Posts Tagged ‘NAD’


Writer and Curator: Larry H. Bernstein, MD, FCAP 

7.8  Sirtuins

7.8.1 Function and regulation of the mitochondrial Sirtuin isoform Sirt5 in Mammalia

7.8.2 Substrates and Regulation Mechanisms for the Human Mitochondrial Sirtuins- Sirt3 and Sirt5

7.8.3 The mTORC1 Pathway Stimulates Glutamine Metabolism and Cell Proliferation by Repressing SIRT4

7.8.4  Rab1A and small GTPases Activate mTORC1

7.8.5 PI3K.Akt signaling in osteosarcoma

7.8.6 The mTORC1-S6K1 Pathway Regulates Glutamine Metabolism through the eIF4B-Dependent Control of c-Myc Translation

7.8.7 Localization of mouse mitochondrial SIRT proteins

7.8.8 SIRT4 Has Tumor-Suppressive Activity and Regulates the Cellular Metabolic Response to DNA Damage by Inhibiting Mitochondrial Glutamine Metabolism

7.8.9 Mitochondrial sirtuins and metabolic homeostasis

7.8.10 Mitochondrial sirtuins

7.8.11 Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling


7.8.1 Function and regulation of the mitochondrial Sirtuin isoform Sirt5 in Mammalia

Gertz M1Steegborn C.
Biochim Biophys Acta. 2010 Aug; 1804(8):1658-65

Sirtuins are a family of protein deacetylases that catalyze the nicotinamide adenine dinucleotide (NAD(+))-dependent removal of acetyl groups from modified lysine side chains in various proteins. Sirtuins act as metabolic sensors and influence metabolic adaptation but also many other processes such as stress response mechanisms, gene expression, and organismal aging. Mammals have seven Sirtuin isoforms, three of them – Sirt3, Sirt4, and Sirt5 – located to mitochondria, our centers of energy metabolism and apoptosis initiation. In this review, we shortly introduce the mammalian Sirtuin family, with a focus on the mitochondrial isoforms. We then discuss in detail the current knowledge on the mitochondrial isoform Sirt5. Its physiological role in metabolic regulation has recently been confirmed, whereas an additional function in apoptosis regulation remains speculative. We will discuss the biochemical properties of Sirt5 and how they might contribute to its physiological function. Furthermore, we discuss the potential use of Sirt5 as a drug target, structural features of Sirt5 and of an Sirt5/inhibitor complex as well as their differences to other Sirtuins and the current status of modulating Sirt5 activity with pharmacological compounds.

removal of acetyl groups from modified lysine side chain

removal of acetyl groups from modified lysine side chain
removal of acetyl groups from modified lysine side chain

sirtuin structure

sirtuin structure
sirtuin structure

7.8.2 Substrates and Regulation Mechanisms for the Human Mitochondrial Sirtuins- Sirt3 and Sirt5

Schlicker C1Gertz MPapatheodorou PKachholz BBecker CFSteegborn C
J Mol Biol. 2008 Oct 10; 382(3):790-801

The enzymes of the Sirtuin family of nicotinamide-adenine-dinucleotide-dependent protein deacetylases are emerging key players in nuclear and cytosolic signaling, but also in mitochondrial regulation and aging. Mammalian mitochondria contain three Sirtuins, Sirt3, Sirt4, and Sirt5. Only one substrate is known for Sirt3 as well as for Sirt4, and up to now, no target for Sirt5 has been reported. Here, we describe the identification of novel substrates for the human mitochondrial Sirtuin isoforms Sirt3 and Sirt5. We show that Sirt3 can deacetylate and thereby activate a central metabolic regulator in the mitochondrial matrix, glutamate dehydrogenase. Furthermore, Sirt3 deacetylates and activates isocitrate dehydrogenase 2, an enzyme that promotes regeneration of antioxidants and catalyzes a key regulation point of the citric acid cycle. Sirt3 thus can regulate flux and anapleurosis of this central metabolic cycle. We further find that the N- and C-terminal regions of Sirt3 regulate its activity against glutamate dehydrogenase and a peptide substrate, indicating roles for these regions in substrate recognition and Sirtuin regulation. Sirt5, in contrast to Sirt3, deacetylates none of the mitochondrial matrix proteins tested. Instead, it can deacetylate cytochrome c, a protein of the mitochondrial intermembrane space with a central function in oxidative metabolism, as well as apoptosis initiation. Using a mitochondrial import assay, we find that Sirt5 can indeed be translocated into the mitochondrial intermembrane space, but also into the matrix, indicating that localization might contribute to Sirt5 regulation and substrate selection.

Mitochondria are central organelles in cellular energy metabolism, but also in processes such as apoptosis, cellular senescence, and lifespan regulation.1 and 2 Failures in mitochondrial function and regulation contribute to aging-related diseases, such as atherosclerosis3 and Parkinson’s disease,4 likely by increasing cellular levels of reactive oxygen species and the damage they cause.1 Emerging players in metabolic regulation and cellular signaling are members of the Sirtuin family of homologs of “silent information regulator 2” (Sir2), a yeast protein deacetylase.5 and 6 Sir2 was found to be involved in aging processes and lifespan determination in yeast,7 and 8 and its homologs were subsequently identified as lifespan regulators in various higher organisms.89 and 10 Sirtuins form class III of the protein deacetylase superfamily and hydrolyze one nicotinamide adenine dinucleotide (NAD +) as cosubstrate for each lysine residue they deacetylate.11 and 12 The coupling of deacetylation to NAD + was proposed to link changes in cellular energy levels to deacetylation activity,13 and 14 which would indicate Sirtuins as metabolic sensors. Other known regulation mechanisms for Sirtuin activity are the modulation of the expression levels of their genes6 and the autoinhibitory effect of an N-terminal region on the yeast Sirtuin “homologous to SIR2 protein 2” (Hst2).15

The seven mammalian Sirtuin proteins (Sirt1–Sirt7) have various substrate proteins that mediate functions in genetic, cellular, and mitochondrial regulation.5 and 6 The best-studied mammalian Sir2 homolog, Sirt1, was shown to regulate, among others, transcription factor p53, nuclear factor-kappa B, and peroxisome proliferator-activated receptor gamma coactivator-1-alpha.6 Three human Sirtuin proteins are known to be located in the mitochondria, Sirt3, Sirt4, and Sirt5,161718 and 19 although Sirt3 was reported to change its localization to nuclear when coexpressed with Sirt5.20 The recent identification of the first substrates for mitochondrial Sirtuins—acetyl coenzyme A synthetase 221 and 22 and glutamate dehydrogenase (GDH)16—as targets of Sirtuins 3 and 4, respectively, revealed that these Sirtuins control a regulatory network that has implications for energy metabolism and the mechanisms of caloric restriction (CR) and lifespan determination.23 Sirt3 regulates adaptive thermogenesis and decreases mitochondrial membrane potential and reactive oxygen species production, while increasing cellular respiration.24 Furthermore, Sirt3 is down-regulated in several genetically obese mice,24 and variability in the human SIRT3 gene has been linked to survivorship in the elderly. 25 In contrast to the deacetylases Sirt3 and Sirt5, Sirt4 appears to be an ADP ribosyltransferase. 16 Through this activity, Sirt4 inhibits GDH and thereby down-regulates insulin secretion in response to amino acids. 16 For Sirt5, however, there is no report yet on its physiological function or any physiological substrate. It is dominantly expressed in lymphoblasts and heart muscle cells,17 and 26 and its gene contains multiple repetitive elements that might make it a hotspot for chromosomal breaks. 26 Interestingly, the Sirt5 gene has been located to a chromosomal region known for abnormalities associated with malignant diseases. 26

A proteomics study found 277 acetylation sites in 133 mitochondrial proteins;27 many of them should be substrates for the mitochondrial Sirtuins mediating their various functions, but up to now, only one physiological substrate could be identified for Sirt3,21 and 22 and none could be identified for Sirt5. Our understanding of substrate selection by Sirtuins is incomplete, and knowledge of specific Sirtuin targets would be essential for a better understanding of Sirtuin-mediated processes and Sirtuin-targeted therapy. A first study on several Sirtuins showed varying preferences among acetylated peptides.28 Structural and thermodynamic analysis of peptides bound to the Sirtuin Sir2Tm from Thermatoga maritima indicated that positions − 1 and + 2 relative to the acetylation site play a significant role in substrate binding. 29 However, these studies were conducted with nonphysiological Sirtuin/substrate pairs, and other studies indicated little sequence specificity; instead, the yeast Sirtuin Hst2 was described to display contextual and conformational specificity: Hst2 deacetylated acetyl lysine only in the context of a protein, and it preferentially deacetylated within flexible protein regions. 30 Finally, statistical analysis of a proteomics study on acetylated proteins identified preferences at various positions such as + 1, − 2, and − 3, and deacetylation sites appeared to occur preferentially in helical regions. 27 Thus, our present knowledge of Sirtuin substrates and of factors determining Sirtuin specificity is incomplete and insufficient for sequence-based identification of physiological substrates.

Here, we describe the identification of novel targets for the mitochondrial deacetylases Sirt3 and Sirt5. We show that Sirt3 can deacetylate and thereby activate the enzymes GDH and isocitrate dehydrogenase (ICDH) 2—two key metabolic regulators in the mitochondrial matrix. We find that the N- and C-terminal regions of Sirt3 influence its activity against GDH and a peptide substrate, indicating roles in regulation and substrate recognition for these regions. Furthermore, we find that Sirt5 can deacetylate cytochrome c, a protein of the mitochondrial intermembrane space (IMS) with a central function in oxidative metabolism and apoptosis.

The upstream sequence contributes to the target specificity of Sirt3 and Sirt5

Sirtuins have been reported to have little sequence specificity,30 but other studies indicated a sequence preference dominated by positions − 1 and + 2.29 We tested the importance of the amino acid pattern preceding the acetylation site for recognition by the mitochondrial Sirtuins Sirt3 and Sirt5 through a fluorescence assay. First, the fluorogenic and commercially available modified p53-derived tetrapeptide QPK-acetylK, originally developed for Sirt2 assays but also efficiently used by Sirt3, was tested. Even 60 μg of Sirt5 did not lead to any deacetylation signal, whereas 0.35 μg of Sirt3 efficiently deacetylated the peptide (Fig. 1a). We then tested Sirt3 and Sirt5 on a second modified p53-derived tetrapeptide, RHK-acetylK. Sirt3 (0.5 μg) showed a slightly increased activity against this substrate as compared to QPK-acetylK (Fig. 1b); more importantly, 0.5 μg of Sirt5 showed significant activity against this peptide. These results show that the mitochondrial Sirtuins Sirt3 and, especially, Sirt5 indeed recognize the local target sequence, and target positions further upstream of − 1 seem to be involved in substrate recognition. For identification of novel substrates for the mitochondrial Sirtuins and further characterization of their target recognition mechanisms, we then turned to testing full-length proteins, as the downstream sequence and the larger protein context of the deacetylation site might also contribute to substrate selection.

Sirtuin substrate specificity

Sirtuin substrate specificity

Fig. 1. Testing the substrate specificity of Sirt3 and Sirt5 with peptides. (a) Sirt3, but not Sirt5, deacetylates the fluorogenic peptide QPK-acetylK. (b) Sirt3 efficiently deacetylates the fluorogenic peptide RHK-acetylK, and Sirt5 also significantly deacetylates this substrate.

Sirt3 deacetylates and activates GDH

In order to identify novel physiological substrates of the mitochondrial Sirtuins, we used proteins isolated in their partly acetylated form from natural sources (i.e., from mammalian mitochondria). These proteins, carrying physiological acetylations, were tested as Sirt3 and Sirt5 substrates in vitro in an ELISA system using an antibody specific for acetylated lysine. In a recent proteomics study, 27 GDH, a central regulator of mitochondrial metabolism, was identified to be acetylated in a feeding-dependent manner. With our ELISA, we found that Sirt3 and Sirt5 can both deacetylate pure GDH isolated from mitochondria, but with very different efficiencies ( Fig. 2a). Sirt3 significantly deacetylated GDH, but even large amounts of Sirt5 decreased the acetylation level of this substrate only slightly. We next tested the effect of GDH deacetylation on its activity. Deacetylation of GDH through incubation with Sirt3 and NAD + before its examination in a GDH activity assay increased its activity by 10%, and a stronger stimulation of GDH activity was seen when larger amounts of Sirt3 were used for deacetylation ( Fig. 2b). GDH is colocalized with Sirt3 in the mitochondrial matrix 1618 and 19 and, thus, likely could be a physiological substrate of this Sirtuin. Indeed, GDH from a Sirt3 knockout mouse was recently shown to be hyperacetylated compared to protein from wild-type mice. 31 Thus, Sirt3 deacetylates GDH in vivo, and our results show that this direct deacetylation of GDH by Sirt3 leads to GDH activation.

sirtuin structure

sirtuin structure

Fig. 2. Sirt3 can deacetylate and thereby activate GDH. (a) Deacetylation of GDH tested in ELISA. Sirt3 efficiently deacetylates GDH, whereas Sirt5 has only a small effect on the acetylation state. (b) GDH activity is increased after deacetylation of the enzyme by Sirt3. The increase in GDH activity depends on the amount of Sirt3 activity used for deacetylation.

Sirt3 can deacetylate and thereby activate ICDH2

In the proteomics study by Kim et al., the mitochondrial citric acid cycle enzymes fumarase and ICDH2 (a key regulator of this metabolic cycle) were found to be acetylated in a feeding-dependent manner. 27 In our ELISA system, we found that Sirt3 efficiently deacetylated the ICDH2 substrate isolated from mitochondria ( Fig. 3a). Western blot analysis (data not shown) and mass spectrometry confirmed that, indeed, the ICDH2 fraction of the partially purified protein was deacetylated by Sirt3. In contrast, even large amounts of Sirt5 did not significantly decrease the acetylation level of this substrate ( Fig. 3a). As expected, deacetylation of ICDH2 by Sirt3 was dependent on NAD +. Fumarase, in contrast, could not be deacetylated as efficiently as ICDH2 through treatment with either Sirt3 or Sirt5 ( Fig. 3b). The low absolute values over background for the ELISA with fumarase, however, might indicate low acetylation levels of the natively purified protein, and a stronger effect might be attainable when testing fumarase with a higher acetylation level.

Fig. 3. Sirt3 deacetylates ICDH2, but not fumarase. (a) Deacetylation of ICDH2 by Sirt3 and Sirt5 tested in ELISA. Sirt3, but not Sirt5, deacetylates ICDH2 in a NAD +-dependent manner. (b) Fumarase acetylation determined through ELISA cannot be significantly decreased by incubation with recombinant Sirt3 or Sirt5. (c) ICDH2 activity measured in a spectrophotometric assay based on the formation of NADPH. ICDH2 activity (continuous line) is increased after deacetylation of the enzyme by Sirt3 (dashed line). (d) The stimulatory effect of deacetylation on ICDH2 activity depends on the amount of deacetylase activity added during pretreatment. (e) ICDH2 with and without Sirt3 treatment analyzed by mass spectrometry after proteolytic digest. The decrease in the signal at 962.3 Da and the increase in signal at 903.5 Da indicate deacetylation at either K211 or K212.

In order to analyze the potential physiological function of ICDH2 deacetylation, we tested the effect of Sirt3-mediated ICDH2 deacetylation on its activity. Incubation of ICDH2 with Sirt3 and NAD + prior to its analysis in an ICDH activity assay increased its activity (Fig. 3c). The stimulation of ICDH2 activity was further increased when larger amounts of Sirt3 were used for deacetylation (Fig. 3d), and no significant increase in ICDH2 activity was observed when the Sirtuin inhibitor dihydrocoumarin was present during incubation with Sirt3 (data not shown). Sirt3 and ICDH2 are colocalized in the mitochondrial matrix,1619 and 32 and we therefore assume that ICDH2 is likely a physiological substrate for Sirt3, which activates ICDH2 by deacetylation.

Sirt3 can deacetylate KK motifs in substrate proteins

In order to identify the site of ICDH2 deacetylation upon treatment with Sirt3, we analyzed ICDH2 by mass spectrometry. For analyzing pure ICDH2, we excised its band from an SDS gel before mass spectrometry analysis. In the proteomics study by Kim et al., two acetylation sites were reported for ICDH2: K75 and K241 (numbering of the partial sequence of the unprocessed precursor; SwissProt entry P33198). 27 After digest of ICDH2, we could not detect peptides comprising K75 and, therefore, could not determine its acetylation status, and we only observed the deacetylated form of K241. We identified an additional acetylation site, however, by detecting signals at m/z = 903.5 and m/z = 962.3 for the peptide QYAIQKK (residues 206–212) carrying one and two acetyl groups, respectively ( Fig. 3e; calculated m/z = 903.5 and 962.5). Sirt3 treatment decreased the signal for the double-acetylated form and increased the signal for the single-acetylated form as compared to internal peptides [e.g., m/z = 890.5 (calculated m/z = 890.5) andm/z = 1041.4 (calculated m/z = 1041.5)]. These data indicate that Sirt3 deacetylates either position K211 or K212 of this KK motif located at a surface-exposed end of a helix that flanks the active site of ICDH2. 33Deacetylation of a KK motif by Sirt3 is consistent with the efficient use of the tested peptide substrates (see above) that both carry KK motifs.

Fig. 4. Increased activity of N- and C-terminally truncated Sirt3. (a) Specific activity against a peptide substrate of the longest Sirt3 form after proteolytic processing that covers residues 102–399. N-terminal truncation increases the specific activity dramatically, and an additional C-terminal truncation activates the catalytic core further. (b) Homology model of Sirt3 based on the crystal structure of Sirt2. The part comprising the catalytic core is shown in red. The NAD + and peptide ligands were manually placed into their binding sides based on the crystal structure of their complex with a bacterial Sir2 homolog from T. maritima. Parts removed in N- and C-terminal truncation constructs are shown in cyan and blue, respectively. (c) Level of acetylation of GDH tested in ELISA. The shortest Sirt3 form Sirt3(114–380) deacetylates more efficiently than Sirt3(114–399) and Sirt3(102–399), which show activities comparable to each other.

Sirt5 can deacetylate cytochrome c

Sirt5 can deacetylate cytochrome c

Sirt5 can deacetylate cytochrome c

The Sirt5 protein that we used for our study comprises residues 34–302, corresponding to the fully active catalytic core determined for Sirt3 (see above). This protein is indeed active against a peptide substrate, but it showed no significant activity against the acetylated mitochondrial matrix proteins tested so far: GDH, ICDH2, and fumarase. We thus picked cytochrome c, a central protein in energy metabolism and apoptosis localized in the mitochondrial IMS, from the list of acetylated mitochondrial proteins 27 for testing as deacetylation substrate. Sirt5 showed deacetylation activity against pure cytochrome c in our ELISA system, whereas Sirt3 had almost no activity against this substrate ( Fig. 5a). Even the more active shortened form of Sirt3(114–380) showed no considerable activity against this substrate.

Fig. 5.  Sirt5 can deacetylate cytochrome c. (a) Deacetylation of cytochrome c tested in ELISA. Sirt5 uses cytochrome c as substrate for deacetylation, whereas Sirt3 treatment leaves the acetylation level of cytochrome c unchanged. (b) Model of the action of the mammalian Sirtuins Sirt3, Sirt4, and Sirt5 in mitochondria. CAC: citric acid cycle. (c) Digest of Sirt5 synthesized in vitro with PK. The protein is fully degraded at proteinase concentrations of 25 μg/ml and above. (d) Import of Sirt5 into isolated yeast mitochondria. Sirt5 reaches an inner mitochondrial compartment in the presence and in the absence of the mitochondrial membrane potential (ΔΨ), whereas Sirt3, as a control for a matrix-targeted protein, is not imported into uncoupled mitochondria. (e) Intramitochondrial localization of Sirt5. Part of the imported Sirt5 is sensitive to PK after swelling (SW) and thus localized in the IMS, but another part of the protein remains protease-resistant and therefore appears to be localized to the matrix. Atp3, a protein localized at the matrix site of the mitochondrial inner membrane, and an IMS-located domain of translocase of inner membrane 23 detected by Western blot analysis served as controls for matrix transport and swelling, respectively. aTim23: anti-Tim23. (f) Scheme of the domain organizations of Sirt3 and Sirt5. Numbers in brackets are residue numbers for boundaries of protein parts. NLS: nuclear localization sequence; MLS: mitochondrial localization sequence; R1, regulatory region 1; R2: regulatory region 2.

Cytochrome c might be a physiological substrate of Sirt5 if this Sirtuin is localized to the mitochondrial IMS (Fig. 5b). A recent study on overexpressed tagged mouse Sirt5 in COS7 cells 20 indeed indicated that Sirt5, at least from mouse, is localized in the IMS. In order to test whether human Sirt5 can be localized to the IMS, we performed import experiments with human Sirt3 and Sirt5 using isolated yeast mitochondria as a model system. 3 Sirt3 and Sirt5 proteins were incubated with mitochondria, followed by PK treatment for degradation of nonimported protein ( Fig. 5d). In a parallel reaction, mitochondria were uncoupled prior to the import reaction by addition of valinomycin (− ΔΨ). Sirt3, a protein known to be located in the mitochondrial matrix, 19 was only efficiently imported in the presence of a membrane potential. Dependence on the mitochondrial potential is a hallmark of matrix import, 38 and the results thus show that Sirt3 is imported into the correct compartment in our experimental system. Sirt5, in contrast, reaches an inner-mitochondrial compartment both in the presence and in the absence of the membrane potential, suggesting that Sirt5 may accumulate in the IMS.

In order to further test the localization of Sirt5, we removed the outer mitochondrial membrane after the import reaction by osmotic swelling, followed by PK digest of then accessible proteins (Fig. 5e). Rupture of the outer membrane was confirmed by monitoring the accessibility of an IMS-exposed domain of endogenous translocase of inner membrane 23 (detected by Western blot analysis). Part of the imported Sirt5 was degraded by PK, indicating its localization in the IMS.

Sirtuins are involved in central physiological regulation mechanisms, many of them with relevance to metabolic regulation and aging processes.5 and 6 Therefore, the seven mammalian Sirtuin isoforms are emerging targets for the treatment of metabolic disorders and aging-related diseases.39 For most Sirtuin effects, however, the specific signaling mechanisms and molecular targets are not yet known. We have identified novel potential targets for Sirtuins in mitochondria, the major metabolic centers in cells. We found that Sirt3 can deacetylate and thereby activate ICDH2, a key regulation point for flux throughout the citric acid cycle. Interestingly, the ICDH isoform regulated by Sirt3 forms NADPH instead of the NADH used for ATP synthesis. This activity is assumed to be important for the NADPH-dependent regeneration of antioxidants,40 and its stimulation by Sirt3 should thus help to slow oxidative damage and cellular aging processes. Furthermore, Sirt3 deacetylates GDH in vitro (this study) and in vivo31 and we find that this modification also stimulates GDH activity that promotes glucose and ATP synthesis by enabling amino acids to be used as fuels for citric acid cycle and gluconeogenesis. 41 Consistently, Sirt3 was reported to increase respiration, 24 which is needed for ATP synthesis but also for conversion of amino acids into glucose and urea. 41 The enzyme previously identified to be activated by Sirt3, acetyl coenzyme A synthetase 2, 21 and 22 also fuels the citric acid cycle independently of glycolysis by activating free acetate (Fig. 5b). Interestingly, a shift away from liver glycolysis is one of the metabolic changes observed under CR, a feeding regimen with 20–40% fewer calories than consumed ad libitum that is found to extend the lifespan of a variety of organisms. 6 CR was previously reported to increase GDH activity in the liver, 42where Sirt3 is highly expressed, 17 and Sirt3 activity is known to be increased by CR. 6 and 24 It thus appears that Sirt3 mediates some of the effects of CR and lifespan regulation, consistent with its implication in survivorship in the elderly 25 and 43 and the prominent role of Sirtuins in CR found for various organisms,6 and 44 and it also appears that GDH activation likely contributes to the Sirt3-dependent effects.

Little is known about additional factors regulating the activity and specificity of Sirtuin enzymes. Their requirement for NAD + indicates that the NAD +/NADH ratio should regulate Sirtuins,13 and 14 but even changes to ratios observed under extreme conditions such as CR appear to influence Sirtuin activity only slightly.35 Furthermore, NAD + levels would influence all Sirtuins similarly, but a more specific tuning of individual Sirtuin activities appears necessary in order to orchestrate the many effects mediated by Sirtuins (see, e.g., discussion above).6 and 45 A deeper insight into the regulation of Sirtuin enzymes would also be required for the development of more specific Sirtuin inhibitors—a prerequisite for Sirtuin-targeted therapy.39 The regulatory parts flanking the catalytic cores might be interesting target sites (Fig. 5f). N-terminal extensions between ∼ 30 and 120 residues are present in all human Sirtuins but show little conservation, indicating that they might respond to various regulators. Our results indicate that the corresponding N-terminal region in Sirt3 also blocks productive binding for small peptides (Fig. 4a), but enables access for entire protein substrates (Fig. 4c). The C-terminal truncated part in our experiments (Sirt3 residues 380–399) is formed by α14 (secondary structure numbering for Sirt236) whose end corresponds to the N-terminus of Hst2 α13 that partly occupies the NAD +binding site.15 In Sirt3, however, the C-terminal truncation alone lowers activity only slightly, and we assume that it has no regulatory function on its own but might instead assist the N-terminal autoinhibitory region. This module of the N-terminus and the C-terminus (Figs. 4b and 5f) appears to contribute to the substrate specificity of the enzyme, and ligands binding to it might enable or block rearrangements opening up the active site and thereby regulate the enzyme’s activity. Alternatively, the flanking parts might be removed by proteolytic processing or alternative splicing, thereby changing Sirtuin activity and specificity.

7.8.3 The mTORC1 Pathway Stimulates Glutamine Metabolism and Cell Proliferation by Repressing SIRT4

Csibi A1Fendt SMLi CPoulogiannis GChoo AYChapski DJ, et al.
Cell. 2013 May 9; 153(4):840-54.

Proliferating mammalian cells use glutamine as a source of nitrogen and as a key anaplerotic source to provide metabolites to the tricarboxylic acid cycle (TCA) for biosynthesis. Recently, mTORC1 activation has been correlated with increased nutrient uptake and metabolism, but no molecular connection to glutaminolysis has been reported. Here, we show that mTORC1 promotes glutamine anaplerosis by activating glutamate dehydrogenase (GDH). This regulation requires transcriptional repression of SIRT4, the mitochondrial-localized sirtuin that inhibits GDH. Mechanistically, mTORC1 represses SIRT4 by promoting the proteasome-mediated destabilization of cAMP response element binding-2 (CREB2). Thus, a relationship between mTORC1, SIRT4 and cancer is suggested by our findings. Indeed, SIRT4 expression is reduced in human cancer, and its overexpression reduces cell proliferation, transformation and tumor development. Finally, our data indicate that targeting nutrient metabolism in energy-addicted cancers with high mTORC1 signaling may be an effective therapeutic approach.

Proliferating mammalian cells use glutamine as a source of nitrogen and as a key anaplerotic source to provide metabolites to the tricarboxylic acid cycle (TCA) for biosynthesis. Recently, mTORC1 activation has been correlated with increased nutrient uptake and metabolism, but no molecular connection to glutaminolysis has been reported. Here, we show that mTORC1 promotes glutamine anaplerosis by activating glutamate dehydrogenase (GDH). This regulation requires transcriptional repression of SIRT4, the mitochondrial-localized sirtuin that inhibits GDH. Mechanistically, mTORC1 represses SIRT4 by promoting the proteasome-mediated destabilization of cAMP response element binding-2 (CREB2). Thus, a relationship between mTORC1, SIRT4 and cancer is suggested by our findings. Indeed, SIRT4 expression is reduced in human cancer, and its overexpression reduces cell proliferation, transformation and tumor development. Finally, our data indicate that targeting nutrient metabolism in energy-addicted cancers with high mTORC1 signaling may be an effective therapeutic approach.

Nutrient availability plays a pivotal role in the decision of a cell to commit to cell proliferation. In conditions of sufficient nutrient sources and growth factors (GFs), the cell generates enough energy and acquires or synthesizes essential building blocks at a sufficient rate to meet the demands of proliferation. Conversely, when nutrients are scarce, the cell responds by halting the biosynthetic machinery and by stimulating catabolic processes such as fatty acid oxidation and autophagy to provide energy maintenance (Vander Heiden et al., 2009). Essential to the decision process between anabolism and catabolism is the highly conserved, atypical Serine/Threonine kinase mammalian Target of Rapamycin Complex 1 (mTORC1), whose activity is deregulated in many cancers (Menon and Manning, 2008). This complex, which consists of mTOR, Raptor, and mLST8, is activated by amino acids (aa), GFs (insulin/IGF-1) and cellular energy to drive nutrient uptake and subsequently proliferation (Yecies and Manning, 2011). The molecular details of these nutrient-sensing processes are not yet fully elucidated, but it has been shown that aa activate the Rag GTPases to regulate mTORC1 localization to the lysosomes (Kim et al., 2008Sancak et al., 2008); and GFs signal through the PI3K-Akt or the extracellular signal-regulated kinase (ERK)-ribosomal protein S6 kinase (RSK) pathways to activate mTORC1 by releasing the Ras homolog enriched in brain (RHEB) GTPase from repression by the tumor suppressors, tuberous sclerosis 1 (TSC1)– TSC2 (Inoki et al., 2002Manning et al., 2002Roux et al., 2004). Finally, low energy conditions inhibit mTORC1 by activating AMPK and by repressing the assembly of the TTT-RUVBL1/2 complex. (Inoki et al., 2003Gwinn et al., 2008Kim et al., 2013).

Glutamine, the most abundant amino acid in the body plays an important role in cellular proliferation. It is catabolized to α-ketoglutarate (αKG), an intermediate of the tricarboxylic acid (TCA) cycle through two deamination reactions in a process termed glutamine anaplerosis (DeBerardinis et al., 2007). The first reaction requires glutaminase (GLS) to generate glutamate, and the second occurs by the action of either glutamate dehydrogenase (GDH) or transaminases. Incorporation of αKG into the TCA cycle is the major anaplerotic step critical for the production of biomass building blocks including nucleotides, lipids and aa (Wise and Thompson, 2010). Recent studies have demonstrated that glutamine is also an important signaling molecule. Accordingly, it positively regulates the mTORC1 pathway by facilitating the uptake of leucine (Nicklin et al., 2009) and by promoting mTORC1 assembly and lysosomal localization (Duran et al., 2012;Kim et al., 2013).

Commonly occurring oncogenic signals directly stimulate nutrient metabolism, resulting in nutrient addiction. Oncogenic levels of Myc have been linked to increased glutamine uptake and metabolism through a coordinated transcriptional program (Wise et al., 2008Gao et al., 2009). Hence, it is not surprising that cancer cells are addicted to glutamine (Wise and Thompson, 2010). Thus, considering the prevalence of mTORC1 activation in cancer and the requirement of nutrients for cell proliferation, understanding how mTORC1 activation regulates nutrient levels and metabolism is critical. Activation of the mTORC1 pathway promotes the utilization of glucose, another nutrient absolutely required for cell growth. However, no study has yet investigated if and how the mTORC1 pathway regulates glutamine uptake and metabolism. Here, we discover a novel role of the mTORC1 pathway in the stimulation of glutamine anaplerosis by promoting the activity of GDH. Mechanistically, mTORC1 represses the transcription of SIRT4, an inhibitor of GDH. SIRT4 is a mitochondrial-localized member of the sirtuin family of NAD-dependent enzymes known to play key roles in metabolism, stress response and longevity (Haigis and Guarente, 2006). We demonstrate that the mTORC1 pathway negatively controls SIRT4 by promoting the proteasome-mediated degradation of cAMP-responsive element-binding (CREB) 2. We reveal that SIRT4 levels are decreased in a variety of cancers, and when expressed, SIRT4 delays tumor development in a Tsc2−/− mouse embryonic fibroblasts (MEFs) xenograft model. Thus, our findings provide new insights into how mTORC1 regulates glutamine anaplerosis, contributing therefore to the metabolic reprogramming of cancer cells, an essential hallmark to support their excessive needs for proliferation.

The mTORC1 pathway regulates glutamine metabolism via GDH

The activation of the mTORC1 pathway has recently been linked to glutamine addiction of cancer cells (Choo et al., 2010), yet it remains to be resolved if mTORC1 serves as a regulator of glutamine anaplerosis. To investigate this possibility, we first determined the effect of mTORC1 activity on glutamine uptake. We measured glutamine uptake rates in Tsc2 wild-type (WT) and Tsc2−/− MEFs. We found that Tsc2−/− MEFs consumed significantly more glutamine (Figure 1A), showing that mTORC1 activation stimulates the uptake of this nutrient. In addition, re-expression of Tsc2 in Tsc2−/− cells reduced glutamine uptake (Figure S1A). Similarly, mTORC1 inhibition with rapamycin resulted in decreased glutamine uptake in MEFs (Figure 1A). The decreased on glutamine uptake was significantly reduced after 6h of rapamycin treatment when compared to control (data not shown). To further confirm the role of mTORC1 on glutamine uptake, we used human embryonic kidney (HEK) 293T cells stably expressing either WT-RHEB or a constitutively active mutant (S16H) of RHEB. Increased mTORC1 signaling, as evidenced by sustained phosphorylation of S6K1 and its target rpS6, was observed in RHEB-expressing cells (Figure S1B). The activation of the mTORC1 pathway nicely correlated with an increase in glutamine consumption, therefore confirming that changes in mTORC1 signaling are reflected in cellular glutamine uptake (Figure S1B). To determine whether the modulation of glutamine uptake by the mTORC1 pathway occurs in cancer cells, we examined glutamine uptake rates in conditions of mTORC1 inhibition in human epithelial tumor cell lines, including the colon carcinoma DLD1, and the prostate cancer DU145. Rapamycin treatment resulted in decreased proliferation (data not shown) and yielded a decreased glutamine uptake in both cell lines (Figure 1B & data not shown). Glutamine is the major nitrogen donor for the majority of ammonia production in cells (Figure 1C) (Shanware et al., 2011). Consistent with decreased glutamine uptake, we found that ammonia levels were also diminished after rapamycin treatment (Figure S1C).

Figure 1  The mTORC1 pathway regulates glutamine metabolism via glutamate dehydrogenase

We next examined the fate of glutamine in conditions of mTORC1 inhibition, using gas chromatography/mass spectrometry (GC/MS) analysis to monitor the incorporation of uniformly labeled [U-13C5]-Glutamine into TCA cycle intermediates. Direct glutamine contribution to I̧KG (m+5), succinate (m+4), malate (m+4) and citrate (m+4) was decreased in rapamycin treated cells (Figure S1D) indicating that rapamycin impaired glutamine oxidation and subsequent carbon contribution into the TCA cycle.

To test whether glutamine uptake or glutamine conversion is limiting, we measured the intracellular levels of glutamine and glutamate in DLD1 cells. Increased levels of glutamine and/or glutamate will show that the catalyzing enzyme activity is limiting and not glutamine transport itself (Fendt et al., 2010). Rapamycin treatment resulted in increased intracellular levels of both glutamine and glutamate, showing that glutamate to αKG conversion is the critical limiting reaction (Figures 1D & 1E). To further confirm the implication of the glutamate catalyzing reaction we also measured αKG levels. If glutamate conversion is indeed critical we expect no alteration in αKG levels. This is expected because αKG is downstream of the potentially limiting glutamate conversion step, and it has been shown that product metabolite concentrations of limiting metabolic enzymes stay unaltered, while the substrate metabolite concentrations change to keep metabolic homeostasis (Fendt et al., 2010). We found that αKG levels were unaltered after rapamycin treatment, corroborating that the limiting enzymatic step is glutamate conversion (Figure 1F). To further confirm the limitation in glutamate-to-αKG conversion, we measured flux through this reaction. Strikingly, this flux was significantly reduced during rapamycin treatment (Figure 1G). Additionally, the inhibition of mTORC1 resulted in increased glutamate secretion (Figure 1H), thus confirming that the glutamate-to-αKG conversion step is a major bottleneck in the glutamine pathway during rapamycin treatment.

Glutamate conversion can be conducted by GDH (Figure 1C), suggesting that the mTORC1 pathway potentially regulates this enzyme. In agreement, rapamycin treatment resulted in decreased GDH activity in DLD1 cells (Figure 1I). To exclude that transaminases play a role in the mTORC1-induced regulation of glutamine metabolism, we used amin ooxyacetate (AOA) at a concentration shown to effectively inhibit the two predominant transaminases, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) (Figure 1C) (Wise et al., 2008), or rapamycin in the presence of α-15N-labeled glutamine. Subsequently, we measured 15N-labeling patterns and metabolite levels of alanine, an amino acid that is predominately produced by a transaminase-catalyzed reaction (Possemato et al., 2011). We found that AOA dramatically decreased 15N contribution and metabolite levels of alanine, while rapamycin only mildly affected the 15N contribution to this amino acid and showed no effect on alanine levels compared to the control condition (Figures 1J & S1E). In conclusion, these data demonstrate that GDH, not transaminases, plays a major role in the regulation of glutamine metabolism downstream of mTORC1.

mTORC1 controls GDH activity by repressing SIRT4

As our results show that mTORC1 regulates glutamate dehydrogenase, we sought to identify the molecular mechanism. SIRT4 is a negative regulator of GDH activity through ADP-ribosylation (Haigis et al., 2006), thus suggesting that mTORC1 potentially controls this step of glutamine metabolism via SIRT4. To test this possibility, we first assessed the ADP-ribosylation status of GDH by introducing biotin-labeled NAD followed by immunoprecipitation using avidin-coated beads. Rapamycin treatment led to an increase in the mono-ADP-ribosylation status of GDH, similar to that observed in cells stably expressing SIRT4 (Figure 2A). Importantly, we found that the knockdown of SIRT4 abrogated the rapamycin-induced decrease in the activity of GDH (Figures 2B & S2A). Strikingly, SIRT4 protein levels were increased upon mTORC1 inhibition in MEFs (Figures 2C). This regulation was confirmed in both DLD1 and DU145 cells (Figures 2D). Remarkably, rapamycin potently increased SIRT4 levels after 6h of treatment (Figure S2B), correlating with reduced glutamine consumption at the same time point (data not shown). In contrast, SIRT4 levels were not influenced by the treatment of MEFs with U0216, an inhibitor of MEK1/2 in the MAPK pathway (Figure S2C). All other mTOR catalytic inhibitors tested in Tsc2−/− MEFs also resulted in increased SIRT4 protein levels (Figure S2D). To evaluate a potential regulation of SIRT4 by mTORC2, we performed RNA interference (RNAi) experiments of either raptor or the mTORC2 component, rictor, in Tsc2−/− MEFs. The knockdown of raptor, but not rictor, was sufficient to increase SIRT4 protein levels, confirming the role of the mTORC1 pathway in the regulation of SIRT4 (Figure 2E). To investigate whether mTORC1 regulation of SIRT4 occurs in tumor samples, a TSC-xenograft model was used. We injected a TSC2−/− rat leiomyoma cell line; ELT3 cells, expressing either an empty vector (V3) or TSC2 (T3), in the flank of nude mice. SIRT4 levels were dramatically increased in TSC2-expressing tumors compared to empty vector samples (Figure S2E). In addition, we assessed the levels of SIRT4 in both ELT3 xenograft tumors and in mouse Tsc2+/− liver tumors after rapamycin treatment. As expected, these tumor samples exhibited robust elevation of SIRT4 after rapamycin treatment (Figures 2F & S2F). Thus, these data demonstrate that the mTORC1 pathway represses SIRT4 in several tumor systems.

Figure 2  mTORC1 controls glutamate dehydrogenase activity by repressing SIRT4

CREB2 regulates the transcription of SIRT4 in an mTORC1-dependent fashion

We next asked whether the mTORC1-dependent regulation of SIRT4 occurred at the mRNA level. Quantitative RT-PCR results show that rapamycin treatment significantly increased the expression of SIRT4mRNA in Tsc2−/− MEFs (Figure 3A). SIRT4 mRNA levels were dramatically reduced in Tsc2−/− MEFs compared to their WT counterpart (Figure 3B). Similar results were obtained from transcriptional profiling analysis of the SIRT4 gene from a previously published dataset (GSE21755) (Figure 3C) (Duvel et al. 2010). Altogether, our data demonstrate that mTORC1 negatively regulates the transcription of SIRT4. To determine whether CREB2 is involved in the mTORC1-dependent regulation of SIRT4, we performed RNAi experiments. The silencing of CREB2 abolished the rapamycin-induced expression of SIRT4 (Figures 3E & S3A). The knockdown of CREB1 did not affect the upregulation of SIRT4 upon mTORC1 inhibition, thus demonstrating the specificity of CREB2 to induce SIRT4 (Figure S3B), and the knockdown of CREB2 significantly abrogated the rapamycin-induced increase in the activity of the SIRT4 promoter.

Figure 3  SIRT4 is regulated at the mRNA level in an mTORC1-dependent fashion

mTORC1 regulates the stability of CREB2

We next investigated whether the mTORC1 pathway regulates CREB2. Although we did not observe major changes in Creb2 mRNA in normal growth conditions (Figure S4A), mTORC1 inhibition resulted in accumulation of CREB2 protein levels by 2h of rapamycin treatment (Figure 4A). U0126 failed to cause the accumulation of CREB2 (Figure S4B). In contrast, CREB1 protein levels were not affected after 24h rapamycin treatment (Figure S4C). As observed for SIRT4, mTOR catalytic inhibitors, and the specific knockdown of mTOR, resulted in upregulation of CREB2 protein levels (Figures S4D & S4E). CREB2 is upregulated in diverse cell types as a response to a variety of stresses, including hypoxia, DNA damage, and withdrawal of GFs, glucose, and aa (Cherasse et al., 2007Rouschop et al., 2010Yamaguchi et al., 2008;Whitney et al., 2009). Interestingly, mTORC1 is negatively regulated by all of these environmental inputs (Zoncu et al., 2011). Since mTORC1 signaling in Tsc2−/− MEFs is insensitive to serum deprivation, we assessed the role of aa withdrawal and re-stimulation on CREB2 levels. As shown in Fig. 4B, CREB2 accumulated upon aa deprivation, and was decreased following aa re-addition. This phenomenon required the action of the proteasome as MG132 efficiently blocked CREB2 degradation following aa re-addition. Importantly, we found that mTORC1 inhibition abrogated the aa-induced decrease of CREB2 (Figure 4B).

Figure 4  mTORC1 regulates the stability of CREB2

mTORC1 activation promotes the binding of CREB2 to βTrCP and modulates CREB2 ubiquitination

Next, we attempted to identify the E3 ubiquitin ligase that might be responsible for CREB2 turnover. Consistent with a recent study, we found CREB2 to bind the E3 ligase, βTrCP (Frank et al., 2010). However, other related E3 ligases including Fbxw2, Fbxw7a, and Fbxw9 did not bind to CREB2 (data not shown). The interaction of CREB2 with Flag-βTrCP1 was enhanced in the presence of insulin, and was abolished by rapamycin pretreatment (Figure 4D). Importantly, insulin treatment promoted the ubiquitination of CREB2 in an mTORC1-dependent fashion (Figure 4E). Altogether, our results support the notion that the mTORC1 pathway regulates the targeting of CREB2 for proteasome-mediated degradation. βTrCP binds substrates via phosphorylated residues in conserved degradation motifs (degrons), typically including the consensus sequence DpSGX(n)pS or similar variants. We found an evolutionary conserved putative βTrCP binding site (DSGXXXS) in CREB2 (Figure 4F). Interestingly, we noted a downward mobility shift in CREB2 protein with mTORC1 inhibition, consistent with a possible decrease in the phosphorylation of CREB2. (Figure 4A). Frank et al. (2010) showed that phosphorylation of the first serine in the degron motif corresponding to Ser218 is required for the CREB2/βTrCP interaction, and this modification acts as a priming site for a gradient of phosphorylation events on five proline-directed residues codons (T212, S223, S230, S234, and S247) that is required for CREB2 degradation during the cell cycle progression (Frank et al., 2010). Consistent with these observations, we found that the mutation of the five residues to alanine (5A mutant) resulted in strong stabilization of CREB2, comparable to the serine-to-alanine mutation on the priming Ser218 phosphorylation site (Figure S4G).

SIRT4 represses bioenergetics and cell proliferation

We observed that glutamine utilization is repressed by rapamycin treatment (Figure 1) and SIRT4 is induced by mTORC1 inhibition (Figure 2). Thus, we tested whether SIRT4 itself directly regulates cellular glutamine uptake. The stable expression of SIRT4 resulted in the repression of glutamine uptake in Tsc2−/− MEFs and DLD1 cells (Figures 5A & 5B). Glucose uptake was not affected by SIRT4 expression (data not shown). Because glutamine can be an important nutrient for energy production, we examined ATP levels in SIRT4 expressing cells. Consistent with reduced glutamine consumption, the expression of SIRT4 in Tsc2−/− cells resulted in decreased ATP/ADP ratio compared to control cells (Figure 5C). Cells produce ATP via glycolysis and oxidative phosphorylation (OXPHOS). To test the contribution of mitochondrial metabolism versus glycolysis to ATP, we measured the ATP/ADP ratio after the treatment with oligomycin, an inhibitor of ATP synthesis from OXPHOS. Importantly, the difference of the ATP/ADP ratio between control and SIRT4 expressing cells was abrogated by oligomycin (Figure 5C), further demonstrating that SIRT4 may repress the ability of cells to generate energy from mitochondrial glutamine catabolism. Mitochondrial glutamine catabolism is essential for energy production and viability in the absence of glucose (Yang et al., 2009Choo et al., 2010). Thus, we examined the effect of SIRT4 on the survival of Tsc2−/− MEFs during glucose deprivation. Control cells remained viable following 48h of glucose deprivation. Conversely, SIRT4 expressing cells showed a dramatic increase in cell death under glucose-free conditions, which was rescued by the addition of the cell permeable dimethyl-I̧KG (DM-I̧KG) (Figure 5D). Conversely, the expression of SIRT4 did not affect the viability of glucose-deprived Tsc2 WT MEFs (Figure S5A). Glucose deprivation also induced death of the human DU145 cancer cell line stably expressing SIRT4 (data not shown).

Figure 5  SIRT4 represses bioenergetics and proliferation

Glutamine is an essential metabolite for proliferating cells, and many cancer cells exhibit a high rate of glutamine consumption (DeBerardinis et al., 2007). Thus, decreased glutamine uptake in DLD1 and DU145 cancer cells expressing SIRT4 might result in decreased proliferation. Indeed, these cells grew significantly slower than did control cells. Remarkably, DM-I̧KG completely abrogated the decreased proliferation of SIRT4 expressing cells (Figure 5E & 5F), suggesting that repressed glutamine metabolism drove the reduced proliferation of cells expressing SIRT4. The expression of SIRT4 also slowed the proliferation of Tsc2−/− MEFs but did not affect Tsc2 WT MEFs (Figures S5B & S5C). Finally, to rule out that the effect on proliferation was due to aberrant localization and to off-target effects of the overexpressed protein, we examined the localization of HA-SIRT4. We found that SIRT4 is co-localized with the MitoTracker, a mitochondrial-selective marker (Figure S5D). Taken together, these data demonstrate that SIRT4 is a critical negative regulator of mitochondrial glutamine metabolism and cell proliferation.

SIRT4 represses TSC-tumor development

Recent studies have demonstrated a major role of glutamine metabolism in driving oncogenic transformation of many cell lines (Gao et al., 2009Wang et al., 2011). Since SIRT4 expression represses glutamine uptake and cell proliferation (Figure 5), we hypothesized that it could affect tumorigenesis. To test this idea, we assessed the role of SIRT4 in cell transformation by using an anchorage-independent growth assay. SIRT4 expression reduced the ability of Tsc2−/−p53−/− MEFs to grow in soft agar. However, the expression of SIRT4 in Tsc2+/+p53−/− did not impair their colony formation properties (Figure 6A). Tumor incidence in mice injected with Tsc2+/+p53−/− MEFs was not affected by SIRT4 (data not shown). Conversely, in the Tsc2−/−p53−/− cohort, SIRT4 reduced tumor incidence by 20 days at median (Figure 6B). SIRT4 expression inTsc2−/−p53−/− MEFs resulted in reduction of Ki-67 positivity by 60% (Figure 6E), consistent with the finding that SIRT4 inhibits the proliferation of these cells in vitro (Figure S5B). Finally, we performed a comprehensive meta-analysis of SIRT4 expression in human tumors and found significantly lower expression levels of SIRT4, relative to normal tissue, in bladder, breast, colon, gastric, ovarian and thyroid carcinomas (Figure 6F). Interestingly, loss of SIRT4 expression showed a strong association with shorter time to metastasis in patients with breast cancer (Figures 6G & 6H). Altogether, these data strongly suggest that SIRT4 delays tumorigenesis regulated by the mTORC1 pathway.

Figure 6
SIRT4 suppresses TSC-tumor development

The pharmacologic inhibition of glutamine anaplerosis synergizes with glycolytic inhibition to induce the specific death of mTORC1 hyperactive cells

The activation of mTORC1 leads to glucose and glutamine addiction as a result of increased uptake and metabolism of these nutrients (Choo et al., 2010Duvel et al., 2010 & Figure 1). These observations suggest that targeting this addiction offers an interesting therapeutic approach for mTORC1-driven tumors. The alkylating agent, mechlorethamine (Mechlo), incites cell toxicity in part by the inhibition of the GAPDH step of glycolysis via poly-ADP ribose polymerase (PARP)-dependent cellular consumption of cytoplasmic NAD+. The ultimate consequence is glycolytic inhibition, thus mimicking glucose deprivation (Zong et al., 2004). Treatment of Tsc2−/− MEFs with Mechlo decreased both NAD levels and lactate production (Figure 7A and data not shown). The decrease in NAD+ levels was rescued by addition of DPQ (Figure 7A), a PARP inhibitor (Zong et al., 2004). We next tested the ability of glutamine inhibition to determine the sensitivity of Tsc2−/− MEFs to Mechlo. As shown in Figure 7B, the treatment with EGCG, a GDH inhibitor (Figure 1G), potently synergized with Mechlo to kill Tsc2−/− MEFs with the greatest effect observed at 30μM (Figure 7B). As a result, this combination dramatically increased the cleavage of PARP, an apoptotic marker (Figure 7E). Similarly, glutamine deprivation sensitized Tsc2−/− MEFs to Mechlo (data not shown). The RNAi-mediated knockdown of GDH also synergized with Mechlo to induce death of Tsc2−/− MEFs (Figure 7D). Importantly, at these concentrations the combination did not induce death of a Tsc2-rescued cell line (Figure 7C).

Figure 7 The combination of glutamine metabolism inhibitors with glycolytic inhibition is an effective therapy to kill Tsc2−/− and PTEN−/− cells

Because the metabolic properties of cells with activated mTORC1 by Tsc2– deficiency can be efficiently targeted, we also examined other cell types in which mTORC1 is hyperactive by the loss of PTEN. We found that the combination of Mechlo and EGCG was also effective to induce specific toxicity of PTEN−/− MEFs, while PTEN+/+ MEFs were not affected (Figures S7A & S7B). In addition, the PTEN-deficient human prostate adenocarcinoma cell line, LNCaP, was also sensitive to treatment with Mechlo and EGCG (Figure 7F). This effect was specifically due to lack of TCA cycle replenishment as pyruvate supplementation completely reversed the synergistic effect (Figure 7F). The combination of Mechlo with the GLS1 inhibitor, BPTES (Figure 1G), also resulted in decreased viability of Tsc2−/− cells but not of Tsc2-reexpressing cells (Figures S7C & S7D). Again, death in Tsc2−/− cells was rescued with pyruvate or OAA (Figure S7E). To further investigate if the potent cell death in Tsc2−/− was restricted to Mechlo, we used 2-DG, a glycolytic inhibitor. The combination of 2-DG with either EGCG or BPTES resulted in enhanced cell death of Tsc2−/− MEFs compared to single agent treatments (Figure S7F). This effect was also specific to Tsc2−/− cells, since this combination was less toxic in Tsc2-reexpressing MEFs (Figure S7G). Taken together, our results demonstrate that the combination treatments aimed at inhibiting glycolysis and glutaminolysis potently synergize to kill cells with hyperactive mTORC1 signaling.

Here, we define a novel mTORC1-regulated pathway that controls glutamine-dependent anaplerosis and energy metabolism (Figure 7G). We discovered that the mTORC1 pathway regulates glutamine metabolism by promoting the activity of GDH (Figures 1​-3).3). We show that this regulation occurs by repressing the expression of SIRT4, an inhibitor of GDH (Figures 2 & 3). Molecularly, this is the result of mTORC1-dependent proteasome-mediated degradation of the SIRT4 transcriptional regulator, CREB2 (Figure 4). Interestingly, the modulation of CREB2 levels correlates with increased sensitivity to glutamine deprivation (Ye et al., 2010Qing et al., 2012), fitting with our model of glutamine addiction as a result of mTORC1 activation (Choo et al., 2010). Our data suggest that mTORC1 promotes the binding of the E3 ligase, βTrCP, to CREB2 (Figure 4D), promoting CREB2 degradation by the proteasome (Figure 4E). A previous study has demonstrated that five residues in CREB2 located next to the βTrCP degron are required for its stability (Frank et al., 2010). Accordingly, the mutation of these residues to alanine resulted in stabilization of CREB2 and SIRT4 following insulin and aa-dependent mTORC1 activation (Figure 4G). Future work is aimed at determining if mTORC1 and/or downstream kinases are directly responsible for the multisite phosphorylation of CREB2.

The identification of CREB2 as an mTORC1-regulated transcription factor increases the repertoire of transcriptional regulators modulated by this pathway including HIF1α (glycolysis), Myc (glycolysis) and SREBP1 (lipid biosynthesis) (Duvel et al., 2010Yecies and Manning, 2011). The oncogene Myc has also been linked to the regulation of glutamine metabolism by increasing the expression of the surface transporters ASCT2 and SN2, and the enzyme GLS. Thus, enhanced activity of Myc correlates with increased glutamine uptake and glutamate production (Wise et al., 2008Gao et al., 2009). Our findings describe a new level of control to this metabolic node as shown by the modulation of the glutamate-to-αKG flux (Figure 2). This regulation is particularly relevant as some cancer cells produce more than 50% of their ATP by oxidizing glutamine-derived αKG in the mitochondria (Reitzer et al JBC, 1979). Therefore, these studies support the notion that Myc and CREB2/SIRT4 cooperate to regulate the metabolism of glutamine to αKG.

7.8.4  Rab1A and small GTPases Activate mTORC1 Rab1A Is an mTORC1 Activator and a Colorectal Oncogene

Thomas JD1Zhang YJ2Wei YH3Cho JH3Morris LE3Wang HY4Zheng XF5.
Cancer Cell. 2014 Nov 10; 26(5):754-69.


  • Rab1A mediates amino acid signaling to activate mTORC1 independently of Rag
  • Rab1A regulates mTORC1-Rheb interaction on the Golgi apparatus
  • Rab1A is an oncogene that is frequently overexpressed in human cancer
  • Hyperactive amino acid signaling is a common driver for cancer

Amino acid (AA) is a potent mitogen that controls growth and metabolism. Here we describe the identification of Rab1 as a conserved regulator of AA signaling to mTORC1. AA stimulates Rab1A GTP binding and interaction with mTORC1 and Rheb-mTORC1 interaction in the Golgi. Rab1A overexpression promotes mTORC1 signaling and oncogenic growth in an AA- and mTORC1-dependent manner. Conversely, Rab1A knockdown selectively attenuates oncogenic growth of Rab1-overexpressing cancer cells. Moreover, Rab1A is overexpressed in colorectal cancer (CRC), which is correlated with elevated mTORC1 signaling, tumor invasion, progression, and poor prognosis. Our results demonstrate that Rab1 is an mTORC1 activator and an oncogene and that hyperactive AA signaling through Rab1A overexpression drives oncogenesis and renders cancer cells prone to mTORC1-targeted therapy. Regulation of TOR by small GTPases

Raúl V Durán1 and Michael N Halla,1
EMBO Rep. 2012 Feb; 13(2): 121–128.

TOR is a conserved serine/threonine kinase that responds to nutrients, growth factors, the bioenergetic status of the cell and cellular stress to control growth, metabolism and ageing. A diverse group of small GTPases including Rheb, Rag, Rac1, RalA and Ryh1 play a variety of roles in the regulation of TOR. For example, while Rheb binds to and activates TOR directly, Rag and Rac1 regulate its localization and RalA activates it indirectly through the production of phosphatidic acid. Here, we review recent findings on the regulation of TOR by small GTPases.

The growth-controlling TOR signalling pathway is structurally and functionally conserved from unicellular eukaryotes to humans. TOR, an atypical serine/threonine kinase, was originally discovered inSaccharomyces cerevisiae as the target of rapamycin (Heitman et al, 1991). It was later described in many other organisms including the protozoan Trypanosoma brucei, the yeast Schizosaccharomyces pombe, photosynthetic organisms such as Arabidopsis thaliana and Chlamydomonas reinhardtii, and in metazoans such as Caenorhabditis elegansDrosophila melanogaster and mammals. TOR integrates various stimuli to control growth, metabolism and ageing (Avruch et al, 2009Kim & Guan, 2011Soulard et al, 2009;Wullschleger et al, 2006Zoncu et al, 2011a). In mammals, mTOR is activated by nutrients, growth factors and cellular energy, and is inhibited by stress. Thus, the molecular regulation of TOR is complex and diverse. Among the increasing number of TOR regulators, small GTPases are currently garnering much attention. Small GTPases (20–25 kDa) are either in an inactive GDP-bound form or an active GTP-bound form (Bos et al, 2007). GDP–GTP exchange is regulated by GEFs, which mediate the replacement of GDP by GTP, and by GAPs, which stimulate the intrinsic GTPase activity of a cognate GTPase to convert GTP into GDP (Fig 1). Upon activation, small GTPases interact with effector proteins, thereby stimulating downstream signalling pathways. Small GTPases constitute a superfamily that comprises several subfamilies, such as the Rho, Ras, Rab, Ran and Arf families. Rheb, Rag, RalA, Rac1 and Ryh1, all members of the small GTPase superfamily, play a role in the concerted regulation of TOR by different stimuli. This review summarizes recent advances in the understanding of TOR regulation by these small GTPases.

Regulation of small GTPases by GEFs and GAPs

Regulation of small GTPases by GEFs and GAPs

Figure 1 Regulation of small GTPases by GEFs and GAPs. A guanine nucleotide exchange factor (GEF) replaces GDP with GTP to activate the signalling function of the GTPase. Conversely, a GTPase-activating protein (GAP) stimulates hydrolysis of GTP into GDP

The TOR complexes

TOR is found in two functionally and structurally distinct multiprotein complexes, named TORC1 and TORC2 (Avruch et al, 2009Kim & Guan, 2011Soulard et al, 2009Wullschleger et al, 2006Zoncu et al, 2011a). TORC1 regulates several cellular processes including protein synthesis, ribosome biogenesis, nutrient uptake and autophagy. TORC2, in turn, regulates actin cytoskeleton organization, cell survival, lipid synthesis and probably other processes. TORC1 and TORC2 are rapamycin-sensitive and rapamycin-insensitive, respectively, although in some organisms, for example A. thaliana and T. brucei, this rule does not apply (Barquilla et al, 2008Mahfouz et al, 2006). Nevertheless, long-term treatment with rapamycin can also indirectly inhibit TORC2 in mammalian cell lines (Sarbassov et al, 2006). Furthermore, there is accumulating evidence that not all TORC1 readouts are rapamycin-sensitive (Choo & Blenis, 2009Dowling et al, 2010Peterson et al, 2011).

Upstream of TOR

Four main inputs regulate mTORC1: nutrients, growth factors, the bioenergetic status of the cell and oxygen availability. It is well established that growth factors activate mTORC1 through the PI3K–AKT pathway. Once activated, AKT phosphorylates and inhibits the heterodimeric complex TSC1–TSC2, a GAP for Rheb and thus an inhibitor of mTORC1 (Avruch et al, 2009). The TSC1–TSC2 heterodimer is a ‘reception centre’ for various stimuli that are then transduced to mTORC1, including growth factor signals transduced through the AKT and ERK pathways, hypoxia through HIF1 and REDD1, and energy status through AMPK (Wullschleger et al, 2006). In addition to the small GTPases Rheb and Rag (see below), PA also binds to and activates mTORC1 (Fang et al, 2001). Pharmacological or genetic inhibition of PA production, through the inhibition of PLD, impairs activation of mTORC1 by nutrients and growth factors (Fang et al, 2001). Moreover, elevated PLD activity leads to rapamycin resistance in human breast cancer cells (Chen et al, 2003), further supporting a role for PA as an mTORC1 regulator. As discussed below, the small GTPase RalA participates in the mechanism by which PA activates mTORC1 (Maehama et al, 2008Xu et al, 2011).

In the case of nutrients, amino acids in particular, several elements mediate the activation of TORC1. As discussed below, the Rag GTPases are necessary to activate TORC1 in response to amino acids (Binda et al, 2009Kim et al, 2008Sancak et al, 2008). In mammals, it has also been proposed that amino acids stimulate an increase in intracellular calcium concentration, which in turn activates mTORC1 through the class III PI3K Vps34 (Gulati et al, 2008).

Downstream of TOR

TORC1 regulates growth-related processes such as transcription, ribosome biogenesis, protein synthesis, nutrient transport and autophagy (Wullschleger et al, 2006). In mammals, the best-characterized substrates of mTORC1 are S6K and 4E-BP1, through which mTORC1 stimulates protein synthesis. mTORC1 activates S6K, which is a positive regulator of protein synthesis, and inhibits 4E-BP1, which is a negative regulator of protein synthesis. Upon phosphorylation by mTORC1, 4E-BP1 releases eIF4E. Once released from 4E-BP1, eIF4E interacts with the eIF4G subunit of the eIF4F complex, allowing initiation of translation. In mammals, 4E-BP1 participates mainly in the regulation of cell proliferation and metabolism (Dowling et al, 2010). In S. cerevisiae, the main substrate of TORC1 is the S6K orthologue Sch9 (Urban et al, 2007). Sch9 is required for the activation of ribosome biogenesis and translation initiation stimulated by TORC1. Furthermore, it participates in TORC1-dependent inhibition of G0 phase entry.

Regulation of TOR by Rheb

The small GTPase Rheb was first identified in 1994 in a screen for genes induced in neurons in response to synaptic activity (Yamagata et al, 1994), and was first described to interact with the Raf1 kinase (Yee & Worley, 1997). A later report showed that loss of Rhb1, the Rheb orthologue in S. pombe, causes a starvation-like growth arrest (Mach et al, 2000). In 2003, several independent groups working with mammalian cells in vitro and Drosophila in vivo demonstrated that Rheb is the target of the TSC1–TSC2 GAP and a TORC1 activator (Avruch et al, 2009).

Interestingly, the Rheb–mTOR interaction both in vivo and in vitro does not depend on GTP loading of Rheb. This is unusual for GTPases as GTP loading usually regulates effector binding. However, GTP loading of Rheb is crucial for the activation of mTOR kinase activity (Sancak et al, 2007). Conversely, mTOR becomes inactive after association with a nucleotide-deficient Rheb (Long et al, 2005a; Fig 2). Similar results were obtained in S. pombe, making use of mutations that hyperactivate Rheb by increasing its overall GTP : GDP binding ratio (Urano et al, 2005). In contrast to the situation in mammals, interaction of Rheb with SpTOR2 in fission yeast is detected only with a hyperactive Rheb mutant. This suggests that, in S. pombe, Rheb binds to SpTOR2 in a GTP-dependent manner.

Rheb activates TORC1

Rheb activates TORC1

Figure 2 Rheb activates TORC1 both directly and indirectly. GTP-bound Rheb interacts directly with TORC1 to activate TORC1 kinase. GTP-bound Rheb also activates RalA, which activates PLD to increase production of PA. PA in turn interacts with TORC1

In addition to the direct interaction between mTOR and Rheb, activation of PA production by Rheb is an additional mechanism by which Rheb might regulate mTORC1. Rheb binds to and activates PLD in a GTP-dependent manner (Sun et al, 2008). PLD produces PA, which binds directly to and upregulates mTORC1. This finding reveals cross-talk between the TSC–Rheb and the PA pathways in the regulation of mTORC1 signalling. A recent study by Yoon and colleagues further demonstrated the role of PLD in mTORC1 regulation (Yoon et al, 2011). They showed that amino acids activate PLD through translocation of PLD to the lysosomal compartment. This translocation is positively regulated by human Vps34 and is necessary for the activation of mTORC1 by amino acids. These authors propose the existence of a Vps34–PLD1 pathway that activates mTORC1 in parallel to the Rag pathway (Yoon et al, 2011).

Although Rheb is required for the activation of mTORC1 by amino acids, Rheb itself does not participate in amino acid sensing, and GTP-loading of Rheb is not affected by amino acid depletion (Long et al, 2005b). Furthermore, amino acid depletion inhibits mTORC1 even in TSC2−/− fibroblasts (Roccio et al, 2006). Nevertheless, interaction of mTORC1 with Rheb depends on amino acid availability (Long et al, 2005b). As discussed below, the current model proposes that amino acids mediate translocation of mTORC1 to the lysosomal surface where mTORC1 interacts with and is activated by GTP-loaded Rheb (Sancak et al, 2008).

Regulation of TOR by Rag

Rag GTPases have unique features among the Ras GTPase subfamily members: they form heterodimers and lack a membrane-targeting sequence (Nakashima et al, 1999Sekiguchi et al, 2001). Gtr1 in S. cerevisiaewas the first member of this GTPase subfamily to be identified (Bun-Ya et al, 1992). The mammalian RagA and RagB GTPases were later described as Gtr1 orthologues (Hirose et al, 1998). Gtr2 in yeast (Nakashima et al, 1999) and its mammalian orthologues RagC and RagD (Sekiguchi et al, 2001) were subsequently discovered due to their ability to form heterodimers with Gtr1 in yeast and RagA and RagB in mammals, respectively. The crystal structure of the Gtr1–Gtr2 complex has been determined recently (Gong et al, 2011). Gtr1 and Gtr2 have similar structures, organized in two domains: an amino-terminal GTPase domain (designated as the G domain) and a carboxy-terminal domain. The Gtr1–Gtr2 heterodimer presents a pseudo-twofold symmetry resembling a horseshoe. The crystal structure reveals that Gtr1–Gtr2 dimerization results from extensive contacts between the C-terminal domains of both proteins, while the G domains do not contact each other (Gong et al, 2011).

Rag proteins mediate the activation of TORC1 in response to amino acids.

Rag proteins mediate the activation of TORC1 in response to amino acids.

Figure 3 Rag proteins mediate the activation of TORC1 in response to amino acids. The RagA/B–RagC/D heterodimer is anchored to the MP1–p14–p18 complex on the surface of the lysosome.

Overexpressed Rheb is mislocalized throughout the cell, and therefore interaction of mTORC1 with Rheb does not require amino-acid-induced translocation of mTORC1 to the lysosome. The model is further supported by observations in Drosophila showing that expression of a constitutively active mutant of RagA significantly increases the size of individual cells, whereas expression of a dominant negative mutant of RagA reduces cell size (Kim et al, 2008). Moreover, Rag plays a role in TORC1-mediated inhibition of autophagy both in Drosophila (Kim et al, 2008) and in human cells (Narita et al, 2011).

mTOR and small GTPases are therapeutic targets in the treatment of cancer (Berndt et al, 2011Dazert & Hall, 2011). Aberrant activation of GTPases, including Ras, Rho, Rab or Ran GTPases, promotes cell transformation and cancer (Agola et al, 2011Ly et al, 2010Pylayeva-Gupta et al, 2011), in some cases by acting in the mTOR pathway. Targeting GTPases by using farnesyltransferase inhibitors or geranylgeranyltransferase inhibitors affects signal transduction pathways, cell cycle progression, proliferation and cell survival. Both types of inhibitor are currently under investigation for cancer therapy, although only a small subset of patients responds to these inhibitors (Berndt et al, 2011). A better understanding of the relationship between GTPases and mTOR is essential for the design of combined therapies.

From a mechanistic point of view, research on TOR in different systems is continually adding new insight on the role of TOR in cell biology. However, what is lacking is an integration of the various proposed regulators of TOR, in particular small GTPases (see Sidebar A).

Sidebar A | In need of answers

  1. How are amino acids sensed by the cell?
  2. What is the mechanism by which amino acids regulate the GTP-loading of Rag proteins? What are the GEF and GAP for the Rag proteins?
  3. Is there a GEF that regulates the GTP-loading of Rheb?
  4. What is the molecular mechanism by which Rheb activates TORC1?
  5. How is the dual effect of Rac1 being both upstream and downstream from TOR regulated?
  6. How are the diverse GTPases that impinge on TOR integrated?

7.8.5 PI3K.Akt signaling in osteosarcoma

Zhang J1Yu XH2Yan YG1Wang C1Wang WJ3.
Clin Chim Acta. 2015 Apr 15; 444:182-192.


  • Activation of the PI3K/Akt signaling regulates various cellular functions.
  • The PI3K/Akt signaling may play a key role in the progression of osteosarcoma.
  • Targeting the PI3K/Akt signaling has therapeutic potential for osteosarcoma.

Osteosarcoma (OS) is the most common nonhematologic bone malignancy in children and adolescents. Despite the advances of adjuvant chemotherapy and significant improvement of survival, the prognosis remains generally poor. As such, the search for more effective anti-OS agents is urgent. The phosphatidylinositol 3-kinase (PI3K)/Akt pathway is thought to be one of the most important oncogenic pathways in human cancer. An increasing body of evidence has shown that this pathway is frequently hyperactivated in OS and contributes to disease initiation and development, including tumorigenesis, proliferation, invasion, cell cycle progression, inhibition of apoptosis, angiogenesis, metastasis and chemoresistance. Inhibition of this pathway through small molecule compounds represents an attractive potential therapeutic approach for OS. The aim of this review is to summarize the roles of the PI3K/Akt pathway in the development and progression of OS, and to highlight the therapeutic potential of targeting this signaling pathway. Knowledge obtained from the application of these compounds will help in further understanding the pathogenesis of OS and designing subsequent treatment strategies.

PK.Akt signaling

PK.Akt signaling

PI3K/Akt signaling

PI3K.Akt signaling pathway

PI3K.Akt signaling pathway

PI3K/Akt signaling pathway

PK.Akt therapeutic target

PK.Akt therapeutic target

PK/Akt therapeutic target

7.8.6 The mTORC1-S6K1 Pathway Regulates Glutamine Metabolism through the eIF4B-Dependent Control of c-Myc Translation

Csibi A1Lee G1Yoon SO1Tong H2,…, Fendt SM4Roberts TM2Blenis J5.
Curr Biol. 2014 Oct 6; 24(19):2274-80.

Growth-promoting signaling molecules, including the mammalian target of rapamycin complex 1 (mTORC1), drive the metabolic reprogramming of cancer cells required to support their biosynthetic needs for rapid growth and proliferation. Glutamine is catabolyzed to α-ketoglutarate (αKG), a tricarboxylic acid (TCA) cycle intermediate, through two deamination reactions, the first requiring glutaminase (GLS) to generate glutamate and the second occurring via glutamate dehydrogenase (GDH) or transaminases. Activation of the mTORC1 pathway has been shown previously to promote the anaplerotic entry of glutamine to the TCA cycle via GDH. Moreover, mTORC1 activation also stimulates the uptake of glutamine, but the mechanism is unknown. It is generally thought that rates of glutamine utilization are limited by mitochondrial uptake via GLS, suggesting that, in addition to GDH, mTORC1 could regulate GLS. Here we demonstrate that mTORC1 positively regulates GLS and glutamine flux through this enzyme. We show that mTORC1 controls GLS levels through the S6K1-dependent regulation of c-Myc (Myc). Molecularly, S6K1 enhances Myc translation efficiency by modulating the phosphorylation of eukaryotic initiation factor eIF4B, which is critical to unwind its structured 5′ untranslated region (5’UTR). Finally, our data show that the pharmacological inhibition of GLS is a promising target in pancreatic cancers expressing low levels of PTEN.


  • The mTORC1 pathway positively regulates GLS and glutamine flux
  • mTORC1 controls the translation efficiency of Myc mRNA
  • S6K1 regulates Myc translation through eIF4B phosphorylation
  • Inhibition of GLS decreases the growth of pancreatic cancer cells

Figure 1. The mTORC1 Pathway Regulates GLS1 (A–C and E) GLS protein levels in whole cell lysates from Tsc2 WT and Tsc22/2 MEFs treated with rapamycin (Rapa) for 8 hr (A); HEK293T cells stably expressing Rheb WT, the mutant S16H Rheb, or EV and treated with rapamycin for 24 hr (B); Tsc22/2 MEFs treated with rapamycin at the indicated time points (C); and Tsc2 WT and Tsc22/2 MEFs treated with the indicated compounds for 8 hr (E). The concentrations of the compounds were as follows: rapamycin, 20 ng/ml; LY294002 (LY), 20 mM; and BEZ235, 10 mM. (D) Time course of glutamine consumption in Tsc22/2 MEFs incubated with or without 20ng/ml rapamycin for 24 hr. Each time data point is an average of triplicate experiments. (F) Intracellular glutamine levels in Tsc22/2 MEFs treated with rapamycin for 24 hr. (G) Glutamineflux inTsc22/2 MEFs expressing an EV or re-expressingTSC2 treated with theindicated compounds for 24hr.The concentrations of the compounds were as follows: rapamycin 20 ng/ml; LY294002, 20 mM; BEZ235, 10 mM; BPTES, 10 mM; and 6-diazo-5-oxo-l-norleucine, 1mM. The mean is shown. Error bars represent the SEM from at least three biological replicates. Numbers below the immunoblot image represent quantification normalized to the loading control. See also Figure S1.

Figure2. The mTORC1 Pathway Regulates GLS1 via Myc GLS and Myc protein levels in whole cell lysates from BxPC3 cells transfected with a nontargeting control (NTC) siRNA or four independent siRNAs against Myc for 72 hr (A), Tsc2 WT and Tsc22/2 MEFs treated with rapamycin (20 ng/ml) for 8 hr (B), and Tsc22/2 MEFs stably expressing Myc or EV and treated with rapamycin (20 ng/ml) for 24 hr (C).

Figure 3. The mTORC1 Substrate S6K1 Controls GLS through Myc mRNA Translation (A) Normalized luciferase light units of Tsc22/2 MEFs stably expressing a Myc-responsive firefly luciferase construct (Myc-Luc) or vector control (pCignal Lenti-TRE Reporter). Myc transcriptional activity was measured after treatment with rapamycin (20 ng/ml) or PF4708671 (10 mM) for 8 hr. (B) GLS and Myc protein levels in whole cell lysates from HEK293T cells expressing HA-S6K1-CA (F5A-R3A-T389E) or EV treated with rapamycin (20 ng/ml) for 24 hr. HA, hemagglutinin. (CandD) Intracellular glutamine levels of Tsc22/2 MEFs stably expressing S6K-CA(F5A/R5A/T389E, mutating either the three arginines or all residues within the RSPRR motif to alanines shows the same effect; [10]) or empty vector and treated with rapamycin (20 ng/ml) or DMSO for 48 hr (C) or transfected with NTC siRNA or siRNA against both S6K1/2 (D). 24 hr posttransfection, cells transfected with NTC siRNA were treated with PF4708671 (10 mM) or DMSO for 48 hr. (E) Glutamine consumption of Tsc22/2 MEFs transfected with NTC siRNA or siRNA against both S6K1/2. 72 hr posttransfection, media were collected, and levels of glutamine in the media were determined. (F) Normalized luciferase light units of Tsc2WTMEFs transfected with thepDL-N reporter construct containing the 50 UTR of Myc under the control of Renilla luciferase. Firefly luciferase was used as an internal control. 48hr posttransfection, cells were treated with rapamycin (20ng/ml) or PF4708671 (10mM) for 8h. (G) Relative levels of Myc, Gls, and Actin mRNA in each polysomal gradient fraction. mRNA levels were measured by quantitative PCR and normalized to the 5S rRNA level. HEK293T cells were treated with rapamycin (20 ng/ml) for 24 hr, and polysomes were fractionated on sucrose density gradients. The values are averaged from two independent experiments performed in duplicate, and the error bars denote SEM (n = 4). (Hand I) GLS and Myc protein levels in whole cell lysates from Tsc22/2 MEFs transfected with NTC siRNA or two independent siRNAs against eIF4B for 72hr (H) and Tsc22/2 MEFs stably expressing eIF4B WT, mutant S422D, or EV) and treated with rapamycin for 24 hr (I). The mean is shown. Error bars represent the SEM from at least three biological replicates. The asterisk denotes a nonspecific band. The numbers below the immunoblot image represent quantification normalized to the loading control. See also Figures S2 and S3.

Figure 4. Inhibition of GLS Reduces the Growth of Pancreatic Cancer Cells (A) GLS and Myc protein levels in whole cell lysates from BxPC3, MIAPaCa-2, or AsPC-1 cells treated with rapamycin (20 ng/ml) or BEZ235 (1 mM) for 24 hr. (B) Glutamine consumption of BxPC3 or AsPC-1 cells 48 hr after plating. (Cand D) Soft agar assays with BxPC3 or AsPC-1 cells treated with BPTES (10 mM), the combination of BPTES (10 mM) + OAA (2 mM) (C) and BxPC3 or AsPC-1 cells treated with BPTES, and the combination of BPTES (10 mM) + NAC (10 mM) (D). NS, not significant. The mean is shown. Error bars represent the SEM from at least three biological replicates.

7.8.7 Localization of mouse mitochondrial SIRT proteins

Nakamura Y1Ogura MTanaka DInagaki N.
Biochem Biophys Res Commun. 2008 Feb 1; 366(1):174-9

Yeast silent information regulator 2 (SIR2) is involved in extension of yeast longevity by calorie restriction, and SIRT3, SIRT4, and SIRT5 are mammalian homologs of SIR2 localized in mitochondria. We have investigated the localization of these three SIRT proteins of mouse. SIRT3, SIRT4, and SIRT5 proteins were localized in different compartments of the mitochondria. When SIRT3 and SIRT5 were co-expressed in the cell, localization of SIRT3 protein changed from mitochondria to nucleus. These results suggest that the SIRT3, SIRT4, and SIRT5 proteins exert distinct functions in mitochondria. In addition, the SIRT3 protein might function in nucleus

Fig. 1. Localization of SIRT3, SIRT4, and SIRT5 in mitochondria. (A) Confocal microscopy. SIRT3-myc (upper panels), SIRT4-myc (middle panels), and SIRT5-FLAG (lower panels) were expressed in COS7 cells and immunostained with anti-myc antibody or anti-FLAG antibody. Mitochondria and nuclei were stained by MitoTracker Red and DAPI, respectively, and fluorescent images were obtained using a confocal microscope. (B) Fractionation of post-nuclear supernatant. SIRT3-myc, SIRT4-myc, and SIRT5-FLAG proteins each was expressed in COS7 cells, and the obtained PNS was fractionated into mitochondria-enriched precipitate (P1), microsome-enriched precipitate (P2), and supernatant (S) fractions. The three fractions were separated by SDS–PAGE and then analyzed by Western blotting using anti-myc antibody for SIRT3-myc and SIRT4-myc or anti-FLAG antibody for SIRT5-FLAG. Hsp60, calnexin, and GAPDH were used as endogenous markers for mitochondria, microsome, and cytosol, respectively. (C) Alkaline treatment of mitochondria. Mitochondria prepared from the COS7 cells expressing each of the SIRT3-myc, SIRT4-myc, and SIRT5-FLAG proteins were treated with Na2CO3. The reaction mixture was centrifuged to separate the precipitate and supernatant fractions, containing membrane-integrated proteins and soluble proteins, respectively. The two fractions were analyzed by Western blotting. Cytochrome c (cytc) and hsp60 were used as endogenous protein markers for mitochondrial soluble protein. (D) Submitochondrial fractionation. The mitochondria from COS7 cells expressing one of three SIRT proteins were treated with either H2O (hypotonic) or TX-100, and then treated with trypsin. The reaction mixtures were analyzed by Western blotting. Cytochrome c and hsp60 were used as endogenous markers for mitochondrial intermembrane space protein and matrix protein, respectively.

Fig. 2. Localization of SIRT3 when co-expressed with SIRT5. (A) Confocal microscopic analysis of COS7 cells expressing two of the three mitochondrial SIRT proteins. SIRT3-myc and SIRT5-FLAG (upper panels), SIRT3-myc and SIRT4-FLAG (middle panels), and SIRT4-myc and SIRT5-FLAG (lower panels) were co-expressed in COS7 cells, and immunostained using antibodies against myc tag and FLAG tag. Nuclei were stained by DAPI. (B) Subcellular fractionation of PNS. PNS of COS7 cells co-expressing SIRT3-myc and SIRT5-FLAG was fractionated into mitochondria-enriched precipitate (P1), microsome-enriched precipitate (P2), and supernatant (S) fractions, and these fractions along with whole cell lysate were analyzed by Western blotting. (C) Subcellular fractionation using digitonin. COS7 cells expressing either SIRT3-myc (left) or SIRT5-FLAG (middle) or both (right) were solubilized by digitonin, and the obtained lysate was centrifuged and fractionated into nuclear-enriched insoluble (INS), and soluble (SOL) fractions. Hsp60 and laminA/C were used as endogenous markers for mitochondria protein and nucleus protein, respectively.

Because the segment containing amino acid residues 66– 88 potentially forms a basic amphiphilic a-helical structure, it could serve as a MTS. To examine the role of this segment, SIRT3 mutant SIRT3mt, in which the four amino acid residues 72–75 were replaced by four alanine residues, was constructed (Fig. 3A). When SIRT3mt alone was expressed in COS7 cells, SIRT3mt protein was not detected in mitochondria but was widely distributed in the cell in confocal microscopic analysis (Fig. 3B, upper panels). In addition, when SIRT3mt and SIRT5 were co-expressed, the distribution of SIRT3mt protein was not changed compared to that expressed alone (Fig. 3B, lower panels). In fractionation of PNS, SIRT3mt protein was fractionated into S fraction both when SIRT3mt was expressed alone and when SIRT3mt and SIRT5 were co-expressed. SIRT5 protein was localized in mitochondria when SIRT3mt and SIRT5 were co-expressed (Fig. 3C). These results indicate that the MTS is necessary not only for targeting SIRT3 to mitochondria in the absence of SIRT5 but also for targeting SIRT3 to nucleus in the presence of SIRT5.

Fig. 3. Effect of disruption of putative mitochondrial targeting signal of SIRT3. (A) Alanine replacement of putative MTS of SIRT3. Four residues of the putative MTS of SIRT3 (amino acid residues 72–75) were replaced with four alanine residues. In the SIRT3mt sequence, amino acid residues identical with wild-type SIRT3 protein are indicated with dots. (B) Confocal microscopy. Immunofluorescent images of COS7 cells expressing SIRT3mt-myc alone (upper panels) or both SIRT3mt-myc and SIRT5-FLAG (lower panels) are shown. Mitochondria and nuclei were stained by MitoTracker Red and DAPI, respectively. (C) Subcellular fractionation of PNS. PNSs of COS7 cells expressing SIRT3mt-myc alone (an upper panel) or co-expressing SIRT3mt-myc and SIRT5-FLAG (middle and lower panels) were centrifuged and fractionated into mitochondria-enriched precipitate (P1), microsome-enriched precipitate (P2), and supernatant (S) fractions. The fractions were analyzed by Western blotting.

Fig. 4. Effect of disruption of putative nuclear localization signal of SIRT3. (A) Comparison of the amino acid sequences of putative NLS of SIRT3, SIRT3nu, and SV40 large T antigen. Three basic amino acid residues of the putative NLS of SIRT3 (amino acid residues 214–216) were replaced with three alanine residues. In the SIRT3nu sequence, amino acid residues identical with wild-type SIRT3 protein are indicated with dots. The classical NLS of SV40 large T antigen also is shown (SV40). (B) Confocal microscopy. Immunofluorescent images of COS7 cells expressing SIRT3nu-myc alone (upper panels) or both SIRT3nu-myc and SIRT5-FLAG (lower panels) are shown. Mitochondria and nuclei were stained by MitoTracker Red and DAPI, respectively. (C) Subcellular fractionation of PNS. PNSs of the COS7 cells expressing SIRT3nu-myc alone (an upper panel) or co-expressing SIRT3numyc and SIRT5-FLAG (middle and lower panels) were fractionated into mitochondria-enriched precipitate (P1), microsome-enriched precipitate (P2), and supernatant (S) fractions. The fractions were analyzed by Western blotting.

The sequence containing amino acid sequence 213-219 of the SIRT3 closely resembles the putative protein classical NLS of the SV40 T antigen (Fig. 4A). To examine whether this sequence functions as a NLS, the mutant SIRT3 protein SIRT3nu, in which the three basic amino acid residues (214–216) in the putative NLS of SIRT3 were replaced by three alanine residues (Fig. 4A), was constructed. When SIRT3nu alone was expressed in COS7 cells, it was localized in mitochondria (Fig. 4B, upper panels). In the cells co-expressing SIRT3nu and SIRT5, a shift of SIRT3nu protein to the nucleus was not observed, and SIRT3nu protein and a part of SIRT5 protein were scattered widely in the cell in confocal microscopic analysis (Fig. 4B, lower panels). In fractionation of PNS, all of the SIRT3nu protein and nearly half of the SIRT5 protein were shifted from P1 fraction to S fraction by co-expression (Figs. 1B and 4C). These results suggest that the segment containing amino acid residues 213–219 of SIRT3 plays an important role in the localization shift of SIRT3 protein to nucleus when co-expressed with SIRT5. Furthermore, SIRT5 may well hamper SIRT3nu localization in mitochondria through interaction with SIRT3nu. However, further study is required to elucidate the mechanism of the localization shift of SIRT3 protein. Interestingly, recent study has reported that human prohibitin 2 (PHB2), known as a repressor of estrogen receptor (ER) activity, is localized in the mitochondrial inner membrane, and translocates to the nucleus in the presence of ER and estradiol [18]. Although the mechanism of regulation of the expression level of SIRT5 remains unknown, SIRT3 might play a role in communication between nucleus and mitochondria in a SIRT5-dependent manner. The function of mitochondrial SIRT proteins is still not well known. In the present study, we determined the exact localization of mouse SIRT3, SIRT4, and SIRT5 proteins in mitochondria. In addition, we demonstrated that SIRT3 can be present in nucleus in the presence of SIRT5. It has been reported that SIRT3 deacetylates proteins that are not localized in mitochondria in vitro such as histone-4 peptide and tubulin [14]. Thus, if SIRT3 is present in nucleus in vivo, SIRT3 protein might well deacetylate nuclear proteins. These results provide useful information for the investigation of the function of these proteins.


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7.8.8 SIRT4 Has Tumor-Suppressive Activity and Regulates the Cellular Metabolic Response to DNA Damage by Inhibiting Mitochondrial Glutamine Metabolism

Jeong SM1Xiao CFinley LWLahusen TSouza ALPierce KLi YH, et al.
Cancer Cell. 2013 Apr 15; 23(4):450-63.

DNA damage elicits a cellular signaling response that initiates cell cycle arrest and DNA repair. Here we find that DNA damage triggers a critical block in glutamine metabolism, which is required for proper DNA damage responses. This block requires the mitochondrial SIRT4, which is induced by numerous genotoxic agents and represses the metabolism of glutamine into TCA cycle. SIRT4 loss leads to both increased glutamine-dependent proliferation and stress-induced genomic instability, resulting in tumorigenic phenotypes. Moreover, SIRT4 knockout mice spontaneously develop lung tumors. Our data uncover SIRT4 as an important component of the DNA damage response pathway that orchestrates a metabolic block in glutamine metabolism, cell cycle arrest and tumor suppression.

DNA damage initiates a tightly coordinated signaling response to maintain genomic integrity by promoting cell cycle arrest and DNA repair. Upon DNA damage, ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and RAD3-related protein (ATR) are activated and induce phosphorylation of Chk1, Chk2 and γ-H2AX to trigger cell cycle arrest and to initiate assembly of DNA damage repair machinery (Abraham, 2001Ciccia and Elledge, 2010Su, 2006). Cell cycle arrest is a critical outcome of the DNA damage response (DDR) and defects in the DDR often lead to increased incorporation of mutations into newly synthesized DNA, the accumulation of chromosomal instability and tumor development (Abbas and Dutta, 2009Deng, 2006Negrini et al., 2010).

The cellular metabolic response to DNA damage is not well elucidated. Recently, it has been shown that DNA damage causes cells to upregulate the pentose phosphate pathway (PPP) to generate nucleotide precursors needed for DNA repair (Cosentino et al., 2011). Intriguingly, a related metabolic switch to increase anabolic glucose metabolism has been observed for tumor cells and is an important component of rapid generation of biomass for cell growth and proliferation (Jones and Thompson, 2009Koppenol et al., 2011). Hence, cells exposed to genotoxic stress face a metabolic challenge; they must be able to upregulate nucleotide biosynthesis to facilitate DNA repair, while at the same time limiting proliferation and inducing cell cycle arrest to limit the accumulation of damaged DNA. The molecular events that regulate this specific metabolic program in response to DNA damage are still unclear.

Sirtuins are a highly conserved family of NAD+-dependent deacetylases, deacylases, and ADP-ribosyltransferases that play various roles in metabolism, stress response and longevity (Finkel et al., 2009;Haigis and Guarente, 2006). In this study, we studied the role of SIRT4, a mitochondria-localized sirtuin, in cellular metabolic response to DNA damage and tumorigenesis.

DNA damage represses glutamine metabolism

To investigate how cells might balance needs for continued nucleotide synthesis, while also preparing for cell cycle arrest, we assessed the metabolic response to DNA damage by monitoring changes in the cellular consumption of two important fuels, glucose and glutamine, after DNA-damage. Strikingly, treatment of primary mouse embryonic fibroblasts (MEFs) with camptothecin (CPT), a topoisomerase 1 inhibitor that causes double-stranded DNA breaks (DSBs), resulted in a pronounced reduction in glutamine consumption (Figure 1A). Glutamine metabolism in mammalian cells is complex and contributes to a number of metabolic pathways. Glutamine is the primary nitrogen donor for protein and nucleotide synthesis, which are essential for cell proliferation (Wise and Thompson, 2010). Additionally, glutamine provides mitochondrial anaplerosis. Glutamine can be metabolized via glutaminase (GLS) to glutamate and NH4+, and further converted to the tricarboxylic acid (TCA) cycle intermediate α-ketoglutarate via glutamate dehydrogenase (GDH) or aminotransferases. This metabolism of glutamine provides an important entry point of carbon to fuel the TCA cycle (Jones and Thompson, 2009), and accounts for the majority of ammonia production in cells (Yang et al., 2009). CPT-induced reduction of glutamine consumption was accompanied by a reduction in ammonia secretion from cells (Figure 1B). Notably, under these conditions, we observed no obvious decrease in glucose uptake and lactate production (Figures 1C and 1D), consistent with previous studies showing that intact glucose utilization through the PPP is important for a normal DNA damage response (Cosentino et al., 2011). Preservation of glucose uptake also suggests that repression of glutamine consumption may be a specific metabolic response to genotoxic stress and not reflective of a non-specific metabolic crisis.

Figure 1 Glutamine metabolism is repressed by genotoxic stress

To examine the metabolic response to other forms of genotoxic stress, we monitored the metabolic response to ultra-violet (UV) exposure in primary MEFs. Similar to CPT treatment, UV exposure reduced glutamine uptake, without significant changes in glucose consumption (Figures 1E and 1F). Similarly two human cell lines, HepG2 and HEK293T, also demonstrated marked reductions in glutamine uptake in response to DNA damaging agents without comparable changes in glucose uptake (Figures 1G and 1HFigures S1A and S1B). Taken together, these results suggest that a variety of primary and tumor cell lines (from mouse or human) respond to genotoxic stress by down-regulating glutamine metabolism.

To examine in more detail the changes in cellular glutamine metabolism after genotoxic stress, we performed a global metabolomic analysis with transformed MEFs before and after DNA damage. As previously reported, we observed that PPP intermediates were increased in response to DNA damage (Figures 1I and 1J). Remarkably, we observed a decrease in measured TCA cycle intermediates after UV exposure (Figures 1I and 1K). Moreover, we found that HepG2 cells showed a similar metabolomic shift in response to DNA damage (Figure S1D). We did not observe a clear, coordinated repression of nucleotides or glutamine-derived amino acids after exposure to DNA damage (Figure S1C).

To determine whether reduction in TCA cycle metabolites was the consequence of reduced glutamine metabolism, we performed a time-course tracer study to monitor the incorporation of [U-13C5]glutamine into TCA cycle intermediates at 0, 2 and 4 hr after UV treatment. We observed that after UV exposure, cells reduced contribution of glutamine to TCA cycle intermediates in a time-dependent manner (Figure 1L). Moreover, the vast majority of the labeled fumarate and malate contained four carbon atoms derived from [U-13 C5]glutamine (Figure S1F, M+3 versus M+4), indicating that most glutamine was used in the non-reductive direction towards succinate, fumarate and malate production. We were able to observe little contribution of glutamine flux into nucleotides or glutathione in control or UV-treated cells at these time points (data not shown), suggesting that the mitochondrial metabolism of glutamine accounts for the majority of glutamine consumption in these cells. Taken together, the metabolic flux analysis demonstrates that DNA damage results in a reduction of mitochondrial glutamine anaplerosis, thus limiting the critical refueling of carbons into the TCA cycle.

To assess the functional relevance of decreased glutamine metabolism after DNA damage, we deprived cells of glucose, thereby shifting cellular dependence to glutamine to maintain viability (Choo et al., 2011Dang, 2010). If DNA damage represses glutamine usage, we reasoned that cells would be more sensitive to glucose deprivation. Indeed, following 72 hr of glucose deprivation, cell death in primary MEFs was significantly elevated at 10 hr after UV exposure (Figure S1E). However, cells cultured with glucose remained viable in these conditions. Thus, these data demonstrate that genotoxic stress limits glutamine entry into the central mitochondrial metabolism of the TCA cycle.

SIRT4 is induced in response to genotoxic stress

Because sirtuins regulate both cellular metabolism and stress responses (Finkel et al., 2009Schwer and Verdin, 2008), we examined whether sirtuins were involved in the metabolic adaptation to DNA damage. We first examined the expression of sirtuins in the response to DNA damage. Specifically, we probed SIRT1, which is involved in stress responses (Haigis and Guarente, 2006), as well as mitochondrial sirtuins (SIRT3–5), which have been shown to regulate amino acid metabolism (Haigis et al., 2006Hallows et al., 2011Nakagawa et al., 2009). Remarkably, SIRT4 mRNA levels were induced by nearly 15-fold at 15 hr after CPT treatment and 5-fold after etoposide (ETS), a topoisomerase 2 inhibitor, in HEK293T cells (Figure 2A). Interestingly, the induction of SIRT4 was significantly higher than the induction of SIRT1 and mitochondrial SIRT3 (~2-fold), sirtuins known to be induced by DNA damage and regulate cellular responses to DNA damage (Sundaresan et al., 2008Vaziri et al., 2001Wang et al., 2006). Moreover, overall mitochondrial mass was increased by only 10% in comparison with control cells (Figure S2A), indicating that the induction of SIRT4 is not an indirect consequence of mitochondrial biogenesis. These data hint that SIRT4 may have an important, previously undetermined role in the DDR.

Figure 2 SIRT4 is induced by DNA damage stimuli

To test the induction of SIRT4 in the general genotoxic stress response, we treated cells with other types of DNA damage, including UV and gamma-irradiation (IR). SIRT4 mRNA levels were also increased by these genotoxic agents (Figures S2B and S2C) and low doses of CPT and UV treatment also induced SIRT4expression (Figures S2D and S2E). We observed similar results with MEFs (Figures 2B and 2DFigure S2F) and HepG2 cells (Figure S2G). DNA damaging agents elevated SIRT4 in p53-inactive HEK293T cells (Figures 2A and 2C) and in p53-null PC3 human prostate cancer cells (Figure S2H), suggesting that SIRT4can be induced in a p53-independent manner.

To examine whether the induction of SIRT4 occurred as a result of cell cycle arrest, we measured SIRT4levels after the treatment of nocodazole, which inhibits microtubule polymerization to block mitosis. While treatment with nocodazole completely inhibited cell proliferation (data not shown), SIRT4 expression was not elevated (Figure S2I). In addition, we analyzed SIRT4 expression in distinct stages of the cell cycle in HepG2 cells synchronized with thymidine block (Figure S2J, Left). SIRT4 mRNA levels were measured at different times after release and were not elevated during G1 or G2/M phases (Figure S2J, Right), suggesting thatSIRT4 is not induced as a general consequence of cell cycle arrest. Next, we re-examined the localization of SIRT4 after DNA damage. SIRT4 localizes to the mitochondria of human and mouse cells under basal, unstressed conditions (Ahuja et al., 2007Haigis et al., 2006). Following CPT treatment, SIRT4 colocalized with MitoTracker, a mitochondrial-selective marker, indicating that SIRT4 retains its mitochondrial localization after exposure to DNA damage (Figure S2K). Taken together, our findings demonstrate that SIRT4 is induced by multiple forms of DNA damage in numerous cell types, perhaps to coordinate the mitochondrial response to genotoxic stress.

SIRT4 represses glutamine anaplerosis

We observed that glutamine anaplerosis is repressed by genotoxic stress (Figure 1) and SIRT4 is induced by DNA damage (Figure 2). Additionally, previous studies reported that SIRT4 represses glutamine anaplerosis (Haigis et al., 2006). We next tested whether SIRT4 directly regulates cellular glutamine metabolism and contribution of glutamine to the TCA cycle. Like DNA damage, SIRT4 overexpression (SIRT4-OE) in HepG2, HeLa or HEK293T cells resulted in the repression of glutamine consumption (Figure 3AFigures S3A–C). Conversely, SIRT4 knockout (KO) MEFs consumed more glutamine than did wild-type (WT) cells (Figure 3B).

Figure 3 SIRT4 represses mitochondrial glutamine metabolism in response to DNA damage

Mitochondrial glutamine catabolism refuels the TCA cycle and is essential for viability in the absence of glucose (Choo et al., 2011Yang et al., 2009). Thus, we examined the effect of SIRT4 on cell survival during glucose deprivation. Overexpression of SIRT4 in HEK293T or HeLa cells increased cell death in glucose-free media compared to control cells (Figure 3CFigure S3D). Importantly, this cell death was completely rescued by the addition of pyruvate or cell permeable dimethyl α-ketoglutarate (DM-KG), demonstrating that SIRT4 overexpression reduced the ability of cells to utilize glutamine for mitochondrial energy production. Moreover, cell death was equally maximized in the absence of glucose and presence of the mitochondrial ATPase inhibitor oligomycin (Figure 3C). These findings are in line with the model that SIRT4 induction with DNA damage limits glutamine metabolism and utilization by the TCA cycle

We next utilized a metabolomic approach to interrogate glutamine usage in the absence of SIRT4. SIRT4 KO MEFs demonstrated elevated levels of TCA cycle intermediates (Figure 3J, WT versus KO), whereas intermediates of glycolysis were comparable with WT cells (data not shown). Nucleotides and other metabolites downstream of glutamine metabolism were not coordinately regulated by SIRT4 loss (Figure S3E and data not shown). Next, we analyzed glutamine flux in WT and SIRT4 KO MEFs in medium containing [U-13C5]glutamine for 2 or 4 hours and measured isotopic enrichment of TCA cycle intermediates. Loss of SIRT4 promoted a higher rate of incorporation of 13C-labeled metabolites derived from [U-13C5]glutamine in all TCA cycle intermediates measured (Figure 3D). These data provide direct evidence that SIRT4 loss drives increased entry of glutamine-derived carbon into the TCA cycle.

Next, we examined the mechanisms involved in this repression of glutamine anaplerosis. GLS is the first required enzyme for mitochondrial glutamine metabolism (Curthoys and Watford, 1995) and its inhibition limits glutamine flux into the TCA cycle (Wang et al., 2010; Le et al., 2012; Yuneva et al., 2012). Treatment with bis-2-(5-phenylacetoamido-1,2,4-thiadiazol-2-yl)ethyl sulfide (BPTES) (Robinson et al., 2007), an inhibitor of GLS1, repressed glutamine uptake and completely rescued the increased glutamine consumption of SIRT4 KO cells (Figure 3E). Moreover, SIRT4 overexpression no longer inhibited glutamine uptake when GLS1 was reduced by using short hairpin RNAs (shRNAs) (Figures 3F and 3G), demonstrating that SIRT4 regulates mitochondrial glutamine metabolism. SIRT4 is a negative regulator of GDH activity (Haigis et al., 2006) and SIRT4 KO MEFs exhibited increased GDH activity in comparison with WT MEFs (Figure S3F). To test whether SIRT4 regulates mitochondrial glutamine metabolism via inhibiting GDH activity, we measured glutamine uptake in WT and SIRT4 KO cells in the presence of EGCG, a GDH inhibitor (Choo et al., 2011Li et al., 2006). The treatment of EGCG partially rescued the increased glutamine uptake of KO cells (Figure S3G), suggesting that GDH contributes to the role of SIRT4 in glutamine metabolism.

SIRT4 represses mitochondrial glutamine metabolism after DNA damage

SIRT4 regulates cell cycle progression and genomic fidelity in response to DNA damage

Figure 4 SIRT4 is involved in cellular DNA damage responses

SIRT4 represses tumor proliferation

Figure 5 SIRT4 has tumor suppressive function

(A and B) Growth curves of WT and SIRT4 KO MEFs (n = 3) cultured in standard media (A) or media supplemented with BPTES (10 μM) (B). Data are means ±SD.

(C and D) Growth curves of Vector and SIRT4-OE HeLa cells (n = 3) cultured in standard media (C) or media supplemented with BPTES (10 μM) (D). Data are means ±SD.

(E) Focus formation assays with transformed WT and SIRT4 KO MEFs (left). Cells were cultured with normal medium or medium without glucose or glutamine for 10 days and stained with crystal violet. The number of colonies was counted (right) (n =3 samples of each condition). n.d., not determined.

(F) Focus formation assays with transformed KO MEFs reconstituted with SIRT4 or a catalytic mutant of SIRT4 (n = 3). Cells were cultured for 8 days and stained with crystal violet.

(G) Contact inhibited cell growth of transformed WT and SIRT4 KO MEFs cultured in the presence of DMSO or BPTES (10 μM) for 14 days (left). The number of colonies was counted (right). Data are means ±SEM. n.s., not significant. *p < 0.05, **p < 0.005. See also Figure S5.

SIRT4 represses tumor formation in vivo

To investigate SIRT4 function in human cancers, we examined changes in SIRT4 expression. SIRT4 mRNA level was reduced in several human cancers, such as small cell lung carcinoma (Garber et al., 2001), gastric cancer (Wang et al., 2012), bladder carcinoma (Blaveri et al., 2005), breast cancer (TCGA) and leukemia (Choi et al., 2007) (Figure 6A). Of note, lower SIRT4 expression associated with shorter time to death in lung tumor patients (Shedden et al., 2008) (Figure 6B). Overall the expression data is consistent with the model that SIRT4 may play a tumor suppressive role in human cancers.

Figure 6 SIRT4 is a mitochondrial tumor suppressor

SIRT4 regulates glutamine metabolism in lung tissue

To test further the biological relevance of this pathway in lung, we examined whether SIRT4 is induced in vivo after exposure to DNA damaging IR treatment. Remarkably, Sirt4 was significantly induced in lung tissue after IR exposure (Figure 7A). We next examined whether IR repressed glutamine metabolism in vivo, as observed in cell culture by examining GDH activity in lung tissue from WT and SIRT4 KO mice with or without IR exposure. GDH activity was elevated in lung tissue extracts from SIRT4 KO mice compared with WT lung tissue (Figure 7B). Importantly, GDH activity was significantly decreased in lung tissue from WT mice after IR exposure, whereas not in lung tissue from KO mice (Figure 7C). Thus, these findings recapitulate our cellular studies and are in line with the model that SIRT4 induction with DNA damage limits mitochondrial glutamine metabolism and utilization.

SIRT4 inhibits mitochondria glutamine metabolism in vivo

SIRT4 inhibits mitochondria glutamine metabolism in vivo

Figure 7 SIRT4 inhibits mitochondria glutamine metabolism in vivo

To assess whether the functions of SIRT4 can be reproduced in these lung tumors, cells derived from SIRT4 KO lung tumors were reconstituted with wild type SIRT4 (Figure S7A). As expected, SIRT4 reconstitution reduced glutamine uptake, but not glucose uptake (Figures 7D and 7E) and repressed proliferation (Figure S7B) of lung tumor cells.

Here, we report that SIRT4 has an important role in cellular metabolic response to DNA damage by regulating mitochondrial glutamine metabolism with important implication for the DDR and tumorigenesis. First, we discovered that DNA damage represses cellular glutamine metabolism (Figure 1). Next, we found that SIRT4 is induced by genotoxic stress (Figure 2) and is required for the repression of mitochondrial glutamine metabolism (Figure 3). This metabolic response contributes to the control of cell cycle progression and the maintenance of genomic integrity in response to DNA damage (Figure 4). Loss of SIRT4 increased glutamine-dependent tumor cell proliferation and tumorigenesis (Figure 5). In mice, SIRT4 loss resulted in spontaneous tumor development (Figure 6). We demonstrate that SIRT4 is induced in normal lung tissue in response to DNA damage where it represses GDH activity. Finally, the glutamine metabolism-genomic fidelity axis is recapitulated in lung tumor cells derived from SIRT4 KO mice via SIRT4 reconstitution (Figure 7). Our studies therefore uncover SIRT4 as a important regulator of cellular metabolic response to DNA damage that coordinates repression of glutamine metabolism, genomic stability and tumor suppression.

The DDR is a highly orchestrated and well-studied signaling response that detects and repairs DNA damage. Upon sensing DNA damage, the ATM/ATR protein kinases are activated to phosphorylate target proteins, leading to cell cycle arrest, DNA repair, transcriptional regulation and initiation of apoptosis (Ciccia and Elledge, 2010Su, 2006). Dysregulation of this pathway is frequently observed in many tumors. Emerging evidence has suggested that cell metabolism also plays key roles downstream of the DDR-induced pathways.


7.8.9 Mitochondrial sirtuins and metabolic homeostasis

Pirinen E1Lo Sasso GAuwerx J.
Best Pract Res Clin Endocrinol Metab. 2012 Dec; 26(6):759-70.

The maintenance of metabolic homeostasis requires the well-orchestrated network of several pathways of glucose, lipid and amino acid metabolism. Mitochondria integrate these pathways and serve not only as the prime site of cellular energy harvesting but also as the producer of many key metabolic intermediates. The sirtuins are a family of NAD+-dependent enzymes, which have a crucial role in the cellular adaptation to metabolic stress. The mitochondrial sirtuins SIRT3, SIRT4 and SIRT5 together with the nuclear SIRT1 regulate several aspects of mitochondrial physiology by controlling posttranslational modifications of mitochondrial protein and transcription of mitochondrial genes. Here we discuss current knowledge how mitochondrial sirtuins and SIRT1 govern mitochondrial processes involved in different metabolic pathways.

Mitochondria are organelles composed of a matrix enclosed by a double (inner and outer) membrane (1). Major cellular functions, such as nutrient oxidation, nitrogen metabolism, and especially ATP production, take place in the mitochondria. ATP production occurs in a process referred to as oxidative phosphorylation (OXPHOS), which involves electron transport through a chain of protein complexes (I-IV), located in the inner mitochondrial membrane. These complexes carry electrons from electron donors (e.g. NADH) to electron acceptors (e.g. oxygen), generating a chemiosmotic gradient between the mitochondrial intermembrane space and matrix. The energy stored in this gradient is then used by ATP synthase to produce ATP (1). One well-known side effect of the OXPHOS process is the production of reactive oxygen species (ROS) that can generate oxidative damage in biological macromolecules (1). However, to neutralize the harmful effects of ROS, cells have several antioxidant enzymes, including superoxide dismutase, catalase, and peroxidases (1). The sirtuin silent information regulator 2 (Sir2), the founding member of the sirtuin protein family, was identified in 1984 (2). Sir2 was subsequently characterized as important in yeast replicative aging (3) and shown to posses NAD+-dependent histone deacetylase activity (4), suggesting it could play a role as an energy sensor. A family of conserved Sir2-related proteins was subsequently identified. Given their involvement in basic cellular processes and their potential contribution to the pathogenesis of several diseases (5), the sirtuins became a widely studied protein family.

In mammals the sirtuin family consists of seven proteins (SIRT1-SIRT7), which show different functions, structure, and localization. SIRT1 is mostly localized in the nucleus but, under specific physiological conditions, it shuttles to the cytosol (6). Similar to SIRT1, also SIRT6 (7) and SIRT7 (8) are localized in the nucleus. On the contrary, SIRT2 is mainly present in the cytosol and shuttles into the nucleus during G2/M cell cycle transition (9). Finally, SIRT3, SIRT4, and SIRT5, are mitochondrial proteins (10).

The main enzymatic activity catalyzed by the sirtuins is NAD+-dependent deacetylation, as known for the progenitor Sir2 (4,11). Along with histones also many transcription factors and enzymes were identified as targets for deacetylation by the sirtuins. Remarkably, mammalian sirtuins show additional interesting enzymatic activities. SIRT4 has an important ADP-ribosyltransferase activity (12), while SIRT6 can both deacetylate and ADP-ribosylate proteins (13,14). Moreover, SIRT5 was recently shown to demalonylate and desuccinylate proteins (15,16), in particular the urea cycle enzyme carbamoyl phosphate synthetase 1 (CPS1) (16). The (patho-)physiological context in which the seven mammalian sirtuins exert their functions, as well as their biochemical characteristics, are extensively discussed in the literature (17,18) and will not be addressed in this review; here we will focus on the emerging roles of the mitochondrial sirtuins, and their involvement in metabolism. Moreover, SIRT1 will be discussed as an important enzyme that indirectly affects mitochondrial physiology.

Sirtuins are regulated at different levels. Their subcellular localization, but also transcriptional regulation, post-translational modifications, and substrate availability, all impact on sirtuin activity. Moreover, nutrients and other molecules could affect directly or indirectly sirtuin activity. As sirtuins are NAD+-dependent enzymes, the availability of NAD+ is perhaps one of the most important mechanisms to regulate their activity. Changes in NAD+ levels occur as the result of modification in both its synthesis or consumption (19). Increase in NAD+ amounts during metabolic stress, as prolonged fasting or caloric restriction (CR) (2022), is well documented and tightly connected with sirtuin activation (4,19). Furthermore, the depletion and or inhibition of poly-ADP-ribose polymerase (PARP) 1 (23) or cADP-ribose synthase 38 (24), two NAD+consuming enzymes, increase SIRT1 action.

Analysis of the SIRT1 promoter region identified several transcription factors involved in up- or down-regulation of SIRT1 expression. FOXO1 (25), peroxisome proliferator-activated receptors (PPAR) α/β (26,27), and cAMP response element-binding (28) induce SIRT1 transcription, while PPARγ (29), hypermethylated in cancer 1 (30), PARP2 (31), and carbohydrate response element-binding protein (28) repress SIRT1 transcription. Of note, SIRT1 is also under the negative control of miRNAs, like miR34a (32) and miR199a (33). Furthermore, the SIRT1 protein contains several phosphorylation sites that are targeted by several kinases (34,35), which may tag the SIRT1 protein so that it only exerts activity towards specific targets (36,37). The beneficial effects driven by the SIRT1 activation – discussed below- led the development of small molecules modulators of SIRT1. Of note, resveratrol, a natural plant polyphenol, was shown to increase SIRT1 activity (38), most likely indirectly (22,39,40), inducing lifespan in a range of species ranging from yeast (38) to high-fat diet fed mice (41). The beneficial effect of SIRT1 activation by resveratrol on lifespan, may involve enhanced mitochondrial function and metabolic control documented both in mice (42) and humans (43). Subsequently, several powerful synthetic SIRT1 agonists have been identified (e.g. SRT1720 (44)), which, analogously to resveratrol, improve mitochondrial function and metabolic diseases (45). The precise mechanism of action of these compounds is still under debate; in fact, it may well be that part of their action is mediated by AMP-activated protein kinase (AMPK) activation (21,22,46), as resveratrol was shown to inhibit ATP synthesis by directly inhibiting ATP synthase in the mitochondrial respiratory chain (47), leading to an energy stress with subsequent activation of AMPK. However, at least in β-cells, resveratrol-mediated SIRT1 activation and AMPK activation seem to regulate glucose response in the opposite direction, pointing to the existence of alternative molecular targets (48).

Another hypothesis to explain the pleitropic effects of resveratrol suggests it inhibits cAMP-degrading phosphodiesterase 4 (PDE4), resulting in the cAMP-dependent activation of exchange proteins activated by cyclic AMP (Epac1) (40). The consequent Epac1-mediated increase of intracellular Ca2+ levels may then activate of CamKKβ-AMPK pathway (40), which ultimately will result in an increase in NAD+ levels and SIRT1 activation (21). Interestingly, also PDE4 inhibitors reproduce some of the metabolic benefits of resveratrol representing yet another putative way to activate SIRT1.

The regulation of the activity of the mitochondrial sirtuins is at present poorly understood. SIRT3 expression is induced in white adipose (WAT) and brown adipose tissues upon CR (49), while it is down-regulated in the liver of high-fat fed mice (50). SIRT3 activity changes also in the muscle after fasting (51) and chronic contraction (52). All these processes are associated with increase (20,53) or decrease (50) in NAD+ levels. From a transcriptional point of view, SIRT3 gene expression in brown adipocytes seems under the control of peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) -estrogen-related receptor α (ERRα) axis, and this effect is crucial for full brown adipocyte differentiation (54,55). SIRT4 expression is reported to be reduced during CR (12), while the impact of resveratrol on SIRT4 is still under debate (56). Finally, upon ethanol exposure, SIRT5 gene expression was shown to be decreased together with the NAD+levels (57), probably explaining the protein hyperacetylation caused by alcohol exposure (58).

Metabolic homeostasis

The maintenance of metabolic homeostasis is critical for the survival of all species to sustain body structure and function. Metabolic homeostasis is achieved through complicated interactions between metabolic pathways that govern glucose, lipid and amino acid metabolism. Mitochondria are organelles, which integrate these metabolic pathways by serving a physical site for the production and recycling of metabolic intermediates.

Glucose metabolism


Glucose homeostasis is regulated through various complex processes including hepatic glucose output, glucose uptake, glucose utilization and storage. The main hormones regulating glucose homeostasis are insulin and glucagon, and the balance between these hormones determines glucose homeostasis. Insulin promotes glucose uptake in peripheral tissues (muscle and WAT), glycolysis and storage of glucose as glycogen in the fed state, while glucagon stimulates hepatic glucose production during fasting. Sirtuins influence many aspects of glucose homeostasis in several tissues such as muscle, WAT, liver and pancreas.


The body’s ability to synthesise glucose is vital in order to provide an uninterrupted supply of glucose to the brain and survive during starvation. Gluconeogenesis is a cytosolic process, in which glucose is formed from non-carbohydrate sources, such as amino acids, lactate, the glycerol portion of fats and tricarboxylic acid (59) cycle intermediates, during energy demand. This process, which occurs mainly in liver and kidney, shares some enzymes with glycolysis but it employs phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to control the flow of metabolites towards glucose production. These three enzymes are stimulated by glucagon, epinephrine and glucocorticoids, whereas their activity is suppressed by insulin.

The role of mitochondrial sirtuins in the control of gluconeogenesis is not well established. SIRT3 is suggested to induce fasting-dependent hepatic glucose production from amino acids by deacetylating and activating the mitochondrial conversion of glutamate into the TCA cycle intermediate α-ketoglutarate, via the enzyme glutamate dehydrogenase (GDH) (Fig. 1A) (60,61). As SIRT3−/− mice do not display changes in GDH activity (62), the mechanism requires further clarification. In contrast to SIRT3, SIRT4 inhibits GDH via ADP-ribosylation under basal dietary conditions (Fig. 1A-B) (12). Conversely, SIRT4 activity is suppressed during CR resulting in activation of GDH, which fuels the TCA cycle and possibly also gluconeogenesis (12). Therefore, mitochondrial sirtuins may function to support gluconeogenesis during energy limitation, but further research is required to understand the exact roles of mitochondrial sirtuins in gluconeogenesis.

Summary of mitochondrial sirtuins’ role in mitochondrial pathways

Summary of mitochondrial sirtuins’ role in mitochondrial pathways

Figure 1 Summary of mitochondrial sirtuins’ role in mitochondrial pathways

Glucose utilization

 Lipid metabolism

Urea metabolism

The recent discoveries in the biology of mitochondria have shed light on the metabolic regulatory roles of the sirtuin family. To maintain proper metabolic homeostasis, sirtuins sense cellular NAD+ levels, which reflect the nutritional status of the cells, and translate this information to adapt the activity of mitochondrial processes via posttranslational modifications and transcriptional regulation. SIRT1 and SIRT3 function to stimulate proper energy production via FAO and SIRT3 also protects from oxidative stress and ammonia accumulation during nutrient deprivation. SIRT4 seems to play role in the regulation of gluconeogenesis, insulin secretion and fatty acid utilization during times of energy limitation, while SIRT5 detoxifies excess ammonia that can accumulate during fasting. However, we are only at the beginning of our understanding of the roles of the mitochondrial sirtuins, SIRT3, SIRT4 and SIRT5 in complex metabolic processes. In the coming years, further research should identify and verify novel sirtuin targets in vivo and in vitro. We need also to elucidate the regulation and tissue-specific functions of these mitochondrial sirtuins, as well as to understand the potential crosstalk and synchrony between the different sirtuins in different subcellular compartments. Ultimately, the understanding of mitochondrial sirtuin functions may open new possibilities, not only for treatment of cancer and metabolic diseases characterized by mitochondrial dysfunction, but also for disease prevention and health maintenance.

7.8.10 Mitochondrial sirtuins

Huang JY1Hirschey MDShimazu THo LVerdin E.
Biochim Biophys Acta. 2010 Aug; 1804(8):1645-51.

Sirtuins have emerged as important proteins in aging, stress resistance and metabolic regulation. Three sirtuins, SIRT3, 4 and 5, are located within the mitochondrial matrix. SIRT3 and SIRT5 are NAD(+)-dependent deacetylases that remove acetyl groups from acetyllysine-modified proteins and yield 2′-O-acetyl-ADP-ribose and nicotinamide. SIRT4 can transfer the ADP-ribose group from NAD(+) onto acceptor proteins. Recent findings reveal that a large fraction of mitochondrial proteins are acetylated and that mitochondrial protein acetylation is modulated by nutritional status. This and the identification of targets for SIRT3, 4 and 5 support the model that mitochondrial sirtuins are metabolic sensors that modulate the activity of metabolic enzymes via protein deacetylation or mono-ADP-ribosylation. Here, we review and discuss recent progress in the study of mitochondrial sirtuins and their targets.

mitochondrial sirtuins

mitochondrial sirtuins

mitochondrial sirtuins
Fig.1 .NAD+ -dependent deacetylation of sirtuins. The two step catalytic reaction mechanism. In this diagram ADPR = acetyl-ADP-ribose, NAM = nicotinamide, 1-O-AADPR = 1-O-acetyl ADP-ribose and βNAD = beta nicotinamide adenine dinucleotide.

Table 1 Shows subcellular localization, substrates and functions of different types of sirtuins.

Fig.2. Sirt3 regulated pathways in mitochondrial metabolism. Schematic diagram demonstrating the different roles of Sirt3 in the regulation of the main metabolic pathways of mitochondria.In this diagram LCAD = long-chain acyl-CoA dehydrogenase, ACeS2 = acetyl coenzyme synthetase 2, Mn SOD = manganese superoxide dismutase, CypD = cyclophilin D, ICDH2 = isocitrate dehydrogenase 2, OTC = ornithine transcarbomylase,TCA = tricaboxylic acid, ROS = reactive oxygen species, mPTP = membrane permeability transition pore, I–V = respiratory chain complex I–V

Fig. 3.(A) Schematic diagram showing different roles of Sirt4 in the regulation of various metabolic pathways. The diagram shows the Sirt4 regulated decrease in insulin level and the increase in availability of ATP inside mitochondria via upregulation of insulin degrading enzyme (IDE) and adenine translocator (ANT). The diagram also shows the Sirt4 regulated decrease in the efficiency of fatty acid oxidation and tricarboxylic acid cycle (TCA) via inhibition of glutamate dehydrogenase (GDH) and malonyl CoA decarboxylase (MCoAD). (B) Schematic diagram indicating the different roles of Sirt5 in regulation of various metabolic pathways. Sirt5 regulates urea production, fatty acid oxidation, tricarboxylic acid cycle (TCA), glycolysis, reactive oxygen species (ROS) metabolism, purine metabolism via regulating carbamoyl phosphate synthetase (CPS), hydroxyl-coenzyme A dehydrogenase (HADH), pyruvate dehydrogenase (PDH), pyruvate kinase (PK), succinate dehydrogenase(SDH) andurate oxidase (UO) respectively

Conclusion and future perspectives

Sirtuins are highly conserved NAD+-dependent protein deacetylases or ADP ribosyl transferases involved in many cellular processes including genome stability, cell survival, oxidative stress responses, metabolism, and aging. Mitochondrial sirtuins, Sirt3, Sirt4 and Sirt5 are important energy sensors and thus can be regarded as master regulators of mitochondrial metabolism. But it is still not known whether specific sirtuins can only function within particular metabolic pathways or two or more sirtuins could affect the same pathways. One of the mitochondrial sirtuins, Sirt3 is a major mitochondrial deacetylase that plays a pivotal role in the acetylation based regulation of numerous mitochondrial proteins. However, the question how mitochondrial proteins become acetylated is still unsolved and the identity of mitochondrial acetyltransferases is mysterious. Although the predominant function of the sirtuins is NAD+ dependent lysine deacetylation, but along with this major function another less characterized activity of these sirtuins includes ADP ribosylation which is mainly done by Sirt4. Moreover, in the case when the mitochondrial sirtuins exhibit both deacetylase and ADP ribosyl transferase activity, the conditions that determine the relative contribution of both of these activities in same or different metabolic pathways require further investigation. Sirt5 another mitochondrial sirtuin, was a puzzle until the recent finding as it possesses unique demalonylase and desuccinylase activities. However, most of the malonylated or succinylated proteins are important metabolic enzymes but as the significance of lysine malonylation and succinylation is still unknown thus it would be interesting to know how lysine malonylation and succinylation alter the functions of various metabolic enzymes. The mitochondrial sirtuins Sirt3, Sirt4 and Sirt5 serve as critical junctions and are required to exert many of the beneficial effect in mitochondrial metabolism. The emerging multidimensional role of mitochondrial sirtuins in regulation of mitochondrial metabolism and bioenergetics may have far-reaching consequences for many diseases associated with mitochondrial dysfunctions. However it is very important to fully elucidate the functions of mitochondrial sirtuins in different tissues to achieve the goal of therapeutic intervention in different metabolic diseases. Although several proteomic studies have provided detailed information that how mitochondrial sirtuin driven modification takes place on various targets in response to different environmental conditions, still the role of sirtuins in mitochondrial physiology and human diseases requires further exploration. Hopefully the progress in the field of sirtuin biology will soon provide insight into the therapeutic applications for targeting mitochondrial sirtuins by bioactive compounds to treat various human age-related diseases.


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7.8.11 Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling

Verdin E1Hirschey MDFinley LWHaigis MC.
Trends Biochem Sci. 2010 Dec; 35(12):669-75.

Sirtuins are a highly conserved family of proteins whose activity can prolong the lifespan of model organisms such as yeast, worms and flies. Mammals contain seven sirtuins (SIRT1-7) that modulate distinct metabolic and stress response pathways. Three sirtuins, SIRT3, SIRT4 and SIRT5, are located in the mitochondria, dynamic organelles that function as the primary site of oxidative metabolism and play crucial roles in apoptosis and intracellular signaling. Recent findings have shed light on how the mitochondrial sirtuins function in the control of basic mitochondrial biology, including energy production, metabolism, apoptosis and intracellular signaling.

Mitochondria play critical roles in energy production, metabolism, apoptosis, and intracellular signaling [13]. These highly dynamic organelles have the ability to change their function, morphology and number in response to physiological conditions and stressors such as diet, exercise, temperature, and hormones [4]. Proper mitochondrial function is crucial for maintenance of metabolic homeostasis and activation of appropriate stress responses. Not surprisingly, changes in mitochondrial number and activity are implicated in aging and age-related diseases, including diabetes, neurodegenerative diseases, and cancer [1]. Despite the important link between mitochondrial dysfunction and human diseases, in most cases, the molecular causes for dysfunction have not been identified and remain poorly understood.

One of the principal bioenergetic functions of mitochondria is to generate ATP through the process of oxidative phosphorylation (OXPHOS), which occurs in the inner-mitochondrial membrane. Mitochondria are unique bi-membrane organelles that contain their own circular genome (mtDNA) encoding 13 protein subunits involved in electron transport. The remainder of the estimated 1000-1500 mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria from the cytoplasm [56]. These imported proteins can be found either in the matrix, associated with inner or outer mitochondrial membranes or in the inner membrane space (Figure 1). Dozens of nuclear-encoded protein subunits form complexes with the mtDNA-encoded subunits to form electron transport complexes I-IV and ATP synthase, again highlighting the need for precise coordination between these two genomes. The transcriptional coactivator PGC-1α, a master regulator of mitochondrial biogenesis and function, is responsive to a variety of metabolic stresses, ensuring that the number and capacity of mitochondria keeps pace with the energetic demands of tissues [7].

Network of mitochondrial sirtuins

Network of mitochondrial sirtuins

Network of mitochondrial sirtuins. Mitochondria can metabolize fuels, such as fatty acids, amino acids, and pyruvate, derived from glucose. Electrons pass through electron transport complexes (I-IV; red) generating a proton gradient, which is used to drive ATP synthase (AS; red) to generate ATP. SIRT3 (gold) binds complexes I and II, regulating cellular energy levels in the cell [4355]. Moreover, SIRT3 binds and deacetylates acetyl-CoA synthetase 2 (AceCS2) [3940] and glutamate dehydrogenase (GDH) [3347], thereby activating their enzymatic activities. SIRT3 also binds and activates long-chain acyl-CoA dehydrogenase (LCAD) [46]. SIRT4 (light purple) binds and represses GDH activity via ADP-ribosylation [21]. In the rate-limiting step of the urea cycle, SIRT5 (light blue) deacetylates and activates carbamoyl phosphate synthetase 1 (CPS1) [4849].

As high-energy electrons derived from glucose, amino acids or fatty acids fuels are passed through a series of protein complexes (I-IV), their energy is used to pump protons from the mitochondrial matrix through the inner membrane into the inner-membrane space, generating a proton gradient known as the mitochondrial membrane potential (Dψm) (Figure 1). Ultimately, the electrons reduce oxygen to form water, and the protons flow down their gradient through ATP synthase, driving the formation of ATP from ADP. Protons can also flow through uncoupling proteins (UCPs), dissipating their potential energy as heat. Reactive oxygen species (ROS) are a normal side-product of the respiration process [18]. In addition, an increase in Dψm, whether caused by impaired OXPHOS or by an overabundance of nutrients relative to ADP, will result in aberrant electron migration in the electron transport chain and elevated ROS production [1]. ROS react with lipids, protein and DNA, generating oxidative damage. Consequently, cells have evolved robust mechanisms to guard against an increase in oxidative stress accompanying ROS production [9].

Mitochondria are the primary site of ROS production within the cell, and increased oxidative stress is proposed to be one of the causes of mammalian aging [1210]. Major mitochondrial age-related changes are observed in multiple tissues and include decreased Dψm, increased ROS production and an increase in oxidative damage to mtDNA, proteins, and lipids [1114]. As a result, mitochondrial bioenergetic changes that occur with aging have been extensively reviewed [1517].

Silent information regulator (SIR) 2 protein and its orthologs in other species, termed sirtuins, promote an increased lifespan in model organisms such as yeast, worms and flies. Mammals contain seven sirtuins (SIRT1–7) that are characterized by an evolutionary conserved sirtuin core domain [1819]. This domain contains the catalytic activity and invariant amino acid residues involved in binding NAD+, a metabolic co-substrate. All sirtuins exhibit two major enzymatic activities in vitro: NAD+-dependent protein deacetylase activity and ADP-ribosyltransferase activity. Except for SIRT4, well-defined acetylated substrates have been identified for the other sirtuins. So far, only ADP-ribosyltransferase activity has been described for SIRT4 [2021]. Thus, these enzymes couple their biochemical and biological functions to an organism’s energetic state via their dependency on NAD+. A decade of research, largely focused on SIRT1, has revealed that mammalian sirtuins regulate metabolism and cellular survival. In brief, SIRT1–7 target distinct acetylated protein substrates and are localized in distinct subcellular compartments. SIRT1, SIRT6 and SIRT7 are found in nucleus, SIRT2 is primarily cytosolic and SIRT3, 4 and 5 are found in the mitochondria. The mitochondrial-only localization of SIRT3 is controversial and other groups have reported non-mitochondrial localization of this sirtuin [2223]. The biology and biochemistry of the seven mammalian sirtuins have been extensively discussed in the literature [2426] and is not the topic of this review. Instead, we focus on the mitochondrial sirtuins, their substrates, and their impact on mitochondrial biology.

The mitochondrial sirtuins, SIRT3–5 [212729], participate in the regulation of ATP production, metabolism, apoptosis and cell signaling. Unlike SIRT1, a 100 kDa protein, the mitochondrial sirtuins are small, ranging from 30–40 kDa. Thus, their amino acid sequence consists mostly of an N-terminal mitochondrial targeting sequence and the sirtuin core domain, with small flanking regions. Whereas, SIRT3 and SIRT5 function as NAD+-dependent deacetylases on well defined substrates, SIRT4 has no identified acetylated substrate and only shows ADP-ribosyltransferase activity. It is likely, however, that SIRT4 possesses substrate-specific NAD+-dependent deacetylase activity, as has been demonstrated for SIRT6 [30,31]. The three-dimensional structures for the core domains of human SIRT3 and human SIRT5 have been solved and reveal remarkable structural conservation with other sirtuins, such as the ancestral yeast protein and human SIRT2 (Figure 2) [3234]. Given its sequence conservation with the other sirtuins [18], it is likely that SIRT4 adopts a similar three-dimensional conformation.

Figure 2 Structure and alignment of sirtuins

Role of mitochondrial sirtuins in metabolism and energy production

The NAD+ dependence of sirtuins provided the first clue that these enzymes function as metabolic sensors. For instance, sirtuin activity can increase when NAD+ levels are abundant, such as times of nutrient deprivation. In line with this model, mass spectrometry studies have revealed that metabolic proteins, such as tricarboxylic acid (TCA) cycle enzymes, fatty acid oxidation enzymes and subunits of oxidative phosphorylation complexes are acetylated in response to metabolic stress [3537].

Fatty acid oxidation

Consistent with the hypothesis that nutrient stress alters sirtuin activity, a recent report identified significant metabolic abnormalities in Sirt3-/- mice during fasting [38]. In this study, hepatic SIRT3 protein expression increased during fasting, suggesting that both its levels and enzymatic activity are elevated during nutrient deprivation. SIRT3 activates hepatic lipid catabolism via deacetylation of long-chain acyl-CoA dehydrogenase (LCAD), a central enzyme in the fatty acid oxidation pathway. Sirt3-/- mice have diminished fatty acid oxidation, develop fatty liver, have low ATP production, and show a defect in thermogenesis and hypoglycemia during a cold test [38].

Surprisingly, many of the phenotypes observed in Sirt3-/- mice were also observed in mice lacking acetyl-CoA synthetase 2 (AceCS2), a previously identified substrate of SIRT3 [3940]. For example, fasting ATP levels were reduced by 50% in skeletal muscle of AceCS2-/- mice, in comparison to wild type (WT) mice. As a result, fasted AceCS2-/- mice were hypothermic and had reduced capacity for exercise. By converting acetate into acetyl CoA, AceCS2 provides an alternate energy source during times of metabolic challenges, such as thermogenesis or fasting. Interestingly, Acadl-deficient mice (Acadl encodes LCAD) also show cold intolerance, reduced ATP, and hypoglycemia under fasting conditions [41]. These overlapping phenotypes between Sirt3-/-AceCS2-/- and Acadl-/- mice indicate that the regulation of LCAD and AceCS2 acetylation by SIRT3 represents an important adaptive signal during the fasting response (Figure 2).

Electron transport chain

Of all mitochondrial proteins, oxidative phosphorylation complexes are among the most heavily acetylated. One study reported that 511 lysine residues in complexes I-IV and ATP synthase are modified by acetylation [37], hinting that a mitochondrial sirtuin might deacetylate these residues. Indeed, SIRT3 interacts with and deacetylates complex I subunits (including NDUFA9) [42], succinate dehydrogenase (complex II) [43]. SIRT3 has also been shown to bind ATP synthase in a proteomic analysis [44]. SIRT3 also regulates mitochondrial translation, a process which can impact electron transport [45]. Mice lacking SIRT3 demonstrate reduced ATP levels in many tissues [42 46]; however, additional work is required to determine if reduced ATP levels in Sirt3-/- mice is a direct result of OX PHOS hyperacetylation or an indirect effect, via decreased fatty acid oxidation, or a combination of both effects.

Less is known about the roles of SIRT4 and SIRT5 in electron transport. SIRT4 binds adenine nucleotide translocator (ANT), which transports ATP into the cytosol and ADP into the mitochondrial matrix, thereby providing a substrate for ATP synthase [20]. SIRT5 physically interacts with cytochrome C. The biological significance of these interactions, however, remains unknown [21].

TCA cycle

Enzymes for the TCA cycle (also called the Kreb’s cycle) are located in the mitochondrial matrix; this compartmentalization provides a way for cells to utilize metabolites from carbohydrates, fats and proteins. Numerous TCA cycle enzymes are modified by acetylation, although the functional consequences of acetylation have been examined for only a few of these proteins. SIRT3 interacts with several TCA cycle enzymes, including succinate dehydrogenase (SDH, see above [43]) and isocitrate dehydrogenase 2 (ICDH2) [33]. ICDH2 catalyzes the irreversible oxidative decarboxylation of isocitrate to form alpha-ketoglutarate and CO2, while converting NAD+ to NADH. Although the biological significance of these interactions is not yet known, it seems possible that SIRT3 might regulate flux through the TCA cycle.

Role of mitochondrial sirtuins in signaling

During cellular stress or damage, mitochondria release a variety of signals to the cytosol and the nucleus to alert the cell of changes in mitochondrial function. In response, the nucleus generates transcriptional changes to activate a stress response or repair the damage. For example, mitochondrial biogenesis requires a sophisticated transcriptional program capable of responding to the energetic demands of the cell by coordinating expression of both nuclear and mitochondrial encoded genes [4]. Unlike anterograde transcriptional control of mitochondria from nuclear transcription regulators such as PGC-1α, the retrograde signaling pathway, from the mitochondria to the nucleus is poorly understood in mammals. Although there is no evidence directly linking sirtuins to a mammalian retrograde signaling pathway, changes in mitochondrial sirtuin activity could influence signals transmitted from the mitochondria. Interestingly, the nuclear sirtuin SIRT1 deacetylates and activates PGC-1α, a key factor in the transcriptional regulation of genes involved in fatty acid oxidation and oxidative phosphorylation (Figure 3) [5051]. Thus, mitochondrial and nuclear sirtuins might exist in a signaling communication loop to control metabolism.



Mitochondria at nexus of cellular signaling. Mitochondria and mitochondrial sirtuins play a central role in intra- and extra-cellular signaling. Circulating fatty acids and acetate provide whole body energy homeostasis. The mitochondrial metabolites NAD+, NADH, ATP, Ca2+, ROS, ketone bodies, and acetyl-CoA participate in intracellular signaling.

Numerous signaling pathways are activated by changes in mitochondrial release of metabolites and molecules, such as Ca2+, ATP, NAD+, NADH, nitric oxide (NO), and ROS (Figure 3). Of these, Ca2+ is the best studied as a mitochondrial messenger. Mitochondria are important regulators of Ca2+ storage and homeostasis, and mitochondrial Ca2+ uptake is directly tied to the membrane potential of the organelle. Membrane potential serves as a gauge of mitochondrial function: disruption of OXPHOS, interruption in the supply or catabolism of nutrients or loss of structural integrity generally result in a fall in membrane potential, and, in turn, decreased mitochondrial Ca2+ uptake. Subsequent increases in cytosolic free Ca2+ will activate calcineurin and several Ca2+-dependent kinases [52] and affect a wide variety of transcription factors to produce appropriate cell-specific transcriptional responses [53]. Through regulation of nutrient oxidation and electron transport or yet to be identified target(s), mitochondrial sirtuins could influence mAlthough the effect of sirtuins on intracellular calcium signaling has not been studied directly, sirtuin effects on ATP production have been shown. ANT facilitates the exchange of mitochondrial ATP with cytosolic ADP. As a result the cytosolic ATP:ADP ratio reflects changes in mitochondrial energy production. A fall in ATP production activates AMP-activated protein kinase (AMPK), which directly stimulates mitochondrial energy production, inhibits protein synthesis through regulation of mammalian target of rapamycin (mTOR), and influences mitochondrial transcriptional programs [54]. SIRT3 regulates ATP levels in a variety of tissues, suggesting that its activity could have an important role in ATP-mediated retrograde signaling [46,55]. Indeed, recent studies have shown that SIRT3 regulates AMPK activation [5658]. Furthermore, SIRT4 interacts with ANT [20], raising the possibility that SIRT4 activity also influences the ATP:ADP ratio or membrane potential and modulates important mitochondrial signals.

NAD+ and NADH levels are intimately connected with mitochondrial energy production and regulate mitochondrial sirtuin activity. Unlike NAD+, however, NADH is not a sirtuin co-substrate. Indeed, changes in the NAD+:NADH ratio can change the redox state of the cell and alter the activity of enzymes such as poly-ADP-ribose polymerases and sirtuins, with subsequent effects on signaling cascades and gene expression [5961]. Changes in mitochondrial sirtuin activity could change the balance of these metabolites within the mitochondria. For example, fatty acid oxidation reduces NAD+ to NADH, which is oxidized back to NAD+ by OXPHOS. However, it is unclear whether changes in NAD+/NADH can be transmitted outside the organelle. The inner mitochondrial membrane is impermeable to NAD+ and NADH; however, the mitochondrial malate-aspartate shuttle could transfer reducing equivalents across the mitochondrial membranes.

Mitochondrial sirtuin control of apoptosis

Apoptosis is a cellular process of programmed cell death. Mitochondria play an important role in apoptosis by the activation of mitochondrial outer membrane permeabilization, which represents the irrevocable point of no return in committing a cell to death. Outer membrane permeabilization leads to the release of caspase-activating molecules, caspase-independent death effectors, and disruption of ATP production. Despite the central role for mitochondria in the control of apoptosis, surprisingly little is known about how mitochondrial sirtuins participate in apoptotic programs. SIRT3 plays a pro-apoptotic role in both BCL2-53- and JNK-regulated apoptosis [63]. Additionally, cells lacking SIRT3 show decreased stress-induced apoptosis, lending further support for a pro-apoptotic role for SIRT3 [62]. Furthermore, recent work points to a tumor suppressive role for SIRT3: SIRT3 levels are decreased in human breast cancers and Sirt3 null mice develop mammary tumors after 12 months [62]. The mechanism for the tumor suppressive function of SIRT3 is incompletely understood, but involves repression of ROS and protection against DNA damage [62]. In conflicting studies, SIRT3 has been shown to be anti-apoptotic. For example, in the cellular response to DNA damage when mitochondrial NAD+ levels fall below critical levels, SIRT3 and SIRT4 display anti-apoptotic activity, protecting cells from death [64]. SIRT3 has also been shown to be cardioprotective, in part by activation of ROS clearance genes [65]. In future studies, it will be important to elucidate the balance achieved by SIRT3 between stress resistance (anti-apoptosis) and tumor suppression (pro-apoptosis). Additionally, the role of SIRT4 and SIRT5 in regulating metabolism suggests that these mitochondrial sirtuins could also contribute to apoptosis in tumor suppressive or stress resistant manners.

Concluding remarks

An elegant coordination of metabolism by mitochondrial sirtuins is emerging where SIRT3, SIRT4 and SIRT5 serve at critical junctions in mitochondrial metabolism by acting as switches to facilitate energy production during nutrient adaptation and stress. Rather than satisfy, these studies lead to more questions. How important are changes in global mitochondrial acetylation to mitochondrial biology and is acetylation status a readout for sirtuin activity? What are other substrates for SIRT4 and SIRT5? What molecular factors dictate substrate specificity for mitochondrial sirtuins? Moreover, further studies will provide insight into the therapeutic applications for targeting mitochondrial sirtuins to treat human diseases. It is clear that many discoveries have yet to be made in this exciting area of biology.

Body of review in energetic metabolic pathways in malignant T cells

Antigen stimulation of T cell receptor (TCR) signaling to nuclear factor (NF)-B is required for T cell proliferation and differentiation of effector cells.
The TCR-to-NF-B pathway is generally viewed as a linear sequence of events in which TCR engagement triggers a cytoplasmic cascade of protein-protein interactions and post-translational modifications, ultimately culminating in the nuclear translocation of NF-B.
Activation of effect or T cells leads to increased glucose uptake, glycolysis, and lipid synthesis to support growth and proliferation.
Activated T cells were identified with CD7, CD5, CD3, CD2, CD4, CD8 and CD45RO. Simultaneously, the expression of CD95 and its ligand causes apoptotic cells death by paracrine or autocrine mechanism, and during inflammation, IL1-β and interferon-1α. The receptor glucose, Glut 1, is expressed at a low level in naive T cells, and rapidly induced by Myc following T cell receptor (TCR) activation. Glut1 trafficking is also highly regulated, with Glut1 protein remaining in intracellular vesicles until T cell activation.

Dr. Aurel,
Targu Jiu

  1. sjwilliamspa

    Wouldn’t then the preferred target be mTORC instead of Sirtuins if mTORC represses Sirtuin activity?

  2. The answer may not be so simple, perhaps a conundrum.

    In conflicting studies, SIRT3 has been shown to be anti-apoptotic. For example, in the cellular response to DNA damage when mitochondrial NAD+ levels fall below critical levels, SIRT3 and SIRT4 display anti-apoptotic activity, protecting cells from death [64].

    For anti-cancer activity, apoptosis is a desired effect. This reminds me of the problem 15 years ago with the drug that would be effective against sepsis, the best paper of the year in NEJM. It failed.

    We tend to not appeciate the intricacies of biological interactions and fail to see bypass reactions. Pleotropy comes up again and again. The seminal work from Britton Chances lab on the NAD+/NADH ratio have been overlooked.


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Mitochondrial Pyridine Nucleotides and Electron Transport Chain

Larry H Bernstein, MD, FCAP, writer and curator

2.1.5 Mitochondrial Pyridine Nucleotides and Electron Transport Chain Mitochondrial function in vivo evaluated by NADH fluorescence

Mayevsky A1, Rogatsky GG.
Am J Physiol Cell Physiol. 2007 Feb; 292(2):C615-40

Normal mitochondrial function is a critical factor in maintaining cellular homeostasis in various organs of the body. Due to the involvement of mitochondrial dysfunction in many pathological states, the real-time in vivo monitoring of the mitochondrial metabolic state is crucially important. This type of monitoring in animal models as well as in patients provides real-time data that can help interpret experimental results or optimize patient treatment. The goals of the present review are the following: 1) to provide an historical overview of NADH fluorescence monitoring and its physiological significance; 2) to present the solid scientific ground underlying NADH fluorescence measurements based on published materials; 3) to provide the reader with basic information on the methodologies used in the past and the current state of the art fluorometers; and 4) to clarify the various factors affecting monitored signals, including artifacts. The large numbers of publications by different groups testify to the valuable information gathered in various experimental conditions. The monitoring of NADH levels in the tissue provides the most important information on the metabolic state of the mitochondria in terms of energy production and intracellular oxygen levels. Although NADH signals are not calibrated in absolute units, their trend monitoring is important for the interpretation of physiological or pathological situations. To understand tissue function better, the multiparametric approach has been developed where NADH serves as the key parameter. The development of new light sources in UV and visible spectra has led to the development of small compact units applicable in clinical conditions for better diagnosis of patients.

UNDERSTANDING THE MITOCHONDRIAL function has been a challenge for many investigators, including cytologists, biochemists, and physiologists, since its discovery more than 120 years ago. In addition to many books regarding the mitochondria, Ernster and Schatz (79) reviewed the history of mitochondrial structure and function studies. In the past two decades, several studies have reported mitochondrial involvement in pathological processes such as stroke (225) or cytoprotection (77). Most of the information on the mitochondrial function has been accumulated from in vitro studies. A relatively small portion of published papers dealt with the monitoring of mitochondrial function in vivo and in real time. Presently, examination of the involvement of the mitochondrial function in many pathological states, such as sepsis, requires monitoring of patients treated in intensive care units. Unfortunately, real-time monitoring of the mitochondrial function in patients has rarely been performed. The current study presents a review of this issue. To evaluate the activity of the respiratory chain in vivo, it is possible to monitor the mitochondrial NADH, FAD, or the cytochrome oxidase oxidation-reduction state. The interference of blood with the monitoring of FAD and cytochrome oxidase is much higher than with NADH (48); therefore, we invest our effort into the monitoring of the mitochondrial NADH redox state. We do not know of any publication showing clearly that Fp fluorescence could be monitored in vivo in blood-perfused organs. In our preliminary report, we showed that in specific brain areas, one can see the fluorescence of Fp but we were not sure how to validate the results. During the past 33 years, we have published >140 papers in this very significant area, including the largest number of studies using NADH redox state monitoring in patients.

Since the discovery of pyridine nucleotides by Harden and Young (94), >1,000 papers have been published on the use of NADH (Fig. 1A) as a marker for mitochondrial function. In 2000, Schleffler et al. (217) reviewed mitochondrial research methods over the past century. A major aspect of mitochondrial function, namely monitoring the energy state of tissues in vivo, was not discussed in that review. Therefore, the present review will summarize 50 years of research, started in 1955 by Chance and Williams (5657), by defining the mitochondrial metabolic state in vitro. To understand mitochondrial function in vivo and under various pathophysiological conditions, it is important to monitor the redox state of the respiratory chain in real time. The present review will discuss the monitoring principles for one of the electron carriers, namely, nicotinamide adenine dinucleotide (NADH). It is well known that mitochondrial dysfunction is involved in many diseases, such as ischemia, hypoxemia, Parkinson’s disease, Alzheimer’s disease, and in the apoptotic process. Therefore, the possibility of monitoring the mitochondrial NADH redox state in experimental animals and patients is of great importance.

inter-conversion of NAD+ and NADH & difference in the absorption spectra of NAD+ and NADH

inter-conversion of NAD+ and NADH & difference in the absorption spectra of NAD+ and NADH

Fig. 1. A: molecular structure of NAD+ and the inter-conversion of NAD+ and NADH. B: difference in the absorption spectra of NAD+ and NADH. C: emission spectra of brain NADH excited by 366 nm light (A1, A2, B1, B2, C1) or 324 nm laser light (C2). C1 and C2 show measurements from a dead brain, for comparison of NADH spectra using two different light sources.

To assess the energy demand, it is necessary to measure different organ-specific parameters. In the brain, the energy demand can be evaluated by measuring the extracellular levels of K+ that reflect the activity of the major ATP consumer: Na+-K+-ATPase (152161). In the heart, most of the energy is consumed by the muscle contraction activity. On the other hand, the energy supply mechanism is the same in all tissues: oxygenated blood reaching the capillary bed releases O2that diffuses into the cells. Therefore, it is possible to evaluate tissue energy supply by monitoring the same four different parameters in all tissues.

The main function of the mitochondria is to convert the potential energy stored in various substrates (e.g., glucose) into ATP. The inner membrane of the mitochondria contains 5 complexes of integral membrane proteins, including NADH dehydrogenase (complex 1). Three of those proteins are involved in the respiratory chain activity. The main function of the respiratory chain is to gradually transfer electrons from NADH and FADH2 (originating from the TCA cycle) to O2. With the addition of protons (H+), H2O is generated in complex 4. NADH (Fig. 1Aright side) is a substrate or a coenzyme for the enzymatic activity of dehydrogenases that form part of the respiratory chain and reside in the inner membrane of the mitochondria.

Spectroscopic Monitoring of NADH: An Historical Overview

The discovery of the optical properties of reduced nicotinamide adenine dinucleotide (NADH; previously known as diphosphopyridine nucleotide or pyridine nucleotide) has led to a very intensive research since the early 1950s. The reduced form of this molecule, NADH, absorbs light at 320–380 nm (Fig. 1B) and emits fluorescent light at the 420–480 nm range (Fig. 1C).

Because the oxidized form NAD+ does not absorb light in this range, it was possible to evaluate the redox state of the mitochondria by monitoring the UV absorbance (see Monitoring UV absorbance by NADH) or blue fluorescence of NADH (see Monitoring NADH fluorescence).

Undoubtedly, the pioneering work of Britton Chance of the Johnson Research Foundation at the University of Pennsylvania in Philadelphia led to the establishment and development of the unique measurement technology and theoretical conceptualization of the mitochondrial function based on NADH redox state monitoring in vitro as well as in vivo.

The foundations for future NADH monitoring in vitro and in vivo were established mainly in the 1950s; thus this period will be discussed in this section.

Monitoring of NADH UV absorbance

In 1951, Theorell and Bonnichsen found a shift in the absorption spectrum of DPNH upon addition of alcohol dehydrogenase (238). In the same year, Theorell and Chance described a new spectrophotometric technique for measuring the formation and disappearance of the compound of alcohol dehydrogenase and NADH (239). In 1952, Chance showed the applicability of this new technique to the measurements of pyridine nucleotide enzymes of muscle homogenate or intact cells (25). In 1954, Chance and Williams briefly described new sensitive differential spectrophotometric methods applied to the study of reduced NADH in isolated rat liver mitochondria and the same approach was used by Connelly and Chance (61) in monitoring NADH in stimulated frog nerve and muscle preparations. The oxidation of NADH in the muscle was similar to its oxidation in isolated mitochondria upon addition of ADP. In a comprehensive paper, “Enzyme mechanisms in living cells,” Chance described in detail the measurements of the respiratory enzymes, including NADH (26).

A major milestone in NADH monitoring was the technique presented in 1954 by Chance (27) using a double beam spectrophotometer to determine the appropriate wavelengths in measurements of respiratory enzymes.

The detailed descriptions of the respiratory chain and oxidative phosphorylation in the mitochondria (published in 1955 by Chance and Williams) established our basic knowledge of the mitochondrial function (57). Chance and Williams defined, for the first time, the metabolic states of isolated mitochondria in vitro, depending on the substrate, oxygen, and ADP levels. In addition, they correlated those metabolic states to the oxidation-reduction levels of the respiratory enzymes. The physiological significance of those metabolic states was discussed in 1956 by Chance and Williams (58).

Monitoring NADH fluorescence

The fact that NADH was monitored by the difference in the absorption spectrum of its reduced form, limited the use of that technique to the study of mitochondria in vitro, and in very thin tissue samples (e.g., muscle) or in cell suspension. To provide a method more specific than absorption spectroscopy, fluorescence spectrophotometry in the near-ultraviolet range was applied for NADH measurement. The initial model of fluorescence recorder was described by Theorell and Nygaard in 1954 (240). The first detailed study using fluorescence spectrophotometry of NADH in intact Baker’s yeast cells and algae cells was published in 1957 by Duysens and Amesz (75).

In the next 5 years (1958–1962), the monitoring of NADH fluorescence was significantly expanded, led by Chance and collaborators. In a first preliminary study, Chance et al. (37) performed simultaneous fluorometric and spectrophotometric measurements of the reaction kinetics of bound pyridine nucleotides (PN) in the mitochondria. In the same year (1958), Chance and Baltscheffsky presented preliminary results of measuring the fluorescence of intramitochondrial PN (34). In this study, they proved the connection between the mitochondrial metabolic state and the redox state of NADH as measured by spectral fluorometry in mitochondria isolated from rat liver (57). The correlation between the enzymatic assay of PN and sensitive spectrophotometry was investigated by Klingeberger et al. (120) by using the rat liver, heart, kidney, and brain.

In 1959, Chance and collaborators were able to expand the use of NADH fluorometry to various experimental models, from isolated mitochondria to intact tissue. To monitor NADH localization in intact cells, Chance and Legallais (42) developed a unique differential microfluorimeter with a very high spatial resolution. This approach was used in various cells to identify the intracellular localization of NADH fluorescence signals (54201). The next step was to apply the fluorometric technique to the higher organization level of animal tissues. Together with Jobsis, Chance measured in vitro changes in muscle NADH fluorescence following stimulation (41). In another paper published by Chance and Theorell (55) the authors came to the very significant conclusion that “The oxidation and reduction state of mitochondrial pyridine nucleotide without a measurable change of cytoplasmic fluorescence suggest that compartmentalization of mitochondrial and cytoplasmic pyridine nucleotide occurs in vivo, at least in the grasshopper spermatid.”

An intensive use of the in vivo NADH monitoring approach started in 1962. The “classic” paper on in vivo monitoring of NADH was published in 1962 by Chance et al. (36). They were able to simultaneously monitor the brain and kidney of anesthetized rats using two microfluorometers. In 1962, Chance and collaborators elaborated on this kind of in vivo monitoring and used it in other rat organs (4350).

Scientific Background And Technological Aspects

The absorption and fluorescence spectra of NADH (the reduced form) have been well characterized at different levels of organization, i.e., in solution, mitochondria and cell suspensions, tissue slices, and organs in vitro and in vivo. NADH has an optical absorption band at about 300 to 380 nm and a fluorescence emission band at 420 to 480 nm (Fig. 1B and C). The spectra are considered the same, although there are small differences in the shape and maxima of the spectra for different environments and measurement conditions. However, there is a universal agreement that the intensity of the fluorescence band, independent of the organization level of the environment, is proportional to the concentration of mitochondrial NADH (the reduced form), particularly when measured in vivo from a tissue.

The biochemical and physiological significance of these spectral qualities is also universally accepted, that is, an increase in the fluorescence intensity indicates a more reduced state of NADH and of the rest of the mitochondrial electron transfer chain. Under various circumstances, changes in the redox state of the electron transport chain can be associated with various conditions.

To monitor NADH fluorescence, it is possible to use one of the two principles available. At the early stage, it was necessary to measure and identify the fluorescence spectrum of NADH. Fluorescence spectra were compared in different in vitro and in vivo preparations. In parallel, the second approach was adopted, namely, measuring the total fluorescence signal accumulated and integrated into a single intensity using appropriate filters. This approach was necessary to measure NADH fluorescence continuously. The following parts of this section describe the fluorescence spectra of NADH measured in various in vitro and in vivo models by different investigators. We present this review of the reported spectra to describe the foundations for the second monitoring approach, namely, the continuous monitoring of integrated spectra.

Fluorescence Emission Spectra of NADH

NADH in solution.

Several investigators have measured NADH fluorescence in solution. Very recently, Alfano’s group (62) performed a calibration test of pure β-NADH in solution, compared it to porcine myocutaneous flap, and found a very significant correlation. The NADH solution spectrum and mitochondrial spectrum were also compared by Chance and Baltscheffsky (34).

Similar spectra of NADH in solution were recorded by Schomacker et al. (219) using 337-nm excitation light for colonic tissue diagnosis.

NADH spectra in isolated mitochondria.

The excitation and emission spectra of NADH (PN) and flavoprotein were measured in frozen samples of pigeon heart mitochondria (52). Using rat liver mitochondria, Chance and Baltscheffsky (34) measured the fluorescence spectra in the three metabolic states defined by Chance and Williams (58). The 330-nm light excitation resulted in a fluorescence peak at 440–450 nm. The same kind of spectra was obtained by other investigators using different fluorometers or mitochondria isolated from various organs. Galeotti et al. (87) measured similar spectra from rat liver mitochondria. Using Rhodamine B as an internal standard for system calibration, Koretsky and Balaban (125) found the same spectra emitted from isolated rat liver mitochondria. Koretsky et al. (126) compared the emitted spectrum from heart homogenates (similar to isolated mitochondria) with that of dissolved heart homogenates (126).

Intact cells.

The use of microfluorimetry to study intact cell metabolism was described in several publications by Kohen and collaborators (see, for example, Ref. 123).

The typical NADH fluorescence spectrum was measured in suspension of ascite tumor cells (87). This study demonstrated that the spectrum of intact cells was similar to that of NADH solution.

Using isolated myocytes, Eng et al. (78) compared the spectra measured under various conditions of the mitochondria. They found that cyanide induced an increase in the spectrum difference, whereas FCCP, used as a typical uncoupler of oxidative phosphorylation, produced a marked decrease in the spectrum.


Principles of NADH monitoring.

As described in the introductory section, NADH can be measured by utilizing its absorption spectrum in the UV range, as well as by the blue fluorescence spectrum under UV illumination. In the early stages, NADH monitoring was based on the difference in the absorption of NADH and NAD+. At the range of 320 to 380 nm, only the reduced form; NADH absorbs light, while NAD+does not (Fig. 1B). Therefore, when a mixture of NADH and NAD+ is illuminated in a cuvette by 320–380 nm, only NADH will affect the absorption spectrum peak at 340 nm. This property of NADH was used in the early 1950s by several investigators, as reviewed in Spectroscopic Monitoring of NADH–Historical Overview. Chance and collaborators utilized this technique to measure NADH in muscle homogenates or intact cells (25) and published many papers concerning the unique absorption spectrum of NADH.

The absorption approach is not practical for measuring NADH in a thick tissue; hence, another property of NADH was used. Since the early 1950s, fluorescence spectrophotometry of NADH has been employed in various in vitro and in vivo models. The emission of NADH fluorescence, under illumination at 320–380 nm, has a very wide spectrum (420–480) with a peak at 450–460 nm (Fig. 1C). NADH fluorescence has been identified by Chance and his collaborators as a good indicator of the intramitochondrial oxidation-reduction state (48).

The review article on in vivo NADH fluorescence monitoring, published in 1992 by Ince et al. (102) included many other technical aspects of the methodology. Nevertheless, here we will elaborate on the historical development of the various models of NADH fluorometers. We recently (155) reported on a new type of NADH fluorometer based on a very small and stable UV light source: a 375-nm light-emitting diode.


In 1959, Chance and Legallais (42) described a differential fluorometer that heralded a new era in monitoring NADH fluorescence in vivo as an indicator of mitochondrial function. They used a microscope, serving as the fluorometer basis, with two light sources: tungsten and mercury lamps with appropriate filters. In 1959, Chance and Jobsis (41) proved that mechanical muscle activity is associated with NADH oxidation measured in excised muscle. This study was the bridge from the subcellular (mitochondria) and cellular (intact cell) monitoring approaches toward actual in vivo applications.

The first in vivo NADH monitoring device was presented in the early 1960s. At that stage, the effects of scattered light and tissue absorption due to blood were not taken into consideration when monitoring NADH fluorescence. The first detailed results of in vivo NADH fluorescence measurements were published in 1962 (36).

These classic papers described two microfluorometers that were modifications of previous designs (4254). This microfluorimeter type employed Leitz “Ultrapack” illumination, which had been used for many years by various groups until the appearance of UV transmitting optical fibers. To avoid movement artifacts, rats were anesthetized deeply and their heads were fixated in a special holder attached to the operation table. Numerous studies utilized the principles of the “Ultrapack” illumination system. The same instrumentation was used in other in vivo studies, including those of Chance’s group (38434459), Dora and Kovach’s group (7192), Rievich’s group (93), Jobsis and collaborators (108110111213), Gosalvez et al. (89), and Anderson and Sundt (5232). This is only a partial list.

Monitoring NADH fluorescence and reflectance.

The effect of blood on NADH fluorescence was discussed early by Chance et al. (36). To monitor NADH in vivo, Chance’s group had to avoid areas containing large blood vessels, which interfere with the emission and excitation light. The monitoring of a second channel in tissue fluorometry in vivo was reported by Chance and Legallais in 1963 (44). They showed that “changes due to the deoxygenation of oxyhemaglobin do not interfere with measurement of the time course of fluorescence changes in the tissue studies.”

The addition of a second monitoring signal, namely, tissue reflectance at the excitation wavelength was reported in 1968 by Jobsis and Stansby (112). It was based on a previous model described by Jobsis et al. in 1966 (107). In two more papers by Jobsis and collaborators (110,111), the measurement of 366-nm reflectance was used for the correction of the NADH fluorescence signal from the brain. The reflectance signal was subtracted from the fluorescence signal. The same type of instrumentation was used by various groups for the measurement of NADH in single cells (124) or in vitro preparations (1319).

Fiber optic fluorometer/reflectometer.

To enable the monitoring of NADH fluorescence in unanesthetized animals or other in vivo preparations, a flexible means was needed to connect the fluorometer with the tested organ, for example the brain. This was achieved in 1972, when UV transmitting quartz fibers became available (Schott Jena Glass). We have used the light guide-based fluorometer for in vivo monitoring of the brain (48157) subjected to anoxia or cortical spreading depression. The historical development of light guide-based fluorometery-reflectometry is shown in Fig. 2. The original device functioned on the time-sharing principle (Fig. 2A), where four filters were placed in front of a two-arms light guide. Filters 1 and 3 enabled the measurement of NADH fluorescence, while filters 2 and 4 were used to measure tissue reflectance at the excitation wavelength. The reflectance trace was used to correct the NADH signal for hemodynamic artifacts, and to indicate changes in the blood volume of the sampled tissue.

Fig. 2. The three stages in the development of the fiber optic fluorometer/reflectometer (started in the early 1970s).


development of the fiber optic fluorometer_reflectometer

development of the fiber optic fluorometer_reflectometer

Factors Affecting NADH Fluorescence and Reflectance Signals

The excitation and emission spectra of NADH are affected by the redox state of this fluorochrome and by other factors, leading to artifacts in the fluorescence measurements. This section will discuss various NADH-unrelated factors, affecting the measured signal. Since most fluorometers involve the measurement of the total backscattered light at the excitation wavelength (i.e., 366 nm), the discussion will concern changes in NADH fluorescence as well as in tissue reflectance.

The following factors may affect the two measured signals, 366-nm reflectance and 450-nm fluorescence: 1) tissue movement due to mechanical or intracranial pressure changes; 2) extracellular space events, such as volume changes or ion shifts between intra- and extracellular space; 3) vascular and intravascular events, for example, oxy-deoxy Hb changes, and blood volume changes due to autoregulatory vasoconstriction under pathological conditions; and 4) intracellular space factors, such as O2 level, ATP turnover rate, substrate availability, and mitochondrial redox state.

Fig. 3. Comparison between the mitochondrial metabolic state, defined by Chance and Williams (56, 57) and responses of the in vivo brain to changes in O2 supply and brain activation.

mitochondrial metabolic state, defined by Chance and Williams (56, 57) and responses of the in vivo brain to changes in O2 supply

mitochondrial metabolic state, defined by Chance and Williams (56, 57) and responses of the in vivo brain to changes in O2 supply

Changes in mitochondrial NADH and tissue metabolic state

The pioneering work of Chance and Williams in the 1950s, led to the definition of the metabolic state of isolated mitochondria in vitro. The foundations for the use of NADH fluorescence as a marker of mitochondrial activity have been posited in detail by Chance and Williams (5657). The left portion of Fig. 6 is a modification of a published table, while the right hand segment demonstrates the responses of NADH fluorescence measured in the brain in vivo under various perturbations. The “resting state” of the mitochondria in vitro was defined as state 4, where NADH was 99% in the reduced form, and ADP was the rate limiting substance. If ADP is added to a suspension of mitochondria, ATP synthesis will be stimulated, O2 consumption will increase, and the rate limit will be determined by the activity of the respiratory chain. During this state 3, or the “active state,” the NADH redox state will decrease or become more oxidized (∼50%). When the resting mitochondria are deprived of O2, the activity of the mitochondria will stop and NADH will reach its maximum redox state (state 5).

A definitive description of the mitochondrial metabolic state has never been given for in vivo conditions. Therefore, we described the in vivo mitochondria conditions as recorded by NADH fluorescence in a representative tissue or organ; e.g., the brain. While the range between minimal NADH (∼0) and its maximal level was determined in vitro, it is almost impossible to determine in the intact brain or other organs in vivo. For example, state 2, with a substrate free medium, could not be achieved in vivo since the tissue would die. On the other hand, the maximal level of NADH (state 5) could be monitored in vivo under complete deprivation of O2 by anoxia or complete ischemia.

We used changes in NADH levels monitored in vivo to create a new scale ranging from a maximal definite point to the minimal level recorded in vivo. Details of this approach have been published (152). As shown in Fig. 3, the maximal NADH level is achieved under complete O2 deprivation that can be induced both under in vitro and in vivo conditions. This signifies that this definitive point can be used to determine state 5 in vivo as well. The problem is to determine the metabolic state of a tissue in an in vivo situation. If we adopt the in vitro value of a resting state (state 4), this would signify that the increase in NADH during state 5, induced by anoxia (0% O2), would be only 1%. According to all in vivo studies, this is not the case, and during anoxia the increase in NADH is lager than the decrease under state 4 to 3 transition. Figure 3right, illustrates that the observed level of NADH increase is indeed larger than the decrease. Therefore, we concluded that, under in vivo conditions, the “resting” metabolic state of the brain is found between states 4 and 3 rather than in state 4 as defined in vitro (152). To determine the maximal and minimal levels of NADH in vivo it is almost impossible to use cyanide or uncoupler (FCCP). Nevertheless, we were able to determine the maximal level by anoxia and the “minimal” level by nonfluorescing uncoupler. We injected the uncoupler pentachlorophenol into the ventricles of the rat’s brain while monitoring the NADH responses to anoxia and spreading depression (146). To perform a reliable study with cyanide, the animal would have to die and the results will not be helpful; therefore, we used the anoxia response to measure the maximal level of NADH. Using fiber optic fluorometry, we were able to monitor both anesthetized and awake rats. This figure will be discussed later on in this review. It is important to note that most of the published data on NADH monitoring, have been accumulated in brain studies. Therefore, we will present our data mainly relating to the brain, though results on other organs will be presented as well. Table 1 lists studies published by various investigators as well as our publications. The papers are classified according to the organ monitored and the type of perturbation used. This table does not include rarely studied types of organs or perturbations. Such studies are cited individually in the text.

Table 1. Effect of O2 delivery and consumption on NADH redox state measured in various intact organs by various investigators

Table 2. Historical milestones in monitoring NADH fluorescence in vivo


Anoxia and Hypoxia.

The responses to hypoxia and anoxia are very similar; therefore, they will be discussed together. According to the definition of Chance and Williams (5657), a shift toward state 5 involves an increase in NADH proportional to a decrease in O2 supply.

It is assumed that the response of NADH fluorescence to hypoxia or anoxia, induced in vivo, should be very similar to the response of isolated mitochondria. As shown in Fig. 4B, when the blood-free brain was exposed to N2, the fluorescence showed a clear increase-decrease cycle depending on the availability of O2. The reflectance trace was not affected at all. In autoregulated blood-perfused organs, it is expected that the lack of O2 will trigger compensation mechanisms that may lead to an increase in the blood flow and volume, or a decrease in thereflectancesignal. We tested, in the same rats, the response to anoxia of the normoxic blood-perfused brain. The results are shown in Fig. 4A. Indeed, reflectance exhibited a large decrease due to the increase in blood volume (vasodilatation of brain vessels). Figure 4C and D, presents the responses to anoxia measured via 2 mm and 1 mm light guides. A small variation can be seen in the reflectance response between the two light guides.

Ischemia, Or Decreased Blood Flow.

Under partial or complete ischemia, blood flow to the monitored organ is decreased and, as a result, O2 delivery is limited or even abolished. The use of ischemia in animal models provides information relevant to critical clinical situations such as brain stroke or heart attack. The primary factor starting the pathological state is the decrease in O2 supply, making the tissue energy balance negative, and preventing the tissue from performing its function. Figure 7 illustrates the effects of ischemia and anoxia on the NADH level in the brain of an anesthetized gerbil. The measurements of NADH in the cerebral hemispheres were correlated to the brain electrical activity (ECoG; electrocorticogram). To test and compare the measurements done in the two hemispheres, we exposed the gerbil to short-term anoxia. As shown, the two responses are very similar and correlate to the depression of the ECoG signal measured in the two hemispheres.


After the introduction of the light guide-based fluorometry, we were able to expose the awake brain to hyperbaric conditions. A clear decrease in NADH (oxidation) was recorded during the shift from 21% to 100% O2, as well as during compression of up to 10 atmospheres 100% O2 (150,152153167177). A similar oxidation was found upon CO2 addition to the gas mixture (94–99% O2) (149). We also found a correlation between the elevated brain PO2 and the oxidation of NADH in awake rats (151). The oxidation of NADH was also recorded under normobaric hyperoxia (113). Furthermore, we tested the effects of hyperbaric oxygenation on carbon monoxide intoxication (212) or cyanide exposure (235).


Responses to energy consumption changes

As shown by Chance and Williams (57, 58), the activation of the mitochondria by increased ADP is coupled with oxidation of NADH (decreased NADH levels) and is known as the state 4 to state 3 transition in isolated mitochondria. Most of the investigations in this field of tissue activation were made on neuronal tissue in vivo. However, studies of other organs, such as the heart or skeletal muscle, were conducted as well. The demand for energy (ATP) by various tissues is dependent on the specific tasks of each organ or tissue. Nevertheless, the stimulation of mitochondrial function is common in all tissues in the body. We will describe the effects of tissue activation on NADH fluorescence under normoxic conditions as well as during limitation of O2 supply in the tissue (hypoxia, ischemia).


Responses to energy consumption changes

As shown by Chance and Williams (5758), the activation of the mitochondria by increased ADP is coupled with oxidation of NADH (decreased NADH levels) and is known as the state 4 to state 3 transition in isolated mitochondria. Most of the investigations in this field of tissue activation were made on neuronal tissue in vivo. However, studies of other organs, such as the heart or skeletal muscle, were conducted as well. The demand for energy (ATP) by various tissues is dependent on the specific tasks of each organ or tissue. Nevertheless, the stimulation of mitochondrial function is common in all tissues in the body. We will describe the effects of tissue activation on NADH fluorescence under normoxic conditions as well as during limitation of O2 supply in the tissue (hypoxia, ischemia).


The effects of pharmacological agents on NADH redox state in various organs were published as well. Kedem et al. researched the influence of various inotropic agents (1) as well as nitroprusside (2), nitroglycerin (76), and propranolol (86).

Osbakken and collaborators (194195) also monitored NADH under various drug exposures. Baron et al. (17) described the effects of lidocaine on NADH, during ischemia in the dog heart. The effects of blood substitute emulsion on NADH in the kidney were reported (260). The influence of radioprotective chemicals on NADH in rat tissue was described in the 1960s (103). The action of various drugs (e.g., the uncoupler Amytal) was studied in the liver exposed to hyperbaric oxygenation (3140).

Monitoring Human Body Organs

The first attempt to apply NADH fluorometry to human tissues in vivo was made in 1971 by Jobsis et al. (111). Using NADH fluorescence microfluorometry, they monitored the exposed brain of neurosurgical patients undergoing treatments for focal cerebral seizures. They correlated the electrocorticographic data to the NADH redox state under direct cortical stimulation of the monitored area. The clear decrease in the NADH signal was interpreted as a change in oxidation. The recorded changes were very similar to those obtained in analogous procedures in the cat brain (213). A few years later, the collaboration between Austin and Chance (8) led to the recording of NADH in the brain of patients subjected to microanastomosis of the superficial temporal artery to the middle cerebral artery. The same group found an improvement of cerebral oxidative metabolism after the anastomosis, which was correlated to the elevated blood flow and increased tissue PO2 (9).

The next step was taken by Barlow et al. (16), who expanded this technique to monitor the heart and the brain. Using a different type of fluorometer, Van Buren et al. showed a decrease in NADH (oxidation) due to cortical stimulation in epileptic patients (251). In 1979, Fein and Jobsis (81) studied the changes in brain energetics in patients undergoing superficial temporal arterial-middle cerebral artery microanastomosis. Fein and Olinger (8283) monitored patients after transient ischemic attacks. The brain of these patients, who had undergone an extracranial-intracranial bypass, was stimulated, and changes in NADH were recorded.


The laser-based fluorimeter developed by Renault (207) was used to monitor NADH redox state in the heart muscle during pharmacological treatments (207), as well as in skeletal muscle (91). Attempts to apply NADH fluorometry in clinical practice (reported in a dozen short publications) did not lead to the development of a proper medical device applicable on a daily basis.

In 1990, our team started developing a unique multiparametric monitoring system that included the measurement of NADH fluorescence, using a light guide-based device. This system was initially applied to monitor neurosurgical patients undergoing brain surgery or those treated in the intensive care unit. In the first paper on the subject (published in 1991), we showed the feasibility of our approach. After a transient short occlusion of one common carotid artery, the increase in NADH was correlated to a decrease in cerebral blood flow (164). It took another 5 years to restart organized clinical testing of our monitoring system.

Monitoring Nadh And The Multiparametric Approach

The need for multiparametric monitoring of other parameters, additional to NADH, results from the basic understanding that NADH is affected by two major factors. The redox state of NADH reflects not only the availability of O2 inside the mitochondria but also the turnover rate of the ATP-ADP cycling activity (state 4 to state 3 transition). The interaction between these two factors affects the nature of NADH response to various conditions. For example, an increase in energy consumption (e.g., cortical spreading depression) under O2 restriction will be manifested as an increase in NADH rather than a decrease (oxidation) measured in normal well-oxygenated tissue. According to Chance and Williams, an increase in ATP production is always recorded as a decrease in NADH (5758). Therefore, the “reduction cycle” measured by the NADH signal in response to CSD can be interpreted as an artifact of some kind. This phenomenon and the fact that the mitochondrial NADH signal cannot yet be calibrated in absolute values prompted us to develop a multiparametric monitoring approach and a probe that could be used in various tissues exposed to different pathophysiological conditions. By this approach, two major advantages were gained. First, it provided the possibility of a better interpretation of the recorded results; second, nonphysiological responses could also be more easily detected. To elaborate on these points, we will consider the following typical example. In the early stage of NADH monitoring using a time sharing fluorometer, we found that a few minutes after complete ischemia was induced by decapitation in a rat model, a large increase in the reflectance signal was recorded in parallel to a clear NADH decrease in the dead monitored brain, apparently indicative of NADH oxidation. We termed this event “the Secondary Reflectance Increase-SRI” (147). It was clear to us that this late “oxidation” of NADH in the dead animal was an artifact of the monitoring system. The same response was recorded also when partial ischemia was induced in a gerbil’s brain. The “oxidation” of NADH in a dead or partially ischemic brain did not have any physiological or biochemical interpretation, so we suspected that this “oxidation” is due to the large increase in the reflectance signal, and to a failure of the fluorescence signal’s correction method. We speculated that the large increase in the reflectance trace (SRI) after ischemia or brain death, resulted from a spasm of blood vessels. Such spasms are known to occur in this type of conditions, namely during cortex depolarization. Only when monitoring other parameters, in addition to NADH, such as extracellular K+ and DC steady potential, were we able to give a substantial explanation for the SRI event (85). On the basis of these experiments, we concluded that the SRI phenomenon is always associated with a negative shift in the DC potential and a large increase in extracellular potassium when energy is not available.


NADH and electrical activity

The first attempt to combine NADH and electrical measurements was made by Chance and Schoener in 1962 (50). They showed the time relationship between the increase in NADH due to anoxia or hypoxia, and the disappearance of electrical activity (ECoG) in rat cerebral cortex. The same type of correlation was reported later by Jobsis et al. (110) for epileptic activity, and by Rosenthal and Somjen (163) and Mayevsky and Chance (157) for CSD. The accumulated results have made it clear that under limited energy or O2 supply, NADH becomes elevated in the brain, while the spontaneous ECoG activity is depressed. The ECoG begins to decelerate when NADH reaches 70%-80% of its maximal increase upon death (157159) or decapitation (160259). The recovery of ECoG after anoxia is completed much later than NADH oxidation, suggesting that energy availability is a prerequisite condition but not the only condition needed for a complete ECoG recovery. Depression of the ECoG is also recorded when the brain is exposed to depolarization due to CSD; however, it is not caused by a lack of O2. Similar correlations between NADH and ECoG were described in cat cerebral cortex exposed to seizures and hemorrhagic hypotension (100).

NADH and respiratory chain components

Since the activities of various respiratory chain components are strongly coupled, the tissue respiratory rate can be better evaluated by monitoring several such components. Very few attempts have been made to correlate NADH responses in vivo, with other components of the respiratory chain. The main reason for this was the stronger interference of blood with Fp or cytochrome oxidase measurements, compared with NADH. The effects of hypotension and anoxia on NADH and cytochrome aa3, were measured in the brain in vivo (99). LaManna et al. showed the effects of Ethanol on brain NADH and cytochrome aa3 in rats and cats (137). Therefore, almost all correlations between Fp and NADH were studied in blood-free organs (49). In 1976, we presented preliminary results indicating that in certain morphological areas of the brain, containing less blood vessels, a good correlation is recorded between NADH and Fp responses to anoxia in vivo (146). The only practical way to measure these two signals together was to freeze the tissue and then analyze the two parameters in the frozen state (168183). Another approach to correlating NADH and Fp redox state was suggested by Paddle et al. (198). They used a NADH/Fp scanning fluorometer to monitor the muscle (198) or rat diaphragm (197). A few papers have been published on the use of flying spot fluorometer to monitor the two fluorescent signals in the brain and other organs (35). Most of the data published in this field have been acquired in vitro (3349) or in blood-free organs such as the liver (218).

In this review, we tried to summarize the scientific background and technological aspects of in vivo NADH fluometry approach for the monitoring of mitochondrial functions. This technology still has some limitations including the need for better correction technique for hemodynamic artefacts as well as a new approach for quantitative calibration of the signals. During the past decade, the preliminary application of the NADH fluorometry to clinical environment was very promising. This stimulates us to improve the technology to provide a practical medical device that will be used by many clinicians after approval by the regulatory agencies around the world. A microscale mathematical model for metabolic symbiosis: Investigating the effects of metabolic inhibition on ATP turnover in tumors

Colin Phipps, Hamid Molavian, Mohammad Kohandel
J Theoret Biol 2015; 366: 103-114

Cancer cells are notorious for their metabolic adaptations to hypoxic and acidic conditions, and especially for highly elevated glycolytic rates in tumor tissues. An end product of glycolysis is lactate, a molecule that cells can utilize instead of glucose to fuel respiration in the presence of oxygen. This could be beneficial to those cells that do not have sufficient oxygen as it conserves glucose for glycolysis. To better quantify this phenomenon we develop a diffusion-reaction mathematical model for nutrient concentrations in cancerous tissue surrounding a single cylindrical microvessel. We use our model to analyze the interdependence between cell populations’ metabolic behaviors on a microscopic scale, specifically the emerging paradigm of metabolic symbiosis that exists between aerobic and glycolytic cells. The ATP turnover rates are calculated as a function of distance from the blood vessel, which exhibit a lactate-consuming population at intermediate distances from the vessel. We also consider the ramifications of the Warburg effect where cells utilize aerobic glycolysis along with this lactate consuming respiration. We also investigate the effect of inhibiting metabolic pathways on cancer cells since insufficient ATP can trigger cell apoptosis. Effects that could be induced by metabolic inhibitors are analyzed by calculating the total ATP turnover in a unit tissue annulus in various parameter regimes that correspond to treatment conditions where specific metabolic pathways are knocked out. We conclude that therapies that target glycolysis, e.g. lactate dehydrogenase inhibitors or glycolytic enzyme inhibition, are the keys to successful metabolic repression.

The extensive metabolic requirements for cancer cell proliferation coupled with the harsh microenvironment in solid tumors culminate in a highly adaptive and complex network for cellular energy production. The genetically altered metabolic behavior of cancer cells has led to a number of emerging metabolic paradigms, in addition to those that are universally exhibited in both cancerous and normal cells. We will investigate this complex metabolic behavior by formulating a minimal mathematical model that includes the essential metabolites of glucose, lactate and oxygen in the tissue surrounding a microvessel. The cylindrical geometry used here has been used in a similar context to consider interactions between metabolites and tumor cells with treatment effects in a simplified setting (e.g. Bertuzzi et al., 2000, 2007a). The model presented here will enable the quantification of various behaviors, such as the symbiotic relationship that exists between lactate producing glycolytic cells and lactate-consuming respiratory cells, and the analysis of metabolic dependence on various physiological conditions such as hypoxia and induced metabolic inhibition. Metabolic inhibition including glycolytic inhibitors among many others targets could be very important for cancer treatment since an ATP deficit can induce apoptosis (Izyumov et al., 2004). The key consideration for addressing this problem with mathematics is the formulation of nutrient consumption rates that encompass the various primary facets of cancer cell metabolism and their corresponding ATP yields. In normal well-oxygenated tissues the primary source of ATP is the process of cellular respiration. The complete conversion of glucose to carbon dioxide and water has an ideal yield of about 29 ATP, although realistically the yield is substantially lower (Brand, 2005). The preliminary stage of cellular respiration is glycolysis, the conversion of glucose to pyruvate; this process directly produces 2 ATP. In hypoxic conditions this pyruvate is preferentially converted into lactate via the enzyme lactate dehydrogenase (LDH) to regenerate the essential cofactor NAD+. In oxygenated conditions this pyruvate is transported across the inner mitochondrial matrix where it is decarboxylated and enters the citric acid cycle; the citric acid cycle directly generates 2 more ATP per glucose. The primary energy payoff is a result of cofactor oxidization that enables the electron transport chain to establish a proton gradient across the inner mitochondrial matrix. ATP synthase utilizes this electrochemical gradient to drive the phosphorylation of approximately 25 additional ATP per glucose molecule.

The aforementioned universal traits that cancer cells and normal cells share include cellular responses to various levels of oxygen, lactate or glucose. Examples include a Crabtree-like effect and a Pasteur-like effect (Casciari et al., 1992a). The Crabtree-like effect is when oxygen consumption decreases as glucose concentration increases. This can be explained by an increasing reliance on glycolysis for ATP when hyperglycemic conditions are encountered. The Pasteur-like effect is decreased glucose consumption as oxygen increases. This is due primarily to the inhibition of various metabolic steps by the presence of elevated ATP and other intermediaries. However, cancer cells are unique in that they preferentially utilize glycolysis, even in the presence of oxygen, coined aerobic glycolysis. This phenomenon is generally referred to as the Warburg effect whereby cells rely primarily on glycolysis even in the presence of sufficient oxygen to perform respiration (Warburg, 1956). There is a perceived inefficiency of this metabolic strategy, namely the dramatically reduced ATP yield, just 2 per glucose instead of 29, however, it has the benefits of faster ATP production and it is likely that much of this glucose is being consumed for proliferative (Vander Heiden et al., 2009) (e.g. by the pentose phosphate pathway) purposes. In addition to the typical glycolytic phenotype exhibited in many cancers, there is also a developing story of a co-operative relationship existing between aerobic and anaerobic  cancer cells. The lactate necessarily produced by glycolytic cells is being pushed back into the respiratory cycle by being converted into pyruvate (summarized in Feron, 2009; Nakajima and Van Houten, 2012); this spatial relationship is shown in Fig. 1. Lactate consumption has been observed in vitro in various models (Bouzier et al.,1998; Katz et al., 1974) as well as in vivo as early as the early 1980s (Sauer et al., 1982). However, a renewed interest in the topic was piqued when Sonveaux et al. (2008) showed that reducing lactate uptake by cancer cells led to hypoxic cell death, a particularly difficult subpopulation to target using traditional methods.

Metabolic phenomena have been studied in great detail by mathematical models, but models of tumor metabolism rarely include the interaction of the transport mechanisms of microvessels with the localized metabolic behavior of cells (with one recent exception McGillen et al., 2013). In the section to follow, we will develop a mathematical model that describes the concentrations of molecules that are important to cellular metabolism in the tissue around a single three-dimensional vessel that exhibits diffusion dominated interstitial transport. We will then use this model to demonstrate how the properties of the tumor cell population, such as glucose, lactate and oxygen consumption rates, affect tumor hypoxia and ATP production around a single vessel. The effects of metabolic inhibitors will be investigated by parameter changes that could be elicited by the application of glycolysis inhibitors, lactate dehydrogenase (LDH) inhibitors or respiratory inhibitors. We are interested in those metabolic inhibitors that could cripple the cells’ ability to produce ATP.

Fig.1. The spatial relationship between the cell populations in the model indicating dominant metabolism as we move away from the vessel. When the glucose and oxygen concentrations are highest near the vessel wall, the cells preferentially utilize glucose-fuelled respiration. When the oxygen supply is depleted far from the vessel, the cells rely on glycolysis. The glycolytic cells produce large quantities of lactate which are consumed by cells at intermediary distances and hypoxic oxygen concentrations. These cells are participating in a behavior that we will refer to as metabolic symbiosis.

A model to describe the concentrations of the major players in the metabolic pathways of respiration and glycolysis, will be outlined here. Its origins lie in a metabolic model developed by Casciari et al. (1992b) that was subsequently applied on the microscale by Molavian et al. (2009). The functional forms for the production rates are similar to those proposed by MendozaJuez et al. (2012) and subsequently extended to a spatial model by McGillen et al. (2013). In hypoxic and anoxic conditions, cells must partially or exclusively rely on metabolic pathways, such as glycolysis, that do not require oxygen for ATP production. In glycolysis, the preliminary stage of respiration, a single glucose molecule (C6H12O6) yields 2 ATP, which we will denote under the reaction arrow with a boxed ATP yield number, with the byproducts of lactate and a proton. Denoting glucose by G and lactate by L C3H5O3, the net reaction is G kG> 2L + 2H+; [2]

where kG (mM/s) is the rate of glucose consumption by glycolysis that results in lactate formation. The accumulation of these hydrogen ions in a solid tumor is a primary contributor to tumor acidosis. In the presence of oxygen (O2), glycolysis is typically followed by the rest of the respiratory process with an ideal energy yield of approximately 29 ATP molecules with carbon dioxide (CO2) and water (H2O) as the only byproducts. The simplified summary reaction is given by G kO à 6O2 6CO2 + 6H2O; [29]

where kO is the rate of glucose consumption that results in cellular respiration. To represent the metabolic symbiosis between cells primarily producing energy via glycolysis and those consuming lactate in well-oxygenated areas, we will link the above two reactions with the lactate-consuming net reaction: L+ H+ + 3O2 kLà  3CO2 + 3H2O; [13.5]

where kL is the rate of lactate consumption. This summarizes the re-entry of lactate, via conversion to pyruvate, into aerobic respiration that yields 13.5 ATP per lactate molecule. The relationships between the summary reactions included in the model are given in Fig. 2.

Fig. 2. The summary reactions included in the metabolism model. Glycolysis proceeds at rate kG and produces 2 ATP from the conversion of glucose to pyruvate. Glucose-fuelled respiration occurs at rate kO in the presence of oxygen, while lactate-fuelled respiration occurs at rate kL (2 kL is present in the diagram to remain consistent with the glycolytic yield of 2 lactate molecules).

Fig. 3. Solution to base case boundary value problem. Nondimensional oxygen o and glucose g concentrations decrease due to metabolic consumption. Lactate  ℓ  increases to almost double its vessel concentration since it is produced by glycolysis at a higher rate than it is consumed by respiration due to a limiting oxygen concentration. This image has been spatially truncated to 300 μm since the concentrations are approximately constant after this point.

Fig. 4. Consumption rates of oxygen, lactate and glucose (QO, QL and QG for the concentrations given in Fig. 3). The glucose and oxygen consumption rates are strictly positive while the consumption rate of lactate is predominantly negative. This indicates that even in regions where lactate is being consumed, it is being produced at a higher rate by glycolysis.

Fig. 5. The base case for ATP turnover (consumption/production) rates corresponding to consumption rates given in Fig. 4. The contributions of the pathways are bounded by the total ATP turnover rate  PATP . Glycolysis dominates in hypoxic/ anoxic regions while glucose-fuelled respiration occurs sparingly near the blood vessel. Lactate-fuelled cells are consuming the byproduct of the glycolytic cells where there is oxygen present.

Warburg effect

In the base case considered above glycolysis is inhibited until the oxygen consumption drops to values that prevent the production of sufficient ATP to maintain cell survival. However, cancer cells will commonly utilize glycolysis as a primary energy source even when there is enough oxygen to ensure cell survival. In the model we characterize the cell’s ability to hold off on utilizing glycolysis in oxygenated areas by the parameter ΛO. Reducing it 400-fold from the base case above (from 4000 to 100) results in spatial ATP turnover rate as given in Fig. 6. Cells near the vessel greedily consume the available resources leaving cells further from the vessel to die from insufficient ATP supply. The ATP production breakdown corresponds to the second bar in Fig. 8 and is slightly higher than the whole tissue considered in the base case above.

Fig. 6. ATP turnover (consumption/production) rates for cells exhibiting the Warburg effect (differs from base case because ΛO = 100 instead of 4000). The contributions of the pathways are bounded by the total ATP turnover rate PATP. Glycolysis is dominant in all regions of the tumor, however, glucose and lactate fueled respiration occur sparingly near the blood vessel where there is oxygen present.

Fig. 7. The optimal metabolic behavior on the microscale given an ATP turnover maximum of X mM=s. This shows glucose-fuelled respiration near the vessel, glycolysis far from the vessel and a lactate-consuming population in between these two

Instead of fixing all of the parameters to the values given in Table 1, we could leave some of the parameters free and optimize the amount of ATP generated from the given metabolites by imposing a maximum constraint on ATP production. For instance, setting all of the parameters initially to those given in Table 1, and then minimizing some function of Z¼PATP θ where θ is the maximum allowed ATP turnover rate would theoretically ensure that the available resources were not being selfishly consumed by oxidative cells near the vessel. Allowing cells to alter their glycolytic parameters: βg, δ and κg along with their lactate–glucose switch parameter λ yields the results shown in Fig. 7. While there was still enough constraint that the system still exhibited a non-constant ATP turnover where it could, this reinforces the suggested optimal strategy of glucose-fuelled respiration near the vessel, glycolysis far from the vessel and a lactate-consuming population in between these two. This optimization procedure most notably resulted in a reduced δ enabling the switch to glycolysis to happen closer to the vessel and a lower κg enabling a later and more drastic shut off of glycolysis; the parameter results of this simulation are presented in Table C1.

The mathematical model presented here can give insight into the effects of blocking various metabolic pathways. The three metabolic pathways that we have considered, namely (i) glucosefuelled respiration, (ii) lactate-fuelled respiration and (iii) glycolysis, could be inhibited by various agents, and the effects on local ATP production will be outlined below. For illustrative purposes we will consider complete inhibition of these pathways, but this will be followed by consideration of the more realistic scenario where these pathways are only partially inhibited. Entirely knocking out lactate metabolism could be achieved by inhibiting lactate dehydrogenase (LDH) which is responsible for the reentry of lactate into respiratory pathways by converting lactate into pyruvate. Successful inhibition would concurrently prevent the conversion of pyruvate to lactate as well, a crucial step for regenerating NAD+ in glycolytic cells. This has been shown to reduce ATP levels and consequently induce cell death in tumors (Le et al., 2010). The complete inhibition of lactate dehydrogenase would eliminate two of the three pathways considered here: lactate-fuelled respiration and glycolysis. Complete inhibition can be reflected in the model by setting BL¼0 and BG¼0, leaving only glucose-fuelled respiration to produce ATP, a physiologically normal condition. However, the hypoxic and hypoglycaemic conditions considered here do not leave enough fuel for cell survival. This scenario corresponds to the third bar in Fig. 8. We could also target glucose transport into the cell, an intermediary of glycolysis or one of the critical enzymes responsible for converting glucose to pyruvate. This is distinct from the strategy noted above of inhibiting LDH which prevents the conversion of lactate to pyruvate and vice versa. This has also been noted as a prime target for cancer therapy (Pelicano et al., 2006; Gatenby and Gillies, 2007) and there are currently many potential targets (Granchi and Minutolo, 2012). Here we will consider the shutdown of glycolysis as preventing both glucose-fuelled respiration and glycolysis since both of these require glucose to be converted into pyruvate. However, it leaves the lactate-fuelled respiratory pathway intact. This could be considered in the model by taking BO¼0 and BG¼0.Similar tothe caseof LDH inhibition this leads to a significant decrease in ATP production as shown in the fourth bar of Fig. 8. The final scenario that we consider corresponds to full inhibition of respiration somewhere along the chain between pyruvate transport into the mitochondria and the electron transport chain. There are numerous potential targets in the mitochondria (Costantini et al., 2000) and we will consider the complete shutdown of respiration by setting BL¼0 and BO¼0. This would result in negligible oxygen consumption and with our base case of ΛO 100-4000 this would lead to repressed glycolysis in the tissue.

Fig. 9. The effects of metabolic repression on total ATP production in a unit annulus of tumor tissue ðΦÞ. Cell metabolism is fully functioning when the relative rate is 1, while the cell metabolism is fully inhibited when the relative rateis 0. Intermediary values correspond to partial inhibition of both affected metabolic rates, e.g. for LDH half-inhibition: BG and BL are half the base case value, and BO remains at its base case value. The legend abbreviations are the same as those used in bars 3–6 in Fig. 8: LDH inhibition (LDH), glycolytic inhibition (Glyc), respiratory inhibition (Resp), and respiratory inhibition with Warburg effect (R-W). The total ATP production begins to significantly decrease for LDH and glycolytic inhibition only once more than half inhibition is reached. For respiratory inhibition, significant decreases are not detected until metabolic rates drop to one-tenth of the base case value.

The functional form for glycolysis given in (8) is similar to that used in McGillen et al. (2013), except where our form uses oxygen as the inhibitory molecule, they use lactate. McGillen et al. (2013) do not include glucose-fuelled respiration at all (as it was deemed to occur at negligible rates), and they use a similar lactate-fuelled respiratory term as used here, that was originally formulated by Mendoza-Juez et al. (2012). Instead of including a Michaelis– Menten oxygen dependence, they introduce a switch parameter that turns oxygen-fuelled metabolism on and off at a threshold oxygen concentration. However, they did enable the cells to use combinations of respiration and glycolysis as opposed to the strict switching between these two pathways modelled by Mendoza Juez et al. (2012). The novel aspects of our model include the introduction of a glycolytic inhibition parameter that can prevent or enable the Warburg effect, an explicit and smoothly defined oxygen dependence for the respiratory pathways, and the inclusion of an accurate ATP yield formula. While our results focus on the energetic consequences of metabolic inhibition, McGillen et al. (2013) focus on the interaction between metabolite consumption and tumor growth.


The mathematical model formulated and analyzed above can give insight into the metabolic behaviors of cancer cells on the microscale. The tumor microenvironment characterized by hypoxia and nutrient deprivation leads to the utilization of highly unregulated glycolytic pathways and the consumption by respiring cells of the lactate produced by these cells. These metabolic scenarios are encompassed by the functional forms proposed for glucose, lactate and oxygen consumption. To consider the effect of altering parameters in the model to the efficiency of energy production we must also consider the rate of ATP turnover in the tissue. To this end a detailed biochemical summary was performed in order to calculate estimates for ATP yields. These energetic landscapes were considered in tissues that utilize anaerobic glycolysis, thus keeping more cells alive, and those that experience the Warburg effect, performing glycolysis in oxygenated areas. The analysis shows that the latter does confer a proliferative advantage by producing more ATP. The effects of metabolic inhibition were taken into account by knocking out the pathways considered in our model. Glycolytic inhibition blocked glycolysis and glucose-fuelled respiration, LDH inhibition blocked glycolysis and lactate-fuelled respiration while respiration inhibition blocked both forms of respiration. Both strategies that block glycolysis lead to appreciable decreases in total ATP production, while those that block respiration are only effective in the base case where the cells are unable to elevate glycolytic rates due to the repressive effect of oxygen in the model. However, when considering a more realistic scenario where cells can adapt to blocked respiratory pathways by upregulating glycolysis via the Warburg effect, we observe that this treatment strategy allows sufficient ATP for cell survival. The work presented here should lead to a reconsideration of the importance of the spatial relationships between cells performing under specific metabolic regimes and provides a minimally parameterized and straightforward basis for future phenomenological metabolite consumption models. Localization and Kinetics of Reduced Pyridine Nucleotide in Living Cells by Microfluorometry J. Biol. Chem.-1959-Chance-3044-50

Britton Chance and Bo Thorell

J Biological Chemistry Nov 1959; 234(11)
On the basis of early studies of the blue fluorescence of living cells and tissues before chemical treatment, l Sjiistrand (1) suggested its association with the mitochondrial bodies. Microspectroscopic observations of prepared tissue sections revealed emission bands of the fluorescent material of axons (1) and acid treated groups of kidney cells; (2) critical evaluations of available spectrograms of purified materials lead to the identification of thiamin and riboflavin, respectively. Although some of the  of the kidney sections, before acid treatment, showed fluorescence bands in the spectrograms that are now regarded as suggestive of reduced pyridine nucleotide, the fluorescence of which was first observed by Warburg (2), insufficient data were available at that time to consider reduced pyridine nucleotide as a possible cause of the tissue fluorescence. Recent studies by Boyer and Theorell (3) and Duysens and Kronenberg (4) on alcohol dehydrogenase show clearly the great enhancement of DPNH fluorescence that is caused by a binding of the coenzyme to the enzyme surface. Furthermore, Duysens and Amesz (5) demonstrate that the intact yeast cell shows a fluorescence characteristic of bound reduced pyridine nucleotide. In more recent experiments, it has been found that intramitochondrial reduced pyridine nucleotide also exhibits the same characteristic fluorescence, calling attention to the possibility of a close relationship between this effect and the blue fluorescence of living cells and tissues (6). The fluorometric result agrees with the spectrophotometrically determined large RPN3 content of mitochondria (7). Furthermore, its binding to a mitochondrial component has been suggested by kinetic studies (7). More recent data show that the fluorescence of intact muscle diminishes upon electrically induced contraction, in agreement with the spectrophotometrically observed oxidation of RPN (8). Thus, there is good evidence that a considerable amount of tissue fluorescence is due to this component. To study the fluorescence of mitochondrial RPN independently of that of the cytoplasm, it has been desirable to develop a microfluorometric method, which, in conjunction with suitable biological materials showing isolation of the mitochondrial bodies, could be used to investigate cytoplasmic-mitochondrial interactions and also to permit the assay of RPN localized in different
1 The term “autofluorescence” is used by Sjostrand and other workers to indicate the fluorescence of a tissue before its treatment with stains, acids, and so forth.
2 F. S. Sjiistrand, unpublished experiments.
* The abbreviation used is: RPN, reduced pyridine nucleotide.

This paper describes such an instrument and its application to the observation of mitochondrial RPN, particularly in highly localized mitochondrial bodies such as the nebenkern4 of the grasshopper spermatid (11). It is now possible to investigate in viva the independent changes of mitochondrial and cytoplasmic pyridine nucleotide in the aerobic-anaerobic transition. In other cells, where mitochondrial localization is not sufficient for independent characterization of cytoplasmic and mitochondrial components of the fluorescence, assays of the oxidation-reduction state of the total pyridine nucleotide in individual cells in different states of metabolism and growth are possible. The combination of this differential fluorometer with the spectrophotometer described elsewhere (12, 13) for the localization of activities of respiratory and glycolytic enzymes in cells affords a new approach to the dynamic aspects of metabolic reactions.

The closure of the switch contacts and the wave form of the photocurrent and light intensity for an AC-operated light source (see below) are indicated in Fig. 1. The fluctuations of the light intensity (~100 per cent modulation) indicated on the top line cause synchronous variations which result in an asymmetrical wave form for the photocurrent, provided the fluorescent object coincides with the extremes of the excursions of the vibrating diaphragm. To measure the fluorescence intensity of the object (M) and that of a nearby “free space” (R), the switch circuit is adjusted so that it closes for a brief interval at the peaks of the photocurrent wave form (Fig. 1). The portions of the photocurrent selected by this switch are used to charge a condenser so that its potential represents the difference of the photocurrents at the two times. This potential is amplified by a “Millivac,” type 17C, and by an Esterline-Angus l-ma. recorder.

FIQ. 1. Wave forms of light intensity and photocurrent relative to the times of switch closure (alternating current operated by lamp). The vibrating diaphragm operates synchronously with the fluctuations in light intensity so that the extremes of its vibration correspond to maxima of light intensity

Fig. 2. Relative fluorescence maxima for suspensions of diploid bakers’ yeast, pentaploid yeast, and ascites tumor cells. These fluorescence emission spectra are obtained with excitation of the cell suspensions by the 366-rnr mercury line passed through the same filter used in the microfluorometer. The energy obtained through the Wratten 2A filter is analyzed by means of a grating monochromator and is plotted as a function of wave length. Significant features of the record are that no measurable energy at 366, 436, or 546 mp is received by the photocell. The cell suspensions are relatively concentrated (60 mg. per cc. for the yeast cell suspensions). The close correspondence of the amplitudes of the peaks is a consequence of adjusting the photocell dynode voltage appropriately (928).

Studies of mitochondria treated with ADP to cause the disappearance of RPN fluorescence show that a relatively small contribution of the flavoprotein of the respiratory chain remains and that flavoprotein fluorescence does not measurably change with its oxidation-reduction state. Thus, it is felt justified in these preliminary studies to attribute the major portion of the fluorescence observed to RPN. Evidence in favor of this view is indicated below, where chemical transitions affecting the oxidation-reduction state and hence the fluorescence of reduced pyridine nucleotide show that most of the fluorescence localized in the mitochondria is affected by this transition and hence is not a “fixed” background fluorescence.

Relative Intensities of Signals-A survey of various biological materials has been made to determine the relative intensities of the signals obtained and to demonstrate the feasibility of studies of their fluorescence. This study is largely incomplete, but the preliminary results summarized in Table I are rather encouraging. These fluorescence intensities range from a small value for the aerobic nebenkern of the grasshopper spermatid to a large value for the anaerobic pentaploid yeast cell. The larger currents give a signal-to-noise ratio of such magnitude that delicate indications are given, not only of the magnitude of the fluorescence, but also of changes that may occur in different metabolic states or in different parts of the cells. At higher currents, accuracies > 100 : 1 are possible. Localization of Fluorescence-The inadequate resolution of the optical microscope and the uniform distribution of the mitochondria throughout the cytoplasm of such cells as bakers’ or pentaploid yeast or ascites tumor cells offer little possibility for localizing the mitochondrial fluorescence as opposed to the cytoplasmic fluorescence.

Table I Summary of fluorescence intensities for various cell types and metabolic states

FIG. 7. Time course of the fluorescence changes of the nebenkern and of the cytoplasm in the aerobic-anaerobic transition. A, the ratio of nebenkern to cytoplasmic fluorescence, plotted as determined by records similar to those of Fig. 6. The numbers in the diagram refer to the cell studied. The abrupt upward discontinuity of the record at approximately 45 minutes occurs when anaerobiosis is expected. B, the individual measurements of the cytoplasmic (0-O) and nebenkern (0-C) fluorescence. The number of the cell used for measurement is also indicated along the scale of the abscissa (922a, b).

A fluorescence with spectral characteristics that are similar to those of reduced pyridine nucleotide of isolated mitochondria has been demonstrated to be localized in three cell configurations which cytologically show mitochondrial aggregation. The oxidation and reduction of mitochondrial pyridine nucleotide without a measurable change of cytoplasmic fluorescence suggest that compartmentalization of mitochondrial and cytoplasmic pyridine nucleotide occurs in viva, at least in the grasshopper spermatid. Studies of other material, particularly pentaploid yeast cells and ascites tumor cells, indicate that similar changes of fluorescence of the single cell are observed in the aerobic-anaerobic transition. In such cells, optical resolution does not permit localization of mitochondrial bodies. Nevertheless, the state of pyridine nucleotide in the individual cell can be investigated.


Radoslav S. Bozov (@Radobozov)

Your interpretations approximates wrong conclusions: 1. Oxygen is processed via mitochondrial Cu2+/3+ metalloproteins , H2O2 (King’s water) electro-negativity processing). 2. Lactate formation is an effect of cancerogenesis, a Lewis base., you lack fundamental understanding pKa issues in science and more accurately in moderns science. Such thing as protons have never been observed directly, that is a concept for explaining pH. All organic acids in bio systems are deprotonated carboxyl functional groups entering resonance state , which allows interpretation of spectra: There i s no way in real chemical science to have measured pH of a compartment and especially nano space! The physiological charge is -1:
Biophysical concepts might be applied in a wrong direction! which is the case of perceiving NADH/Pyruavte/Lactate triangle , you lack conceptual frames of systems applicability in expanded biological space/energies – proteins, nucleotides, and meta states! Pyridines have nothing to do with energy states, pyridines are nitrogen capacitors , they have nothing to do with origin and implications of mutation/evolution, regulation! You lack fundamental understanding of physical implications today!
Lactate is a compensatory mechanism of the genome for copying with disregulated supply of pyruvate for synthesizing negative methyl groups, energy processed in biospaces via compression/decompressing bio systems! Remember, quantum chemistry and implications of quantum physics is not one and the same! General Relativity is applied only towards statistical cloud delocalization, that implicates induction vs deductive reasoning! Classic mechanics of optics is a neat way to do math, nothing more than that of accepting reality of none observable parameters! Lactic acid was considered an end product of metabolism and physiological fatigue for a long time! Now, we know that is not true! To contrary lactic acid is used to have healthy pluripotecy differentiation of bone marrow derived cell lines. LDH proteins demonstrate high similarity motif selection with a range of transcriprion factors via blast studies. In general DATA IS MESSED UP and likely WRONGLY INTERPRETED!

Larry H Bernstein,

I am quite sure that what I presented is the best that science has produced.  Whether there is a theoretical issue in physical interpretation is another matter.  Two key papers are by Mayekovsky and by Britton Chance.  Britton Chance only died recently at nearly 100, but he was a giant in biochemistry, and my final exam question in freshman biochemistry was – should B Chance get the Nobel Prize.  His conception was then controversial, and the ETC won out.  Nevertheless, his contributions went far beyond the explanation for the H+ transfer role in ETC.  When I was a resident in pathology, my mentor (who identified the difference between myokinase and liver AK) commented that  the only reason that Chance had not been awarded was because his work was so technologically focused. I had studied the malate dehydrogenase reaction in Nate Kaplan’s lab, and I carried out stop-flow studies of the inhibition of the mitochondrial isoenzyme by oxaloacetate.  When I went to Washington, DC at the end of the Vietnam War and the time of Watergate, I had the good fortune to be introduced to Chance in a visit to Philadelphia.  I think that I do understand acidemia, cationic and anionic balance, which is not a simple matter – after some 35 years in pathology, with a main focus on clinical pathology.   If you could step back and give a point by point elucidation of where the experimental interpretation is in error, and a point by point highlight of your explanation, it would be very helpful. I know that I am quite knowledgable about the mechanism of reactions of the pyridine nucleotide linked dehydrogenases, and the isoenzymes, and the abortive ternary complexes.  I also published in the Brit J Cancer in the 1970’s on an abnormality in the cytoplasmic MDH in fast growing murine hepatomas, and in human cancer.  I spent many months purifying the heart mitochondrial MDH to purity, and established that there was no histidine residue at the active site.

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Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

Reviewer and Curator: Larry H. Bernstein, MD, FCAP

Pentose Shunt, Electron Transfer, Galactose, and other Lipids in brief

This is a continuation of the series of articles that spans the horizon of the genetic
code and the progression in complexity from genomics to proteomics, which must
be completed before proceeding to metabolomics and multi-omics.  At this point
we have covered genomics, transcriptomics, signaling, and carbohydrate metabolism
with considerable detail.In carbohydrates. There are two topics that need some attention –
(1) pentose phosphate shunt;
(2) H+ transfer
(3) galactose.
(4) more lipids
Then we are to move on to proteins and proteomics.

Summary of this series:

The outline of what I am presenting in series is as follows:

  1. Signaling and Signaling Pathways
  2. Signaling transduction tutorial.
  3. Carbohydrate metabolism

Selected References to Signaling and Metabolic Pathways published in this Open Access Online Scientific Journal, include the following:

  1. Lipid metabolism

4.1  Studies of respiration lead to Acetyl CoA

4.2 The multi-step transfer of phosphate bond and hydrogen exchange energy

5.Pentose shunt, electron transfers, galactose, and other lipids in brief

6. Protein synthesis and degradation

7.  Subcellular structure

8. Impairments in pathological states: endocrine disorders; stress
hypermetabolism; cancer.

Section I. Pentose Shunt

Bernard L. Horecker’s Contributions to Elucidating the Pentose Phosphate Pathway

Nicole Kresge,     Robert D. Simoni and     Robert L. Hill

The Enzymatic Conversion of 6-Phosphogluconate to Ribulose-5-Phosphate
and Ribose-5-Phosphate (Horecker, B. L., Smyrniotis, P. Z., and Seegmiller,
J. E.      J. Biol. Chem. 1951; 193: 383–396

Bernard Horecker

Bernard Leonard Horecker (1914) began his training in enzymology in 1936 as a
graduate student at the University of Chicago in the laboratory of T. R. Hogness.
His initial project involved studying succinic dehydrogenase from beef heart using
the Warburg manometric apparatus. However, when Erwin Hass arrived from Otto
Warburg’s laboratory he asked Horecker to join him in the search for an enzyme
that would catalyze the reduction of cytochrome c by reduced NADP. This marked
the beginning of Horecker’s lifelong involvement with the pentose phosphate pathway.

During World War II, Horecker left Chicago and got a job at the National Institutes of
Health (NIH) in Frederick S. Brackett’s laboratory in the Division of Industrial Hygiene.
As part of the wartime effort, Horecker was assigned the task of developing a method
to determine the carbon monoxide hemoglobin content of the blood of Navy pilots
returning from combat missions. When the war ended, Horecker returned to research
in enzymology and began studying the reduction of cytochrome c by the succinic
dehydrogenase system.

Shortly after he began these investigation changes, Horecker was approached by
future Nobel laureate Arthur Kornberg, who was convinced that enzymes were the
key to understanding intracellular biochemical processes
. Kornberg suggested
they collaborate, and the two began to study the effect of cyanide on the succinic
dehydrogenase system. Cyanide had previously been found to inhibit enzymes
containing a heme group, with the exception of cytochrome c. However, Horecker
and Kornberg found that

  • cyanide did in fact react with cytochrome c and concluded that
  • previous groups had failed to perceive this interaction because
    • the shift in the absorption maximum was too small to be detected by
      visual examination.

Two years later, Kornberg invited Horecker and Leon Heppel to join him in setting up
a new Section on Enzymes in the Laboratory of Physiology at the NIH. Their Section on Enzymes eventually became part of the new Experimental Biology and Medicine
Institute and was later renamed the National Institute of Arthritis and Metabolic

Horecker and Kornberg continued to collaborate, this time on

  • the isolation of DPN and TPN.

By 1948 they had amassed a huge supply of the coenzymes and were able to
present Otto Warburg, the discoverer of TPN, with a gift of 25 mg of the enzyme
when he came to visit. Horecker also collaborated with Heppel on 

  • the isolation of cytochrome c reductase from yeast and 
  • eventually accomplished the first isolation of the flavoprotein from
    mammalian liver.

Along with his lab technician Pauline Smyrniotis, Horecker began to study

  • the enzymes involved in the oxidation of 6-phosphogluconate and the
    metabolic intermediates formed in the pentose phosphate pathway.

Joined by Horecker’s first postdoctoral student, J. E. Seegmiller, they worked
out a new method for the preparation of glucose 6-phosphate and 6-phosphogluconate, 
both of which were not yet commercially available.
As reported in the Journal of Biological Chemistry (JBC) Classic reprinted here, they

  • purified 6-phosphogluconate dehydrogenase from brewer’s yeast (1), and 
  • by coupling the reduction of TPN to its reoxidation by pyruvate in
    the presence of lactic dehydrogenase
  • they were able to show that the first product of 6-phosphogluconate oxidation,
  • in addition to carbon dioxide, was ribulose 5-phosphte.
  • This pentose ester was then converted to ribose 5-phosphate by a
    pentose-phosphate isomerase.

They were able to separate ribulose 5-phosphate from ribose 5- phosphate and demonstrate their interconversion using a recently developed nucleotide separation
technique called ion-exchange chromatography. Horecker and Seegmiller later
showed that 6-phosphogluconate metabolism by enzymes from mammalian
tissues also produced the same products

Bernard Horecker

Bernard Horecker

Over the next several years, Horecker played a key role in elucidating the

  • remaining steps of the pentose phosphate pathway.

His total contributions included the discovery of three new sugar phosphate esters,
ribulose 5-phosphate, sedoheptulose 7-phosphate, and erythrose 4-phosphate, and
three new enzymes, transketolase, transaldolase, and pentose-phosphate 3-epimerase.
The outline of the complete pentose phosphate cycle was published in 1955
(2). Horecker’s personal account of his work on the pentose phosphate pathway can
be found in his JBC Reflection (3).1

Horecker’s contributions to science were recognized with many awards and honors
including the Washington Academy of Sciences Award for Scientific Achievement in
Biological Sciences (1954) and his election to the National Academy of Sciences in
1961. Horecker also served as president of the American Society of Biological
Chemists (now the American Society for Biochemistry and Molecular Biology) in 1968.


  • 1 All biographical information on Bernard L. Horecker was taken from Ref. 3.
  • The American Society for Biochemistry and Molecular Biology, Inc.


  1. ↵Horecker, B. L., and Smyrniotis, P. Z. (1951) Phosphogluconic acid dehydrogenase
    from yeast. J. Biol. Chem. 193, 371–381FREE Full Text
  2. Gunsalus, I. C., Horecker, B. L., and Wood, W. A. (1955) Pathways of carbohydrate
    metabolism in microorganisms. Bacteriol. Rev. 19, 79–128  FREE Full Text
  3. Horecker, B. L. (2002) The pentose phosphate pathway. J. Biol. Chem. 277, 47965–
    47971 FREE Full Text

The Pentose Phosphate Pathway (also called Phosphogluconate Pathway, or Hexose
Monophosphate Shunt) is depicted with structures of intermediates in Fig. 23-25
p. 863 of Biochemistry, by Voet & Voet, 3rd Edition. The linear portion of the pathway
carries out oxidation and decarboxylation of glucose-6-phosphate, producing the
5-C sugar ribulose-5-phosphate.

Glucose-6-phosphate Dehydrogenase catalyzes oxidation of the aldehyde
(hemiacetal), at C1 of glucose-6-phosphate, to a carboxylic acid in ester linkage
(lactone). NADPserves as electron acceptor.

6-Phosphogluconolactonase catalyzes hydrolysis of the ester linkage (lactone)
resulting in ring opening. The product is 6-phosphogluconate. Although ring opening
occurs in the absence of a catalyst, 6-Phosphogluconolactonase speeds up the
reaction, decreasing the lifetime of the highly reactive, and thus potentially
toxic, 6-phosphogluconolactone.

Phosphogluconate Dehydrogenase catalyzes oxidative decarboxylation of
6-phosphogluconate, to yield the 5-C ketose ribulose-5-phosphate. The
hydroxyl at C(C2 of the product) is oxidized to a ketone. This promotes loss
of the carboxyl at C1 as CO2.  NADP+ again serves as oxidant (electron acceptor).

pglucose hd

pglucose hd

Reduction of NADP+ (as with NAD+) involves transfer of 2e- plus 1H+ to the
nicotinamide moiety.


NADPH, a product of the Pentose Phosphate Pathway, functions as a reductant in
various synthetic (anabolic) pathways, including fatty acid synthesis.

NAD+ serves as electron acceptor in catabolic pathways in which metabolites are
oxidized. The resultant NADH is reoxidized by the respiratory chain, producing ATP.


Glucose-6-phosphate Dehydrogenase is the committed step of the Pentose
Phosphate Pathway. This enzyme is regulated by availability of the substrate NADP+.
As NADPH is utilized in reductive synthetic pathways, the increasing concentration of
NADP+ stimulates the Pentose Phosphate Pathway, to replenish NADPH.

The remainder of the Pentose Phosphate Pathway accomplishes conversion of the
5-C ribulose-5-phosphate to the 5-C product ribose-5-phosphate, or to the 3-C
glyceraldehyde -3-phosphate and the 6-C fructose-6-phosphate (reactions 4 to 8
p. 863).

Transketolase utilizes as prosthetic group thiamine pyrophosphate (TPP), a
derivative of vitamin B1.



Thiamine pyrophosphate binds at the active sites of enzymes in a “V” conformation.The amino group of the aminopyrimidine moiety is close to the dissociable proton,
and serves as the proton acceptor. This proton transfer is promoted by a glutamate
residue adjacent to the pyrimidine ring.

The positively charged N in the thiazole ring acts as an electron sink, promoting
C-C bond cleavage. The 3-C aldose glyceraldehyde-3-phosphate is released.
2-C fragment remains on TPP.

FASEB J. 1996 Mar;10(4):461-70.


The importance of this pathway can easily be underestimated.  The main source for
energy in respiration was considered to be tied to the

  • high energy phosphate bond in phosphorylation and utilizes NADPH, converting it to NADP+.

glycolysis n skeletal muscle in short term, dependent on muscle glycogen conversion
to glucose, and there is a buildup of lactic acid – used as fuel by the heart.  This
pathway accounts for roughly 5% of metabolic needs, varying between tissues,
depending on there priority for synthetic functions, such as endocrine or nucleic
acid production.

The mature erythrocyte and the ocular lens both are enucleate.  85% of their
metabolic energy needs are by anaerobic glycolysis.  Consider the erythrocyte
somewhat different than the lens because it has iron-based hemoglobin, which
exchanges O2 and CO2 in the pulmonary alveoli, and in that role, is a rapid
regulator of H+ and pH in the circulation (carbonic anhydrase reaction), and also to
a lesser extent in the kidney cortex, where H+ is removed  from the circulation to
the urine, making the blood less acidic, except when there is a reciprocal loss of K+.
This is how we need a nomogram to determine respiratory vs renal acidosis or
alkalosis.  In the case of chronic renal disease, there is substantial loss of
functioning nephrons, loss of countercurrent multiplier, and a reduced capacity to
remove H+.  So there is both a metabolic acidosis and a hyperkalemia, with increased
serum creatinine, but the creatinine is only from muscle mass – not accurately
reflecting total body mass, which includes visceral organs.  The only accurate
measure of lean body mass would be in the linear relationship between circulating
hepatic produced transthyretin (TTR).

The pentose phosphate shunt is essential for

  • the generation of nucleic acids, in regeneration of red cells and lens – requiring NADPH.

Insofar as the red blood cell is engaged in O2 exchange, the lactic dehydrogenase
isoenzyme composition is the same as the heart. What about the lens of and cornea the eye, and platelets?  The explanation does appear to be more complex than
has been proposed and is not discussed here.

Section II. Mitochondrial NADH – NADP+ Transhydrogenase Reaction

There is also another consideration for the balance of di- and tri- phospopyridine
nucleotides in their oxidized and reduced forms.  I have brought this into the
discussion because of the centrality of hydride tranfer to mitochondrial oxidative
phosphorylation and the energetics – for catabolism and synthesis.

The role of transhydrogenase in the energy-linked reduction of TPN 

Fritz HommesRonald W. Estabrook∗∗

The Wenner-Gren Institute, University of Stockholm
Stockholm, Sweden
Biochemical and Biophysical Research Communications 11, (1), 2 Apr 1963, Pp 1–6

In 1959, Klingenberg and Slenczka (1) made the important observation that incubation of isolated

  • liver mitochondria with DPN-specific substrates or succinate in the absence of phosphate
    acceptor resulted in a rapid and almost complete reduction of the intramitochondrial TPN.

These and related findings led Klingenberg and co-workers (1-3) to postulate

  • the occurrence of an ATP-controlled transhydrogenase reaction catalyzing the reduction of
    mitochondrial TPN by DPNH. A similar conclusion was reached by Estabrook and Nissley (4).

The present paper describes the demonstration and some properties of an

  • energy-dependent reduction of TPN by DPNH, catalyzed by submitochondrial particles.

Preliminary reports of some of these results have already appeared (5, 6 ) , and a
complete account is being published elsewhere (7).We have studied the energy- dependent reduction of TPN by PNH with submitochondrial particles from both
rat liver and beef heart. Rat liver particles were prepared essentially according to
the method of Kielley and Bronk (8), and beef heart particles by the method of
Low and Vallin (9).


(From the McCollum-Pratt Institute, The Johns Hopkins University, Baltimore,
Maryland)  J. Biol. Chem. 1952, 195:107-119.

NO Kaplan

NO Kaplan

Sidney Colowick

Sidney Colowick

Elizabeth Neufeld

Elizabeth Neufeld

Kaplan studied carbohydrate metabolism in the liver under David M. Greenberg at the
University of California, Berkeley medical school. He earned his Ph.D. in 1943. From
1942 to 1944, Kaplan participated in the Manhattan Project. From 1945 to 1949,
Kaplan worked with Fritz Lipmann at Massachusetts General Hospital to study
coenzyme A. He worked at the McCollum-Pratt Institute of Johns Hopkins University
from 1950 to 957. In 1957, he was recruited to head a new graduate program in
biochemistry at Brandeis University. In 1968, Kaplan moved to the University of
California, San Diego
, where he studied the role of lactate dehydrogenase in cancer. He also founded a colony of nude mice, a strain of laboratory mice useful in the study
of cancer and other diseases. [1] He was a member of the National Academy of
Sciences.One of Kaplan’s students at the University of California was genomic
researcher Craig Venter.[2]3]  He was, with Sidney Colowick, a founding editor of the scientific book series Methods
in Enzymology

Colowick became Carl Cori’s first graduate student and earned his Ph.D. at
Washington University St. Louis in 1942, continuing to work with the Coris (Nobel
Prize jointly) for 10 years. At the age of 21, he published his first paper on the
classical studies of glucose 1-phosphate (2), and a year later he was the sole author on a paper on the synthesis of mannose 1-phosphate and galactose 1-phosphate (3). Both papers were published in the JBC. During his time in the Cori lab,

Colowick was involved in many projects. Along with Herman Kalckar he discovered
myokinase (distinguished from adenylate kinase from liver), which is now known as
adenyl kinase. This discovery proved to be important in understanding transphos-phorylation reactions in yeast and animal cells. Colowick’s interest then turned to
the conversion of glucose to polysaccharides, and he and Earl Sutherland (who
will be featured in an upcoming JBC Classic) published an important paper on the
formation of glycogen from glucose using purified enzymes (4). In 1951, Colowick
and Nathan Kaplan were approached by Kurt Jacoby of Academic Press to do a
series comparable to Methodem der Ferment Forschung. Colowick and Kaplan
planned and edited the first 6 volumes of Methods in Enzymology, launching in 1955
what became a series of well known and useful handbooks. He continued as
Editor of the series until his death in 1985.

The Structure of NADH: the Work of Sidney P. Colowick

Nicole KresgeRobert D. Simoni and Robert L. Hill

On the Structure of Reduced Diphosphopyridine Nucleotide

(Pullman, M. E., San Pietro, A., and Colowick, S. P. (1954)

J. Biol. Chem. 206, 129–141)

Elizabeth Neufeld
·  Born: September 27, 1928 (age 85), Paris, France
·  EducationQueens College, City University of New YorkUniversity of California,

In Paper I (l), indirect evidence was presented for the following transhydrogenase
reaction, catalyzed by an enzyme present in extracts of Pseudomonas


The evidence was obtained by coupling TPN-specific dehydrogenases with the
transhydrogenase and observing the reduction of large amounts of diphosphopyridine nucleotide (DPN) in the presence of catalytic amounts of triphosphopyridine
nucleotide (TPN).

In this paper, data will be reported showing the direct

  • interaction between TPNHz and DPN, in thepresence of transhydrogenase alone,
  • to yield products having the propertiesof TPN and DPNHZ.

Information will be given indicating that the reaction involves

  • a transfer of electrons (or hydrogen) rather than a phosphate 

Experiments dealing with the kinetics and reversibility of the reaction, and with the
nature of the products, suggest that the reaction is a complex one, not fully described
by the above formulation.

Materials and Methods [edited]

The TPN and DPN used in these studies were preparations of approximately 75
percent purity and were prepared from sheep liver by the chromatographic procedure
of Kornberg and Horecker (unpublished). Reduced DPN was prepared enzymatically with alcohol dehydrogenase as described elsewhere (2). Reduced TPN was prepared by treating TPN with hydrosulfite. This treated mixture contained 2 pM of TPNHz per ml.
The preparations of desamino DPN and reduced desamino DPN have been
described previously (2, 3). Phosphogluconate was a barium salt which was kindly
supplied by Dr. B. F. Horecker. Cytochrome c was obtained from the Sigma Chemical Company.

Transhydrogenase preparations with an activity of 250 to 7000 units per mg. were
used in these studies. The DPNase was a purified enzyme, which was obtained
from zinc-deficient Neurospora and had an activity of 5500 units per mg. (4). The
alcohol dehydrogenase was a crystalline preparation isolated from yeast according to the procedure of Racker (5).

Phosphogluconate dehydrogenase from yeast and a 10 per cent pure preparation of the TPN-specific cytochrome c reductase from liver (6) were gifts of Dr. B. F.

DPN was assayed with alcohol and crystalline yeast alcohol dehydrogenase. TPN was determined By the specific phosphogluconic acid dehydrogenase from yeast and also by the specific isocitric dehydrogenase from pig heart. Reduced DPN was
determined by the use of acetaldehyde and the yeast alcohol dehydrogenase.
All of the above assays were based on the measurement of optical density changes
at 340 rnp. TPNHz was determined with the TPN-specific cytochrome c reductase system. The assay of the reaction followed increase in optical density at 550 rnp  as a measure of the reduction of the cytochrome c after cytochrome c
reductase was added to initiate the reaction. The changes at 550 rnp are plotted for different concentrations of TPNHz in Fig. 3, a. The method is an extremely sensitive and accurate assay for reduced TPN.

[No Figures or Table shown]

Formation of DPNHz from TPNHz and DPN-Fig. 1, a illustrates the direct reaction between TPNHz and DPN to form DPNHZ. The reaction was carried out by incubating TPNHz with DPN in the presence of the
transhydrogenase, yeast alcohol dehydrogenase, and acetaldehyde. Since the yeast dehydrogenase is specific for DPN,

  • a decrease in absorption at340 rnp can only be due to the formation of reduced DPN. It can
    be seen from the curves in Fig. 1, a that a decrease in optical density occurs only in the
    presence of the complete system.

The Pseudomonas enzyme is essential for the formation of DPNH2. It is noteworthy
that, under the conditions of reaction in Fig. 1, a,

  • approximately 40 per cent of theTPNH, reacted with the DPN.

Fig. 1, a also indicates that magnesium is not required for transhydrogenase activity.  The reaction between TPNHz and DPN takes place in the absence of alcohol
dehydrogenase and acetaldehyde
. This can be demonstrated by incubating the
two pyridine nucleotides with the transhydrogenase for 4 8 12 16 20 24 28 32 36

FIG. 1. Evidence for enzymatic reaction of TPNHt with DPN.

  • Rate offormation of DPNH2.

(b) DPN disappearance and TPN formation.

(c) Identification of desamino DPNHz as product of reaction of TPNHz with desamino DPN.  (assaying for reduced DPN by the yeast alcohol dehydrogenase technique.

Table I (Experiment 1) summarizes the results of such experiments in which TPNHz was added with varying amounts of DPN.

  • In the absence of DPN, no DPNHz was formed. This eliminates the possibility that TPNH 2 is
    converted to DPNHz
  • by removal ofthe monoester phosphate grouping.

The data also show that the extent of the reaction is

  • dependent on the concentration of DPN.

Even with a large excess of DPN, only approximately 40 per cent of the TPNHzreacts to form reduced DPN. It is of importance to emphasize that in the above
experiments, which were carried out in phosphate buffer, the extent of  the reaction

  • is the same in the presence or absence of acetaldehyde andalcohol dehydrogenase.

With an excess of DPN and different  levels of TPNHZ,

  • the amount of reduced DPN which is formed is
  • dependent on the concentration of TPNHz(Table I, Experiment 2).
  • In all cases, the amount of DPNHz formed is approximately
    40 per cent of the added reduced TPN.

Formation of TPN-The reaction between TPNHz and DPN should yield TPN as well as DPNHz.
The formation of TPN is demonstrated in Table 1. in Fig. 1, b. In this experiment,
TPNHz was allowed to react with DPN in the presence of the transhydrogenase
(PS.), and then alcohol and alcohol dehydrogenase were added . This
would result in reduction of the residual DPN, and the sample incubated with the
transhydrogenase contained less DPN. After the completion of the alcohol
dehydrogenase reaction, phosphogluconate and phosphogluconic dehydrogenase (PGAD) were added to reduce the TPN. The addition of this TPN-specific
dehydrogenase results in an

  • increase inoptical density in the enzymatically treated sample.
  • This change represents the amount of TPN formed.

It is of interest to point out that, after addition of both dehydrogenases,

  • the total optical density change is the same in both

Therefore it is evident that

  • for every mole of DPN disappearing  a mole of TPN appears.

Balance of All Components of Reaction

Table II (Experiment 1) shows that,

  • if measurements for all components of the reaction are made, one can demonstrate
    that there is
  • a mole for mole disappearance of TPNH, and DPN, and
  • a stoichiometric appearance of TPN and DPNH2.
  1. The oxidized forms of the nucleotides were assayed as described
  2. the reduced form of TPN was determined by the TPNHz-specific cytochrome c reductase,
  3. the DPNHz by means of yeast alcohol dehydrogenase plus

This stoichiometric balance is true, however,

  • only when the analyses for the oxidized forms are determined directly on the reaction

When analyses are made after acidification of the incubated reaction mixture,

  • the values found forDPN and TPN are much lower than those obtained by direct analysis.

This discrepancy in the balance when analyses for the oxidized nucleotides are
carried out in acid is indicated in Table II (Experiment 2). The results, when
compared with the findings in Experiment 1, are quite striking.

Reaction of TPNHz with Desamino DPN

Desamino DPN

  • reacts with the transhydrogenase system at the same rate as does DPN (2).

This was of value in establishing the fact that

  • the transhydrogenase catalyzesa transfer of hydrogen rather than a phosphate transfer reaction.

The reaction between desamino DPN and TPNHz can be written in two ways.

TPN f desamino DPNHz

TPNH, + desamino DPN

DPNH2 + desamino TPN

If the reaction involved an electron transfer,

  • desamino DPNHz would be
  • Phosphate transfer would result in the production of reduced

Desamino DPNHz can be distinguished from DPNHz by its

  • slowerrate of reaction with yeast alcohol dehydrogenase (2, 3).

Fig. 1, c illustrates that, when desamino DPN reacts with TPNH2, 

  • the product of the reaction is desamino DPNHZ.

This is indicated by the slow rate of oxidation of the product by yeast alcohol
dehydrogenase and acetaldehyde.

From the above evidence phosphate transfer 

  • has been ruled out as a possible mechanism for the transhydrogenase reaction.

Inhibition by TPN

As mentioned in Paper I and as will be discussed later in this paper,

  • the transhydrogenase reaction does not appear to be readily reversible.

This is surprising, particularly since only approximately 

  • 40 per cent of the TPNHz undergoes reaction with DPN
    under the conditions described above. It was therefore thought that
  • the TPN formed might inhibit further transfer of electrons from TPNH2.

Table III summarizes data showing the

  • strong inhibitory effect of TPN on thereaction between TPNHz and DPN.

It is evident from the data that

  • TPN concentration is a factor in determining the extent of the reaction.

Effect of Removal of TPN on Extent of Reaction

A purified DPNase from Neurospora has been found

  • to cleave the nicotinamide riboside linkagesof the oxidized forms of both TPN and DPN
  • without acting on thereduced forms of both nucleotides (4).

It has been found, however, that

  • the DPNase hydrolyzes desamino DPN at a very slow rate (3).

In the reaction between TPNHz and desamino DPN, TPN and desamino DPNH:,

  • TPNis the only component of this reaction attacked by the Neurospora enzyme
    at an appreciable rate

It was  thought that addition of the DPNase to the TPNHZ-desamino DPN trans-
hydrogenase reaction mixture

  • would split the TPN formed andpermit the reaction to go to completion.

This, indeed, proved to be the case, as indicated in Table IV, where addition of
the DPNase with desamino DPN results in almost

  • a stoichiometric formation of desamino DPNHz
  • and a complete disappearance of TPNH2.

Extent of Reaction in Buffers Other Than Phosphate

All the reactions described above were carried out in phosphate buffer of pH 7.5.
If the transhydrogenase reaction between TPNHz and DPN is run at the same pH
in tris(hydroxymethyl)aminomethane buffer (TRIS buffer)

  • with acetaldehydeand alcohol dehydrogenase present,
  • the reaction proceeds muchfurther toward completion 
  • than is the case under the same conditions ina phosphate medium (Fig. 2, a).

The importance of phosphate concentration in governing the extent of the reaction
is illustrated in Fig. 2, b.

In the presence of TRIS the transfer reaction

  • seems to go further toward completion in the presence of acetaldehyde
    alcohol dehydrogenase
  • than when these two components are absent.

This is not true of the reaction in phosphate,

  • in which the extent is independent of the alcoholdehydrogenase system.

Removal of one of the products of the reaction (DPNHp) in TRIS thus

  • appears to permit the reaction to approach completion,whereas
  • in phosphate this removal is without effect on the finalcourse of the reaction.

The extent of the reaction in TRIS in the absence of alcohol dehydrogenase
and acetaldehyde

  • somewhat greater than when the reaction is run in phosphate.

TPN also inhibits the reaction of TPNHz with DPN in TRIS medium, but the inhibition

  • is not as marked as when the reaction is carried out in phosphate buffer.

Reversibility of Transhydrogenase Reaction;

Reaction between DPNHz and TPN

In Paper I, it was mentioned that no reversal of the reaction could be achieved in a system containing alcohol, alcohol dehydrogenase, TPN, and catalytic amounts of

When DPNH, and TPN are incubated with the purified transhydrogenase, there is

  • no evidence for reversibility.

This is indicated in Table V which shows that

  • there is no disappearance of DPNHz in such a system.

It was thought that removal of the TPNHz, which might be formed in the reaction,
could promote the reversal of the reaction. Hence,

  • by using the TPNHe-specific cytochrome c reductase, one could
  1. not only accomplishthe removal of any reduced TPN,
  2. but also follow the course of the reaction.

A system containing DPNH2, TPN, the transhydrogenase, the cytochrome c
reductase, and cytochrome c, however, gives

  • no reduction of the cytochrome

This is true for either TRIS or phosphate buffers.2

Some positive evidence for the reversibility has been obtained by using a system

  • DPNH2, TPNH2, cytochrome c, and the cytochrome creductase in TRIS buffer.

In this case, there is, of course, reduction of cytochrome c by TPNHZ, but,

  • when the transhydrogenase is present.,there is
  • additional reduction over and above that due to the added TPNH2.

This additional reduction suggests that some reversibility of the reaction occurred
under these conditions. Fig. 3, b shows

  • the necessity of DPNHzfor this additional reduction.

Interaction of DPNHz with Desamino DPN-

If desamino DPN and DPNHz are incubated with the purified Pseudomonas enzyme,
there appears

  • to be a transfer of electrons to form desamino DPNHz.

This is illustrated in Fig. 4, a, which shows the

  • decreased rate of oxidation by thealcohol dehydrogenase system
  • after incubation with the transhydrogenase.
  • Incubation of desamino DPNHz with DPN results in the formation of DPNH2,
  • which is detected by the faster rate of oxidation by the alcohol dehydrogenase system
  • after reaction of the pyridine nucleotides with thetranshydrogenase (Fig. 4, b).

It is evident from the above experiments that

the transhydrogenase catalyzes an exchange of hydrogens between

  • the adenylic and inosinic pyridine nucleotides.

However, it is difficult to obtain any quantitative information on the rate or extent of
the reaction by the method used, because

  • desamino DPNHz also reacts with the alcohol dehydrogenase system,
  • although at a much slower rate than does DPNH2.


The results of the balance experiments seem to offer convincing evidence that
the transhydrogenase catalyzes the following reaction.


Since desamino DPNHz is formed from TPNHz and desamino DPN,

  • thereaction appears to involve an electron (or hydrogen) transfer
  • rather thana transfer of the monoester phosphate grouping of TPN.

A number of the findings reported in this paper are not readily understandable in
terms of the above simple formulation of the reaction. It is difficult to understand
the greater extent of the reaction in TRIS than in phosphate when acetaldehyde
and alcohol dehydrogenase are present.

One possibility is that an intermediate may be involved which is more easily converted
to reduced DPN in the TRIS medium. The existence of such an intermediate is also
suggested by the discrepancies noted in balance experiments, in which

  • analyses of the oxidized nucleotides after acidification showed
  • much lower values than those found by direct analysis.

These findings suggest that the reaction may involve

  • a 1 electron ratherthan a 2 electron transfer with
  • the formation of acid-labile free radicals as intermediates.

The transfer of hydrogens from DPNHz to desamino DPN

  • to yield desamino DPNHz and DPN and the reversal of this transfer
  • indicate the unique role of the transhydrogenase
  • in promoting electron exchange between the pyridine nucleotides.

In this connection, it is of interest that alcohol dehydrogenase and lactic
dehydrogenase cannot duplicate this exchange  between the DPN and
the desamino systems.3  If one assumes that desamino DPN behaves
like DPN,

  • one might predict that the transhydrogenase would catalyze an
    exchange of electrons (or hydrogen) 3.

Since alcohol dehydrogenase alone

  • does not catalyze an exchange of electrons between the adenylic
    and inosinic pyridine nucleotides, this rules out the possibility
  • that the dehydrogenase is converted to a reduced intermediate
  • during electron between DPNHz and added DPN.

It is hoped to investigate this possibility with isotopically labeled DPN.
Experiments to test the interaction between TPN and desamino TPN are
also now in progress.

It seems likely that the transhydrogenase will prove capable of

  • catalyzingan exchange between TPN and TPNH2, as well as between DPN and

The observed inhibition by TPN of the reaction between TPNHz and DPN may

  • be due to a competition between DPN and TPNfor the TPNH2.


  1. Direct evidence for the following transhydrogenase reaction. catalyzedby an
    enzyme from Pseudomonas fluorescens, is presented.


Balance experiments have shown that for every mole of TPNHz disappearing
1 mole of TPN appears and that for each mole of DPNHz generated 1 mole of
DPN disappears. The oxidized nucleotides found at the end of the reaction,
however, show anomalous lability toward acid.

  1. The transhydrogenase also promotes the following reaction.

TPNHz + desamino DPN -+ TPN + desamino DPNH,

This rules out the possibility that the transhydrogenase reaction involves a
phosphate transfer and indicates that the

  • enzyme catalyzes a shift of electrons (or hydrogen atoms).

The reaction of TPNHz with DPN in 0.1 M phosphate buffer is strongly
inhibited by TPN; thus

  • it proceeds only to the extent of about40 per cent or less, even
  • when DPNHz is removed continuously by meansof acetaldehyde
    and alcohol dehydrogenase.
  • In other buffers, in whichTPN is less inhibitory, the reaction proceeds
    much further toward completion under these conditions.
  • The reaction in phosphate buffer proceedsto completion when TPN
    is removed as it is formed.
  1. DPNHz does not react with TPN to form TPNHz and DPN in the presence
    of transhydrogenase. Some evidence, however, has been obtained for
    the reversibility by using the following system:
  • DPNHZ, TPNHZ, cytochromec, the TPNHz-specific cytochrome c reductase,
    and the transhydrogenase.
  1. Evidence is cited for the following reversible reaction, which is catalyzed
    by the transhydrogenase.

DPNHz + desamino DPN fi DPN + desamino DPNHz

  1. The results are discussed with respect to the possibility that the
    transhydrogenase reaction may
  • involve a 1 electron transfer with theformation of free radicals as intermediates.



  1. Coiowick, S. P., Kaplan, N. O., Neufeld, E. F., and Ciotti, M. M., J. Biol. Chem.,196, 95 (1952).
  2. Pullman, 111. E., Colowick, S. P., and Kaplan, N. O., J. Biol. Chem., 194, 593(1952).
  3. Kaplan, N. O., Colowick, S. P., and Ciotti, M. M., J. Biol. Chem., 194, 579 (1952).
  4. Kaplan, N. O., Colowick, S. P., and Nason, A., J. Biol. Chem., 191, 473 (1951).
  5. Racker, E., J. Biol. Chem., 184, 313 (1950).
  6. Horecker, B. F., J. Biol. Chem., 183, 593 (1950).

Section !II. 


The Leloir pathway: a mechanistic imperative for three enzymes to change
the stereochemical configuration of a single carbon in galactose.

Frey PA.
FASEB J. 1996 Mar;10(4):461-70.

The biological interconversion of galactose and glucose takes place only by way of
the Leloir pathway and requires the three enzymes galactokinase, galactose-1-P
uridylyltransferase, and UDP-galactose 4-epimerase.
The only biological importance of these enzymes appears to be to

  • provide for the interconversion of galactosyl and glucosyl groups.

Galactose mutarotase also participates by producing the galactokinase substrate
alpha-D-galactose from its beta-anomer. The galacto/gluco configurational change takes place at the level of the nucleotide sugar by an oxidation/reduction
mechanism in the active site of the epimerase NAD+ complex. The nucleotide portion
of UDP-galactose and UDP-glucose participates in the epimerization process in two ways:

1) by serving as a binding anchor that allows epimerization to take place at glycosyl-C-4 through weak binding of the sugar, and

2) by inducing a conformational change in the epimerase that destabilizes NAD+ and
increases its reactivity toward substrates.

Reversible hydride transfer is thereby facilitated between NAD+ and carbon-4
of the weakly bound sugars.

The structure of the enzyme reveals many details of the binding of NAD+ and
inhibitors at the active site

The essential roles of the kinase and transferase are to attach the UDP group
to galactose, allowing for its participation in catalysis by the epimerase. The
transferase is a Zn/Fe metalloprotein
, in which the metal ions stabilize the
structure rather than participating in catalysis. The structure is interesting
in that

  • it consists of single beta-sheet with 13 antiparallel strands and 1 parallel strand
    connected by 6 helices.

The mechanism of UMP attachment at the active site of the transferase is a double
, with the participation of a covalent UMP-His 166-enzyme intermediate
in the Escherichia coli enzyme. The evolution of this mechanism appears to have
been guided by the principle of economy in the evolution of binding sites.

PMID: 8647345 Free full text

Section IV.

More on Lipids – Role of lipids – classification

  • Energy
  • Energy Storage
  • Hormones
  • Vitamins
  • Digestion
  • Insulation
  • Membrane structure: Hydrophobic properties

Lipid types

lipid types

lipid types

nat occuring FAs in mammals

nat occuring FAs in mammals

Read Full Post »

Author: Larry H. Bernstein, MD, FACP

Nathan Oram Kaplan

Continuation of a portrait

Notable Investigations

When Alan Wilson joined Nate’s laboratory, perticularly interested in molecular evolution they carried out studies that revealed many interesting taxonomic and enzymatic relationships. For example, the flatfish, halibut, flounder, and sole have only the anaerobic type of LDH(M4) in their tissues as adults. Since they bury themselves in the sand and live in an anaerobic environment, one can see why the M-type enzyme is present in the heart of these fish. When the flatfish larvae hatch they are free-living forms. They have one eye on each side, but at the time when one of the eyes move from one side to the other there is also a change in the lactic acid dehydrogenase. The young fish have the H type present in heart and other tissues and at the time of the eye movement there is a change to the M form. When Nate and Alan examined a number of invertebrates, they found that the arthropods, particularly the lobsters and crabs, had a very unusual LDH.

Margaret Ciotti worked with Kaplan on the horseshoe Crab (Limmulus). The rate of enzymatic lactate oxidation with NAD was very slow, but this group of arthropods had high activity with the acetylpyridine analog of NAD (AP-DPN). To their dismay that this LDH reacted very well with the natural coenzyme in contrast to other crabs. It was simple! Limmulus isn’t a crab. An examination of spiders, scorpions, and tarantulas revealed that all had enzymes similar to horseshoe crab. It soon became apparent to Nate that the horseshoe crab was related to the spider species and not to the lobster-crab group. It was very surprising to Nate that he would be able to classify an organism using enzymological techniques which agreed with the taxonomic classification. In addition, the Limmulus enzyme would not work with pure L-lactate. Pure L-lactate was not a good substrate but D-lactate was very effective because the LDH for Limmulus was D-LDH. This was surprising, because almost all animal LDH’s are of the L-configuration and are tetrameric.

A major publication about the structural differences between the H4 and M4 isoenzymes and the active site was published in PNAS 1974. Eventoff et al.
Proc. Natl. Acad. Sci. USA 1977; 74(7):2677-2681 [Biochemistry]
The changes in the hydrophobic adenosine binding pocket [residues 96(94), 119(116), and 55(54)] tend to reduce the size of the amino acid side chains in the H4 isozyme, increasing the volume within the pocket. Thus, in the initial binding of the cofactor (38), the adenosine will bind with reduced affinity to the H4, as compared to the M4, molecule. One substantial difference is the presence of Gln 31 in the heart enzyme and Ala in the muscle enzyme. The glutamine could form a hydrogen bond with the nicotinamide phosphate (thus increasing the energy of binding for the heart-isozyme) and move the nicotinamide end of the coenzyme out of the active center by at least 1 A. Unfortunately, the evidence for this important change is not clear in the electron density maps. The relative position of the substrate and the nicotinamide would favor the formation of the NAD-pyruvate covalent adduct between the methyl group of pyruvate and carbon 4 of nicotinamide in the H4 isozyme. Thus, the inhibition by pyruvate due to the formation of the abortive ternary complex LDH:NAD-pyruvate can occur more easily.

Nate received a telephone call from the Bureau of Fisheries in Boston inquiring if they could distinguish between haddock and cod using their techniques. There was a suspicion that the filets being sold in the market were not haddock but mostly cod. Haddock sold at four times the cost of cod. Most of the fillets contained almost exclusively cod muscle LDH. Today all the filets of haddock are tested for the presence of cod. These observations were put into the Congressional Record as an indication and illustration of how molecular biology could be of value to the average consumer.

A fresh endeavor

In the 1970s, he and Gordon Sato (previously at Brandeis) established a successful colony of athymic mice. Since these mice lacked a thymus, human tumors were not rejected and tumor xenografts could be grown in the animals.The mice were used to examine anti-cancer agents making this facility an important component of the UCSD Cancer Center“.

What transcends his scientific accomplishments was the warm and inspiring influence that Nate Kaplan had on those who worked with him. Young investigators from the world over were drawn to his laboratory, where they were accommodated with excellent research problems, excellent facilities, and the qualities of the man himself. These qualities were a combination of warmth, understanding, keen insight, and a contagious enthusiasm for biochemistry which permeated all of his professional activities.

Correspondence with Johannes Everse, Emeritus Professor of Biochemistry, Texas Tech Univiversity, Lubbock, TX

What strikes you about the unique character of Nathan Kaplan?

I would like to emphasize one more of Nate’s qualities: not only did he have an extraordinary keen ability to recognize good people, once you were part of his group, he did go out of his way to help anyone who was in trouble or who wanted do more than he expected of them. I believe in Yiddish they would call him a MENSCH. I worked with Nate for 16 years, from 1960 till 1976, and I owe him my career.

One of the best examples of his ability to pick up good people was Francis Stolzenbach. Fran came to Nate’s lab in Baltimore as a high school graduate with nothing to recommend him. Nate needed someone to do some routine laboratory chores. After a short time Nate realized that Fran was not only smart, he also learned fast and could work accurately, but he could always count on Francis that the work got done. Francis got himself involved in a nasty divorce, had a drinking problem, and a few other things like that, but Nate was always ready to help him out of his problems. As you know, when Nate moved to Brandeis, he asked Francis to go with him and later the same when he moved to San Diego. You know that Nate trusted Francis with keeping the research going, even when Nate went to Israel for a few months. Without any formal education, Francis became an excellent researcher who knew how to move a project forward and was capable of supervising even postdoctoral fellows when asked to do so. I give Nate credit for recognizing that Francis had the ability to do that not long after Francis joined him in Baltimore.

Let me also tell you what Nate did for me while I was in his laboratory. I started my career as a laboratory technician. After high school I first worked for 3 years in the lab of a factory like Del Monte, where they taught me how to do quality control. That ended when I was drafted for the Army, which lasted only one year. After that, I found a job at a pharmaceutical factory near Amsterdam, where I worked on a procedure to synthesize Vitamin A for four years, while I earned my technician certificate in organic chemistry. After that I moved to the biochemistry laboratory, where I worked for another 4 years earning my certificate in biochemistry. At that point I was 28 years old and had climbed the corporate ladder as far as possible; the next step up required a university degree, which I did not have and could not get. The Company had a very nice policy: they hired professors from the University of Amsterdam and Utrecht to come and give courses in the evenings for employees that were interested. After completing the course and taking an exam, one got a certificate of completion. There were lots of different courses on different scientific topics. I took a number of these courses during those 8 years.

But I felt unhappy that at the age of 28 I had no way to advance my career further. At that time (1959) the company research labs were always looking forward to the latest issues of Science and Nature and other scientific journals in order to pick up the latest methodology and findings. The USA had the reputation of being the best country in the world for research. So I talked with my supervisor about me taking a leave of absence and go spend a few years in the States to learn how they do research. He thought I was crazy, but after some more talking he agreed. So I started applying for any position that was advertised in Science that seemed suitable for an experienced laboratory technician. After trying for about 6 months, I got a phone call from the secretary of a professor in Amsterdam, who wanted to know if I would like to be interviewed by the professor for a job that a friend had available in the USA. I went and about a month later I got a letter from Dr. Lowenstein at Brandeis University, telling me that they were offering me a job. I had never heard of either Dr. Lowenstein or Brandeis, but I knew that a job at a University would be far preferable to a job at some company. So I accepted, figuring that if this was not the right job, I could always look for something better once I was in the States. In the meantime, Brandeis had started the procedure to get me a first preference visum, and one day I got a big envelope with lots of papers that I had to take to the US Consulate in Rotterdam. It was the visum application, but that application was signed by Nathan O. Kaplan. I knew that name! So I arrived at Brandeis in June 1960, while Nate was in Israel for the summer. When he came back, he introduced me to Dr. Lenny Brand, then a postdoc, to be his assistant. A year later, when Lenny went to Johns Hopkins, I became Kaplan’s assistant. By that time I had forgotten about going back to Holland. I felt like I had joined one of the best research groups in the world.

Then in 1963 I decided one day to listen in on the biochemistry course that was given to the first year students. I discovered that they were using the same biochemistry textbook that I had used in Holland for my technician certificate. I figured that if the graduate students start at that level, then I should also be able to do these studies. So I took a tranquilizer to calm my nerves, went to Nate’s office, and asked him if there was any possibility for me to earn a university degree. I expected that he would smile at me and tell me to get back to work, but instead he told me to sit down and started to ask me lots of questions about my background. Remember, I came to the US with nothing more than a Dutch high school diploma, two technician certificates and a bunch of certificates that I had taken various courses, all things that nobody could read. I of course realized earlier that I was invited to come to Brandeis almost solely on the recommendation of that prof in Amsterdam and my own explanation of what the requirements were to earn the technician certificates. It was simply: OK, you are here now, let’s see what you can do!

After Nate questioned me for about an hour, he told me to my surprise that he would talk to the Dean! A few days later he told me that the Dean wanted to be assured that I could do academic work, and wanted me to take an undergraduate course of my choice. I chose to take math 101, because I knew nothing about differentials and integrals. The instructor was told that I was a “special” unregistered student, but I was to take all the assignments and exams as a regular students and graded accordingly. I got an A in the course. Then the Dean agreed to accept me as a “special” graduate student, while Nate agreed that I could take time off to take the required courses, one at a time, and make up the time during evenings and weekends. My point is that it must have taken an awful lot of persuasion by Nate to get the Dean to agree to admit someone to graduate school without ever being in an undergraduate school and with mostly papers that nobody could read or verify, just taking Nate’s word for it. Brandeis is not known as a school that is generous in handing out degrees.
Eventually, when Nate moved to San Diego, I wanted to continue working for my degree at UCSD. But UCSD, being a state school, had strict rules about requiring an undergraduate degree in order to get into graduate school. Nate moved heaven and earth trying to overcome this obstacle, but no success. About a year later, when Drs. Lawrence Levine and Bill Jencks from Brandeis came to visit UCSD and I told them about my predicament, they went back to Brandeis and convinced the department to recommend to the Dean to grant me a Masters degree. I got that in the mail in 1971. In 1973 I got my Ph.D. at UCSD. My dissertation subject: NAD adducts and ternary complexes.

Granted, Nate went out of his way for me. I often thought that he sort of had adopted me as a son or something. But during my 16 years with him I have seen him help others in a similar way when he thought they deserved a helping hand. More than anybody I have ever met, this guy had a heart of gold.

How did Methods in Enzymology come about?

Nate and Sidney Colowick learned to know each other when they both were postdoctoral fellows at the McCollum Pratt Institute at Johns Hopkins. Other people that worked there told me that Sidney was the experimentalist, whereas Nate spend more time figuring out how to approach a scientific question. In the process, Nate figured out that the most important asset in a laboratory is to have ready access to methods and procedures. At that time these were published in scientific journals, but making copies was expensive and the copies lasted only for a few months. So it was hard to remember where who had published a method for this or a procedure for that. To overcome this problem, Nate started keeping a collection of all the methods and procedures that he found in the literature and that he thought may be useful some day. Soon he had a sizeable collection, and people learned about that. So he was constantly asked “Nate, do you know how to do this? or Nate, do you have a procedure for that? It was Bill McElroy, at that time the director of the Institute, who suggested to Nate that this constant demand for the latest procedures and methods could be overcome by putting his collection into a book, so everybody would have them available. McElroy knew someone at Academic Press and that resulted in the birth of Methods in Enzymology. The initial issue consisted of 4 volumes and a few years later the series was updated with newer methods in Volumes 5 and 6. By that time Nate had found out how much time is involved in publishing a book, which left him not much time for research. Also, at that time he had been approached by Brandeis to take the chairmanship of a new biochemistry department, which would be the third such department in the US. So the series was completed with Volume 7, which was just an index of the 6 existing volumes.

But the series was extremely successful. For example, at that time I worked in the research laboratories of a pharmaceutical company in Holland, and we had the complete series in our library, where they were heavily used! Since science moves forward, Nate got constantly called upon to further update the series. But at Brandeis he could not afford the time any more. Then someone, I believe it was Willis Wood, suggested to Nate to let others edit additional volumes, while he and Sidney would become Editors-in-Chief. As such, they would still have to approve any plans for new volumes as well as approve the final product, but others would do all the “footwork” of getting the volumes together. Nate and Sidney thought that it was a great idea and, as they say, the rest is history.

There is no question that the Methods in Enzymology series has been by far the most successful series of books ever published in biochemistry and possibly in other sciences as well. It was Nate’s insight that accomplished that feat by realizing that the “rate-limiting step” in research at that time was the lack of readily available methods and procedures.

There was a lot of work on the adducts. Please comment on that.

Concerning your follow-up: The story of the NAD-adducts indeed is an interesting one, and I had a lot to do with it.

It started back in the 1950’s when someone in Nate’s laboratory made an adduct of NAD with, I believe, acetone or acetaldehyde. But except for trying to learn about the chemical properties of NAD, nothing was done with it. Then in the early 1960’s, shortly after I joined Nate’s group, a technician found that when she kept a solution of NADH in the freezer overnight, the NADH had lost most of its activity when she did her LDH assays. From that point on NADH solutions were made fresh every day. But one of the postdocs, Peter Fawcett, took a look at a frozen solution and found that it still had its original UV spectrum, ruling out that the NADH was oxidized. Then he found that the frozen NADH actually was a potent inhibitor of an LDH assay when added to a normal NADH-pyruvate assay. Peter published a short note in Biochim. Biophys Acta about this LDH inhibitor formed from NADH. But it triggered Nate’s interest in terms of what actually happened to the NADH. He put me to work on trying to find out, since I originally worked as an organic chemist in Holland. I soon showed that nothing had happened to the adenine moiety, and the riboses and phosphates were also still in place and intact. Hence, the change had to be in the nicotinamide ring. The UV spectrum indicated that it still had the dihydropyridine structure of NADH, suggesting no changes to the ring itself. I then tested for the presence of an intact amide group and got a negative result. A few more tests indicated that some carbonyl compound had reacted with the amide group and the 4-position of the nicotinamide ring. The project was set aside for a time.
Over the years I often thought about the adduct project, in part because I was a bit unhappy about having worked hard on that project for about 9 months with nothing to show for it. I already had figured out that the acetone could not react with NADH; the NADH had to be oxidized to NAD first, then it could react with acetone. This would result in no changes in the UV spectrum, but of course all NADH activity would be lost. I also knew from my organic chemistry background that for acetone to react with NAD it had to be in the enol-form instead of in the keto-form. Since it is normal for these carbonyl compounds to be present in both forms, that would not be a problem. That would mean that NAD should be able to form analogous adducts with many carbonyl compounds, especially with alpha-keto-acids. For example, a solution of pyruvate consists of 95% keto-pyruvate and 5% enol-pyruvate.
At that time we had also learned about the abortive ternary complex of LDH-NAD-pyruvate as an inhibitor of the LDH activity. This complex, when prepared in a cuvette, also showed the characteristic UV absorbance at 340 nm of NADH, suggesting that the nicotinamide ring was in the dihydro-form in the complex. So I was wondering if the abortive complex actually was an enzyme-bound NAD-pyruvate adduct. So I had Estelle Zoll prepare the pyruvate adduct of NAD and then tested it as an inhibitor of LDH. It showed potent inhibition. I then asked her to prepare the adduct of NAD with oxaloacetate, which is different from pyruvate by a single –CH2- group. This adduct had no effect on LDH, but she showed it to be a potent inhibitor of malate dehydrogenase. That made us wonder if this specific inhibition indicated that the enzymes were recognizing their respective substrates when it was bound chemically to NAD; i.e., that the adducts bound to both the coenzyme binding site and the substrate binding site of the enzymes. We then made a series of NAD adducts, using substrates of enzymes that we had access to, and found that indeed each enzyme recognized its substrates in the adducts. I was jubilant and felt very happy when I showed Nate these results.
At the same time, Dr. Michael Rossmann at Purdue was trying very hard to determine the structure of dogfish muscle LDH, using x-ray crystallography, as well as the location of the coenzyme and, if possible, the substrate. So I felt like we were approaching the same problem, using two different techniques. He used the physical technique of x-ray crystallography, whereas I was using chemistry. Eventually we got together and our results were published in a PNAS article in 1973. A detailed description of the results with the adducts and ternary complex was published in Advances in Enzymology, vol. 37, also of 1973. I can mail you reprints of these articles if you wish.

Representative Early Publications

(Nathan O. Kaplan Papers. MSS 0099. UC San Diego::Mandeville Special Collections Library)
Nicotinic acid analogue of diphosphopyridine nucleotide 1958. N box 38, folder 68.
Enzyme-coenzyme-substrate complex. of pyridine nucleotide depend. dehydrogenases 1958. box 39, folder 5.
Chemical properties of 3-substitited pyridine analogues of dpn 1959. box 39, folder 11.
Enzymatic studies with analogues of diphosphopyridine nucleotide 1959. box 39, folder 12.
Molecular heterogeneity and evolution of enzymes 1960. box 39, folder 17.
Mechanism of depletion of mitochondrial pyridine nucleotides 1960. box 39, folder 24.
Measurements of enzymes in the diagnosis of acute myocardial infarction 1961. box 39, folder 28.
Pyridine nucleotide transhydrogenase VIII. Properties of the transhydrogenase reactions of an enzyme complex isolated from beef heart mitochondria 1961. box 39, folder 33.
Heterogeneity of the lactic dehydrogenases of new-born and adult rat heart as determined with enzyme analogs 1961. box 39, folder 37.
Regulatory effects of enzyme action 1961. box 39, folder 38.
Inhibition of dehydrogenase reactions by a substance formed from reduced dpn 1961. box 39, folder 40.
Nature and development of lactic dehydrogenases 1962. box 39, folder 44.
Functions of the two forms of lactic dehydrogenase in the breast muscle of birds 1963. box 39, folder 52.
Substituted nicotinamide analogues of nicotinamide adenine dinucleotide 1963. box 39, folder 56.
Alterations of tissue lactate dehydrogenase in human neoplasms 1963. box 39, folder 65.
Lactic dehydrogenases: functions of the two types 1964. box 39, folder 67.
Evolution of lactic dehydrogenases 1964. box 40, folder 1.
Lactate dehydrogenase – structure and function. 1964. box 40, folder 4.
Lactic dehydrogenase in cancer 1964. box 40, folder 5.

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