Posts Tagged ‘TNF-a’

Liver Endoplasmic Reticulum Stress and Hepatosteatosis

Larry H Bernstein, MD, FCAP


1. Absence of adipose triglyceride lipase protects from hepatic endoplasmic reticulum stress in mice.

Fuchs CD, Claudel T, Kumari P, Haemmerle G, et al.
LabExpMol Hepatology, Medical Univ of Graz, Austria.
Hepatology. 2012 Jul;56(1):270-80. Epub 2012 May 29.

Nonalcoholic fatty liver disease (NAFLD) is characterized by

  • triglyceride (TG) accumulation and
  • endoplasmic reticulum (ER) stress.

Fatty acids (FAs) may trigger ER stress, therefore,

  •  the absence of adipose triglyceride lipase (ATGL/PNPLA2)-
    • the main enzyme for intracellular lipolysis,
  • releasing FAs, and
  • closest homolog to adiponutrin (PNPLA3)

recently implicated in the pathogenesis of NAFLD-

  • could protect against hepatic ER stress.

Wild-type (WT) and ATGL knockout (KO) mice

  •  were challenged with tunicamycin (TM) to induce ER stress.

Markers of hepatic

  •  lipid metabolism,
  • ER stress, and
  • inflammation were explored
    • for gene expression by
    •  serum biochemistry,
    • hepatic TG and FA profiles,
    • liver histology,
    • cell-culture experiments were performed in Hepa1.6 cells
  • after the knockdown of ATGL before FA and TM treatment.

TM increased hepatic TG accumulation in ATGL KO, but not in WT mice. Lipogenesis and β-oxidation
were repressed at the gene-expression level
(sterol regulatory element-binding transcription factor 1c,
fatty acid synthase, acetyl coenzyme A carboxylase 2, and carnitine palmitoyltransferase 1 alpha) in
both WT and ATGL KO mice. Genes for very-low-density lipoprotein (VLDL) synthesis (microsomal
triglyceride transfer protein and apolipoprotein B)

  •  were down-regulated by TM in WT
  • and even more in ATGL KO mice,
  • which displayed strongly reduced serum VLDL cholesterol levels.

ER stress markers were induced exclusively in TM-treated WT, but not ATGL KO, mice:

  •  glucose-regulated protein,
  • C/EBP homolog protein,
  • spliced X-box-binding protein,
  • endoplasmic-reticulum-localized DnaJ homolog 4, and
  • inflammatory markers Tnfα and iNos.

Total hepatic FA profiling revealed a higher palmitic acid/oleic acid (PA/OA) ratio in WT mice.
Phosphoinositide-3-kinase inhibitor-

  • known to be involved in FA-derived ER stress and
  • blocked by OA-
  • was increased in TM-treated WT mice only.

In line with this, in vitro OA protected hepatocytes from TM-induced ER stress. Lack of ATGL may protect from
hepatic ER stress through alterations in FA composition. ATGL could constitute a new therapeutic strategy
to target ER stress in NAFLD.
PMID: 22271167 Diabetes Obes Metab. 2010 Oct;12 Suppl 2:83-92.

2. Hepatic steatosis: a role for de novo lipogenesis and the transcription factor SREBP-1c.
Ferré P, Foufelle F. INSERM, and Université Pierre et Marie Curie-Paris, Paris, France.    PMID: 21029304

Excessive availability of plasma fatty acids and lipid synthesis from glucose (lipogenesis) are important determinants of steatosis.
Lipogenesis is an insulin- and glucose-dependent process that is under the control of specific transcription factors,

Insulin induces the maturation of SREBP-1c in the endoplasmic reticulum (ER).

  • SREBP-1c in turn activates glycolytic gene expression,
    • allowing glucose metabolism, and
    • lipogenic genes in conjunction with ChREBP.

Lipogenesis activation in the liver of obese markedly insulin-resistant steatotic rodents is then paradoxical.
It appears the activation of SREBP-1c and thus of lipogenesis is

  •  secondary in the steatotic liver to an ER stress.

The ER stress activates the

  •  cleavage of SREBP-1c independent of insulin,
  • explaining the paradoxical stimulation of lipogenesis
  • in an insulin-resistant liver.

Inhibition of the ER stress in obese rodents

  •  decreases SREBP-1c activation and lipogenesis and
  • improves markedly hepatic steatosis and insulin sensitivity.
  • ER is thus worth considering as a potential therapeutic target for steatosis and metabolic syndrome.

3. SREBP-1c transcription factor and lipid homeostasis: clinical perspective
Ferré P, Foufelle F
Inserm, Centre de Recherches Biomédicales des Cordeliers, Paris, France.
Horm Res. 2007;68(2):72-82. Epub 2007 Mar 5. PMID:17344645

Insulin has long-term effects on glucose and lipid metabolism through its control on the expression of specific genes.
In insulin sensitive tissues and particularly in the liver,

  •  the transcription factor sterol regulatory element binding protein-1c (SREBP-1c) transduces the insulin signal, which is
  • synthetized as a precursor in the membranes of the endoplasmic reticulum
  • which requires post-translational modification to yield its transcriptionally active nuclear form.

Insulin activates the transcription and the proteolytic maturation of SREBP-1c, which induces the

  •  expression of a family of genes
  • involved in glucose utilization and fatty acid synthesis and
  • can be considered as a thrifty gene.

Since a high lipid availability is

  •  deleterious for insulin sensitivity and secretion,
  • a role for SREBP-1c in dyslipidaemia and type 2 diabetes
  • has been considered in genetic studies.

SREBP-1c could also participate in

  •  hepatic steatosis observed in humans
  • related to alcohol consumption and
  • hyperhomocysteinemia
  • concomitant with a ER-stress and
  • insulin-independent SREBP-1c activation.

4. Hepatic steatosis: a role for de novo lipogenesis and the transcription factor SREBP-1c
Ferré P, Foufelle F
INSERM, Centre de Recherches des Cordeliers and Université Pierre et Marie Curie-Paris, Paris, France.
Diabetes Obes Metab. 2010 Oct;12 Suppl 2:83-92. PMID: 21029304

Lipogenesis in liver steatosis is

  •  an insulin- and glucose-dependent process
  • under the control of specific transcription factors,
  • sterol regulatory element binding protein 1c (SREBP-1c),
  • activated by insulin and carbohydrate response element binding protein (ChREBP)

Insulin induces the maturation of SREBP-1c in the endoplasmic reticulum (ER).
SREBP-1c in turn activates glycolytic gene expression, allowing –

  •  glucose metabolism in conjunction with ChREBP.

activation of SREBP-1c and lipogenesis is secondary in the steatotic liver to ER stress, which

  •  activates the cleavage of SREBP-1c independent of insulin,
  • explaining the stimulation of lipogenesis in an insulin-resistant liver.
  • Inhibition of the ER stress in obese rodents decreases SREBP-1c activation and improves
  • hepatic steatosis and insulin sensitivity.

ER is thus a new partner in steatosis and metabolic syndrome

5. Pharmacologic ER stress induces non-alcoholic steatohepatitis in an animal model
Jin-Sook Leea, Ze Zhenga, R Mendeza, Seung-Wook Hac, et al.
Wayne State University SOM, Detroit, MI
Toxicology Letters 20 May 2012; 211(1):29–38

Endoplasmic reticulum (ER) stress refers to a condition of

  •  accumulation of unfolded or misfolded proteins in the ER lumen, which is known to
  • activate an intracellular stress signaling termed
  • Unfolded Protein Response (UPR).

A number of pharmacologic reagents or pathophysiologic stimuli

  •  can induce ER stress and activation of the UPR signaling,
  • leading to alteration of cell physiology that is
  • associated with the initiation and progression of a variety of diseases.

Non-alcoholic steatohepatitis (NASH), characterized by hepatic steatosis and inflammation, has been considered the
precursor or the hepatic manifestation of metabolic disease. In this study, we delineated the

  • toxic effect and molecular basis
  • by which pharmacologic ER stress,
  • induced by a bacterial nucleoside antibiotic tunicamycin (TM),
  • promotes NASH in an animal model.

Mice of C57BL/6J strain background were challenged with pharmacologic ER stress by intraperitoneal injection of TM. Upon TM injection,

  •  mice exhibited a quick NASH state characterized by
  • hepatic steatosis and inflammation.

TM-treated mice exhibited an increase in –

  •  hepatic triglycerides (TG) and a –
  • decrease in plasma lipids, including
  • plasma TG,
  • plasma cholesterol,
  • high-density lipoprotein (HDL), and
  • low-density lipoprotein (LDL),

In response to TM challenge,

  •  cleavage of sterol responsive binding protein (SREBP)-1a and SREBP-1c,
  •  the key trans-activators for lipid and sterol biosynthesis,
  • was dramatically increased in the liver.

Consistent with the hepatic steatosis phenotype, expression of

  •  some key regulators and enzymes in de novo lipogenesis and lipid droplet formation was up-regulated,
  • while expression of those involved in lipolysis and fatty acid oxidation was down-regulated
  • in the liver of mice challenged with TM.

TM treatment also increased phosphorylation of NF-κB inhibitors (IκB),

  •  leading to the activation of NF-κB-mediated inflammatory pathway in the liver.

Our study not only confirmed that pharmacologic ER stress is a strong “hit” that triggers NASH, but also demonstrated

  •  crucial molecular links between ER stress,
  • lipid metabolism, and
  • inflammation in the liver in vivo.

► Pharmacologic ER stress induced by tunicamycin (TM) induces a quick NASH state in vivo.
► TM leads to dramatic increase in cleavage of sterol regulatory element-binding protein in the liver.
► TM up-regulates lipogenic genes, but down-regulates the genes in lipolysis and FA oxidation.
► TM activates NF-κB and expression of genes encoding pro-inflammatory cytokines in the liver.
ER, endoplasmic reticulum; TM, tunicamycin; NASH, non-alcoholic steatohepatitis; NAFLD,
non-alcoholic fatty liver disease; TG, triglycerides; SREBP, sterol responsive binding protein;
NF-κB, activation of nuclear factor-kappa B; IκB, NF-κB inhibitor
Keywords: ER stress; Non-alcoholic steatohepatitis; Tunicamycin; Lipid metabolism; Hepatic inflammation
Figures and tables from this article:

Fig. 1. TM challenge alters lipid profiles and causes hepatic steatosis in mice. (A) Quantitative real-time RT-PCR analysis of liver mRNA isolated from mice challenged with TM or vehicle control. Total liver mRNA was isolated at 8 h or 30 h after injection with vehicle or TM (2 μg/g body weight) for real-time RT-PCR analysis. Expression values were normalized to β-actin mRNA levels. Fold changes of mRNA are shown by comparing to one of the control mice. Each bar denotes the mean ± SEM (n = 4 mice per group); **P < 0.01. Edem1, ER degradation enhancing, mannosidase alpha-like 1. (B) Oil-red O staining of lipid droplets in the livers of the mice challenged with TM or vehicle control (magnification: 200×). (C) Levels of TG in the liver tissues of the mice challenged with TM or vehicle control. (D) Levels of plasma lipids in the mice challenged with TM or vehicle control. TG, triglycerides; TC, total plasma cholesterol; HDL, high-density lipoproteins; VLDL/LDL, very low and low density lipoproteins. For C and D, each bar denotes mean ± SEM (n = 4 mice per group); *P < 0.05; **P < 0.01.

 F options

Fig. 2. TM challenge leads to a quick NASH state in mice. (A) Histological examination of liver tissue sections of the mice challenged with TM (2 μg/g body weight) or vehicle control. Upper panel, hematoxylin–eosin (H&E) staining of liver tissue sections; the lower panel, Sirius staining of collagen deposition of liver tissue sections (magnification: 200×). (B) Histological scoring for NASH activities in the livers of the mice treated with TM or vehicle control. The grade scores were calculated based on the scores of steatosis, hepatocyte ballooning, lobular and portal inflammation, and Mallory bodies. The stage scores were based on the liver fibrosis. Number of mice examined is given in parentheses. Mean ± SEM values are shown. P-values were calculated by Mann–Whitney U-test.

Fig. 3. TM challenge significantly increases levels of cleaved/activated forms of SREBP1a and SREBP1c in the liver. Western blot analysis of protein levels of SREBP1a (A) and SREBP1c (B) in the liver tissues from the mice challenged with TM (2 μg/g body weight) or vehicle control. Levels of GAPDH were included as internal controls. For A and B, the values below the gels represent the ratios of mature/cleaved SREBP signal intensities to that of SREBP precursors. The graph beside the images showed the ratios of mature/cleaved SREBP to precursor SREBP in the liver of mice challenged with TM or vehicle. The protein signal intensities shown by Western blot analysis were quantified by NIH imageJ software. Each bar represents the mean ± SEM (n = 3 mice per group); **P < 0.01. SREBP-p, SREBP precursor; SREBP-m, mature/cleaved SREBP.

Fig. 4. TM challenge up-regulates expression of genes involved in lipogenesis but down-regulates expression of genes involved in lipolysis and FA oxidation. Quantitative real-time RT-PCR analysis of liver mRNAs isolated from the mice challenged with TM (2 μg/g body weight) or vehicle control, which encode regulators or enzymes in: (A) de novo lipogenesis: PGC1α, PGC1β, DGAT1 and DGAT2; (B) lipid droplet production: ADRP, FIT2, and FSP27; (C) lipolysis: ApoC2, Acox1, and LSR; and (D) FA oxidation: PPARα. Expression values were normalized to β-actin mRNA levels. Fold changes of mRNA are shown by comparing to one of the control mice. Each bar denotes the mean ± SEM (n = 4 mice per group); **P < 0.01. (E and F) Isotope tracing analysis of hepatic de novo lipogenesis. Huh7 cells were incubated with [1-14C] acetic acid for 6 h (E) or 12 h (F) in the presence or absence of TM (20 μg/ml). The rates of de novo lipogenesis were quantified by determining the amounts of [1-14C]-labeled acetic acid incorporated into total cellular lipids after normalization to cell numbers.

Fig. 5. TM activates the inflammatory pathway through NF-κB, but not JNK, in the liver. Western blot analysis of phosphorylated Iκ-B, total Iκ-B, phosphorylated JNK, and total JNK in the liver tissues from the mice challenged with TM (2 μg/g body weight) or vehicle control. Levels of GAPDH were included as internal controls. The values below the gels represent the ratios of phosphorylated protein signal intensities to that of total proteins.

Fig. 6. TM induces expression of pro-inflammatory cytokines and acute-phase responsive proteins in the liver. Quantitative real-time RT-PCR analyses of liver mRNAs isolated from the mice challenged with TM (2 μg/g body weight) or vehicle control, which encode: (A) pro-inflammatory cytokine TNFα and IL6; and (B) acute-phase protein SAP and SAA3. Expression values were normalized to β-actin mRNA levels. Fold changes of mRNA are shown by comparing to one of the control mice. (C–E) ELISA analyses of serum levels of TNFα, IL6, and SAP in the mice challenged with TM or vehicle control for 8 h ELISA. Each bar denotes the mean ± SEM (n = 4 mice per group); *P < 0.05, **P < 0.01.

Corresponding author at: Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA. Tel.: +1 313 577 2669; fax: +1 313 577 5218.

The SREBP regulatory pathway. Brown MS, Goldst...

The SREBP regulatory pathway. Brown MS, Goldstein JL (1997). “The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor”. Cell 89 (3) : 331–340. doi:10.1016/S0092-8674(00)80213-5. PMID 9150132. (Photo credit: Wikipedia)

English: Structure of the SREBF1 protein. Base...

English: Structure of the SREBF1 protein. Based on PyMOL rendering of PDB 1am9. (Photo credit: Wikipedia)

The SREBP regulatory pathway

The SREBP regulatory pathway (Photo credit: Wikipedia)

English: Diagram of rough endoplasmic reticulu...

English: Diagram of rough endoplasmic reticulum by Ruth Lawson, Otago Polytechnic. (Photo credit: Wikipedia)

Micrograph demonstrating marked (macrovesicula...

Micrograph demonstrating marked (macrovesicular) steatosis in non-alcoholic fatty liver disease. Masson’s trichrome stain. (Photo credit: Wikipedia)



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Biochemistry of the Coagulation Cascade and Platelet Aggregation: Nitric Oxide: Platelets, Circulatory Disorders, and Coagulation Effects

Curator/Editor/Author: Larry H. Bernstein, MD, FCAP 



Subtitle: Nitric Oxide: Platelets, Circulatory Disorders, and Coagulation Effects.  (Part I)

Summary: This portion of the Nitric Oxide series on PharmaceuticalIntelligence( is the first of a two part treatment of platelets, the coagulation cascade, and protein-membrane interactions with low flow states, local and systemic inflammatory disease, and hematologic disorders.  It is highly complex as the lines separating intrinsic and extrinsic pathways become blurred as a result of endothelial shear stress, distinctly different than penetrating or traumatic injury.  In addition, other factors that come into play are also considered.  The 2nd piece will be concerned with oxidative stress and the diverse effects on NO on the vasoactive endothelium, on platelet endothelial interaction, and changes in blood viscosity.

Coagulation Pathway

The workhorse tests of the modern coagulation laboratory, the prothrombin time (PT) and the activated partial thromboplastin time (aPTT), are the basis for the published extrinsic and intrinsic coagulation pathways.  This is, however, a much simpler model than one encounters delving into the mechanism and interactions involved in hemostasis and thrombosis, or in hemorrhagic disorders.

We first note that there are three components of the hemostatic system in all vertebrates:

  • Platelets,
  • vascular endothelium, and
  • plasma proteins.

The liver is the largest synthetic organ, which synthesizes

  • albumin,
  • acute phase proteins,
  • hormonal and metal binding proteins,
  • albumin,
  • IGF-1, and
  • prothrombin, mainly responsible for the distinction between plasma and serum (defibrinated plasma).

According to WH Seegers [Seegers WH,  Postclotting fates of thrombin.  Semin Thromb Hemost 1986;12(3):181-3], prothrombin is virtually all converted to thrombin in clotting, but Factor X is not. Large quantities of thrombin are inhibited by plasma and platelet AT III (heparin cofactor I), by heparin cofactor II, and by fibrin.  Antithrombin III, a serine protease, is a main inhibitor of thrombin and factor Xa in blood coagulation. The inhibitory function of antithrombin III is accelerated by heparin, but at the same time antithrombin III activity is also reduced. Heparin retards the thrombin-fibrinogen reaction, but otherwise the effectiveness of heparin as an anticoagulant depends on antithrombin III in laboratory experiments, as well as in therapeutics. The activation of prothrombin is inhibited, thereby inactivating  any thrombin or other vulnerable protease that might otherwise be generated. [Seegers WH, Antithrombin III. Theory and clinical applications. H. P. Smith Memorial Lecture. Am J Clin Pathol. 1978;69(4):299-359)].  With respect to platelet aggregation, platelets aggregate with thrombin-free autoprothrombin II-A. Aggregation is dependent on an intact release mechanism since inhibition of aggregation occurred with adenosine, colchicine, or EDTA. Autoprothrombin II-A reduces the sensitivity of platelets to aggregate with thrombin, but enhances epinephrine-mediated aggregation. [Herman GE, Seegers WH, Henry RL. Autoprothrombin ii-a, thrombin, and epinephrine: interrelated effects on platelet aggregation. Bibl Haematol 1977;44:21-7.]

A tetrapeptide, residues 6 to 9 in normal prothrombin, was isolated from the NH(2)-terminal, Ca(2+)-binding part of normal prothrombin. The peptide contained two residues of modified glutamic acid, gamma-carboxyglutamic acid. This amino acid gives normal prothrombin the Ca(2+)-binding ability that is necessary for its activation.

Abnormal prothrombin, induced by the vitamin K antagonist, dicoumarol, lacks these modified glutamic acid residues and that this is the reason why abnormal prothrombin does not bind Ca(2+) and is nonfunctioning in blood coagulation. [Stenflo J, Fernlund P, Egan W, Roepstorff P. Vitamin K dependent modifications of glutamic acid residues in prothrombinProc Natl Acad Sci U S A. 1974;71(7):2730-3.]

Interestingly, a murine monoclonal antibody (H-11) binds a conserved epitope found at the amino terminal of the vitamin K-dependent blood proteins prothrombin, factors VII and X, and protein C. The sequence of polypeptide recognized contains 2 residues of gamma-carboxyglutamic acid, and binding of the antibody is inhibited by divalent metal ions.  The antibody bound specifically to a synthetic peptide corresponding to residues 1-12 of human prothrombin that was synthesized as the gamma-carboxyglutamic acid-containing derivative, but binding to the peptide was not inhibited by calcium ion. This suggested that binding by divalent metal ions is not due simply to neutralization of negative charge by Ca2+. [Church WR, Boulanger LL, Messier TL, Mann KG. Evidence for a common metal ion-dependent transition in the 4-carboxyglutamic acid domains of several vitamin K-dependent proteins. J Biol Chem. 1989;264(30):17882-7.]

Role of vascular endothelium.

I have identified the importance of prothrombin, thrombin, and the divalent cation Ca 2+ (1% of the total body pool), mention of heparin action, and of vitamin K (inhibited by warfarin).  Endothelial functions are inherently related to procoagulation and anticoagulation. The subendothelial matrix is a complex of many materials, most important related to coagulation being collagen and von Willebrand factor.

What about extrinsic and intrinsic pathways?  Tissue factor, when bound to factor VIIa, is the major activator of the extrinsic pathway of coagulation. Classically, tissue factor is not present in the plasma but only presented on cell surfaces at a wound site, which is “extrinsic” to the circulation.  Or is it that simple?

Endothelium is the major synthetic and storage site for von Willebrand factor (vWF).  vWF is…

  • secreted from the endothelial cell both into the plasma and also
  • abluminally into the subendothelial matrix, and
  • acts as the intercellular glue binding platelets to one another and also to the subendothelial matrix at an injury site.
  • acts as a carrier protein for factor VIII (antihemophilic factor).
  • It  binds to the platelet glycoprotein Ib/IX/V receptor and
  • mediates platelet adhesion to the vascular wall under shear. [Lefkowitz JB. Coagulation Pathway and Physiology. Chapter I. in Hemostasis Physiology. In ( ???), pp1-12].

Ca++ and phospholipids are necessary for all of the reactions that result in the activation of prothrombin to thrombin. Coagulation is initiated by an extrinsic mechanism that

  • generates small amounts of factor Xa, which in turn
  • activates small amounts of thrombin.

The tissue factor/factorVIIa proteolysis of factor X is quickly inhibited by tissue factor pathway inhibitor (TFPI).The small amounts of thrombin generated from the initial activation feedback

  • to create activated cofactors, factors Va and VIIIa, which in turn help to
  • generate more thrombin.
  • Tissue factor/factor VIIa is also capable of indirectly activating factor X through the activation of factor IX to factor IXa.
  • Finally, as more thrombin is created, it activates factor XI to factor XIa, thereby enhancing the ability to ultimately make more thrombin.


Coagulation Cascade

The procoagulant plasma coagulation cascade has traditionally been divided into the intrinsic and extrinsic pathways. The Waterfall/Cascade model consists of two separate initiations,

  • intrinsic (contact) and
    • The intrinsic pathway is initiated by a complex activation process of the so-called contact phase components,
      • prekallikrein,
      •  high-molecular weight kininogen (HMWK) and
      • factor XII

Activation of the intrinsic pathway is promoted by non-biological surfaces, such as glass in a test tube, and is probably not of physiological importance, at least not in coagulation induced by trauma.

Instead, the physiological activation of coagulation is mediated exclusively via the extrinsic pathway, also known as the tissue factor pathway.

  • extrinsic pathways,

Tissue factor (TF) is a membrane protein which is normally found in tissues. TF forms a procoagulant complex with factor VII, which activates factor IX and factor X.

  • which ultimately merge at the level of Factor Xa (common pathway).

Regulation of thrombin generation. Coagulation is triggered (initiation) by circulating trace amounts of fVIIa and locally exposed tissue factor (TF). Subsequent formations of fXa and thrombin are regulated by a tissue factor pathway inhibitor (TFPI) and antithrombin (AT). When the threshold level of thrombin is exceeded, thrombin activates platelets, fV, fVIII, and fXI to augment its own generation (propagation).

Activated factors IX and X (IXa and Xa) will activate prothrombin to thrombin and finally the formation of fibrin. Several of these reactions are much more efficient in the presence of phospholipids and protein cofactors factors V and VIII, which thrombin activates to Va and VIIIa by positive feedback reactions.

We depict the plasma coagulation emphasizing the importance of membrane surfaces for the coagulation processes. Coagulation is initiated when tissue factor (TF), an integral membrane protein, is exposed to plasma. TF is expressed on subendothelial cells (e.g. smooth muscle cells and fibroblasts), which are exposed after endothelium damage. Activated monocytes are also capable of exposing TF.

A small amount, approximately 1%, of activated factor VII (VIIa) is present in circulating blood and binds to TF. Free factor VIIa has poor enzymatic activity and the initiation is limited by the availability of its cofactor TF. The first steps in the formation of a blood clot is the specific activation of factor IX and X by the TF-VIIa complex. (Initiation of coagulation: Factor VIIa binds to tissue factor and activates factors IX and X). Coagulation is propagated by procoagulant enzymatic complexes that assemble on the negatively charged membrane surfaces of activated platelets. (Propagation of coagulation: Activation of factor X and prothrombin).  Once thrombin has been formed it will activate the procofactors, factor V and factor VIII, and these will then assemble in enzyme complexes. Factor IXa forms the tenase complex together with its cofactor factor VIIIa, and factor Xa is the enzymatic component of the prothrombinase complex with factor Va as cofactor.

Activation of protein C takes place on the surface of intact endothelial cells. When thrombin (IIa) reaches intact endothelium it binds with high affinity to a specific receptor called thrombomodulin. This shifts the specific activity of thrombin from being a procoagulant enzyme to an anticoagulant enzyme that activates protein C to activated protein C (APC).  The localization of protein C to the thrombin-thrombomodulin complex can be enhanced by the endothelial protein C receptor (EPCR), which is a transmembrane protein with high affinity for protein C.  Activated protein C (APC) binds to procoagulant surfaces such as the membrane of activated platelets where it finds and degrades the procoagulant cofactors Va and VIIIa, thereby shutting down the plasma coagulation.  Protein S (PS) is an important nonenzymatic  cofactor to APC in these reactions. (Degradation of factors Va and VIIIa).

The common theme in activation and regulation of plasma coagulation is the reduction in dimensionality. Most reactions take place in a 2D world that will increase the efficiency of the reactions dramatically. The localization and timing of the coagulation processes are also dependent on the formation of protein complexes on the surface of membranes. The coagulation processes can also be controlled by certain drugs that destroy the membrane binding ability of some coagulation proteins – these proteins will be lost in the 3D world and not able to form procoagulant complexes on surfaces.

Assembly of proteins on membranes – making a 3D world flat

• The timing and efficiency of coagulation processes are handled by reduction in dimensionality

– Make 3 dimensions to 2 dimensions

• Coagulation proteins have membrane binding capacity

• Membranes provide non-coagulant and procoagulant surfaces

– Intact cells/activated cells

• Membrane binding is a target for anticoagulant drugs

– Anti-vitamin K (e.g. warfarin)

Modern View

It can be divided into the phases of initiation, amplification and propagation.

  • In the initiation phase, small amounts of thrombin can be formed after exposure of tissue factor to blood.
  • In the amplification phase, the traces of thrombin will be inactivated or used for amplification of the coagulation process.

At this stage there is not enough thrombin to form insoluble fibrin. In order to proceed further thrombin  activates platelets, which provide a procoagulant surface for the coagulation factors. Thrombin will also activate the vital cofactors V and VIII that will assemble on the surface of activated platelets. Thrombin can also activate factor XI, which is important in a feedback mechanism.

In the final step, the propagation phase, the highly efficient tenase and prothrombinase complexes have been assembled on the membrane surface. This yields large amounts of thrombin at the site of injury that can cleave fibrinogen to insoluble fibrin. Factor XI activation by thrombin then activates factor IX, which leads to the formation of more tenase complexes. This ensures enough thrombin is formed, despite regulation of the initiating TF-FVIIa complex, thus ensuring formation of a stable fibrin clot. Factor XIII stabilizes the fibrin clot through crosslinking when activated by thrombin.

English: Gene expression pattern of the VWF gene.

English: Gene expression pattern of the VWF gene. (Photo credit: Wikipedia)

Coagulation cascade

Coagulation cascade (Photo credit: Wikipedia)

Blood Coagulation (Thrombin) and Protein C Pat...

Fibrinolytic pathway

Fibrinolysis is the physiological breakdown of fibrin to limit and resolve blood clots. Fibrin is degraded primarily by the serine protease, plasmin, which circulates as plasminogen. In an auto-regulatory manner, fibrin serves as both the co-factor for the activation of plasminogen and the substrate for plasmin.

In the presence of fibrin, tissue plasminogen activator (tPA) cleaves plasminogen producing plasmin, which proteolyzes the fibrin. This reaction produces the protein fragment D-dimer, which is a useful marker of fibrinolysis, and a marker of thrombin activity because fibrin is cleaved from fibrinogen to fibrin.

Bleeding after Coronary Artery bypass Graft

Cardiac surgery with concomitant CPB can profoundly alter haemostasis, predisposing patients to major haemorrhagic complications and possibly early bypass conduit-related thrombotic events as well. Five to seven percent of patients lose more than 2 litres of blood within the first 24 hours after surgery, between 1% and 5% require re-operation for bleeding. Re-operation for bleeding increases hospital mortality 3 to 4 fold, substantially increases post-operative hospital stay and has a sizeable effect on health care costs. Nevertheless, re-exploration is a strong risk factor associated with increased operative mortality and morbidity, including sepsis, renal failure, respiratory failure and arrhythmias.

(Gábor Veres. New Drug Therapies Reduce Bleeding in Cardiac Surgery. Ph.D. Doctoral Dissertation. 2010. Semmelweis University)

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Curator & Author: Larry H. Bernstein, MD, FCAP

Leaders in Pharmaceutical Intelligence

Subtitle: Nitric Oxide, Peroxinitrite, and NO donors in Renal Function Loss

Summary: The criticality of renal function is traced to the emergence of animal forms from the sea to land. It also becomes acutely and/or chronically dysfunctional in metabolic, systemic inflammatory and immunological diseases of man. We have already described the key role that nitric oxide and the NO synthases play in reduction of oxidative stress, and we have seen that a balance has to be struck between pro- and anti-oxidative as well as inflammatory elements for avoidance of diseases, specifically involving the circulation, but effectively not limited to any organ system. In this discussion we shall look at kidney function, NO and NO donors. This is an extension of a series of posts on NO and NO related disorders.


Part I. The evolution of kidney structure and Function Evolution of kidney function

In fish the nerves that activate breathing take a short journey from an ancient part of the brain, the brain stem, to the throat and gills. For the ancient tadpole, the nerve controlling a reflex related to hiccup in man served a useful purpose, allowing the entrance to the lung to remain open when breathing air but closing it off when gulping water – which would then be directed only to the gills.

For humans and other mammals it provides a bit of evidence of our common ancestry. DNA evidence has pinned iguanas and chameleons as the closest relatives to snakes. In utero, we develop three separate kidneys in succession, absorbing the first two before we wind up with the embryonic kidney that will become our adult kidney. The first two of these reprise embryonic kidneys of ancestral forms, and in the proper evolutionary order.

The pronephric kidney does not function in human and other mammalian embryos. It disappears and gives rise to the Mesonephric kidney. This kidney filters wastes from the blood and excretes them to the outside of the body via a pair of tubes called the mesonephric ducts (also “Wolffian ducts”). The mesonephric kidney goes on to develop into the adult kidney of fish and amphibians.

This kidney does function for a few weeks in the human embryo, but then disappears as our final kidney forms, which is the Metanephric kidney. This begins developing about five weeks into gestation, and consists of an organ that filters wastes from the blood and excretes them to the outside through a pair ureters. In the embryo, the wastes are excreted directly into the amniotic fluid. The metanephric kidney is the final adult kidney of reptiles, birds, and mammals.

The first two kidneys resemble, in order, those of primitive aquatic vertebrates (lampreys and hagfish) and aquatic or semiaquatic vertebrates (fish and amphibians): an evolutionary order.

The explanation, then, is that we go through developmental stages that show organs resembling those of our ancestors. Take a step back and we see that fresh water fish have glomerular filtration. Cardiac contraction provides the pressure to force the water, small molecules, and ions into the glomerulus as nephric filtrate. The essential ingredients are then reclaimed by the tubules, returning to the blood in the capillaries surrounding the tubules. The amphibian kidney also functions chiefly as a device for excreting excess water.

But the problem is to conserve water, not eliminate it. The frog adjusts to the varying water content of its surroundings by adjusting the rate of filtration at the glomerulus. When blood flow through the glomerulus is restricted, a renal portal system is present to carry away materials reabsorbed through the tubules. Bird kidneys function like those of reptiles (from which they are descended). Uric acid is also their chief nitrogenous waste. All mammals share our use of urea as their chief nitrogenous waste. Urea requires much more water to be excreted than does uric acid. Mammals produce large amounts of nephric filtrate but are able to reabsorb most of this in the tubules. But even so, humans lose several hundred ml each day in flushing urea out of the body.

In his hypothesis of the evolution of renal function Homer Smith proposed that the formation of glomerular nephron and body armor had been adequate for the appearance of primitive vertebrates in fresh water and that the adaptation of homoiotherms to terrestrial life was accompanied by the appearance of the loop of Henle.

In the current paper, the increase in the arterial blood supply and glomerular filtration rate and the sharp elevation of the proximal reabsorption are viewed as important mechanisms in the evolution of the kidney. The presence of glomeruli in myxines and of nephron loops in lampreys suggests that fresh water animals used the preformed glomerular apparatus of early vertebrates, while mechanisms of urinary concentration was associated with the subdivision of the kidney into the renal cortex and medulla. The principles of evolution of renal functions can be observed at several levels of organizations in the kidney.

Natochin YV. Evolutionary aspects of renal function. Kidney International 1996; 49: 1539–1542; doi:10.1038/ki.1996.220. Smith HW: From Fish to Philosopher. Boston, Little, Brown, 1953.


The Kidney: Anatomy and Physiology

The kidney lies in the lower abdomen capped by the adrenal glands. It has an outer cortex and an inner medulla. The basic unit is the nephron, which filters blood at the glomerulus, and not only filters urine eliminating mainly urea, also uric acid, and other nitrogenous waste, but also reabsorbs Na+ in exchange for H+/(reciprocal K+) through the carbonic anhydrase of the epithelium. In addition, it serves as a endocrine organ and receptor through the renin-angiotensin/aldosterone system, sensitivity to water loss controlled by antidiuretic hormone, and is sensitive to the natriuretic peptides of the heart. The kidney is an elegant structure with a high concentration of glomeruli in the cortex, and in the medulla one finds a U-shaped tube that is critical in a countercurrent multiplier system with a descending limb, Loop of Henley, and ascending limb.

As the filtrate flows through the glomerulus into the descending limb, there is reabsorption of glucose and of H+ by the carbonic anhydrase conversion to water and CO2, except with serious acidemia, in which K+ is reabsorbed with H+ loss to the filtrate, resulting in a hyperkalemia. In the descending limb Na+ is absorbed into the interstitium, and the hypertonic interstitium draws water back for circulation, regulated by the action of ADH on the epithelium of the ascending limb. The result in terms of basic urinary clearance, the volume of urine loss is moderated by the amount needed for circulation (10 units of whole blood) without dehydration, and an amount sufficient for metabolite loss (including drug metabolites). The urine flows into the kidney pelvis and flow down the ureters.

The renal blood flow needs mention. The blood reaches the glomerulus by way of the afferent arteriole and leaves by way of the efferent arteriole. In a book by the Harvard Pathologist Shields Warren on diabetes he made a distinction between hypertension and diabetes in that efferent arteriolar sclerosis is present in both, but diabetes is uniquely identified by afferent arteriolar sclerosis. In diabetes you also have a typical glomerulosclerosis, which might be related to the same hyalinization found in the pancreatic islets – a secondary amyloidosis.


English: Nephron, Diagram of the urine formati...

English: Nephron, Diagram of the urine formation. The number inside tubular urin concentration in mOsm/l – when ADH acts Polski: Nefron, Schemat tworzenia moczu. Cyfry wewnątrz kanalików oznaczają lokalne stężenie w mOsm/l – gdy działa ADH (dochodzi do zagęszczania moczu). (Photo credit: Wikipedia)

Loop of Henle (Grey's Anatomy book)

Loop of Henle (Grey’s Anatomy book) (Photo credit: Wikipedia)

Frontal section through the kidney

Frontal section through the kidney (Photo credit: Wikipedia)


_ Part IIa. Nitric Oxide role in renal tubular epithelial cell function Tubulointerstitial Nephritides

As part of the exponential growth in our understanding of nitric oxide (NO) in health and disease over the past 2 decades, the kidney has become appreciated as a major site where NO may play a number of important roles. Although earlier work on the kidney focused more on effects of NO at the level of larger blood vessels and glomeruli, there has been a rapidly growing body of work showing critical roles for NO in tubulointerstitial disease. In this review we discuss some of the recent contributions to this important field.

Mattana J, Adamidis A, Singhal PC. Nitric oxide and tubulointerstitial nephritides. Seminars in Nephrology 2004; 24(4):345-353.

Nitric oxide donors and renal tubular (subepithelial) matrix

Nitric oxide (NO) and its metabolite, peroxynitrite (ONOO-), are involved in renal tubular cell injury. If NO/ONOO- has an effect to reduce cell adhesion to the basement membrane, does this effect contribute to tubular obstruction and would it be partially responsible for the harmful effect of NO on the tubular epithelium during acute renal failure (ARF)?

Wangsiripaisan A, et al. examined the effect of the NO donors

  • [1] (z)-1-[2-(2-aminoethyl)-N-(2-ammonioethyl)amino]diazen-1- ium-1, 2-diolate (DETA/NO),
  • [2] spermine NONOate (SpNO), and
  • [3] the ONOO- donor 3-morpholinosydnonimine (SIN-1) on

cell-matrix adhesion to collagen types I and IV, and also fibronectin using three renal tubular epithelial cell lines:

  • [1] LLC-PK1,
  • [2] BSC-1, and
  • [3] OK.

It was only the exposure to SIN-1 that caused a dose-dependent impairment in cell-matrix adhesion.

Similar results were obtained in the different cell types and matrix proteins. The effect of SIN-1 (500 microM) on LLC-PK1 cell adhesion was not associated with either cell death or alteration of matrix protein and was attenuated by either

  • [1] the NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide,
  • [2] the superoxide scavenger superoxide dismutase, or
  • [3] the ONOO- scavenger uric acid in a dose-dependent manner.

These investigators concluded in this seminal paper that ONOO- generated in the tubular epithelium during ischemia/reperfusion has the potential to impair the adhesion properties of tubular cells, which then may contribute to the tubular obstruction in ARF.

Wangsiripaisan A, Gengaro PE, Nemenoff RA, Ling H, et al. Effect of nitric oxide donors on renal tubular epithelial cell-matrix adhesion. Kidney Int 1999; 55(6):2281-8.

Coexpressed Nitric Oxide Synthase and Apical β1 Integrins

In sepsis-induced acute renal failure, actin cytoskeletal alterations result in shedding of proximal tubule epithelial cells (PTEC) and tubular obstruction.

This study examined the hypothesis that inflammatory cytokines, released early in sepsis, cause PTEC cytoskeletal damage and alter integrin-dependent cell-matrix adhesion. The question of whether the intermediate nitric oxide (NO) modulates these cytokine effects was also examined. After exposure of human PTEC to tumor necrosis factor-α, interleukin-1α, and interferon-γ, the actin cytoskeleton was disrupted and cells became elongated, with extension of long filopodial processes.

Cytokines induced shedding of viable, apoptotic, and necrotic PTEC, which was dependent on NO synthesized by inducible NO synthase (iNOS) produced as a result of cytokine actions on PTEC. Basolateral exposure of polarized PTEC monolayers to cytokines induced maximal NO-dependent cell shedding, mediated in part through NO effects on cGMP. Cell shedding was accompanied by dispersal of basolateral β1 integrins and E-cadherin, with corresponding upregulation of integrin expression in clusters of cells elevated above the epithelial monolayer.

These cells demonstrated coexpression of iNOS and apically redistributed β1 integrins. These authors point out that the major ligand involved in cell anchorage was laminin, probably through interactions with the integrin α3β1.

This interaction was downregulated by cytokines but was not dependent on NO. They posulate a mechanism by which inflammatory cytokines induce PTEC damage in sepsis, in the absence of hypotension and ischemia.

Glynne PA, Picot J and Evans TJ. Coexpressed Nitric Oxide Synthase and Apical β1 Integrins Influence Tubule Cell Adhesion after Cytokine-Induced Injury. JASN 2001; 12(11): 2370-2383.

Potentiation by Nitric Oxide of Apoptosis in Renal Proximal Tubule Cells

Proximal tubular epithelial cells (PTEC) exhibit a high sensitivity to undergo apoptosis in response to proinflammatory stimuli and immunosuppressors and participate in the onset of several renal diseases. This study examined the expression of inducible nitric oxide (NO) synthase after challenge of PTEC with bacterial cell wall molecules and inflammatory cytokines and analyzed the pathways that lead to apoptosis in these cells by measuring changes in the mitochondrial transmembrane potential and caspase activation.

The data show that the apoptotic effects of proinflammatory stimuli mainly were due to the expression of inducible NO synthase. Cyclosporin A and FK506 inhibited partially NO synthesis.

However, both NO and immunosuppressors induced apoptosis, probably through a common mechanism that involved the irreversible opening of the mitochondrial permeability transition pore. Activation of caspases 3 and 7 was observed in cells treated with high doses of NO and with moderate concentrations of immunosuppressors.

The conclusion is that the cooperation between NO and immunosuppressors that induce apoptosis in PTEC might contribute to the renal toxicity observed in the course of immunosuppressive therapy.

Hortelano S, Castilla M, Torres AM, Tejedor A, and Bosca L.  Potentiation by Nitric Oxide of Cyclosporin A and FK506- Induced Apoptosis in Renal Proximal Tubule Cells. J Am Soc Nephrol 2000; 11: 2315–2323.


Part IIb. Related studies with ROS and/or RNS on nonrenal epithelial cells

Reactive nitrogen species block cell cycle re-entry Endogenous sources of reactive nitrogen species (RNS) act as second messengers in a variety of cell signaling events, whereas environmental sources of RNS like nitrogen dioxide (NO2) inhibit cell survival and growth through covalent modification of cellular macromolecules. Murine type II alveolar cells arrested in G0 by serum deprivation were exposed to either NO2 or SIN-1, a generator of RNS, during cell cycle re-entry.

In serum-stimulated cells, RNS blocked cyclin D1 gene expression, resulting in cell cycle arrest at the boundary between G0 and G1. Dichlorofluorescin diacetate (DCF) fluorescence indicated that RNS induced sustained production of intracellular hydrogen peroxide (H2O2), which normally is produced only transiently in response to serum growth factors.

Loading cells with catalase prevented enhanced DCF fluorescence and rescued cyclin D1 expression and S phase entry.

These studies indicate environmental RNS interfere with cell cycle re-entry through an H2O2-dependent mechanism that influences expression of cyclin D1 and progression from G0 to the G1 phase of the cell cycle.

Yuan Z, Schellekens H, Warner L, Janssen-Heininger Y, Burch P, Heintz NH. Reactive nitrogen species block cell cycle re-entry through sustained production of hydrogen peroxide. Am J Respir Cell Mol Biol. 2003;28(6):705-12. Epub 2003 Jan 10.

Peroxynitrite modulates MnSOD gene expression

Peroxynitrite (ONOO-) is a strong oxidant derived from nitric oxide (‘NO) and superoxide (O2.-), reactive nitrogen (RNS) and oxygen species (ROS) present in inflamed tissue. Other oxidant stresses, e.g., TNF-alpha and hyperoxia,   induce mitochondrial, manganese-containing superoxide dismutase (MnSOD) gene expression.   3-morpholinosydnonimine HCI (SIN-1) (10 or 1000 microM) increased MnSOD mRNA, but did not change hypoxanthine guanine phosphoribosyl transferase (HPRT) mRNA.   Authentic peroxynitrite (ONOO ) (100-500 microM) also increased MnSOD mRNA but did not change constitutive HPRT mRNA expression.   ONOO stimulated luciferase gene expression driven by a 2.5 kb fragment of the rat MnSOD gene 5′ promoter region.

MnSOD gene induction due to ONOO- was

  • [1] inhibited effectively by L-cysteine (10 mM) and
  • [2] partially inhibited by N-acetyl cysteine (NAC)(50 mM) or
  • [3] pyrrole dithiocarbamate (10 mM).

.NO from 1-propanamine, 3-(2-hydroxy-2-nitroso-1-propylhydrazine) (PAPA NONOate) (100 or 1000 microM) did not change MnSOD or HPRT mRNA, nor did either H202 or NO2-, breakdown products of SIN-1 and ONOO, have any effect on MnSOD mRNA expression; ONOO- and SIN-1 also did not increase detectable MnSOD protein content or increase MnSOD enzymatic activity.

Nevertheless, increased steady state [O2.-] in the presence of .NO yields ONOO , and ONOO has direct, stimulatory effects on MnSOD transcript expression driven at the MnSOD gene 5′ promoter region inhibited completely by L-cysteine and partly by N-acetyl cysteine in lung epithelial cells. This raises a question of whether the same effect is seen in renal tubular epithelium.

Jackson RM, Parish G, Helton ES. Peroxynitrite modulates MnSOD gene expression in lung epithelial cells. Free Radic Biol Med. 1998; 25(4-5):463-72.

Comparative impacts of glutathione peroxidase-1 gene knockout on oxidative stress

Selenium-dependent glutathione peroxidase-1 (GPX1) protects against reactive-oxygen-species (ROS)-induced oxidative stress in vivo, but its role in coping with reactive nitrogen species (RNS) is unclear. Primary hepatocytes were isolated from GPX1-knockout (KO) and wild-type (WT) mice to test protection of GPX1 against cytotoxicity of

  • [1] superoxide generator diquat (DQ),
  • [2]NO donor S-nitroso-N-acetyl-penicillamine (SNAP) and
  • [3] peroxynitrite generator 3-morpholinosydnonimine (SIN-1).

Treating cells with SNAP in addition to DQ produced synergistic cytotoxicity that minimized differences in apoptotic cell death and oxidative injuries between the KO and WT cells. Less protein nitrotyrosine was induced by 0.05-0.5 mM DQ+0.25 mM SNAP in the KO than in the WT cells.

Total GPX activity in the WT cells was reduced by 65 and 25% by 0.5 mM DQ+0.1 mM SNAP and 0.5 mM DQ, respectively. Decreases in Cu,Zn-superoxide dismutase (SOD) activity and increases in Mn-SOD activity in response to DQ or DQ+SNAP were greater in the KO cells than in the WT cells.

The study indicates GPX1 was more effective in protecting hepatocytes against oxidative injuries mediated by ROS alone than by ROS and RNS together, and knockout of GPX1 did not enhance cell susceptibility to RNS-associated cytotoxicity. Instead, it attenuated protein nitration induced by DQ+SNAP.

To better understand the mechanism(s) underlying nitric oxide (. NO)-mediated toxicity, in the presence and absence of concomitant oxidant exposure, postmitotic terminally differentiated NT2N cells (which are incapable of producing . NO) were exposed to [1]PAPA-NONOate (PAPA/NO) and [2] 3-morpholinosydnonimine (SIN-1).

Exposure to SIN-1, which generated peroxynitrite (ONOO) in the range of 25-750 nM/min, produced a concentration- and time-dependent delayed cell death.   In contrast, a critical threshold concentration (>440 nM/min) was required for . NO to produce significant cell injury.   There is a largely necrotic lesion after ONOO exposure and an apoptotic-like morphology after . NO exposure.

Cellular levels of reduced thiols correlated with cell death, and pretreatment with N-acetylcysteine (NAC) fully protected from cell death in either PAPA/NO or SIN-1 exposure. NAC given within the first 3 h posttreatment further delayed cell death and increased the intracellular thiol level in SIN-1 but not . NO-exposed cells.

Cell injury from . NO was independent of cGMP, caspases, and superoxide or peroxynitrite formation.   Overall, exposure of non-. NO-producing cells to . NO or peroxynitrite results in delayed cell death, which, although occurring by different mechanisms,   appears to be mediated by the loss of intracellular redox balance.

Gow AJ, Chen Q, Gole M, Themistocleous M, Lee VM, Ischiropoulos H. Two distinct mechanisms of nitric oxide-mediated neuronal cell death show thiol dependency. Am J Physiol Cell Physiol. 2000; 278(6):C1099-107.

NO2 effect on phosphatidyl choline   Nitrogen dioxide (NO2) inhalation affects the extracellular surfactant as well as the structure and function of type II pneumocytes.

The studies had differences in oxidant concentration, duration of exposure, and mode of NO2 application. This study evaluated the influence of the NO2 application mode on the phospholipid metabolism of type II pneumocytes. Rats were exposed to identical NO2 body doses (720 ppm x h), which were applied continuously (10 ppm for 3 d), intermittently (10 ppm for 8 h per day, for 9 d), and repeatedly (10 ppm for 3 d, 28 d rest, and then 10 ppm for 3 d). Immediately after exposure, type II cells were isolated and evaluated for cell yield, vitality, phosphatidylcholine (PC) synthesis, and secretion.

Type II pneumocyte cell yield was only increased from animals that had been continuously exposed to NO2, but vitality of the isolated type II pneumocytes was not affected by the NO2 exposure modes. Continuous application of 720 ppm x h NO2 resulted in increased activity of the cytidine-5-diphosphate (CDP)-choline pathway.   After continuous NO2 application,

  • [1] specific activity of choline kinase,
  • [2] cytidine triphosphate (CTP):cholinephosphate cytidylyltransferase,
  • [3] uptake of choline, and
  • [4] pool sizes of CDP-choline and PC   were significantly increased over those of controls.

Intermittent application of this NO2 body dose provoked less increase in PC synthesis and the synthesis parameters were comparable to those for cells from control animals after repeated exposure. Whereas PC synthesis in type II cells was stimulated by NO2, their secretory activity was reduced.   Continuous exposure reduced the secretory activity most, whereas intermittent exposure nonsignificantly reduced this activity as compared with that of controls. The repeated application of NO2 produced no differences.

The authors conclude that…. type II pneumocytes adapt to NO2 atmospheres depending on the mode of its application, at least for the metabolism of PC and its secretion from isolated type II pneumocytes.

The reader asks whether this effect could also be found in renal epithelial cells, for which PC is not considered vital as for type II pneumocytes and possibly related to surfactant activity in the lung.

Müller B, Seifart C, von Wichert P, Barth PJ. Adaptation of rat type II pneumocytes to NO2: effects of NO2 application mode on phosphatidylcholine metabolism. Am J Respir Cell Mol Biol. 1998; 18(5): 712-20.

iNOS involved in immediate response to anaphylaxis

The generation of large quantities of nitric oxide (NO) is implicated in the pathogenesis of anaphylactic shock. The source of NO, however, has not been established and conflicting results have been obtained when investigators have tried to inhibit its production in anaphylaxis.

This study analyzed the expression of inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) in a mouse model of anaphylaxis.   BALB/c mice were sensitized and challenged with ovalbumin to induce anaphylaxis. Tissues were removed from the heart and lungs, and blood was drawn at different time points during the first 48 hours after induction of anaphylaxis. The Griess assay was used to measure nitric oxide generation.

Nitric oxide synthase expression was examined by reverse transcriptase polymerase chain reaction and immunohistochemistry. A significant increase in iNOS mRNA expression and nitric oxide production was evident as early as 10 to 30 minutes after allergen challenge in both heart and lungs.

In contrast, expression of eNOS mRNA was not altered during the course of the experiment. The results support involvement of iNOS in the immediate physiological response of anaphylaxis.

Sade K, Schwartz IF, Etkin S, Schwartzenberg S, et al. Expression of Inducible Nitric Oxide Synthase in a Mouse Model of Anaphylaxis. J Investig Allergol Clin Immunol 2007; 17(6):379-385.


Part IIc. Additional Nonrenal Related NO References

1. Nitrogen dioxide induces death in lung epithelial cells in a density-dependent manner. Persinger RL, Blay WM, Heintz NH, Hemenway DR, Janssen-Heininger YM. Am J Respir Cell Mol Biol. 2001 May;24(5):583-90. PMID: 11350828 [PubMed – indexed for MEDLINE] Free Article

2. Molecular mechanisms of nitrogen dioxide induced epithelial injury in the lung. Persinger RL, Poynter ME, Ckless K, Janssen-Heininger YM. Mol Cell Biochem. 2002 May-Jun;234-235(1-2):71-80. Review. PMID: 12162462 [PubMed – indexed for MEDLINE]

3. Nitric oxide and peroxynitrite-mediated pulmonary cell death. Gow AJ, Thom SR, Ischiropoulos H. Am J Physiol. 1998 Jan;274(1 Pt 1):L112-8. PMID: 9458808 [PubMed – indexed for MEDLINE] Free Article

4. Mitogen-activated protein kinases mediate peroxynitrite-induced cell death in human bronchial epithelial cells. Nabeyrat E, Jones GE, Fenwick PS, Barnes PJ, Donnelly LE. Am J Physiol Lung Cell Mol Physiol. 2003 Jun;284(6):L1112-20. Epub 2003 Feb 21. PMID: 12598225 [PubMed – indexed for MEDLINE] Free Article

5. Peroxynitrite inhibits inducible (type 2) nitric oxide synthase in murine lung epithelial cells in vitro. Robinson VK, Sato E, Nelson DK, Camhi SL, Robbins RA, Hoyt JC. Free Radic Biol Med. 2001 May 1;30(9):986-91. PMID: 11316578 [PubMed – indexed for MEDLINE]

6. Nitric oxide-mediated chondrocyte cell death requires the generation of additional reactive oxygen species. Del Carlo M Jr, Loeser RF. Arthritis Rheum. 2002 Feb;46(2):394-403. PMID: 11840442 [PubMed – indexed for MEDLINE]

7. Colon epithelial cell death in 2,4,6-trinitrobenzenesulfonic acid-induced colitis is associated with increased inducible nitric-oxide synthase expression and peroxynitrite production.

Yue G, Lai PS, Yin K, Sun FF, Nagele RG, Liu X, Linask KK, Wang C, Lin KT, Wong PY. J Pharmacol Exp Ther. 2001 Jun;297(3):915-25. PMID: 11356911 [PubMed – indexed for MEDLINE] Free Article


Part IIIa. Acute renal failure   Acute renal failure (ARF), characterized by sudden loss of the ability of the kidneys to [1] excrete wastes, [2] concentrate urine, [3] conserve electrolytes, and [4] maintain fluid balance, is a frequent clinical problem, particularly in the intensive care unit, where it is associated with a mortality of between 50% and 80%.

This clinical entity was described as an acute loss of kidney function that occurred in severely injured crush victims because of histological evidence for patchy necrosis of renal tubules at autopsy. In the clinical setting, the terms ATN and acute renal failure (ARF) are frequently used interchangeably. However, ARF does not include increases in blood urea due to [1] reversible renal vasoconstriction (prerenal azotemia) or [2] urinary tract obstruction (postrenal azotemia). Acute hemodialysis was first used clinically during the Korean War in 1950 to treat military casualties, and this led to a decrease in mortality of the ARF clinical syndrome from about 90% to about 50%.   In the half century that has since passed, much has been learned about the pathogenesis of ischemic and nephrotoxic ARF in experimental models, but there has been very little improvement in mortality. This may be explained by changing demographics: [1] the age of patients with ARF continues to rise, and [2] comorbid diseases are increasingly common in this population. Both factors may obscure any increased survival related to improved critical care. Examining the incidence of ARF in several military conflicts does, however, provide some optimism. The incidence of ARF in seriously injured casualties decreased between World War II and the Korean War, and again between that war and the Vietnam War, despite the lack of any obvious difference in the severity of the injuries. What was different was the rapidity of the fluid resuscitation of the patients? Fluid resuscitation on the battlefield with the rapid evacuation of the casualties to hospitals by helicopter began during the Korean War and was optimized further during the Vietnam War. For seriously injured casualties the incidence of ischemic ARF was one in 200 in the Korean War and one in 600 in the Vietnam War. This historical sequence of events suggests that early intervention could prevent the occurrence of ARF, at least in military casualties.   In experimental studies it has been shown that progression from an azotemic state associated with renal vasoconstriction and intact tubular function (prerenal azotemia) to established ARF with tubular dysfunction occurs if the renal ischemia is prolonged. Moreover, early intervention with fluid resuscitation was shown to prevent the progression from prerenal azotemia to established ARF. Diagnostic evaluation of ARF One important question, therefore, is how to assure that an early diagnosis of acute renal vasoconstriction can be made prior to the occurrence of tubular dysfunction, thus providing the potential to prevent progression to established ARF. In this regard, past diagnostics relied on observation of the patient response to a fluid challenge: [1] decreasing levels of blood urea nitrogen (BUN) indicated the presence of reversible vasoconstriction, [2] while uncontrolled accumulation of nitrogenous waste products, i.e., BUN and serum creatinine, indicated established ARF.

This approach, however, frequently led to massive fluid overload in the ARF patient with resultant

  • [1] pulmonary congestion,
  • [2] hypoxia, and
  • [3] premature need for mechanical ventilatory support and/or hemodialysis.

On this background the focus turned to an evaluation of urine sediment and urine chemistries to differentiate between renal vasoconstriction with intact tubular function and established ARF.

It was well established that if tubular function was intact, renal vasoconstriction was associated with enhanced tubular sodium reabsorption. Specifically, the fraction of filtered sodium that is rapidly reabsorbed by normal tubules of the vasoconstricted kidney is greater than 99%.

Thus, when nitrogenous wastes, such as creatinine and urea, accumulate in the blood due to a fall in glomerular filtration rate (GFR) secondary to renal vasoconstriction with intact tubular function, the fractional excretion of filtered sodium (FENa = [(urine sodium × plasma creatinine) / (plasma sodium × urine creatinine)]) is less than 1%. An exception to this physiological response of the normal kidney to vasoconstriction is when the patient is receiving a diuretic, including mannitol, or has glucosuria, which decreases tubular sodium reabsorption and increases FENa.

It has recently been shown in the presence of diuretics that a rate of fractional excretion of urea (FEurea) of less than 35 indicates intact tubular function, thus favoring renal vasoconstriction rather than established ARF as a cause of the azotemia.


English: Physiology of Nephron

English: Physiology of Nephron (Photo credit: Wikipedia)

Structures of the kidney: 1.Renal pyramid 2.In...

Structures of the kidney: 1.Renal pyramid 2.Interlobar artery 3.Renal artery 4.Renal vein 5.Renal hilum 6.Renal pelvis 7.Ureter 8.Minor calyx 9.Renal capsule 10.Inferior renal capsule 11.Superior renal capsule 12.Interlobar vein 13.Nephron 14.Minor calyx 15.Major calyx 16.Renal papilla 17.Renal column (no distinction for red/blue (oxygenated or not) blood, arteriole is between capilaries and larger vessels (Photo credit: Wikipedia)



Mechanisms of ARF

Based on the foregoing comments, this discussion of mechanisms of ARF will not include nitrogenous-waste accumulation due to renal vasoconstriction with intact tubular function (prerenal azotemia) or urinary tract obstruction (postrenal azotemia). The mechanisms of ARF involve both vascular and tubular factors. An ischemic insult to the kidney will in general be the cause of the ARF. While a decrease in renal blood flow with diminished oxygen and substrate delivery to the tubule cells is an important ischemic factor, it must be remembered that a relative increase in oxygen demand by the tubule is also a factor in renal ischemia.

Approximately 30–70% of these shed epithelial tubule cells in the urine are viable and can be grown in culture. Recent studies using cellular and molecular techniques have provided information relating to the structural abnormalities of injured renal tubules that occur both in vitro and in vivo. In vitro studies using chemical anoxia have revealed abnormalities in the proximal tubule cytoskeleton that are associated with translocation of Na+/K+-ATPase from the basolateral to the apical membrane.

A comparison of cadaveric transplanted kidneys with delayed versus prompt graft function has also provided important results regarding the role of Na+/K+-ATPase in ischemic renal injury. This study demonstrated that, compared with kidneys with prompt graft function, those with delayed graft function had a significantly greater cytoplasmic concentration of Na+/K+-ATPase and actin-binding proteins — spectrin (also known as fodrin) and ankyrin — that had translocated from the basolateral membrane to the cytoplasm.

Such a translocation of Na+/K+-ATPase from the basolateral membrane to the cytoplasm could explain the decrease in tubular sodium reabsorption that occurs with ARF. An important focus of research is the mechanisms whereby the critical residence of Na+/K+-ATPase in the basolateral membrane (which facilitates vectorial sodium transport) is uncoupled by hypoxia or ischemia.  The actin-binding proteins,

  • spectrin and
  • ankyrin,

serve as substrates for the calcium-activated cysteine protease calpain.


In vitro studies in proximal tubules have shown a rapid rise in cytosolic calcium concentration during acute hypoxia, which antedates the evidence of tubular injury as assessed by lactic dehydrogenase (LDH) release. There is further evidence to support the importance of the translocation of Na+/K+-ATPase from the basolateral membrane to the cytoplasm during renal ischemia/reperfusion.

Specifically, calpain-mediated breakdown products of the actin-binding protein spectrin occur with renal ischemia. Calpain activity was demonstrated to increase during hypoxia in isolated proximal tubules. Measurement of LDH release following calpain inhibition indicated attenuation of hypoxic damage to proximal tubules. There was no evidence of an increase in cathepsin, a (cysteine protease) in proximal tubules during hypoxia , but there is a calcium-independent pathway for calpain activation during hypoxia.

Calpastatin, an endogenous cellular inhibitor of calpain activation, was shown to be diminished during hypoxia in association with the rise in another cysteine protease, caspase.

This effect of diminished calpastatin activity could be reversed by caspase inhibition. Proteolytic pathways appear to be involved in calpain-mediated proximal tubule cell injury during hypoxia. Calcium activation of phospholipase A has also been shown to contribute to renal tubular injury during ischemia.


Tubular obstruction during ARF

The existence of proteolytic pathways involving cysteine proteases, namely calpain and caspases, may therefore explain

  • the decrease in proximal tubule sodium reabsorption and
  • increased FENa

secondary to proteolytic uncoupling of Na+/K+-ATPase from its basolateral membrane anchoring proteins.

This tubular perturbation alone, however, does not explain the fall in GFR that leads to nitrogenous-waste retention and thus the rise in BUN and serum creatinine.   Decreased proximal tubule sodium reabsorption may lead to a decreased GFR during ARF. First of all, brush border membranes and cellular debris could provide the substrate for intraluminal obstruction in the highly resistant portion of distal nephrons.

In fact, microdissection of individual nephrons of kidneys from patients with ARF demonstrated obstructing casts in distal tubules and collecting ducts. This observation could explain the dilated proximal tubules that are observed upon renal biopsy of ARF kidneys. The intraluminal casts in ARF kidneys stain prominently for Tamm-Horsfall protein (THP), which is produced in the thick ascending limb. Importantly, THP is secreted into tubular fluid as a monomer but subsequently may become a polymer that forms a gel-like material in the presence of increased luminal Na+ concentration, as occurs in the distal nephron during clinical ARF with the decrease in tubular sodium reabsorption.

Thus, the THP polymeric gel in the distal nephron provides an intraluminal environment for distal cast formation involving viable, apoptotic, and necrotic cells.

The loss of the tubular epithelial cell barrier and/or the tight junctions between viable cells during acute renal ischemia could lead to a leak of glomerular filtrate back into the circulation. (If this occurs and normally non-reabsorbable substances, such as inulin, leak back into the circulation, then a falsely low GFR will be measured as inulin clearance. It should be noted, however, that the degree of extensive tubular damage observed in experimental studies demonstrating tubular fluid backleak is rarely observed with clinical ARF in humans). Moreover, dextran sieving studies in patients with ARF demonstrated that, at best, only a 10% decrease in GFR could be explained by backleak of filtrate. Cadaveric transplanted kidneys with delayed graft function, however, may have severe tubular necrosis, and thus backleak of glomerular filtration may be more important in this setting.

Inflammation and NO

There is now substantial evidence for the involvement of inflammation in the pathogenesis of the decreased GFR associated with acute renal ischemic injury. In this regard, there is experimental evidence that iNOS may contribute to tubular injury during ARF. Hypoxia in isolated proximal tubules has been shown to increase NO release, and there is increased iNOS protein expression in ischemic kidney homogenates. An antisense oligonucleotide was shown to block the upregulation of iNOS and afford functional protection against acute renal ischemia. Moreover, when isolated proximal tubules from iNOS, eNOS, and neuronal NO synthase (nNOS) knockout mice were exposed to hypoxia, only the tubules from the iNOS knockout mice were protected against hypoxia, as assessed by LDH release. The iNOS knockout mice were also shown to have lower mortality during ischemia/reperfusion than wild-type mice.  The scavenging of NO by oxygen radicals produces peroxynitrite causing tubule damage during ischemia. While iNOS may contribute to ischemic injury of renal tubules,  the vascular effect of eNOS in the glomerular afferent arteriole is protective against ischemic injury. In this regard, eNOS knockout mice are more sensitive to endotoxin-related injury than normal mice.

Moreover, the protective role of vascular eNOS may be more important than the deleterious effect of iNOS at the tubule level during renal ischemia.   This is because treatment of mice with the nonspecific NO synthase (NOS) inhibitor L-NAME, which blocks both iNOS and eNOS, worsens renal ischemic injury. NO may downregulate eNOS and is a potent inducer of heme oxygenase-1, which has been shown to be cytoprotective against renal injury. The MAPK pathway also appears to be involved in renal oxidant injury. Activation of extracellular signal–regulated kinase (ERK) or inhibition of JNK ameliorates oxidant injury–induced necrosis in mouse renal proximal tubule cells in vitro. Upregulation of ERK may also be important in the effect of preconditioning whereby early ischemia affords protection against a subsequent ischemia/reperfusion insult. Alterations in cell cycling are also involved in renal ischemic injury. Upregulation of p21, which inhibits cell cycling, appears to allow cellular repair and regeneration, whereas homozygous p21 knockout mice demonstrate enhanced cell necrosis in response to an ischemic insult.

Prolonged duration of the ARF clinical course and the need for dialysis are major factors projecting a poor prognosis. Patients with ARF who require dialysis have a 50–70% mortality rate. Infection and cardiopulmonary complications are the major causes of death in patients with ARF. Excessive fluid administration in patients with established ARF may lead to pulmonary congestion, hypoxia, the need for ventilatory support, pneumonia, and multiorgan dysfunction syndrome, which has an 80–90% mortality rate. Until means to reverse the diminished host defense mechanisms in azotemic patients with clinical ARF are available, every effort should be made to avoid invasive procedures such as the placement of bladder catheters, intravenous lines, and mechanical ventilation. Over and above such supportive care, it may be that combination therapy will be necessary to prevent or attenuate the course of ARF. Such combination therapy must involve agents with potential beneficial effects on vascular tone, tubular obstruction, and inflammation.

Schrier RW, Wang W, Poole B, and Mitra A. Acute renal failure: definitions, diagnosis, pathogenesis, and therapy. The Journal of Clinical Investigation 2004; 114(1):5-14.


Part IIIb. Additional Related References on NO, oxidative stress and Kidney

Shelgikar PJ, Deshpande KH, Sardeshmukh AS, Katkam RV, Suryakarl AN. Role of oxidants and antioxidants in ARF patients undergoing hemodialysis. Indian J Nephrol 2005;15: 73-76.

Lee JW. Renal Dysfunction in Patients with Chronic Liver Disease. Electrolytes Blood Press 7:42-50, 2009ㆍdoi: 10.5049/EBP.2009.7.2.42.

Saadat H, et al. Endothelial Nitric Oxide Function and Tubular Injury in Premature Infants. Int J App Sci and Technol 2012; 7(6): 77-81.

Amerisan MS. Cardiovascular disease in chronic kidney disease. Indian J Nephrol 2005;15: 1-7.


Traditional risk factors for CVD in CKD

  • Hypertension
  • Older Age
  • Diabetes Mellitus
  • Male gender
  • High LDL
  • White Race
  • Low HDL
  • Physical inactivity
  • Smoking
  • Menopause
  • LVH

CKD Related CV Risk Factors

  • Blood Pressure
  • ? Homocysteinemia
  • Anemia
  • ? Inflammation
  •   Ca++ x P++
  • ? NO synthesis
  • Na+ Retention
  • ? Lp (a)
  • Hypervolemia
  • ? Insulin Resistance
  • Proteinuria & Hypoalbuminemia
  • Iron over load
  • ? Adeponectin
  • ??Vit. C or E
  • ? 5 Lipoxygenase
  • ROS
  • Genetic factors
  • ADMA (Asymmetric Dimethyl Arginine)

S Vikrant, SC Tiwari. Essential Hypertension – Pathogenesis and Pathophysiology. J Indian Acad Clinical Medicine 2001; 2(3):141-161. Scheme for pathogenesis of salt dependent hypertension.

The hypothesis proposes that early hypertension is episodic and is mediated by a hyperactive sympathetic nervous system or activated renin-angiotensin system.

Cell membrane alterations

Hypotheses linking abnormal ionic fluxes to increased peripheral resistance through increase in cell sodium, calcium, or pH.   The hypertension that is more common in obese people may arise in large part from the insulin resistance and resultant hyperinsulinaemia that results from the increased mass of fat. However, rather unexpectedly, insulin resistance may also be involved in hypertension in non-obese people.

Overall scheme for the mechanisms by which obesity, if predominantly upper body or visceral in location, could promote


  • diabetes,
  • dyslipidemia and
  • hypertension via hyperinsulinemia.

The explanation for insulin resistance found in as many as half of nonobese hypertensive is not obvious and may involve one or more aspects of insulin’s action


Proposed mechanisms by which insulin resistance and/or hyperinsulinemia may lead to increased blood pressure.

  1. Enhanced renal sodium and water reabsorption.
  2. Increased blood pressure sensitivity to dietary salt intake
  3. Augmentation of the pressure and
  4. aldosterone responses to AII
  5. Changes in transmembrane electrolyte transport
  • a. Increased intracellular sodium
  • b. Decreased Na+/K+ – ATPase activity
  • c. Increased intracellular Ca2+ pump activity
  • d. Increased intracellular Ca2+ accumulation
  • e. Stimulation of growth factors


Part IV. New Insights on NO donors

This study investigated the involvement of nitric oxide (NO) into the irradiation-induced increase of cell attachment. These experiments explored the cellular mechanisms of low-power laser therapy. HeLa cells were irradiated with a monochromatic visible-tonear infrared radiation (600–860 nm, 52 J/m2) or with a diode laser (820 nm, 8–120 J/m2) and the number of cells attached to a glass matrix was counted after 30 minute incubation at 37oC. The NO donors

  1. sodium nitroprusside (SNP),
  2. glyceryl trinitrate (GTN), or
  3. sodium nitrite (NaNO2)

were added to the cellular suspension before or after irradiation. The action spectra and the concentration and fluence dependencies obtained were compared and analyzed.

The well-structured action spectrum for the increase of the adhesion of the cells, with maxima at 619, 657, 675, 740, 760, and 820 nm, points to the existence of a photoacceptor responsible for the enhancement of this property (supposedly cytochrome c oxidase, the terminal respiratory chain enzyme), as well as signaling pathways between the cell mitochondria, plasma membrane, and nucleus.

Treating the cellular suspension with SNP before irradiation significantly modifies the action spectrum for the enhancement of the cell attachment property (band maxima at 642, 685, 700, 742, 842, and 856 nm). The action of SNP, GTN, andNaNO2 added before or after irradiation depends on their concentration and radiation fluence.

The NO donors added to the cellular suspension before irradiation eliminate the radiation induced increase in the number of cells attached to the glass matrix, supposedly by way of binding NO to cytochrome c oxidase. NO added to the suspension after irradiation can also inhibit the light-induced signal downstream. Both effects of NO depend on the concentration of the NO donors added.

The results indicate that NO can control the irradiation-activated reactions that increase the attachment of cells.

Karu TI, Pyatibrat LV, and Afanasyeva NI. Cellular Effects of Low Power Laser Therapy Can be Mediated by Nitric Oxide. Lasers Surg. Med 2005; 36:307–314.

IFNa-2b (IFN-a) effect on barrier function of renal tubular epithelium

IFNa treatment can be accompanied by impaired renal function and capillary leak. This study shows IFNa produced dose-dependent and time-dependent decrease in transepithelial resistance (TER) ameliorated by tyrphostin, an inhibitor of phosphotyrosine kinase with increased expression of occludin and E-cadherin. In conclusion, IFNa can directly affect barrier function in renal epithelial cells via ovewrexpression or missorting of the junctional proteins occludin and E-cadherin.

Lechner J, Krall M, Netzer A, Radmayr C, et al. Effects of interferon a-2b on barrier function and junctional complexes of renal proximal tubulat LLC-pK1 cells. Kidney Int 1999; 55:2178-2191.

Ischemia-reperfusion injury

The pathophysiology of acute renal failure (ARF) is complex and not well understood. Numerous models of ARF suggest that oxygen-derived reactive species are important in renal ischemia-reperfusion (I-R) injury, but the nature of the mediators is still controversial. Treatment with oxygen radical scavengers, antioxidants, and iron chelators such as

  • superoxide dismutase,
  • dimethylthiourea,
  • allopurinol, and
  • deferoxamine

are protective in some models, and suggest a role for the hydroxyl radical formation. However, these compounds are not protective in all models of I-R injury, and direct evidence for the generation of hydroxyl radical is absent. Furthermore, these inhibitors have another property in common.

They all directly scavenge or inhibit the formation of peroxynitrite (ONOO−), a highly toxic species derived from nitric oxide (NO) and superoxide. Thus, the protective effects seen with these inhibitors may be due in part to their ability to inhibit ONOO− formation. Even though reactive oxygen species are thought to participate in ischemia-reperfusion (I-R) injury, induction of and production of high levels of  inducible nitric oxide (NO)  also contribute to this injury.

NO combines with superoxide to form the potent oxidant peroxynitrite (ONOO−). NO and ONOO− were investigated in a rat model of renal I-R injury using the selective iNOS inhibitor L-N6-(1-iminoethyl)lysine (L-NIL).

I-R surgery significantly increased plasma creatinine levels to 1.9 ± 0.3 mg/dl (P < .05) and caused renal cortical necrosis. L-NIL administration (3 mg/kg) in animals subjected to I-R significantly decreased plasma creatinine levels to 1.2 ± 0.10 mg/dl (P < .05 compared with I-R) and reduced tubular damage.

ONOO− formation was evaluated by detecting 3-nitrotyrosine-protein adducts (3NTyPAs), a stable biomarker of ONOO− formation.   The kidneys from I-R animals had increased levels of 3NTyPAs compared with control animals   L-NIL-treated rats (3 mg/kg) subjected to I-R showed decreased levels of 3NTyPAs.

These results suggests that iNOS-generated NO mediates damage in I-R injury possibly through ONOO− formation.


In summary,

  1. 3-nitrotyrosine-protein adducts were detected in renal tubules after I-R injury.
  2. Selective inhibition of iNOS by L-NIL decreased injury, improved renal function, and decreased apparent ONOO− formation.
  3. Reactive nitrogen species should be considered potential therapeutic targets in the prevention and treatment of renal I-R injury.


Walker LM, Walker PD, Imam SZ, et al. Evidence for Peroxynitrite Formation in Renal Ischemia-Reperfusion Injury: Studies with the Inducible Nitric Oxide Synthase InhibitorL-N6-(1-Iminoethyl)lysine1. 2000.

Role of TNFa independent of iNOS Renal failure is a frequent complication of sepsis, mediated by renal vasoconstrictors and vasodilators. Endotoxin induces several proinflammatory cytokines, among which tumor necrosis factor (TNF) is thought to be of major importance. Tumor necrosis factor (TNF) has been suggested to be a factor in the acute renal failure in sepsis or endotoxemia. Passive immunization by anti-TNFa prevented development of septic shock in animal experiments.The development of ARF involves excessive intrarenal vasoconstriction. Involvement of nitric oxide (NO), generated by inducible NO synthase (iNOS), is still a factor in the pathogenesis of endotoxin-induced renal failure. TNF-a leads to a decrease in glomerular filtration rate (GFR).

This study tested the hypothesis that the role of TNF-a in endotoxic shock related ARF is mediated by iNOS-derived NO.   An injection of lipopolysaccharide (LPS) constituent of gram-negative bacteria to wild-type mice resulted in a 70% decrease in glomerular filtration rate (GFR) and in a 40% reduction in renal plasma flow (RPF) 16 hours after the injection.   The results occurred independent of hypotension, morphological changes, apoptosis, and leukocyte accumulation. In mice pretreated with TNFsRp55, only a 30% decrease in GFR was observed without a significant change in RPF as compared with controls. Pretreatment with TNKsRp55 on renal function Wild-type mice were pretreated with TNFsRp55(10 mg/kg IP)  for one hour before the administration of 5 mg/kg intraperitoneal endotoxin. GFR and RPF were determined 16 hours thereafter. Data are expressed as mean 6, SEM, N 5 6. *P , 0.05 vs. Control; §P , 0.05 vs. LPS, by ANOVA.

The serum NO concentration was significantly lower in endotoxemic wild-type mice pretreated with TNFsRp55, as compared with untreated endotoxemic wild-type mice. In LPS-injected iNOS knockout mice and wild-type mice treated with a selective iNOS inhibitor, 1400W, the development of renal failure was similar to that in wild-type mice. As in wild-type mice,TNFsRp55 significantly attenuated the decrease in GFR (a 33% decline, as compared with 75% without TNFsRp55) without a significant change in RPF in iNOS knockout mice given LPS. These results demonstrate a role of TNF in the early renal dysfunction (16 h) in a septic mouse model independent of iNOS,

  • hypotension,
  • apoptosis,
  • leukocyte accumulation,and
  • morphological alterations,

thus suggesting renal hypoperfusion secondary to an imbalance between, as yet to be defined renal vasoconstrictors and vasodilators.

Knotek M, Rogachev B, Wang W,….., Edelstein CL, Dinarello CA, and Schrier RW. Endotoxemic renal failure in mice: Role of tumor necrosis factor independent of inducible nitric oxide synthase. Kidney International 2001; 59:2243–2249

Ischemic acute renal failure

Inflammation plays a major role in the pathophysiology of acute renal failure resulting from ischemia. This review discusses the contribution of

  • endothelial
  • epithelial cells and
  • leukocytes

to this inflammatory response. The roles of cytokines/chemokines in the injury and recovery phase are reviewed. The protection of mouse kidney prior to exposure to ischemia or urinary tract obstruction is  a potential model to  search for pharmacologic agents to protect the kidney against injury by inflammatory mediators produced by tubular epithelial cells and activated leukocytes in renal ischemia/reperfusion (I/R) injury. Tubular epithelia produce

  • TNF-a,
  • IL-1,
  • IL-6,
  • IL-8,
  • TGF-b,
  • MCP-1,
  • ENA-78,
  • RANTES, and
  • fractalkines,

whereas leukocytes produce

  • TNF-a,
  • IL-1,
  • IL-8,
  • MCP-1,
  • ROS, and
  • eicosanoids.

The release of these chemokines and cytokines serve as effectors for a positive feedback pathway enhancing inflammation and cell injury, the cycle of tubular epithelial cell injury and repair following renal ischemia/reperfusion.   Tubular epithelia are typically cuboidal in shape and apically-basally polarized; the Na+/K+-ATPase localizes to basolateral plasma membranes, whereas cell adhesion molecules, such as integrins localize basally. In response to ischemia reperfusion,

  • the Na+/K+-ATPase appears apically, and
  • integrins are detected on lateral and basal plasma membranes.

Some of the injured epithelial cells undergo necrosis and/or apoptosis detaching from the underlying basement membrane into the tubular space where they contribute to tubular occlusion. Viable cells that remain attached, dedifferentiate, spread, and migrate to repopulate the denuded basement membrane. With cell proliferation, cell-cell and cell-matrix contacts are restored, and the epithelium redifferentiates and repolarizes, forming a functional, normal epithelium Inflammation is a significant component of renal I/R injury, playing a considerable role in its pathophysiology.

Although significant progress has been made in defining the major components of this process, the complex cross-talk between endothelial cells, inflammatory cells, and the injured epithelium with each generating and often responding to cytokines and chemokines is not well understood. In addition, we have not yet taken full advantage of the large body of data on inflammation in other organ systems.

Furthermore, preconditioning the kidney to afford protection to subsequent bouts of ischemia may serve as a useful model challenging us to therapeutically mimic endogenous mechanisms of protection.

Understanding the inflammatory response prevalent in ischemic kidney injury will facilitate identification of molecular targets for therapeutic intervention.

Bonventre JV and Zuk A. Ischemic acute renal failure: An inflammatory disease? Forefronts in Nephrology 2002;.. :480-485

Gene expression profiles in renal proximal tubules In kidney disease renal proximal tubular epithelial cells (RPTEC) actively contribute to the progression of tubulointerstitial fibrosisby mediating both

  • an inflammatory response and
  • via epithelial-to-mesenchymal transition.

Using laser capture microdissection we specifically isolated RPTEC from cryosections of the healthy parts of kidneys removed owing to renal cell carcinoma and from kidney biopsies from patients with proteinuric nephropathies. RNA was extracted and hybridized to complementary DNA microarrays after linear RNA amplification. Statistical analysis identified 168 unique genes with known gene ontology association, which separated patients from controls. Besides distinct alterations in signal-transduction pathways (e.g. Wnt signalling), functional annotation revealed a significant upregulation of genes involved in


  • cell proliferation and cell cycle control (like insulin-like growth factor 1 or cell division cycle 34),
  • cell differentiation (e.g. bone morphogenetic protein 7),
  • immune response,
  • intracellular transport and
  • metabolism


in RPTEC from patients.

The study also revealed differential expression of a number of genes responsible for cell adhesion (like BH-protocadherin) with a marked downregulation of most of these transcripts. In summary, the results obtained from RPTEC revealed a differential regulation of genes, which are likely to be involved in either pro-fibrotic or tubulo-protective mechanisms in proteinuric patients at an early stage of kidney disease.

Rudnicki M, Eder S, Perco P, Enrich J, et al. Gene expression profiles of human proximal tubular epithelial cells in proteinuric nephropathies. Kidney International 2006; xx:1-11. Kidney International advance online publication, 20 December 2006; doi:10.1038/

Oxidative stress involved with diabetic nephropathy

Diabetic Nephropathy (DN) poses a major health problem. There is strong evidence for a potential role of the eNOS gene. This case control study investigated the possible role of genetic variants of the endothelial Nitric Oxide Synthase (eNOS) gene and oxidative stress in the pathogenesis of nephropathy in patients with diabetes mellitus. The study included 124 diabetic patients;

  1. 68 of these patients had no diabetic nephropathy (group 1) while
  2. 56 patients exhibited symptoms of diabetic nephropathy (group 2).
  3. Sixty two healthy non-diabetic individuals were also included as a control group.

Blood samples from subjects and controls were analyzed to investigate the eNOS genotypes and to estimate

  • the lipid profile and
  • markers of oxidative stress such as malondialdehyde (MDA) and nitric oxide (NO).

No significant differences were found in the frequency of eNOS genotypes between diabetic patients (either in group 1 or group 2) and controls (p >0.05). Also, no significant differences were found in the frequency of eNOS genotypes between group 1 and group 2 (p >0.05). Both group 1 and group 2 had significantly higher levels of nitrite and MDA when compared with controls (all p = 0.0001). Also group 2 patients had significantly higher levels of nitrite and MDA when compared with group 1 (p = 0.02, p = 0.001 respectively).

The higher serum level of the markers of oxidative stress in diabetic patients particularly those with diabetic nephropathy suggest that oxidative stress and not the eNOS gene polymorphism is involved in the pathogenesis of the diabetic nephropathy in this subset of patients

Badawy A, Elbaz R, Abbas AM, Ahmed Elgendy A, et al. Oxidative stress and not endothelial Nitric Oxide Synthase gene polymorphism involved in diabetic nephropathy. Journal of Diabetes and Endocrinology 2011; 2(3): 29-35.

Metformin in renal ischemia reperfusion

Renal ischemia plays an important role in renal impairment and transplantation. Metformin is a biguanide used in type 2 diabetes, it inhibits hepatic glucose production and increases peripheral insulin sensitivity. While the mode of action of metformin is incompletely understood, it appears to have anti-inflammatory and antioxidant effects involved in its beneficial effects on insulin resistance.   Control, Sham, ischemia/reperfusion (I/R) and Metformin treated I /R groups   A renal I/R injury was done by a left renal pedicle occlusion to induce ischemia for 45 min followed by 60 min of reperfusion with contralateral nephrectomy. Metformin pretreated I/R rats in a dose of 200 mg/kg/day for three weeks before ischemia induction.

  • Nitric oxide (NO),
  • tumor necrosis factor alpha (TNF α) ,
  • catalase (CAT) and
  • reduced glutathione (GSH) activities

were determined in renal tissue, while

  • creatinine clearance (CrCl) ,
  • blood urea nitrogen (BUN) were measured and

5 hour urinary volume and electrolytes were estimated . BUN and CrCl levels in the I/R group were significantly higher than in control rats (p<0.05) table (1).


Table 1: Creatinine clearance (Cr Cl) and blood urea nitrogen (BUN) levels in control and test groups.
(Mean ± SD)

Groups CrCl   (ml/min) BUN (mg/dl)
Control group 1.30 ±0.11 14.30±0.25
Sham group+ metformin 1.27±0.09 15.70±0.19
I/R group (P1) 1.85±0.25 (<0.001 ) 28.00±0.62 (<0.001)
I/R+ metformin group (P2,P3) 1.55±0.22 (0.001, 0.028) 18.10±1.00 (<0.001, <0.001)
  • P1: Statistical significance between control
    group and saline treated I/R group.
  • P2 Statistical significance between control
    group and Metformin treated I/R group.
  • P3 Statistical significance between saline treated
    I/R group and Metformin treated I/R group


When metformin was administered before I/R, BUN and CrCl levels were still significantly higher than control group but their elevation were significantly lower in comparison to I/R group alone (P<0.05).   TNF α and NO levels were significantly higher in the I/R group than those of the control group (Table 2). Pre-treatment with metformin significantly lowered their levels in comparison to I/R group (P<0.05).


Table 2: Tumor necrosis factor α (TNF α) and inducible nitric oxide (iNO) levels in control and test groups.
(Mean ± SD)

Groups TNF α (pmol/mg tissue) iNO (nmol/ mg tissue)
Control group 1 7.60 ±5.98 2.54 ± 0.82
Sham group+ metformin 16.70 ±5.50 2.35 ±0.80
I/R group (P1) 54. 00±6.02 (<0.001) 4.50±0.89 (<0.001)
I/R+metformin group (P2,P3) 39 ± 14.01 (<0.001, 0.006) 3.53±0.95 (0.02, 0.03)


  • P1: Statistical significance between control group
    and saline treated I/R group.
  • P2 Statistical significance between control group
    and Metformin treated I/R group.
  • P3 Statistical significance between saline treated
    I/R group and Metformin treated I/R group


These results showed significant increase in NO,TNF α, BUN , CrCl and significant decrease in urinary volume , electrolytes, CAT and GSH activities in the I/R group than those in the control group. Metformin decreased significantly NO, TNF α, BUN and CrCl while increased urinary volume, electrolytes, CAT and GSH activities.   Lipid peroxidation is related to I/R induced tissue injury. Production of inducible NO synthase (NOS) under lipid peroxidation and inflammatory conditions results in the induction of NO which react with O2 liberating peroxynitrite (OONO-). NO itself inactivates the antioxidant enzyme system CAT and GSH. Alteration in NO synthesis have been observed in other kidney injuries as nephrotoxicity and acute renal failure induced by endotoxins.

Treatment with iNOS inhibitors improved renal function and decreased peroxynitrite radical which is believed to be responsible for the shedding of proximal convoluted tubules in I/R.   Metformin produced anti-inflammatory renoprotective effect on CrCl and diuresis in renal I/R injury.

Malek HA. The possible mechanism of action of metformin in renal ischemia reperfusion in rats. The Pharma Research Journal 2011; 6(1):42-49.

Possible role of NO donors in ARFThe L-arginine-nitric oxide (NO) pathway has been implicated in many physiological functions in the kidney, including

  • regulation of glomerular hemodynamics,
  • mediation of pressure-natriuresis,
  • maintenance of medullary perfusion,
  • blunting of tubuloglomerular feedback (TGF),
  • inhibition of tubular sodium reabsorption and
  • modulation of renal sympathetic nerve activity

Its net effect in the kidney is to promote natriuresis and diuresis, contributing to adaptation to variations of dietary salt intake and maintenance of normal blood pressure. Nitric oxide has been implicated in many physiologic processes that influence both acute and long-term control of kidney function. Its net effect in the kidney is to promote natriuresis and diuresis, contributing to adaptation to variations of dietary salt intake and maintenance of normal blood pressure. A pretreatment with nitric oxide donors or L-arginine may prevent the ischemic acute renal injury. In chronic kidney diseases, the systolic blood pressure is correlated with the plasma level of asymmetric dimethylarginine, an endogenous inhibitor of nitric oxide synthase. A reduced production and biological action of nitric oxide is associated with an elevation of arterial pressure, and conversely, an exaggerated activity may represent a compensatory mechanism to mitigate the hypertension.

JongUn Lee. Nitric Oxide in the Kidney : Its Physiological Role and Pathophysiological Implications. Electrolyte & Blood Pressure 2008; 6:27-34.

Renal Hypoxia and Dysoxia following Reperfusion

Acute renal failure (ARF) is a common condition which develops in 5% of hospitalized patients. Of the patients who develop ARF, ~10% eventually require renal replacement therapy. Among critical care patients who have acute renal failure and survive, 2%-10% develop terminal renal failure and require long-term dialysis.   The kidneys are particularly susceptible to ischemic injury in many clinical conditions such as renal transplantation, treatment of suprarenal aneurysms, renal artery reconstructions, contrast-agent induced nephropathy, cardiac arrest, and shock. One reason for renal sensitivity to ischemia is that the kidney microvasculature is highly complex and must meet a high energy demand.

Under normal, steady state conditions, the oxygen (O2) supply to the renal tissues is well in excess of oxygen demand.   Under pathological conditions, the delicate balance of oxygen supply versus demand is easily disturbed due to the unique arrangement of the renal microvasculature and its increasing numbers of diffusive shunting pathways.  

The renal microvasculature is serially organized, with almost all descending vasa recta emerging from the efferent arterioles of the juxtamedullary glomeruli. Adequate tissue oxygenation is thus partially dependent on the maintenance of medullary perfusion by adequate cortical perfusion. This, combined with the low amount of medullary blood flow (~10% of total renal blood flow) in the U-shaped microvasculature of the medulla allows O2 shunting between the descending and ascending vasa recta and contributes to the high sensitivity of the medulla and cortico-medullary junction to decreased O2 supply.

Whereas past investigations have focused mainly on tubular injury as the main cause of ischemia-related acute renal failure, increasing evidence implicates alterations in the intra-renal microcirculation pathway and in the O2 handling. Indeed, although acute tubular necrosis (ATN) has classically been believed to be the leading cause of ARF, data from biopsies in patients with ATN have shown few or no changes consistent with tubular necrosis.

The role played by microvascular dysfunction, however, has generated increasing interest. The complex pathophysiology of ischemic ARF includes the inevitable

  • reperfusion phase associated with oxidative stress,
  • cellular dysfunction and
  • altered signal transduction.

During this process, alterations in oxygen transport pathways can result in cellular hypoxia and/or dysoxia. In this context, the distinction between hypoxia and dysoxiais that

  • cellular hypoxia refers to the condition of decreased availability of oxygen due to inadequate convective delivery from the microcirculation.
  • Cellular dysoxia, in contrast, refers to a pathological condition where the ability of mitochondria to perform oxidative phosphorylation is limited, regardless of the amount of available oxygen.


The latter condition is associated with mitochondrial failure and/or activation of alternative pathways for oxygen consumption. Thus, we would expect that an optimal balance between oxygen supply and demand is essential to reducing damage from renal ischemia-reperfusion (I/R) injury. Complex interactions exist between

  • tubular injury,
  • microvascular injury, and
  • inflammation after renal I/R.

On the one hand, insults to the tubule cells promotes the liberation of a number of inflammatory mediators, such as TNF-á, IL-6, TGF-â, and chemotactic cytokines(RANTES, monocyte chemotactic protein-1, ENA-78, Gro-á, and IL-8). On the other hand, chemokine production can promote

  • leukocyte-endothelium interactions and
  • leukocyte activation,

resulting in…..

  • renal blood flow impairment and
  • the expansion of tubular damage
  • impaired renal hemodynamics and
  • electrolyte reabsorption

Adequate medullary tissue oxygenation, in terms of balanced oxygen supply and demand, is dependent on the maintenance of medullary perfusion by adequate cortical perfusion and also on the high rate of O2 consumption required for active electrolyte transport. Furthermore, renal blood flow is closely associated with renal sodium transport, mitochondrial activity and NO-mediated O2 consumption In addition to having a limited O2 supply due to the anatomy of the microcirculation anatomy, the sensitivity of the medulla to hypoxic conditions results from this high O2 consumption.

Renal sodium transport is the main O2-consuming function of the kidney and is closely linked to renal blood flow for sodium transport, particularly in the thick ascending limbs of the loop of Henle and the S3 segments of the proximal tubules. Medullary renal blood flow is also highly dependent on cortical perfusion, with almost all descending vasa recta emerging from the efferent arteriole of juxta medullary glomeruli. A profound reduction in cortical perfusion can disrupt medullary blood flow and lead to an imbalance between O2 supply and O2 consumption. On theother hand, inhibition of tubular reabsorption by diuretics increases medullary pO2 by decreasing the activity of Na+/K+-ATPases and local O2 consumption.

Mitochondrial activity and NO-mediated O2 consumption

The medulla has been found to be the main site of production of NO in the kidney. In addition to the actions described above, NO appears to be a key regulator of renal tubule cell metabolism by inhibiting the activity of the Na+-K+-2Cl- cotransporter and reducing Na+/H+ exchange. Since superoxide (O2-) is required to inhibit solute transport activity, it was assumed that these effects were mediated by peroxynitrite (OONO-). Indeed, mitochondrial nNOS upregulation, together with an increase in NO production, has been shown to increase mitochondrial peroxynitrite generation, which in turn, can induce cytochrome c release and promote apoptosis. NO has also been shown to directly compete with O2 at the mitochondrial level. These findings support the idea that NO acts as an endogenous regulator to match O2 supply to O2 consumption, especially in the renal medulla.   NO reversibly binds to the O2 binding site of cytochrome oxidase, and acts as a potent, rapidMitochondrial activity and NO-mediated O2 consumption, and reversible inhibitor of cytochrome oxidase in competition with molecular O2. This inhibition could be dependent on the O2 level, since the IC50 (the concentration of NO that reduces the specified response by half) decreases with reduction in O2 concentration. The inhibition of electron flux at the cytochrome oxidase level switches the electron transport chain to a reduced state, and consequently leads to depolarization of the mitochondrial membrane potential and electron leakage.

To summarize, while the NO/O2 ratio can act as a regulator of cellular O2 consumption by matching decreases in O2 delivery to decreases in cellular O2 cellular, the inhibitory effect of NO on mitochondrial respiration under hypoxic conditions further impairs cellular aerobic metabolism. This leads to a state of “cytopathic hypoxia,” as described in the sepsis literature.   Only cell-secreted NO competes with O2 and to regulate mitochondrial respiration. In addition to the 3 isoforms (eNOS, iNOS, cnNOS), an α-isoform of neuronal NOS, the mitochondrial isoform (mNOS) located in the inner mitochondrial membrane, has also been shown to regulate mitochondrial respiration. These data support a role for NO in the balanced regulation of renal O2 supply and O2 consumption after renal I/R However, the relationships between the determinants of O2 supply, O2 consumption, and renal function, and their relation to renal damage remain largely unknown.

Sustained endothelial activation Ischemic renal failure leads to persistent endothelial activation, mainly in the form of endothelium-leukocyte interactions and the activation of adhesion molecules. This persistent activation can compromise renal blood flow, prevent the recovery of adequate tissue oxygenation, and jeopardize tubular cell survival despite the initial recovery of renal tubular function. A 30-50% reduction in microvascular density was seen 40 weeks after renal ischemic injury in a rat model. Vascular rarefaction has been proposed to induce chronic hypoxia resulting in tubulointerstitial fibrosis via the molecular activation of fibrogenic factors such as transforming growth factor (TGF)-β, collagen, and fibronectin, all of which may play an important role in the progression of chronic renal disease.

Adaptation to hypoxia Over the last decade, the role of hypoxia-inducible factors (HIFs) in O2 supply and adaptation to hypoxic conditions has found increasing support. HIFs are O2-sensitive transcription factors involved in O2-dependent gene regulation that mediate cellular adaptation to O2 deprivation and tissue protection under hypoxic conditions in the kidney.   NO generation can promote HIF-1α accumulation in a cGMP-independent manner. However, Hagen et al. (2003) showed that NO may reduce the activation of HIF in hypoxia via the inhibitory effect of NO on cytochrome oxidase.

Therefore, it seems that NO has pleiotropic effects on HIF expression, with various responses related to different pathways. HIF-1α upregulates a number of factors implicated in cytoprotection, including angiogenic growth factors, such as vascular endothelial growth factors (VEGF), endothelial progenitor cell recruitment via the endothelial expression of SDF-1, heme-oxygenase-1 (HO-1), and erythropoietin (EPO), and vasomotor regulation.

HO-1 produces carbon monoxide (a potent vasodilator) while degrading heme, which may preserve tissue blood flow during reperfusion. Thus, it has been suggested that the induction of HO-1 can protect the kidney from ischemic damage by decreasing oxidative damage and NO generation.

Finally, in addition to its anti-apoptotic properties, EPO may protect the kidney from ischemic damage by restoring the renal microcirculation by stimulating the mobilization and differentiation of progenitor cells toward an endothelial phenotype and by inducing NO release from eNOS.

Pharmacological interventions

Use of pharmacological interventions which act at the microcirculatory level may be a successful strategy to overcome ischemia-induced vascular damage and prevent ARF. Activated protein C (APC), an endogenous vitamin K-dependent serine protease with multiple biological activities, may meet these criteria. Along with antithrombotic and profibrinolytic properties, APC can reduce the chemotaxis and interactions of leukocytes with activated endothelium.

However, renal dysfunction was not improved in the largest study published so far. In addition, APC has been discontinued by Lilly for the use intended in severe sepsis. Moreover, neither drugs with renal vasodilatory effects (i.e., dopamine, fenoldopam, endothelin receptors blockers, adenosine antagonists) nor agents that decrease renal oxygen consumption (i.e., loop diuretics) have been shown to protect the kidney from ischemic damage. We have to bear in mind that a magic bullet to treat the highly complex condition of which is renal I/R is not in sight.

We can expect that understanding the balance between O2 delivery and O2 consumption, as well as the function of O2-consuming pathways (i.e., mitochondrial function, reactive oxygen species generation) will be central to this treatment strategy.

Take home point

The deleterious effects of NO are thought to be associated with the NO generated by the induction of iNOS and its contribution to oxidative stress both resulting in vascular dysfunction and tissue damage. Ischemic injury also leads to structural damage to the endothelium and leukocyte infiltration. Consequently, renal tissue hypoxia is proposed to promote the initial tubular damage, leading to acute organ dysfunction.   Comment: I express great appreciation for refeering to this work, which does provide enormous new insights into hypoxia-induced acute renal failure, and ties together the anatomy, physiology, and gene regulation through signaling pathways.

Ince C, Legrand M, Mik E , Johannes T, Payen D. Renal Hypoxia and Dysoxia following Reperfusion of the Ischemic Kidney. Molecular Medicine (Proof) 2008; pp36.

Nitric oxide and non-hemodynamic functions of the kidney

One of the major scientific advances in the past decade in understanding of the renal function and disease is the prolific growth of literature incriminating nitric oxide (NO) in renal physiology and pathophysiology. NO was first shown to be identical with endothelial derived relaxing factor (EDRF) in 1987 and this was followed by a rapid flurry of information defining the significance of NO in not only vascular physiology and hemodynamics but also in neurotransmission, inflammation and immune defense systems. Although most actions of NO are mediated by cyclic guanosine monophosphate (cGMP) signaling, S-nitrosylation of cysteine residues in target proteins constitutes another well defined non-cGMP dependent mechanism of NO effects. Recent years have witnessed a phenomenal scientific interest in the vascular biology, particularly the relevance of nitric oxide (NO) in cardiovascular and renal physiology and pathophysiology. Although hemodynamic actions of NO received initial attention, a variety of non-hemodynamic actions are now known to be mediated by NO in the normal kidney, which include

  • tubular transport of electrolyte and water,
  • maintenance of acid-base homeostasis,
  • modulation of glomerular and interstitial functions,
  • renin-angiotensin activation and
  • regulation of immune defense mechanism in the kidney.


Table 1 : Functions of NO in the kidney

  • 1. Renal macrovascular and microvascular dilatation (afferent > efferent)
  • 2. Regulation of mitochondrial respiration.
  • 3. Modulation renal medullary blood flow
  • 4. Stimulation of fluid, sodium and HCO3 – reabsorption in the proximal tubule
  • 5. Stimulation of renal acidification in proximal tubule by stimulation of NHE activity
  • 6. Inhibition of Na+, Cl- and HCO3 – reabsorption in the mTALH
  • 7. Inhibition of Na+ conductance in the CCD
  • 8. Inhibition of H+-ATPase in CCD


One of the renal regulatory mechanisms related to maintenance of arterial blood pressure involves the phenomenon of pressure-natriuresis in response to elevation of arterial pressure. This effect implies inhibition of tubular sodium reabsorption resulting in natriuresis, in an effort to lower arterial pressure. Experimental evidence from indicates that intra-renal NO modulates pressure natriuresis.

Furthermore many studies have confirmed the role of intra renal NO in mediating tubulo-glomerular feedback (TGF). In vivo micropuncture studies have shown that NO derived from nNOS in macula densa specifically inhibits the TGF responses leading to renal afferent arteriolar vasoconstriction in response to sodium reabsorption in the distal tubule. Other recent studies support the inhibitory role of NO from eNOS and iNOS in mTALH segment on TGF effects.

Recent observations in vascular biology have yielded new information that endothelial dysfunction early in the course might contribute to the pathophysiology of acute renal failure.  Structural and functional changes in the vascular endothelium are demonstrable in early ischemic renal failure. Altered NO production and /or decreased bioavailability of NO comprise the endothelial function in acute renal failure.

Several studies have indicated imbalance of NOS activity with enhanced expression and activity of iNOS and decreased eNOS in ischemic kidneys.

The imbalance results from enhanced iNOS activity and attenuated eNOS activity in the kidney.  

Many experimental studies support a contributory role for NO in glomerulonephritis (GN). Evidence from recent studies pointed out that NO may be involved in peroxynitrite formation, pro-inflammatory chemokines and signaling pathways in addition to direct glomerular effects that promote albumin permeability in GN. Although originally macrophages and other leukocytes were first considered as the source renal NO production in GN, it is now clear iNOS derived NO from glomerular mesangial cells are the primary source of NO in GN.

In most pathological states, the role of NO is dependent by the stage of the disease, the nitric oxide synthase (NOS) isoform involved and the presence or absence of other modifying intrarenal factors. Additionally NO may have a dual role in several disease states of the kidney such as acute renal failure, inflammatory nephritides, diabetic nephropathy and transplant rejection.

A rapidly growing body of evidence supports a critical role for NO in tubulointerstitial nephritis (TIN). In the rat model of autoimmune TIN, Gabbai et al. demonstrated increased iNOS expression in the kidney and NO metabolites in urine and plasma. However the effects of iNOS on renal damage in TIN seem to have a biphasic effect- since iNOS specific inhibitors (eg. L-Nil) are renoprotective in the acute phase while they actually accelerated the renal damage in the chronic phase.

Thus chronic NOS inhibition is used to induce chronic tubulointerstitial injury and fibrosis along with mild glomerulosclerosis and hypertension.

Major pathways of L-arginine metabolism.

L-arginine may be metabolized by the urea cycle enzyme arginase to L-ornithine and urea by arginine decarboxylase to agmatine and CO2 or by NOS to nitric oxide (NO) and L-citrulline.

Adapted from Klahr S: Can L-arginine manipulation reduce renal disease? Semin Nephrol 1999; 61:304-309.

It is obvious that kidney is not only a major source of arginine and nitric oxide but NO plays an important role in the water and electrolyte balance and acid-base physiology and many other homeostatic functions in the kidney. Unfortunately we are far from a precise understanding of the significance of NO alterations in various disease states primarily due to conflicting data from the existing literature.

Therapeutic potential for manipulation of L-arginine- nitric oxide axis in renal disease states has been discussed. More studies are required to elucidate the abnormalities in NO metabolism in renal diseases and to confirm the therapeutic potential of L-arginine.

Sharma SP. Nitric oxide and the kidney. Indian J Nephrol 2004;14: 77-84

Inhibition of Constitutive Nitric Oxide Synthase

Excess NO generation plays a major role in the hypotension and systemic vasodilatation characteristic of sepsis. Yet the kidney response to sepsis is characterized by vasoconstriction resulting in renal dysfunction. We have examined the roles of inducible nitric oxide synthase (iNOS) and endothelial NOS (eNOS) on the renal effects of lipopolysaccharide administration by comparing the effects of specific iNOS inhibition, L-N6-(1-iminoethyl)lysine (L-NIL), and 2,4-diamino-6-hydroxy-pyrimidine vs. nonspecific NOS inhibitors (nitro-L-arginine-methylester). cGMP responses to carbamylcholine (CCh) (stimulated, basal) and sodium nitroprusside in isolated glomeruli were used as indices of eNOS and guanylate cyclase (GC) activity, respectively. LPS significantly decreased blood pressure and GFR (P =0.05) and inhibited the cGMP response to CCh.

GC activity was reciprocally increased. L-NIL and 2,4-diamino-6-hydroxy-pyrimidine administration prevented the decrease in GFR, restored the normal response to CCh, and GC activity was normalized. In vitro application of L-NIL also restored CCh responses in LPS glomeruli. Neuronal NOS inhibitors verified that CCh responses reflected eNOS activity.

L-NAME, a nonspecific inhibitor, worsened GFR, a reduction that was functional and not related to glomerular thrombosis, and eliminated the CCh response. No differences were observed in eNOS mRNA expression among the experimental groups. Selective iNOS inhibition prevents reductions in GFR, whereas nonselective inhibition of NOS further decreases GFR.

These findings suggest that the decrease in GFR after LPS is due to local inhibition of eNOS by iNOS, possibly via NO autoinhibition.

Schwartz D, Mendonca M, Schwartz I, Xia Y, et al. Inhibition of Constitutive Nitric Oxide Synthase (NOS) by Nitric Oxide Generated by Inducible NOS after Lipopolysaccharide Administration Provokes Renal Dysfunction in Rats. J. Clin. Invest. 1997; 100:439–448.

Salt-Sensitivity and Hypertension Renin-angiotensin system (RAS) plays a key role in the regulation of renal function, volume of extracellular fluid and blood pressure. The activation of RAS also induces oxidative stress, particularly superoxide anion (O2-) formation.

Although the involvement of O2 – production in the pathology of many diseases is known for long, recent studies also strongly suggest its physiological regulatory function of many organs including the kidney. However, a marked accumulation of O2- in the kidney alters normal regulation of renal function and may contribute to the development of salt-sensitivity and hypertension.

In the kidney, O2- acts as vasoconstrictor and enhances tubular sodium reabsoption. Nitric oxide (NO), another important radical that exhibits opposite effects than O2 -, is also involved in the regulation of kidney function. O2- rapidly interacts with NO and thus, when O2- production increases, it diminishes the bioavailability of NO leading to the impairment of organ function. As the activation of RAS, particularly the enhanced production of angiotensin II, can induce both O2- and NO generation, it has been suggested that physiological interactions of

  • RAS,
  • NO and
  • O2-

provide a coordinated regulation of kidney function.   The imbalance of these interactions is critically linked to the pathophysiology of salt-sensitivity and hypertension.

Kopkan L, Červenka L. Renal Interactions of Renin-Angiotensin System, Nitric Oxide and Superoxide Anion: Implications in the Pathophysiology of Salt-Sensitivity and Hypertension. Physiol. Res. 2009; 58 (Suppl. 2): S55-S67.


In this review I attempted to evaluate complex and still incomplete and conflicting conclusions from many studies. I thus broke the report into three major portions:


  • 1 The kidney and its anatomy, physiology, and ontogeny.
  • 2 The pathological disease variation affecting the kidney
  • a: a tie in to eNON and iNos, nitric oxide, cGMP and glutaminase – in acute renal failure, hypertension, chronic renal failure, dialysis the pathology of acute tubular necrosis, glomerular function, efferent arteriolar and kidney medullary circulatory impairment, and cast formation related to Tamm Horsfall protein
  • b :The role of NO, eNOS and iNOS in disorders of the lund alveolar cell and subendothelial matrix, and of liver disease also affecting the kidney, and the heart. c Additional references
  • 3.     a Acute renal failure, oxidate stress, ischemia-reperfusion injury, tubulointerstitial chronic inflammation
  • 3       b Additional references 4. Nitric oxide donors – opportunities for therapeutic targeting? As we see this in as full a context as possible, it is hard to distinguish the cart from the horse.


We know that there is an unquestionable role of NO, and a competing balance to be achieved between eNOS, iNOS, an effect on tubular water and ion-cation reabsorptrion, a role of TNFa, and consequently an important role in essential/malignant hypertension, with the size of the effect related to the stage of disorder, the amount of interstitial fibrosis, the remaining nephron population, the hypertonicity of the medulla, the vasodilation of the medullary circulation, and the renin-angiotensin-aldosterone system. Substantial data and multiple patients with many factors per patient would be need to extract the best model using a supercomputer.

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Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Original description - :Cartoon representation...

Original description – :Cartoon representation of ubiquitin protein, highlighting the secondary structure. α-helices are coloured in blue and the β-sheet in green. The normal attachment point for a further ubiquitin molecule in polyubiquitin chain formation, lysine 48, is shown in pink. :Image was created using PyMOL (Photo credit: Wikipedia)

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Larry H Bernstein, MD, FACP, Curator, Reporter, AEW

The work reviewed follows a seminal contribution by two Israeli and an American molecular biologists who shared the Nobel Prize in Chemistry in 2004.

The Royal Swedish Academy of Sciences awarded the Nobel Prize in Chemistry for 2004 “for the discovery of ubiquitin-mediated protein degradation” jointly to Aaron Ciechanover Technion – Israel Institute of Technology, Haifa, Israel, Avram Hershko Technion – Israel Institute of Technology, Haifa, Israel and Irwin Rose – University of California, Irvine, USA.

Aaron Ciechanover, born 1947 (57 years) in Haifa, Israel (Israeli citizen) received a Doctor’s degree in medicine in 1975 at Hebrew University of Jerusalem, and in biology in 1982 at the Technion (Israel Institute of Technology), Haifa. He is a Distinguished Professor at the Center for Cancer and Vascular Biology, and the Rappaport Faculty of Medicine and Research Institute at the Technion, Haifa,

Avram Hershko, born 1937 (67 years) in Karcag, Hungary (Israeli citizen) earned the Doctor’s degree in medicine in 1969 at the Hadassah and the Hebrew University Medical School, Jerusalem.  He is a Distinguished Professor at the Rappaport Family Institute for Research in Medical Sciences at the Technion (Israel Institute of Technology), Haifa, Israel.

Irwin Rose, born 1926 (78 years) in New York, USA (American citizen) achieved a Doctor’s degree in 1952 at the University of Chicago, USA. Specialist at the Department of Physiology and Biophysics, College of Medicine, University of California, Irvine, USA.

Proteins labelled for destruction
Proteins build up all living things: plants, animals and therefore us humans. In the past few decades biochemistry has come a long way towards explaining how the cell produces all its various proteins. But as to the breaking down of proteins, not so many researchers were interested. Aaron Ciechanover, Avram Hershko and Irwin Rose went against the stream and at the beginning of the 1980s discovered one of the cell’s most important cyclical processes, regulated protein degradation. For this, they are being rewarded
with the 2004 Nobel Prize in Chemistry.

The label consists of a molecule called ubiquitin. This fastens to the protein to be destroyed, accompanies it to the proteasome where it is recognised as the key in a lock, and signals that a protein is on the way for disassembly. Shortly before the protein is squeezed into the proteasome, its ubiquitin label is disconnected for re-use.

Aaron Ciechanover, Avram Hershko and Irwin Rose have brought us to realise that the cell functions as a highly-efficient checking station where proteins are built up and broken down at a furious rate. The degradation is not indiscriminate but takes place through a process that is controlled in detail so that the proteins to be broken down at any given moment are given a molecular label, a ‘kiss of death’, to be dramatic. The labelled proteins are then fed into the cells’ “waste disposers”, the so called proteasomes, where they are chopped into small pieces and destroyed.

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Thanks to the work of the three Laureates it is now possible to understand at  molecular level how the cell controls a number of central processes by breaking down certain proteins and not others. Examples of processes governed by ubiquitin-mediated protein degradation are cell division, DNA repair, quality control of newly-produced proteins, and important parts of the immune defence. When the degradation does not work correctly, we fall ill. Cervical cancer and cystic fibrosis are two examples. Knowledge of
ubiquitin-mediated protein degradation offers an opportunity to develop drugs against these diseases and others.

Aaron Ciechanover and Ronen Ben-Saadon. N-terminal ubiquitination: more protein substrates join in. TRENDS in Cell Biology 2004; 14 (3):103-106.

The ubiquitin–proteasome system (UPS) is involved in selective targeting of innumerable cellular proteins through a complex pathway that plays important roles in a broad array of processes. An important step in the proteolytic cascade is specific recognition of the substrate by one of many ubiquitin ligases, E3s, which is followed by generation of the polyubiquitin degradation signal. For most substrates, it is believed that the first ubiquitin moiety is conjugated, through its C-terminal Gly76 residue, to an 1-NH2 group of an internal Lys residue. Recent findings indicate that, for several proteins, the first ubiquitin moiety is fused linearly to the a-NH2 group of the N-terminal residue.

The ubiquitin–proteasome system (UPS). Ubiquitin is first activated to a high-energy intermediate by E1. It is then transferred to a member of the E2 family of enzymes. From E2 it can be transferred directly to the substrate (S, red) that is bound specifically to a member of the ubiquitin ligase family of proteins, E3

  • (a). This occurs when the E3 belongs to the RING finger family of ligases. In the case of a HECT-domain-containing ligase
  • (b), the activated ubiquitin is transferred first to the E3 before it is conjugated to the E3-bound substrate . Additional ubiquitin moieties are added successively to the previously conjugated moiety to generate a polyubiquitin chain.
  • The polyubiquitinated substrate binds to the 26S proteasome complex (comprising 19S and 20S sub-complexes): the substrate is degraded to short peptides, and free and reusable ubiquitin is released through the activity of de-ubiquitinating enzymes (DUBs).

Ubiquitination on an internal lysine and on the N-terminal residue of the target substrate.

  • (a) The first ubiquitin moiety is conjugated, through its C-terminal Gly76 residue, to the 1-NH2 group of an internal lysine residue of the target substrate (Kn).
  • (b) The first ubiquitin moiety is conjugated to a free a-NH2 group of the N-terminal residue, X.
  • In both cases, successive addition of activated ubiquitin moieties to internal Lys48 on the previously conjugated ubiquitin moiety leads to the synthesis of a  polyubiquitin chain that serves as the degradation signal for the 26S proteasome


A UPS Autophagy Review

Summary: This discussion is another in a series discussing mitochondrial metabolism, energetics and regulatory function, and dysfunction, and the process leading to apoptosis and a larger effect on disease, with a specific targeting of neurodegeneration. Why neurological and muscle damage are more sensitive than other organs is not explained easily, but recall in the article on mitochondrial oxidation-reduction reactions and repair that there are organ specific differences in the rates of organelle mutation errors and in the rates of repair. In addition, consider the effect of iron-binding in the function of the cell, and Ca2+ binding in the creation of the mechanic work or signal transmission carried out by the neuromuscular system. We target the previously mentioned role of ubiquitin-proteosome, and interaction with autophagy, mitophagy, and disease.

Keywords: autophagy, ubiquitin-proteosome, UPS, protein degradation, defective organelle removal, selective degradation, E3, neurodegenerative disease, mitochondria, mitophagy, proteolysis, ribosomes, apoptosis, Ca++, rapamycin, TORC1, atg1p kinase, ubiqitization, trafficking pathways, unfolded protein response (UPS), p52/sequestrome, IC3, nitrogen starvation, acetaldehyde dehydrogenase (Ald6p), Ut1hp, toxisomes, Pex3/14 proteins, Bax, E3 Ligase, TRAP1, TNF-a, NFkB.

Ubiquitin-Proteosome Pathway
Three recent papers, describing three apparently independent biological processes, highlight the role of the ubiquitin-proteasome system as a major, however selective, proteolytic and regulatory pathway. Using specific inhibitors to the proteasome, Rock et al. (1994) demonstrate a role for this protease in the degradation of the major bulk of cellular proteins. They also showed that antigen processing requires the ubiquitin-activating enzyme, El. This indicates that antigen processing is both ubiquitin dependent and proteasome dependent. Furthermore, inhibitors to the proteasome prevent tumor necrosis factor a (TNFa)-induced activation of mature NFKB and its entry into the nucleus. The two studies clearly demonstrate that the ubiquitin-proteasome system is involved not only in complete destruction of its protein substrates, but also in limited proteolysis and posttranslational processing in which biologically active peptides or fragments are generated. In addition, the unstable c-Jut but not the stable v-Jun, is multiubiquitinated and degraded. The escape of the oncogenic v-Jun from ubiquitin-dependent degradation suggests a novel route to malignant transformation. Presented here is a review of the components, mechanisms of action, and cellular physiology of the ubiquitin-proteasome pathway.

Experimental evidence implicates the ubiquitin system in the degradation of

  • mitotic cyclins,
  • oncoproteins,
  • the tumor suppressor protein p53,
  • several cell surface receptors,
  • transcriptional regulators, and
  • mutated and damaged proteins.

Some of the proteolytic processes occur throughout the cell cycle, whereas others are tightly programmed and occur following cell cycle-dependent posttranslational modifications of the components involved. Signaling and degradation of other proteins (cell surface receptors, for example) may occur only following structural changes or modification(s) in the target molecule that results from ligand binding. Cell cycle-and modification-dependent degradation, as well the ability of the system to destroy completely or only partially its protein substrates, reflects the complexity involved in regulated intracellular protein degradation.

Enzymes of the System
The reaction occurs in two distinct steps:

  1. signaling of the protein by covalent attachment of multiple ubiquitin molecules and
  2. degradation of the targeted protein with the release of free and reutilizable ubiquitin.

Conjugation of ubiquitin to proteins destined for degradation proceeds, in general, in a three-step mechanism.

  1. Initially, the C-terminal Gly of ubiquitin is activated by ATP to a high energy thiol ester intermediate in a reaction catalyzed by the ubiquitin-activating enzyme, El.
  2. Following activation, E2 (ubiquitin carrier protein or ubiquitin-conjugating enzyme [USC]) transfers ubiquitin from El to the substrate that is bound to a ubiquitin-protein ligase, E3.
  3. Here an isopeptide bond is formed between the activated C-terminal Gly of ubiquitin and an c-NH2 group of a Lys residue of the substrate.

As E3 enzymes specifically synthesized by processive transfer of ubiquitin moieties to Lys-48 of the previous (and already conjugated) ubiquitin molecule. In many cases, E2 transfers activated ubiquitin directly to the protein substrate. Thus, E2 enzymes also play an important role in substrate recognition, although, in most cases, this modification is of the monoubiquitin type.

The Ubiquitin-Mediated Proteolytic Pathway
(1) Activation of ubiquitin by El and E2.
(2) Binding of the protein substrate to E3.
(3) EP dependent but EM independent monoubiquitination.
(4) EP-dependent but EM independent polyubiquitination?
(5) Ed-dependent polyubiquitination.
(6) Degradation of ubiquitin-protein conjugate by the 26s protease.
(7) “Correction” function of C-terminal hydrolase(s).
(6) Release of ubiquitin from terminal proteolytic products by &terminal hydrolase(s).

It is essential for the system that ubiquitin recycles. This function is carried out by ubiquitin C-terminal hydrolases (isopeptidases). In protein degradation, hydrolase(s) is required to release ubiquitin from isopeptide linkage with Lys residues of the protein substrate at the final stage of the proteolytic process. A ubiquitin C-terminal hydrolytic activity is also required to disassemble polyubiquitin chains linked to the protein substrate, following or during the degradative process. A “proofreading” function has been proposed for hydrolases to release free protein from “incorrectly” ubiquitinated proteins. Another possibility is that ubiquitin C-terminal hydrolases are required for trimming polyubitin chains.

Hydrolases are probably required for the processing of biosynthetic precursors of ubiquitin, since most ubiquitin genes are arranged either in linear polyubiquitin arrays or are fused to ribosomal proteins. Yet another hydrolase may be required for the removal of extra amino acid residues that are encoded by certain genes at the C-termini of some polyubiquitin molecules. Ubiquitin C-terminal hydrolases may have other functions as well. High energy El-ubiquitin and E2-ubiquitin thiol esters may react with intracellular nucleophiles (such as glutathione or polyamines). Such reactions may lead to rapid depletion of free ubiquitin unless such side products are rapidly cleaved.

Recognition of Substrates
Short-lived proteins contain a region enriched with Pro, Glu, Ser, and Thr (PEST region). However, it has not been shown that this region indeed serves as a consensus proteolysis targeting signal. An interesting problem involves the evolution of the N-end rule pathway and its physiological roles. Proteins that are derived from processing of polyproteins (Sindbis virus RNA polymerase, for example) may contain destabilizing N-termini and thus are proteolyzed via the N-end rule pathway.

Using a “synthetic lethal” screen, Ota and Varshavsky attempted to isolate a mutant that requires the N-end rule pathway for viability. They characterized an extragenic suppressor of the mutation and found that it encodes a protein with a strong correlation to protein phosphotyrosine phosphatase. The target protein or the connection between dephosphorylation of phosphotyrosine and the N-end rule pathway is still obscure. In an additional study, these researchers have shown that a missense mutation in SLNI, a member of a two-component signal transduction system in yeast, is lethal in the absence, but not in the presence, of the N-end rule pathway. Further studies are required to isolate the target protein and identify the signal transduction pathway.

Two recent studies have shed light on the role of the ubiquitin system and the proteasome in the process. Michalek et al. (1993) have shown that a mutant cell that harbors a thermolabile El cannot present peptides derived from ovalbumin following inactivation of the enzyme. In contrast, presentation of a minigene-expressed antigene peptide or presentation of exogenous similar peptide was not perturbed at the nonpermissive temperature. The important conclusion of the researchers is that the processing of the protein to peptides requires the complete ubiquitin pathway. In a complementary study, Rock et al. (1994) have shown that inhibitors that block the chymotryptic activity of the proteasome also block antigen presentation, most probably by inhibiting proteolysis of the antigen (ovalbumin). Thus, it appears that processing of MHC restricted class I antigens requires both ubiquitination and subsequent degradation by the proteasome. It is likely that the proteasome catalyzes processing of these antigens as part of the 26s protease complex.
Ciechanover A. The Ubiquitin-Proteasome Proteolytic Pathway. Cell 1994; 79:13-21.
Regulation of autophagy
The protein content of the cell is determined by the balance between protein synthesis and protein degradation. At constant intracellular protein concentration, i.e. at steady state, rates of protein synthesis and degradation are equal. Although turnover of protein results in energy dissipation, regulation at the level of protein degradation effectively controls protein levels.
Intracellular proteins to be degraded in the lysosomes can get access to these organelles by the following processes:

  • macroautophagy,
  • microautophagy,
  • crinophagy and selective,
  • chaperonin mediated, direct uptake of proteins.

Overview of the involvement of signal transduction in the regulation of macroautophagic proteolysis by amino acids and cell swelling.

  1. Amino acids (AA) stimulate a protein kinase cascade via a plasma membrane receptor.
  2. Receptor activation results in activation of PtdIns 3-kinase (PI3K), possibly via a heterotrimeric Gái3 protein.
  3. followed by activation of PKC-æ, PKB/Akt, p70S6 kinase (p70S6k) and finally phosphorylation of ribosomal protein S6 (S6P).
  4. The GDP-bound form of Gái3 is required for autophagic sequestration, whereas the GTP-bound form is inhibitory.
  5. The constitutively formed phosphatidylinositol 3-phosphate (PI3P) is also required for autophagic sequestration. Therefore,

inhibition of PtdIns 3-kinase activity by

  • wortmannin (W),
  • LY294002 (LY) or
  • 3-methyladenine (3MA) prevents autophagic sequestration.

Activation of PKC-æ and PKB/Akt is mediated by the 3,4- and 3,4,5-phosphate forms of phosphatidylinositol (PI3,4P2 and PI3,4,5P3) that are produced upon activation of PtdIns 3-kinase.

As a result of this, the first step of the macroautophagic pathway is

  • inhibited by components of the cascade that are downstream of PtdIns 3-kinase.
  • inhibition of this downstream cascade by rapamycin (RAPA) accelerates autophagic sequestration.
  • cell swelling potentiates the effect of amino acids via a change in the receptor owing to membrane stretch.

Furthermore, the site of action of the different effectors of the cytoskeleton (okadaic acid, cytochalasin, nocodazole, vinblastin and colchicine) are indicated.

  • AVi,
  • initial autophagic vacuole;
  • AVd,
  • mature degradative autophagic vacuole,
  • ER, endoplasmic reticulum.

The rate of proteolysis , an important determinant of the intracellular protein content, and part of its degradation occurs in the lysosomes and is mediated by macroautophagy. In liver, macroautophagy is very active and almost completely accounts for starvation-induced proteolysis. Factors inhibiting this process include

  • amino acids,
  • cell swelling and
  • insulin.

In the mechanisms controlling macroautophagy, protein phosphorylation plays an important role.

  • Activation of a signal transduction pathway, ultimately
  • leading to phosphorylation of ribosomal protein S6,
  • accompanies Inhibition of macroautophagy.

Components of this pathway may include

  • a heterotrimeric Gi3-protein,
  • phosphatidylinositol 3-kinase and
  • p70S6 kinase.

Selectivity of Autophagy
It has been assumed for a long time that macroautophagy is a non-selective process, in which macromolecules are randomly degraded in the same ratio as they occur in the cytoplasm . However, recent observations strongly suggest that this may not always be the case, and that macroautophagy can be selective. Lysosomal protein degradation can selectively occur via ubiquitin-dependent and -independent pathways. In the perfused liver, although autophagic breakdown of protein and RNA (mainly ribosomal RNA) is sensitive to inhibition by amino acids and insulin, glucagon accelerates proteolysis but has no effect on RNA degradation.

Another example of selective autophagy is the degradation of superfluous peroxisomes in hepatocytes from clofibrate-treated rats. When hepatocytes from these rats, in which the number of peroxisomes is greatly increased, are incubated in the absence of amino acids to ensure maximal flux through the macroautophagic pathway, peroxisomes are degraded at a relative rate that exceeds that of any other component in the liver cell. The accelerated degradation of peroxisomes was sensitive to inhibition by 3-methyladenine, a specific autophagic sequestration inhibitor. Interestingly, the accelerated removal of peroxisomes was prevented by long-chain but not short-chain fatty acids. Since long-chain fatty acids are substrates for peroxisomal â-oxidation, this indicates that these organelles are removed by autophagy when they are functionally redundant.  Our hypothesis is that acylation (palmitoylation?) of a peroxisomal membrane protein protects the peroxisome against autophagic sequestration.

Under normal conditions macroautophagy may be largely unselective and serves, for example, to produce amino acids for gluconeogenesis and the synthesis of essential proteins in starvation. When cell structures are functionally redundant or when they become damaged, the autophagic system is able to recognize this and is able to degrade the structure concerned. As yet, nothing is known about the recognition signals. A possibility is that ubiquitination of membrane proteins is required to mark the structure to be degraded for autophagic sequestration.

Ubiquitin may be involved in macroautophagy
Ubiquitin not only contributes to extralysosomal proteolysis but is also involved in autophagic protein degradation. Thus, in fibroblasts ubiquitin–protein conjugates can be found in the lysosomes, as shown by immunohistochemistry and immunogold electron microscopy. Free ubiquitin can also be found inside lysosomes. Accumulations of ubiquitin–protein conjugates in filamentous, presumably lysosomal, structures are also found in a large number of neurodegenerative diseases. Mallory bodies in the liver of alcoholics also contain ubiquitin–protein conjugates.

This presence of ubiquitin–protein conjugates in filamentous inclusions in neurons and other cells can be caused by a defect in the extralysosomal ubiquitin-dependent proteolytic pathway. However, it is also possible that these filamentous inclusions represent an attempt of the cell to get rid of unwanted material (proteins, organelles) via autophagy. Direct evidence that ubiquitin may be involved in the control of macroautophagy came from experiments with CHO cells with a temperature-sensitive mutation in the ubiquitin-activating enzyme E1. Wild-type cells increased their rate of proteolysis in response to stress (amino acid depletion, increased temperature). This was prevented by the acidotropic agent ammonia or by the autophagic sequestration inhibitor 3-methyladenine, indicating that the accelerated proteolysis occurred by autophagy. In the mutant cells, there was no such increase in proteolysis in response to stress at the restrictive temperature.

Autophagy and carcinogenesis
In cancer development, cell growth is mainly induced by inhibition of protein degradation, since differences in the rate of protein synthesis between tumorigenic cells and their normal counterparts are rather small. A striking example of how reduced autophagic proteolysis can contribute to cell growth can be found in the development of liver carcinogenesis. This decrease in autophagic flux results from a decrease in the rate of autophagic sequestration and is already detectable in the early preneoplastic stage. Autophagic flux is then hardly inhibitable by amino acids nor is it inducible by catabolic stimuli
and declines in the more advanced stage of cancer development to a rate of less than 20% of that seen in normal hepatocytes. The fact that the addition of 3-methyladenine to hepatocytes from normal rats increased hepatocyte viability to the same level as observed for the tumour cells strongly suggests that the fall in autophagic proteolysis contributes to the rapid growth rate of these cells and gives them a selective advantage over the normal hepatocytes.

Underlying control mechanisms for autophagy are gradually being unravelled. It is perhaps not surprising that protein phosphorylation and signal transduction are key elements in these mechanisms. The discovery of an amino acid receptor in the plasma membrane of the hepatocyte with a signal transduction pathway coupled to it may have important repercussions, not only for the control of macroautophagy but also for the control of other pathways.

It remains to be seen whether the details of the mechanisms controlling the process in yeast are similar to those in mammalian cells. For example, it is not known whether amino acids are able to control the process as they do in mammalian cells.

Blommaart EFC, Luiken JJFP, Meijer AJ. Autophagic proteolysis: control and specificity. Histochemical Journal (1997); 29:365–385.
A Novel Type of Selective Autophagy
Eukaryotic cells use autophagy and the ubiquitin–proteasome system (UPS) as their major protein degradation pathways. Whereas the UPS is required for the rapid degradation of proteins when fast adaptation is needed, autophagy pathways selectively remove protein aggregates and damaged or excess organelles. However, little is known about the targets and mechanisms that provide specificity to this process. Here we show that mature ribosomes are rapidly degraded by autophagy upon nutrient starvation in Saccharomyces cerevisiae. Surprisingly, this degradation not only occurs by a nonselective mechanism, but also involves a novel type of selective autophagy, which we term ‘ribophagy’. A genetic screen revealed that selective degradation of ribosomes requires catalytic activity of the Ubp3p/Bre5p ubiquitin protease. Although Ubp3p and Bre5p cells strongly accumulate 60S ribosomal particles upon starvation, they are proficient in starvation sensing and in general trafficking and autophagy pathways. Moreover, ubiquitination of several ribosomal subunits and/or ribosome associated proteins was specifically enriched in Ubp3p cells, suggesting that the regulation of ribophagy by ubiquitination may be direct. Interestingly, Ubp3p cells are sensitive to rapamycin and nutrient starvation, implying that selective degradation of ribosomes is functionally important in vivo. Taken together, our results suggest a link between ubiquitination and the regulated degradation of mature ribosomes by autophagy.
Kraft C, Deplazes A, Sohrmann M,Peter M. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nature Cell Biology 2008; 10(5): 603-609. DOI: 10.1038/ncb1723.

Mitochondrial Failure and Protein Degradation

Progressive mitochondrial failure is tightly associated with the the development of most age-related human diseases including neurodegenerative diseases, cancer, and type 2 diabetes.

This tight connection results from the double-edged sword of mitochondrial respiration, which is responsible for generating both ATP and ROS, as well as from risks that are inherent to mitochondrial biogenesis. To prevent and treat these diseases, a precise understanding of the mechanisms that maintain functional mitochondria is necessary. Mitochondrial protein quality control is one of the mechanisms that protect mitochondrial integrity, and increasing evidence implicates the cytosolic ubiquitin/proteasome system (UPS) as part of this surveillance network. In this review, we will discuss our current understanding of UPS-dependent mitochondrial protein degradation, its roles in diseases progression, and insights into future studies.

While mitochondria have their own genome, about 99% of the roughly 1000 mitochondrial proteins are encoded in the nuclear genome. Most mitochondrial proteins are therefore

  • synthesized in the cytoplasm,
  • unfolded,
  • transported across one or both mitochondrial membranes,
  • then refolded and/or assembled into complexes (Tatsuta, 2009).

Failure of this complex series of events generates unfolded or misfolded proteins within mitochondria, often disrupting critical functions.

Mitochondrial oxidative phosphorylation generates usable cellular energy in the form of ATP, but also produces reactive oxygen species (ROS) . ROS tend to react quickly, so their predominant sites of damage are mitochondrial macromolecules that are localized nearby the source of ROS production.

Exposure to oxidative stress facilitates misfolding and aggregation of these mitochondrial proteins, leading to disassembly of protein complexes and eventual loss of mitochondrial integrity.

The clearance of misfolded and aggregated proteins is constantly needed to maintain functional mitochondria.
There are several systems promoting this turnover.

  1. Mitophagy, a selective mitochondrial autophagy, mediates a bulk removal of damaged mitochondria.
  2. mitochondria intrinsically contain proteases in each of their compartments and these proteases recognize misfolded mitochondrial proteins and mediate their degradation.

Accumulating evidence shows that the ubiquitin proteasome system (UPS) plays an important role in mitochondrial protein degradation. At various cellular sites, the UPS is involved in protein degradation. With the help of ubiquitin E1–E2–E3 enzyme cascades, target proteins destined for destruction are marked by conjugation of K48-linked poly-ubiquitin chain. This poly-ubiquitinated protein is then targeted to the proteasome for degradation.

Cells treated with proteasome inhibitors exhibit elevated levels of ubiquitinated mitochondrial proteins, suggesting the potentially important roles of the proteasome on mitochondrial protein degradation. Studies have also identified mitochondrial substrates of the UPS.

  • Fzo1, an outer mitochondrial membrane (OMM) protein involved in mitochondrial fusion, is partially dependent on the proteasome for its degradation in yeast.
  • The F box protein Mdm30 mediates ubiquitination of Fzo1 by Skp1-Cullin-F-boxMdm30 ligase, which leads to proteasomal degradation.

The UPS has also been implicated in mitochondrial protein degradation in higher organisms. In mammals,

  • the OMM proteins mitofusin 1 and 2 (Mfn1/2; the mammalian orthologs of Fzo1) and Mcl1 are polyubiquitinated and degraded by the proteasome.
  • VDAC1, Tom20 and Tom70 were also suggested as targets of proteasomal degradation as they are stabilized by proteasome inhibition.
  •  inactivation of the proteasome also induces accumulation of intermembrane space (IMS) proteins and, consistent with this, the proteasome plays a role in degradation of the IMS protein, Endonuclease G.

Turnover of some inner mitochondrial membrane (IMM) proteins is also dependent upon the proteasome. Uncoupling proteins (UCPs) 2 and 3 exhibit an unusually short half-life compared with other IMM proteins, and Brand and colleagues showed that inactivation of the proteasome prevents their turnover in vivo and in a reconstituted in vitro system. Finally, mitochondrial matrix proteins can also be degraded by the proteasome.

Cdc48/p97 is involved in many cellular processes through its role in protein degradation and is targeted to different subcellular sites by adaptor proteins. For example, Cdc48/p97 is recruited to the endoplasmic reticulum with the help of two adaptor proteins, Npl4 and Ufd1. This implies the existence of specific adaptors that recruit Cdc48/p97 to mitochondria. Consistent with this notion, the authors recently identified a mitochondrial adaptor protein for Cdc48, which we named Vms1 (VCP/Cdc48-associated mitochondrial stress responsive 1). Vms1 interacts with Cdc48/p97 and Npl4, but not with Ufd1, which indicates that the Cdc48/p97–Npl4–Ufd1 complex functions in ER protein degradation while the Vms1–Cdc48/p97–Npl4 complex acts in mitochondria. In agreement with this notion, overexpression of Cdc48 or Npl4 rescues the Vms1 mutant phenotype while Ufd1 has no effect.

Normally, Vms1 is cytoplasmic. Upon mitochondrial stress, however, Vms1 recruits Cdc48 and Npl4 to mitochondria. In agreement with the role of Cdc48/p97 in OMM protein degradation, loss of the Vms1 system results in accumulation of ubiquitin-conjugated proteins in purified mitochondria as well as stabilization of Fzo1 under mitochondrial stress conditions. Accumulation of damaged and misfolded mitochondrial proteins disturbs the normal physiology of the mitochondria, leading to mitochondrial dysfunction. As expected, the Vms1 mutants progressively lose mitochondrial respiratory activity, eventually leading to cell death. The VMS1 gene is broadly conserved in eukaryotes, implying an important functional role in a wide range of organisms. The C. elegans Vms1 homolog exhibits a similar pattern of mitochondrial stress responsive translocation and is required for normal lifespan. Additionally, mammalian Vms1 also forms a stable complex with p97. Combining these observations, the authors conclude that Vms1 is a conserved component of the UPS-dependent mitochondrial protein quality control system.

The UPS regulates mitochondrial dynamics and initiation of mitophagy
The UPS regulates mitochondrial dynamics. Major proteins involved in mitochondrial fission or fusion (e.g. Mfn1/2, Drp1 and Fis1) are degraded by the UPS.  MITOL, a mitochondrial E3 ubiquitin ligase, is required for Drp1-dependent mitochondrial fission as depletion or inactivation of MITOL blocks mitochondrial fragmentation. Moreover, knockdown of USP30, an OMM-localized deubiquitinating enzyme, induces an elongated mitochondrial morphology, suggesting a defect in fission. Through this regulatory process, the UPS controls mitochondrial dynamics. Parkin, an E3 ligase involved in mitophagy, utilizes the UPS to enhance mitochondrial fission through degradation of components of the fusion machinery. By facilitating fragmentation of damaged mitochondria, which is essential for initiation of mitophagy, Parkin stimulates mitophagy. The underlying mechanisms linking the UPS to the regulation of mitochondrial dynamics remain unclear.

Accumulation of aberrant proteins and human diseases
In neurodegenerative diseases wherein aberrant pathological proteins accumulate throughout the cell, including sites in mitochondria. Amyloid precursor protein (APP), a protein associated with Alzheimer’s disease, accumulates within mitochondria and is implicated in blockade of mitochondrial protein import. A, a neurotoxic APP cleavage product, can also facilitate the formation of the mitochondrial permeability transition pore (mPTP) by binding to mPTP components VDAC1, CypD and ANT, which provokes cell death.
-Synuclein, a protein associated with the development of Parkinson’s disease, is targeted to the IMM where it binds to the mitochondrial respiratory complex I and impairs its function. -Synuclein interferes with mitochondrial dynamics as its unique interaction with the mitochondrial membrane disturbs the fusion process. Finally, in Huntington’s disease, increased association of the mutant huntingtin protein with mitochondria can impair mitochondrial trafficking. Moreover, accumulation of mutant huntingtin protein disrupts cristae structure and it facilitates mitochondrial fragmentation by activation of Drp1. These examples demonstrate the crucial importance of prompt removal of dysfunctional and/or aberrant proteins in maintaining functional mitochondria.

UPS-mediated mitochondrial protein degradation.
Misfolded and/or damaged mitochondrial proteins destined for proteasomal degradation in the cytosol are recruited to the outer mitochondrial membrane (OMM) from each mitochondrial compartment by unknown mechanisms. Upon reaching the OMM, these proteins are presented to the proteasome through a series of events. They are K48 polyubiquitinated by the cytoplasmic (e.g. Parkin) or mitochondrial ubiquitin E3 ligases. For proteasomal degradation, polyubiquitinated mitochondrial substrate proteins need to be retrotranslocated to the cytoplasm, probably, either by the proteasome per se or by the help of UPS components such as Vms1, Cdc48/p97 and Npl4. Following dislocation to the cytoplasm, these substrate proteins are degraded by the proteasome.

Treatment of diseases that arise from defects in protein quality control will depend on greater depth in our understanding of this process, which could contribute to the development of novel therapeutic approaches. For instance, both mutant SOD1, a misfolded mitochondrial protein associated with the onset of amyotrophic lateral sclerosis, and polyglutamine expanded ataxin-3, a pathogenic protein causing Machado-Joseph disease, are ubiquitinated by MITOL and then degraded by the proteasome. Facilitating the proteasomal degradation of these aberrant proteins might therefore efficiently control diseases progression and, eventually, cure the diseases. Answering these questions would partially unveil the mysterious physiology of mitochondria, which, in turn, would facilitate the development of therapeutics to prevent and cure devastating human diseases.

Heo JM, Rutter J. Ubiquitin-dependent mitochondrial protein degradation. The International Journal of Biochemistry & Cell Biology 2011; 43:1422– 1426.
UPS Inhibitors and Apoptotic Machinery
Over the past decade, the promising results of UPSIs (UPS inhibitors) in eliciting apoptosis in various cancer cells, and the approval of the first UPSI (Bortezomib/Velcade/PS-341) for the treatment of multiple myeloma have raised interest in assessing the death program activated upon proteasomal blockage. Several reports indicate that UPSIs stimulate apoptosis in malignant cells by operating at multiple levels, possibly by inducing different types of cellular stress. Normally cellular stress signals converge on the core elements of the apoptotic machinery to trigger the cellular demise. In addition to eliciting multiple stresses, UPSIs can directly operate on the core elements of the apoptotic machinery to control their abundance. Alterations in the relative levels of anti and pro-apoptotic factors can render cancer cells more prone to die in response to other anti-cancer treatments. Aim of the present review is to discuss those core elements of the apoptotic machinery that are under the control of the UPS.

The UPS (Ubquitin-Proteasome System)
To fulfill the protein-degradation process two branches, operating at different levels, principally comprise the UPS.

  • The first branch is formed by the enzymatic activities responsible for delivering the substrate to the degradative machinery: the targeting branch.
  • The second branch is represented by the proteolytic machinery, which ultimately fragments the protein substrate into small oligopeptides.

Oligopeptides are further digested to single amino acids by cytosolic proteases.
It is important to remember that conjugation of ubiquitin to a specific protein is not sufficient to determine its degradation. In fact, mono-ubiquitination or poly-monoubiquitination and in certain cases also poly-ubiquitination of proteins are post-translational modifications related to various cellular functions including DNA repair or membrane trafficking . To deliver polypeptides for proteasomal degradation poly-ubiquitin chains of more than 4 ubiquitins must be assembled through lysine-48 linkages.

There are 3 catalytic sites for each polyubiquitin chain. These sites show specific requirements in terms of substrate specificities and catalytic activities, and they are identified as

  1. trypsin-like, which prefer to cleave after hydrophobic bonds, chymotrypsin-like, which cleave at basic residues and
  2. postglutamyl peptide hydrolase-like or
  3. caspase-like activities, which cut after acidic amino acid.

Each proteasome active site uses the side chain hydroxyl group of an NH2-terminal threonine as the catalytic nucleophile, a mechanism that distinguishes the proteasome from other cellular proteases. The presence of substrate proteolysis small size peptides ranging from 3 to 22 residues are generated. Alternative catalytic sites guarantees the efficient processing of several different substrates.

UPS Inhibitors
By UPS inhibitors (UPSI) we mean small molecules that share the ability to target and inhibit specific activities of the UPS, causing the accumulation of poly-ubiquitinated proteosomal substrates. UPSIs are heterogeneous compounds and among them bortezomib is the only one used in clinical practice.

PR-171, a modified peptide related to the natural product epoxomicin, is composed of two key elements:

  1. a peptide portion that selectively binds with high affinity in the substrate binding pocket(s) of the proteasome and
  2. an epoxyketone pharmacophore that stereospecifically interacts with the catalytic threonine residue and irreversibly inhibits enzyme activity.

In comparison to bortezomib, PR-171 exhibits equal potency, but greater selectivity, for the chymotrypsin-like activity of the proteasome. In cell culture PR-171 is more cytotoxic than bortezomib. In mice PR-171 is well tolerated and shows stronger anti-tumor activity when compared with bortezomib . Clinical studies are in progress to test the safety of PR-171 at different dose levels on some hematological cancers.

Cell Death by UPSI
In vitro experiments have unambiguously established that incubation of neoplastic cells with UPSIs including bortezomib triggers their death. Apoptosis or type I cell death relies on the timed activation of caspases, a group of cysteine proteases, which cleave selected cellular substrates after aspartic residues. Two main apoptotic pathways keep in check caspase activation.

The turnover of a large number of cellular proteins is under the control of the UPS. Thus in principle any proteosomal substrate could contribute directly or indirectly to the cell death phenotype. This is perfectly exemplified by two master regulators of cell life and death, p53 and NFkB.  UPSIs cause

  • NF-kB inhibition through reduced IkB degradation and,
  • in opposition; they promote stabilization and accumulation of p53.

c-FLIP is the most important element of the extrinsic pathway under the direct control of the UPS. Two different FLIP isoforms exist:

  1. c-FLIPL (Long) and
  2. c-FLIPS (Short).

c-FLIPL is highly homologus to caspase-8 and contains two tandem repeat Death Effector Domains (DED) and a catalytically inactive caspase-like domain. Both FLIPs can be degraded by the UPS; however they display distinct half-lives and the unique C terminus of c-FLIPS possesses a destabilizing function. The regulation of c-FLIP levels in response to UPSIs is rather controversial. Some reports indicate that UPSIs can reduce c-FLIP levels and in this manner synergize with TRAIL to promote apoptosis.

UPSIs activate multiple cellular responses and different stress signals that ultimately cause cell death. For this reason they represent broad inducers of apoptosis. In addition, since many of the available UPSIs alter the proteolytic activity of the proteasome, they represent non-specific modulators of the expression/activity of various components of the apoptotic machinery. Paradoxically they can simultaneously favor the accumulation of pro- and anti-apoptotic factors.
Brancolini C. Inhibitors of the Ubiquitin-Proteasome System and the Cell Death Machinery: How Many Pathways are Activated? Current Molecular Pharmacology, 2008; 1:24-37.

Mitochondrial Quality Control
The PINK1–Parkin pathway plays a critical role in mitochondrial quality control by selectively targeting damaged mitochondria for autophagy. The AAA-type ATPase p97 acts downstream of PINK1 and Parkin to segregate fusion-incompetent mitochondria for turnover. [Tanaka et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201007013)]. p97 acts by targeting the mitochondrial fusion-promoting factor mitofusin for degradation through an endoplasmic reticulum–associated degradation (ERAD)-like mechanism.

Pallanck LJ. Culling sick mitochondria from the herd. J Cell Biol 2012;191(7):1225–1227.

PINK1 and Parkin and Parkinson’s Disease

Studies of the familial Parkinson disease-related proteins PINK1 and Parkin have demonstrated that these factors promote the fragmentation and turnover of mitochondria following treatment of cultured cells with mitochondrial depolarizing agents. Whether PINK1 or Parkin influence mitochondrial quality control under normal physiological conditions in dopaminergic neurons, a principal cell type that degenerates in Parkinson disease, remains unclear. To address this matter, we developed a method to purify and characterize neural subtypes of interest from the adult Drosophila brain.

Using this method, we find that dopaminergic neurons from Drosophila parkin mutants accumulate enlarged, depolarized mitochondria, and that genetic perturbations that promote mitochondrial fragmentation and turnover rescue the mitochondrial depolarization and neurodegenerative phenotypes of parkin mutants. In contrast, cholinergic neurons from parkin mutants accumulate enlarged depolarized mitochondria to a lesser extent than dopaminergic neurons, suggesting that a higher rate of mitochondrial damage, or a deficiency in alternative mechanisms to repair or eliminate damaged mitochondria explains the selective vulnerability of dopaminergic neurons in Parkinson disease.

Our study validates key tenets of the model that PINK1 and Parkin promote the fragmentation and turnover of depolarized mitochondria in dopaminergic neurons. Moreover, our neural purification method provides a foundation to further explore the pathogenesis of Parkinson disease, and to address other neurobiological questions requiring the analysis of defined neural cell types.

Burmana JL, Yua S, Poole AC, Decala RB , Pallanck L. Analysis of neural subtypes reveals selective mitochondrial dysfunction in dopaminergic neurons from parkin mutants.

Autophagy in Parkinson’s Disease.
Parkinson’s disease is a common neurodegenerative disease in the elderly. To explore the specific role of autophagy and the ubiquitin-proteasome pathway in apoptosis, a specific proteasome inhibitor and macroautophagy inhibitor and stimulator were selected to investigate pheochromocytoma (PC12) cell lines transfected with human mutant (A30P) and wildtype (WT) -synuclein.

The apoptosis ratio was assessed by flow cytometry. LC3, heat shock protein 70 (hsp70) and caspase-3 expression in cell culture were determined by Western blot. The hallmarks of apoptosis and autophagy were assessed with transmission electron microscopy. Compared to the control group or the rapamycin (autophagy stimulator) group, the apoptosis ratio in A30P and WT cells was significantly higher after treatment with inhibitors of the proteasome and macroautophagy. The results of Western blots for caspase-3 expression were similar to those of flow cytometry; hsp70 protein was significantly higher in the proteasome inhibitor group than in control, but in the autophagy inhibitor and stimulator groups, hsp70 was similar to control. These findings show that inhibition of the proteasome and autophagy promotes apoptosis, and the macroautophagy stimulator rapamycin reduces the apoptosis ratio. And inhibiting or stimulating autophagy has less impact on hsp70 than the proteasome pathway.

In conclusion, either stimulation or inhibition of macroautophagy, has less impact on hsp70 than on the proteasome pathway. This study found that rapamycin decreased apoptotic cells in A30P cells independent of caspase-3 activity. Although several lines of evidence recently demonstrated crosstalk between autophagy and caspase-independent apoptosis, we could not confirm that autophagy activation protects cells from caspase-independent cell death. Undoubtedly, there are multiple connections between the apoptotic and autophagic processes.

Inhibition of autophagy may subvert the capacity of cells to remove damaged organelles or to remove misfolded proteins, which would favor apoptosis. However, proteasome inhibition activated macroautophagy and accelerated apoptosis. A likely explanation is inhibition of the proteasome favors oxidative reactions that trigger apoptosis, presumably through

1. a direct effect on mitochondria, and
2. the absence of NADPH2 and ATP

which may deinhibit the activation of caspase-2 or MOMP. Another possibility is that aggregated proteins induced by proteasome inhibition increase apoptosis.

Yang F, Yanga YP, Maoa CJ, Caoa BY, et al. Role of autophagy and proteasome degradation pathways in apoptosis of PC12 cells overexpressing human -synuclein. Neuroscience Letters 2009; 454:203–208. doi:10.1016/j.neulet.2009.03.027.

Parkin-dependent Ubiquitination of Endogenous Bax 

Autosomal recessive loss-of-function mutations within the PARK2 gene functionally inactivate the E3 ubiquitin ligase parkin, resulting in neurodegeneration of catecholaminergic neurons and a familial form of Parkinson disease. Current evidence suggests both a mitochondrial function for parkin and a neuroprotective role, which may in fact be interrelated. The antiapoptotic effects of Parkin have been widely reported, and may involve fundamental changes in the threshold for apoptotic cytochrome c release, but the substrate(s) involved in Parkin dependent protection had not been identified. Here, we demonstrate the Parkin-dependent ubiquitination of endogenous Bax comparing primary cultured neurons from WT and Parkin KO mice and using multiple Parkin-overexpressing cell culture systems. The direct ubiquitination of purified Bax was also observed in vitro following incubation with recombinant parkin. The authors found that Parkin prevented basal and apoptotic stress induced translocation of Bax to the mitochondria. Moreover, an engineered ubiquitination-resistant form of Bax retained its apoptotic function, but Bax KO cells complemented with lysine-mutant Bax did not manifest the antiapoptotic effects of Parkin that were observed in cells expressing WT Bax. These data suggest that Bax is the primary substrate responsible for the antiapoptotic effects of Parkin, and provide mechanistic insight into at least a subset of the mitochondrial effects of Parkin.

Johnson BN, Berger AK, Cortese GP, and LaVoie MJ. The ubiquitin E3 ligase Parkin regulates the proapoptotic function of Bax. PNAS 2012, pp 6.
Parkin Promotes Mitochondrial Loss in Autophagy
Parkin, an E3 ubiquitin ligase implicated in Parkinson’s disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular approaches, we show that upon translocation to mitochondria, Parkin activates the ubiquitin–proteasome system (UPS) for widespread degradation of outer membrane proteins. This is evidenced by an increase in K48-linked polyubiquitin on mitochondria, recruitment of the 26S proteasome and rapid degradation of multiple outer membrane proteins. The degradation of proteins by the UPS occurs independently of the autophagy pathway, and inhibition of the 26S proteasome completely abrogates Parkin-mediated mitophagy in HeLa, SH-SY5Y and mouse cells. Although the mitofusins Mfn1 and Mfn2 are rapid degradation targets of Parkin, degradation of additional targets is essential for mitophagy. These results indicate that remodeling of the mitochondrial outer membrane proteome is important for mitophagy, and reveal a causal link between the UPS and autophagy, the major pathways for degradation of intracellular substrates.

Chan NC, Salazar AM, Pham AH, Sweredoski MJ, et al. Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy. Human Molecular Genetics 2011; 20(9): 1726–1737. doi:10.1093/hmg/ddr048.

TRAP1 and TBP7 Interaction in Refolding of Damaged Proteins
TRAP1 is a mitochondrial antiapoptotic heat shock protein. The information available on the TRAP1 pathway describes just a few well-characterized functions of this protein in mitochondria. However, our group’s use of mass spectrometry analysis identified TBP7, an AAA-ATPase of the 19S proteasomal subunit, as a putative TRAP1-interacting protein. Surprisingly, TRAP1 and TBP7 co-localize in the endoplasmic reticulum (ER), as demonstrated by biochemical and confocal/electron microscopy analyses, and directly interact, as confirmed by FRET analysis. This is the first demonstration of TRAP1 presence in this cellular compartment. TRAP1 silencing by shRNAs, in cells exposed to thapsigargin-induced ER stress, correlates with up-regulation of BiP/Grp78, thus suggesting a role of TRAP1 in the refolding of damaged proteins and in ER stress protection. Consistently, TRAP1 and/or TBP7 interference enhanced stress-induced cell death and increased intracellular protein ubiquitination. These experiments led us to hypothesize an involvement of TRAP1 in protein quality control for mistargeted/misfolded mitochondria-destined proteins, through interaction with the regulatory proteasome protein TBP7. Remarkably, the expression of specific mitochondrial proteins decreased upon TRAP1 interference as a consequence of increased ubiquitination. The proposed TRAP1 network has an impact in vivo, since it is conserved in human colorectal cancers, is controlled by ER-localized TRAP1 interacting with TBP7 and provides a novel model of ER-mitochondria crosstalk.


VMS1 and Mitochondrial Protein Degradation
We show that Ydr049 (renamed VCP/Cdc48-associated mitochondrial stress-responsive—Vms1), a member of an unstudied pan-eukaryotic protein family, translocates from the cytosol to mitochondria upon mitochondrial stress. Cells lacking Vms1 show progressive mitochondrial failure, hypersensitivity to oxidative stress, and decreased chronological life span. Both yeast and mammalian Vms1 stably interact with Cdc48/VCP/p97, a component of the ubiquitin/proteasome system with a well-defined role in endoplasmic reticulum-associated protein degradation (ERAD), wherein misfolded ER proteins are degraded in the cytosol. We show that oxidative stress triggers mitochondrial localization of Cdc48 and this is dependent on Vms1. When this system is impaired by mutation of Vms1,

  • ubiquitin-dependent mitochondrial protein degradation,
  • mitochondrial respiratory function,and
  • cell viability are compromised.

We demonstrate that Vms1 is a required component of an evolutionarily conserved system for mitochondrial protein degradation, which is
necessary to maintain

  • mitochondrial,
  • cellular, and
  • organismal viability.

Heo JM, Livnat-Levanon N, Taylor EB, Jones KT. A Stress-Responsive System
for Mitochondrial Protein Degradation. Molecular Cell 2010; 40:465–480.
DOI 10.1016/j.molcel.2010.10.021

Mitochondrial Protein Degradation
The biogenesis of mitochondria and the maintenance of mitochondrial functions depends on an autonomous proteolytic system in the organelle which is highly conserved throughout evolution. Components of this system include processing

  • peptidases and
  • ATP-dependent proteases, as well as
  • molecular chaperone proteins and
  • protein complexes with apparently regulatory functions.

While processing peptidases mediate maturation of nuclear-encoded mitochondrial preproteins, quality control within various subcompartments of mitochondria is ensured by ATP-dependent proteases which selectively remove non-assembled or misfolded polypeptides. Moreover, these proteases appear to control the activity- or steady-state levels of specific regulatory proteins and thereby ensure mitochondrial genome integrity, gene expression and protein assembly.

Kaser M and Langer T. Protein degradation in mitochondria. CELL & DEVELOPMENTAL BIOLOGY 2000; 11:181–190. doi: 10.1006/10.1006/scdb.2000.0166.

RING finger E3s

Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member of the family contains any other previously described domain. Although the study of a few members in A. thaliana and O. sativa has been reported, the role of this family in the life cycle of a plant is still vague.

To provide tools to advance on the functional analysis of this family we have undertaken a phylogenetic analysis of ATLs in twenty-four plant genomes. ATLs were found in all the 24 plant species analyzed, in numbers ranging from 20–28 in two basal species to 162 in soybean. Analysis of ATLs arrayed in tandem indicates that sets of genes are expanding in a species-specific manner. To
get insights into the domain architecture of ATLs we generated 75 pHMM LOGOs from 1815 ATLs, and unraveled potential protein-protein interaction regions by means of yeast two-hybrid assays. Several ATLs were found to interact with DSK2a/ubiquilin through a region at the amino-terminal end, suggesting that this is a widespread interaction that may assist in the mode of action of ATLs; the region was traced to a distinct sequence LOGO. Our analysis provides significant observations on the evolution and expansion of the ATL family in addition to information on the domain structure of this class of ubiquitin-ligases that may be involved in plant adaptation to environmental stress.

Aguilar-Hernandez V, Aguilar-Henonin L, Guzman P. Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments. PLoS ONE 2011; 6(8): e23934. doi:10.1371/journal.pone.0023934
UPS Proteolytic Function Inadequate in Proteinopathies
Proteinopathies are a family of human disease caused by toxic aggregation-prone proteins and featured by the presence of protein aggregates in the affected cells. The ubiquitin-proteasome system (UPS) and autophagy are two major intracellular protein degradation pathways. The UPS mediates the targeted degradation of most normal proteins after performing their normal functions as well as the removal of abnormal, soluble proteins. Autophagy is mainly responsible for degradation of defective organelles and the bulk degradation of cytoplasm during starvation. The collaboration between the UPS and autophagy appears to be essential to protein quality control in the cell.

UPS proteolytic function often becomes inadequate in proteinopathies which may lead to activation of autophagy, striving to remove abnormal proteins especially the aggregated forms. HADC6, p62, and FoxO3 may play an important role in mobilizing this proteolytic consortium. Benign measures to enhance proteasome function are currently lacking; however, enhancement of autophagy via pharmacological intervention and/or lifestyle change has shown great promise in alleviating bona fide proteinopathies in the cell and animal models. These pharmacological interventions are expected to be applied clinically to treat human proteinopathies in the near future.

Zheng Q, Li J, Wang X. Interplay between the ubiquitin-proteasome system and
autophagy in proteinopathies. Int J Physiol Pathophysiol Pharmacol 2009;1:127-142.

Ubiquitin-associated Protein-Protein Interactions

Applicability of in vitro biotinylated ubiquitin for evaluation of endogenous ubiquitin conjugation and analysis of ubiquitin-associated protein-protein interactions has been investigated. Incubation of rat brain mitochondria with biotinylated ubiquitin followed by affinity chromatography on avidin-agarose, intensive washing, tryptic digestion of proteins bound to the affinity sorbent and their mass spectrometry analysis resulted in reliable identification of 50 proteins belonging to mitochondrial and extramitochondrial compartments. Since all these proteins were bound to avidin-agarose only after preincubation of the mitochondrial fraction with biotinylated ubiquitin, they could therefore be referred to as specifically bound proteins. A search for specific
ubiquitination signature masses revealed several extramitochondrial and intramitochondrial ubiquitinated proteins representing about 20% of total number of proteins bound to avidin-agarose. The interactome analysis suggests that the identified non-ubiquitinated proteins obviously form tight complexes either with ubiquitinated proteins or with their partners and/or mitochondrial membrane components. Results of the present study demonstrate that the use of biotinylated ubiquitin may be considered as the method of choice for in vitro evaluation of endogenous ubiquitin-conjugating machinery in particular
subcellular organelles and changes in ubiquitin/organelle associated interactomes. This may be useful for evaluation of changes in interactomes induced by protein ubiquitination.

Buneeva OA, Medvedeva MV, Kopylov AT, Zgoda VG, Medvedev AE. Use of Biotinylated Ubiquitin for Analysis of Rat Brain Mitochondrial Proteome and Interactome. Int J Mol Sci 2012; 13: 11593-11609; doi:10.3390/ijms130911593
IL-6 regulation on mitochondrial remodeling/dysfunction

Muscle protein turnover regulation during cancer cachexia is being rapidly defined, and skeletal muscle mitochondria function appears coupled to processes regulating muscle wasting. Skeletal muscle oxidative capacity and the expression of proteins regulating mitochondrial biogenesis and dynamics are disrupted in severely cachectic ApcMin/+ mice. It has not been determined if these changes occur at the onset of cachexia and are necessary for the progression of muscle wasting. Exercise and anti-cytokine therapies have proven effective in preventing cachexia development in tumor bearing mice, while their effect on mitochondrial content, biogenesis and dynamics is not well understood.

The purposes of this study were to

1) determine IL-6 regulation on mitochondrial remodeling/dysfunction during the progression of cancer cachexia and
2) to determine if exercise training can attenuate mitochondrial dysfunction and the induction of proteolytic pathways during IL-6 induced cancer cachexia.

ApcMin/+ mice were examined during the progression of cachexia, after systemic interleukin (IL)-6r antibody treatment, or after IL-6 over-expression with or without exercise. Direct effects of IL-6 on mitochondrial remodeling were examined in cultured C2C12 myoblasts.

Mitochondrial content was not reduced during the initial development of cachexia, while muscle PGC-1α and fusion (Mfn1, Mfn2) protein expression was repressed.

With progressive weight loss mitochondrial content decreased, PGC-1α and fusion proteins were further suppressed, and fission protein (FIS1) was induced.

IL-6 receptor antibody administration after the onset of cachexia

  • improved mitochondrial content,
  • PGC-1α,
  • Mfn1/Mfn2 and
  • FIS1 protein expression.

IL-6 over-expression in pre-cachectic mice

  • accelerated body weight loss and muscle wasting, without reducing mitochondrial content,
  • while PGC-1α and Mfn1/Mfn2 protein expression was suppressed
  • and FIS1 protein expression induced.

Exercise normalized these IL-6 induced effects. C2C12 myotubes administered IL-6 had

  • increased FIS1 protein expression,
  • increased oxidative stress, and
  • reduced PGC-1α gene expression
  • without altered mitochondrial protein expression.

Altered expression of proteins regulating mitochondrial biogenesis and fusion are early events in the initiation of cachexia regulated by IL-6, which precede the loss of muscle mitochondrial content. Furthermore, IL-6 induced mitochondrial remodeling and proteolysis can be rescued with moderate exercise training even in the presence of high circulating IL-6 levels.

White JP, Puppa MJ, Sato S, Gao S. IL-6 regulation on skeletal muscle mitochondrial remodeling during cancer cachexia in the ApcMin/+ mouse. Skeletal Muscle 2012; 2:14-30.

Starvation-induced Autophagy
Upon starvation cells undergo autophagy, a cellular degradation pathway important in the turnover of whole organelles and long lived proteins. Starvation-induced protein degradation has been regarded as an unspecific bulk degradation process. We studied global protein dynamics during amino acid starvation-induced autophagy by quantitative mass spectrometry and were able to record nearly 1500 protein profiles during 36 h of starvation. Cluster analysis of the recorded protein profiles revealed that cytosolic proteins were degraded rapidly, whereas proteins annotated to various complexes and organelles were degraded later at different time periods. Inhibition of protein degradation pathways identified the lysosomal/autophagosomal system as the main degradative route.

Thus, starvation induces degradation via autophagy, which appears to be selective and to degrade proteins in an ordered fashion and not completely arbitrarily as anticipated so far.

Kristensen AR, Schandorff S, Høyer-Hansen M, Nielsen MO, et al. Ordered Organelle Degradation during Starvation-induced Autophagy. Molecular & Cellular Proteomics 2008; 7:2419–2428.

Skeletal Muscle Macroautophagy
Skeletal muscles are the agent of motion and one of the most important tissues responsible for the control of metabolism. Coordinated movements are allowed by the highly organized structure of the cytosol of muscle fibers (or myofibers), the multinucleated and highly specialized cells of skeletal muscles involved in contraction. Contractile proteins are assembled into repetitive structures, the basal unit of which is the sarcomere, that are well packed into the myofiber cytosol. Myonuclei are located at the edge of the myofibers, whereas the various organelles such as mitochondria and sarcoplasmic reticulum are embedded among the myofibrils. Many different changes take place in the cytosol of myofibers during catabolic conditions:

  • proteins are mobilized
  • organelles networks are reorganized for energy needs
  • the setting of myonuclei can be modified.


  • strenuous physical activity,
  • improper dietary regimens and
  • aging

lead to mechanical and metabolic damages of myofiber organelles, especially mitochondria, and contractile proteins. During aging the protein turnover is slowed down, therefore it is easier to accumulate aggregates of dysfunctional proteins. Therefore, a highly dynamic tissue such as skeletal muscle requires a rapid and efficient system for the removal of altered organelles, the elimination of protein aggregates, and the disposal of toxic products.

The two major proteolytic systems in muscle are the ubiquitin-proteasome and the autophagy-lysosome pathways. The proteasome system requires

  • the transcription of the two ubiquitin ligases (atrogin-1 and MuRF1) and
  • the ubiquitination of the substrates.

Therefore, the ubiquitin-proteasome system can provide the rapid elimination of single proteins or small aggregates. Conversely, the autophagic system is able to degrade entire organelles and large proteins aggregates. In the autophagy-lysosome system, double-membrane vesicles named autophagosomes are able to engulf a portion of the cytosol and fuse with lysosomes, where their content is completely degraded by lytic enzymes.

The autophagy flux can be biochemicaly monitored following LC3 lipidation and p62 degradation. LC3 is the mammalian homolog of the yeast Atg8 gene, which is lipidated when recruited for the double-membrane commitment and growth. p62 (SQSTM-1) is a polyubiquitin-binding protein involved in the proteasome system and that can either reside free in the cytosol and nucleus or occur within autophagosomes and lysosomes. The GFP-LC3 transgenic mouse model allows easy detection of autophagosomes by simply monitoring the presence of bright GFP-positive puncta inside the myofibrils and beneath the plasma membrane of the myofibers, thus investigate the activation of autophagy in skeletal muscles with different contents of slow and fast-twitching myofibers and in response to stimuli such as fasting. For example, in the fast-twiching extensor digitorum longus muscle few GFP-LC3 dots were observed before starvation, while many small GFP-LC3 puncta appeared between myofibrils and in the perinuclear regions after 24 h starvation. Conversely, in the slow-twitching soleus muscle, autophagic puncta were almost absent in standard condition and scarcely induced after 24 h starvation.
Autophagy in Muscle Homeostasis
The autophagic flux was found to be increased during certain catabolic conditions, such as fasting, atrophy , and denervation , thus contributing to protein breakdown. Food deprivation is one of the strongest stimuli known to induce autophagy in muscle. Indeed skeletal muscle, after the liver, is the most responsive tissue to autophagy activation during food deprivation. Since muscles are the biggest reserve of amino acids in the body, during fasting autophagy has the vital role to maintain the amino acid pool by digesting muscular protein and organelles. In mammalian cells, mTORC1, which consists of

  • mTOR and
  • Raptor,

is the nutrient sensor that negatively regulates autophagy.

During atrophy, protein breakdown is mediated by atrogenes, which are under the forkhead box O (FoxO) transcription factors control, and activation of autophagy seems to aggravate muscle loss during atrophy. In vivo and in vitro studies demonstrated that several genes coding for components of the autophagic machinery, such as

  • LC3,
  • Vps34,
  • Atg12 and
  • Bnip3,

are controlled by FoxO3 transcription factor. FoxO3 is able to regulate independently the ubiquitin-proteasome system and the autophagy-lysosome machinery in vivo and in vitro. Denervation is also able to induce autophagy in skeletal muscle, although at a slower rate than fasting. This effect is mediated by RUNX1, a transcription factor upregulated during autophagy; the lack of RUNX1 results in excessive autophagic flux in denervated muscle and leads to atrophy. The generation of Atg5 and Atg7 muscle-specific knockout mice have shown that with suppression of autophagy both models display muscle weakness and atrophy and a significant reduction of weight, which is correlated with the important loss of muscle tissue due to an atrophic condition. An unbalanced autophagy flux is highly detrimental for muscle, as too much induces atrophy whereas too little leads to muscle weakness and degeneration. Muscle wasting associated with autophagy inhibition becomes evident and symptomatic only after a number of altered proteins and dysfunctional organelles are accumulated, a condition that becomes evident after months or even years. On the other hand, the excessive increase of autophagy flux is able to induce a rapid loss of muscle mass (within days or weeks).
Alterations of autophagy are involved in the pathogenesis of several myopathies and dystrophies.

The maintenance of muscle homeostasis is finely regulated by the balance between catabolic and anabolic process. Macroautophagy (or autophagy) is a catabolic process that provides the degradation of protein aggregation and damaged organelles through the fusion between autophagosomes and lysosomes. Proper regulation of the autophagy flux is fundamental for the homeostasis of skeletal muscles during physiological situations and in response to stress. Defective as well as excessive autophagy is harmful for muscle health and has a pathogenic role in several forms of muscle diseases.
Grumati P, Bonaldo P. Autophagy in Skeletal Muscle Homeostasis and in Muscular Dystrophies. Cells 2012, 1, 325-345; doi:10.3390/cells1030325. ISSN 2073-4409.

Parkinson’s Disease Mutations
Mutations in parkin, a ubiquitin ligase, cause early-onset familial Parkinson’s disease (AR-JP). How Parkin suppresses Parkinsonism remains unknown. Parkin was recently shown to promote the clearance of impaired mitochondria by autophagy, termed mitophagy. Here, we show that Parkin promotes mitophagy by catalyzing mitochondrial ubiquitination, which in turn recruits ubiquitin-binding autophagic components, HDAC6 and p62, leading to mitochondrial clearance.

During the process, juxtanuclear mitochondrial aggregates resembling a protein aggregate-induced aggresome are formed. The formation of these “mito-aggresome” structures requires microtubule motor-dependent transport and is essential for efficient mitophagy. Importantly, we show that AR-JP–causing Parkin mutations are defective in supporting mitophagy due to distinct defects at

  • recognition,
  • transportation, or
  • ubiquitination of impaired mitochondria,

thereby implicating mitophagy defects in the development of Parkinsonism. Our results show that impaired mitochondria and protein aggregates are processed by common ubiquitin-selective autophagy machinery connected to the aggresomal pathway, thus identifying a mechanistic basis for the prevalence of these toxic entities in Parkinson’s disease.
Lee JY,Nagano Y, Taylor JP,Lim KL, and Yao TP. Disease-causing mutations in Parkin impair mitochondrial ubiquitination, aggregation, and HDAC6-dependent mitophagy. J Cell Biol 2010; 189(4):671-679.

Drosophila Parkin Requires PINK1

Loss of the E3 ubiquitin ligase Parkin causes early onset Parkinson’s disease, a neurodegenerative disorder of unknown etiology. Parkin has been linked to multiple cellular processes including

  • protein degradation,
  • mitochondrial homeostasis, and
  • autophagy;

however, its precise role in pathogenesis is unclear. Recent evidence suggests that Parkin is recruited to damaged mitochondria, possibly affecting

  • mitochondrial fission and/or fusion,
  • to mediate their autophagic turnover.

The precise mechanism of recruitment and the ubiquitination target are unclear. Here we show in Drosophila cells that PINK1 is required to recruit Parkin to dysfunctional mitochondria and promote their degradation. Furthermore, PINK1 and Parkin mediate the ubiquitination of the profusion factor Mfn on the outer surface of mitochondria. Loss of Drosophila PINK1 or parkin causes an increase in Mfn abundance in vivo and concomitant elongation of mitochondria. These findings provide a molecular mechanism by which the PINK1/Parkin pathway affects mitochondrial fission/fusion as suggested by previous genetic interaction studies. We hypothesize that Mfn ubiquitination may provide a mechanism by which terminally damaged mitochondria are labeled and sequestered for degradation by autophagy.

Ziviani E, Tao RN, and Whitworth AJ. Drosophila Parkin requires PINK1 for mitochondrial translocation and ubiquitinates Mitofusin. PNAS 2010. Pp6

Dynamin-related protein 1 (Drp1) in Parkinson’s
Mutations in Parkin, an E3 ubiquitin ligase that regulates protein turnover, represent one of the major causes of familial Parkinson’s disease (PD), a neurodegenerative disorder characterized by the loss of dopaminergic neurons and impaired mitochondrial functions. The underlying mechanism by which pathogenic parkin mutations induce mitochondrial abnormality is not fully understood. Here we demonstrate that Parkin interacts with and subsequently ubiquitinates dynamin-related protein 1 (Drp1), for promoting its proteasome-dependent degradation. Pathogenic mutation or knockdown of Parkin inhibits the ubiquitination and degradation of Drp1, leading to an increased level of Drp1 for mitochondrial fragmentation. These results identify Drp1 as a novel substrate of Parkin and suggest a potential mechanism linking abnormal Parkin expression to mitochondrial dysfunction in the pathogenesis of PD.

Wang H, Song P, Du L, Tian W. Parkin ubiquitinates Drp1 for proteasome-dependent degradation: implication of dysregulated mitochondrial dynamics in Parkinson’s disease.
JBC Papers in Press. Published on February 3, 2011 as Manuscript M110.144238.

Pink1, Parkin, and DJ-1 Form a Complex
Mutations in the genes PTEN-induced putative kinase 1 (PINK1), PARKIN, and DJ-1 cause autosomal recessive forms of Parkinson disease (PD), and the Pink1/Parkin pathway regulates mitochondrial integrity and function. An important question is whether the proteins encoded by these genes function to regulate activities of other cellular compartments. A study in mice, reported by Xiong et al. in this issue of the JCI, demonstrates that Pink1, Parkin, and DJ-1 can form a complex in the cytoplasm, with Pink1 and DJ-1 promoting the E3 ubiquitin ligase activity of Parkin to degrade substrates via the proteasome (see the related article, doi:10.1172/ JCI37617).

This protein complex in the cytosol may or may not be related to the role of these proteins in regulating mitochondrial function or oxidative stress in vivo.
Three models for the role of the PPD complex. In this issue of the JCI, Xiong et al. report that Pink1, Parkin, and DJ-1 bind to each other and form a PPD E3 ligase complex in which Pink1 and DJ-1 modulate Parkin-dependent ubiquitination and subsequent degradation of substrates via the proteasome. Previous work suggests that the Pink1/Parkin pathway regulates mitochondrial integrity and promotes mitochondrial fission in Drosophila.

(A) Parkin and DJ-1 may be recruited to the mitochondrial outer membrane during stress and interact with Pink1. These interactions may facilitate the ligase activity of Parkin, thereby facilitating the turnover of molecules that regulate mitochondrial dynamics and mitophagy. The PPD complex may have other roles in the cytosol that result in degradative ubiquitination and/or relay information from mitochondria to other cellular compartments.
(B) Alternatively, Pink1 may be released from mitochondria after cleavage to interact with DJ-1 and Parkin in the cytosol.
A and B differ in the site of action of the PPD complex and the cleavage status of Pink1.
The complex forms on the mitochondrial outer membrane potentially containing full-length Pink1 in A, and in the cytosol with cleaved Pink1 in B.
Lack of DJ-1 function results in phenotypes that are distinct from the mitochondrial phenotypes observed in null mutants of Pink1 or Parkin in Drosophila. Thus, although the PPD complex is illustrated here as regulating mitochondrial fission, the role of DJ-1 in vivo remains to be clarified.
(C) It is also possible that the action occurs in the cytosol and is independent of the function of Pink1/Parkin in regulating mitochondrial integrity and function.

The Xiong et al. study offers an entry point for explorations of the role of Pink1, Parkin, and DJ-1 in the cytoplasm. It remains to be shown whether Parkin, in complex with Pink1 and DJ-1, carries out protein degradation in vivo.

Li H, and Guo M. Protein degradation in Parkinson disease revisited: it’s complex. commentaries. J Clin Invest.  doi:10.1172/JCI38619.

Xiong, H., et al. Parkin, PINK1, and DJ-1 form a ubiquitin E3 ligase complex promoting unfolded protein degradation. J. Clin. Invest. 2009; 119:650–660.

 Mitochondrial Ubiquitin Ligase, MITOL, protects neuronal cells

Nitric oxide (NO) is implicated in neuronal cell survival. However, excessive NO production mediates neuronal cell death, in part via mitochondrial dysfunction. Here, we report that the mitochondrial ubiquitin ligase, MITOL, protects neuronal cells from mitochondrial damage caused by accumulation of S-nitrosylated microtubule associated protein 1B-light chain 1 (LC1). S-nitrosylation of LC1 induces a conformational change that serves both to activate LC1 and to promote its ubiquination by MITOL, indicating that microtubule
stabilization by LC1 is regulated through its interaction with MITOL. Excessive NO production can inhibit MITOL, and MITOL inhibition resulted in accumulation of S-nitrosylated LC1 following stimulation of NO production by calcimycin and N-methyl-D-aspartate. LC1 accumulation under these conditions resulted in mitochondrial dysfunction and neuronal cell death. Thus, the balance between LC1 activation by S-nitrosylation and down-regulation by MITOL is critical for neuronal cell survival. Our findings may contribute significantly to an understanding of the mechanisms of neurological diseases caused by nitrosative stress-mediated mitochondrial dysfunction.

Yonashiro R, Kimijima Y, Shimura T, Kawaguchi K, et al. Mitochondrial ubiquitin ligase MITOL blocks S-nitrosylated MAP1B-light chain 1-mediated mitochondrial dysfunction and neuronal cell death. PNAS; 2012. pp 6.

Ubiquitin–Proteasome System in Neurodegeneration
A common histopathological hallmark of most neurodegenerative diseases is the presence of aberrant proteinaceous inclusions inside affected neurons. Because these protein aggregates are detected using antibodies against components of the ubiquitin–proteasome system (UPS), impairment of this machinery for regulated proteolysis has been suggested to be at the root of neurodegeneration. This hypothesis has been difficult to prove in vivo owing to the lack of appropriate tools. The recent report of transgenic mice with ubiquitous expression of a UPS-reporter protein should finally make it possible to test in vivo the role of the UPS in neurodegeneration.

Hernandez F, Dıaz-Hernandez M, Avila J and Lucas JJ. Testing the ubiquitin–proteasome hypothesis of neurodegeneration in vivo. TRENDS in Neurosciences 2004; 27(2): 66-68.

ALP in Parkinson’s
The ubiquitin-proteasome system (UPS) and autophagy-lysosome pathway (ALP) are the two most important mechanisms that normally repair or remove abnormal proteins. Alterations in the function of these systems to degrade misfolded and aggregated proteins are being increasingly recognized as playing a pivotal role in the pathogenesis of many neurodegenerative disorders such as Parkinson’s disease. Dysfunction of the UPS has been already strongly implicated in the pathogenesis of this disease and, more recently, growing interest has been shown in identifying the role of ALP in neurodegeneration. Mutations of a-synuclein and the increase of intracellular concentrations of non-mutant a-synuclein have been associated with Parkinson’s disease phenotype.

The demonstration that a-synuclein is degraded by both proteasome and autophagy indicates a possible linkage between the dysfunction of the UPS or ALP and the occurrence of this disorder.The fact that mutant a-synucleins inhibit ALP functioning by tightly binding to the receptor on the lysosomal membrane for autophagy pathway further supports the assumption that impairment of the ALP may be related to the development of Parkinson’s disease.

In this review, we summarize the recent findings related to this topic and discuss the unique role of the ALP in this neurogenerative disorder and the putative therapeutic potential through ALP enhancement.

Pan Y, Kondo S, Le W, Jankovic J. The role of autophagy-lysosome pathway in
neurodegeneration associated with Parkinson’s disease. Brain 2008; 131: 1969-1978. doi:10.1093/brain/awm318.

Ubiquitin-Proteasome System in Parkinson’s

There is growing evidence that dysfunction of the mitochondrial respiratory chain and failure of the cellular protein degradation machinery, specifically the ubiquitin-proteasome system, play an important role in the pathogenesis of Parkinson’s disease. We now show that the corresponding pathways of these two systems are linked at the transcriptomic level in Parkinsonian substantia nigra. We examined gene expression in medial and lateral substantia nigra (SN) as well as in frontal cortex using whole genome DNA oligonucleotide microarrays. In this study, we use a hypothesis-driven approach in analysing microarray data to describe the expression of mitochondrial and ubiquitin-proteasomal system (UPS) genes in Parkinson’s disease (PD).

Although a number of genes showed up-regulation, we found an overall decrease in expression affecting the majority of mitochondrial and UPS sequences. The down-regulated genes include genes that encode subunits of complex I and the Parkinson’s-disease-linked UCHL1. The observed changes in expression were very similar for both medial and lateral SN and also affected the PD cerebral cortex. As revealed by “gene shaving” clustering analysis, there was a very significant correlation between the transcriptomic profiles of both systems including in control brains.

Therefore, the mitochondria and the proteasome form a higher-order gene regulatory network that is severely perturbed in Parkinson’s disease. Our quantitative results also suggest that Parkinson’s disease is a disease of more than one cell class, i.e. that it goes beyond the catecholaminergic neuron and involves glia as well.

Duke DC, Moran LB, Kalaitzakis ME, Deprez M, et al. Transcriptome analysis reveals link between proteasomal and mitochondrial pathways in Parkinson’s disease. Neurogenetics 2006; 7:139-148.
Bax Degradation a Novel Mechanism for Survival in Bcl-2 overexpressed cancer cells
The authors previously reported that proteasome inhibitors were able to overcome Bcl-2-mediated protection from apoptosis, and now show that inhibition of the proteasome activity in Bcl-2-overexpressing cells accumulates the proapoptotic Bax protein to mitochondrial cytoplasm, where it interacts to Bcl-2 protein. This event was followed by release of mitochondrial cytochrome c into the cytosol and activation of caspase-mediated apoptosis. In contrast, proteasome inhibition did not induce any apparent changes in Bcl-2 protein levels. In addition, treatment with a proteasome inhibitor increased levels of ubiquitinated forms of Bax protein, without any effects on Bax mRNA expression. They also established a cell-free Bax degradation assay in which an in vitro-translated, 35S-labeled Bax protein can be degraded by a tumor cell protein extract, inhibitable by addition of a proteasome inhibitor or depletion of the proteasome or ATP. The Bax degradation activity can be reconstituted in the proteasome-depleted supernatant by addition of a purified 20S proteasome or proteasome-enriched fraction. Finally, by using tissue samples of human prostate adenocarcinoma, they demonstrated that increased levels of Bax degradation correlated well with decreased levels of Bax protein and increased Gleason scores of prostate cancer. These studies strongly suggest that ubiquitin-proteasome-mediated Bax degradation is a novel survival mechanism in human cancer cells and that selective targeting of this pathway should provide a unique approach for treatment of human cancers, especially those overexpressing Bcl-2.
In the current study, These investigators report that

  • (i) proteasome inhibition results in Bax accumulation before release of cytochrome c and induction of apoptosis, which is associated with the ability of proteasome inhibitors to overcome Bcl-2-mediated antiapoptotic function;
  • (ii) Bax is regulated by an ATP-ubiquitin-proteasome-dependent degradation pathway; and
  • (iii) decreased levels of Bax protein correlate with increased levels of Bax degradation in aggressive human prostate cancer.

Li B and Dou QP. Bax degradation by the ubiquitin-proteasome-dependent pathway: Involvement in tumor survival and progression. PNAS 2000; 97(8): 3851-3855.

p97 and DBeQ, ATP-competitive p97 inhibitor
A major limitation to current studies on the biological functions of p97/Cdc48 is that there is no method to rapidly shut off its ATPase activity. Given the range of cellular processes in which Cdc48 participates, it is difficult to determine whether any particular phenotype observed in the existing mutants is due to a direct or indirect effect. Moreover, inhibition of p97 activity in animal cells by siRNA or expression of a dominant-negative version is challenged by its high abundance and is not suited to evaluating proximal phenotypic effects of p97 loss of function.

A specific small-molecule inhibitor of p97 would provide an important tool to investigate diverse functions of this essential ATPase associated with diverse cellular activities (AAA) ATPase and to evaluate its potential to be a therapeutic target in human disease. Cancer cells may be particularly sensitive to killing by suppression of protein degradation mechanisms, because they may exhibit a heightened dependency on these mechanisms to clear an elevated burden of quality-control substrates. For example, some cancers produce high levels of a specific protein that is a prominent quality-control substrate (e.g., Ig light chains in multiple myeloma) or produce high levels of reactive oxygen species, which can result in excessive protein damage via oxidation. Therefore, a specific p97 inhibitor would be a valuable research tool to investigate p97 function in cells.

We carried out a high-throughput screen to identify inhibitors of p97 ATPase activity. Dual-reporter cell lines that simultaneously express p97-dependent and p97-independent proteasome substrates were used to stratify inhibitors that emerged from the screen. N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ) was identified as a selective,potent, reversible, and ATP-competitive p97 inhibitor.

DBeQ blocks multiple processes that have been shown by RNAi to depend on p97, including degradation of ubiquitin fusion degradation and endoplasmic reticulum-associated degradation pathway reporters, as well as autophagosome maturation. DBeQ also potently inhibits cancer cell growth and is more rapid than a proteasome inhibitor at mobilizing the executioner caspases-3 and -7.

Simultaneous inhibition of proteasome and histone deacetylase 6 (HDAC6) [which is required for autophagy results in synergistic killing of multiple myeloma cells]. Interestingly, more than one dozen human clinical trials ( combine bortezomib with the broad-spectrum HDAC inhibitor vorinostat, which is active toward HDAC6. Targeting p97
may provide an alternative route to achieving the same objective. Our results provide a rationale for targeting p97 in cancer therapy. Future work will provide molecular insight into how inhibition of p97 activity by DBeQ results in apoptosis and could strengthen the rationale for a p97-targeted cancer therapeutic.

Chou TF, Brown SJ, Minond D, Nordin BE, et al. Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways. PNAS 2011; pp 6

The causes of various neurodegenerative diseases, particularly sporadic cases, remain unknown, but increasing evidence suggests that these diseases may share similar molecular and cellular mechanisms of pathogenesis. One prominent feature common to most neurodegenerative diseases is the accumulation of misfolded proteins in the form of insoluble protein aggregates or inclusion bodies. Although these aggregates have different protein compositions, they all contain ubiquitin and proteasome subunits, implying a failure of the ubiquitin-proteasome system (UPS) in the removal of misfolded proteins.

A direct link between UPS dysfunction and neurodegeneration has been
provided by recent findings that genetic mutations in UPS components cause several rare, familial forms of neurodegenerative diseases. Furthermore, it is becoming increasingly clear that oxidative stress, which results from aging or exposure to environmental toxins, can directly damage UPS components, thereby contributing to the pathogenesis of sporadic forms of neurodegenerative diseases.

Aberrations in the UPS often result in defective proteasome-mediated protein degradation, leading to accumulation of toxic proteins and eventually to neuronal cell death. Interestingly, emerging evidence has begun to suggest that impairment in substrate-specific components of the UPS, such as E3 ubiquitin-protein ligases, may cause aberrant ubiquitination and neurodegeneration in a proteasome-independent manner. This provides an overview of the molecular components of the UPS and their impairment in familial and sporadic forms of neurodegenerative diseases, and summarizes present knowledge about the pathogenic mechanisms of UPS dysfunction in neurodegeneration.

Molecular mechanisms of protein ubiquitination and degradation by the UPS. Ubiquitination involves a highly specific enzyme cascade in which

  • ubiquitin (Ub) is first activated by the ubiquitinactivating enzyme (E1),
  • then transferred to an ubiquitin-conjugating enzyme (E2), and
  • finally covalently attached to the substrate by an ubiquitin-protein ligase (E3).

Ubiquitination is a reversible posttranslational modification in which the removal of Ub is mediated by a deubiquitinating enzyme (DUB).

  • Substrate proteins can be either monoubiquitinated or polyubiquitinated through successive conjugation of Ub moieties to an internal lysine residue in Ub.
  • K48-linked poly-Ub chains are recognized by the 26S proteasome, resulting in degradation of the substrate and recycling of Ub.
  • Monoubiquitination or K63-linked polyubiquitination plays a number of regulatory roles in cells that are proteasome-independent.


Loss-of-function mutations in parkin, a 465-amino-acid RING-type E3 ligase, were first identified as the cause for autosomal recessive juvenile Parkinsonism (AR-JP) and subsequently found to account for ~50% of all recessively transmitted early-onset PD cases. Interestingly, patients with parkin mutations do not exhibit Lewy body pathology.

Possible pathogenic mechanisms by which impaired UPS components cause neurodegeneration. Genetic mutations or oxidative stress from aging and/or exposure to environmental toxins have been shown to impair the ubiquitination machinery (particularly E3 ubiquitin-protein ligases) and deubiquitinating enzymes (DUBs), resulting in abnormal ubiquitination. Depending on the type of ubiquitination affected, the impairment could cause neurodegeneration through two different mechanisms.

In the first model, aberrant K48-linked polyubiquitination resulting from impaired E3s or DUBs alters protein degradation by the proteasome, leading to accumulation of toxic proteins and subsequent neurodegeneration. The proteasomes could be directly damaged by oxidative stress or might be inhibited by protein aggregation, which exacerbates the neurotoxicity.

In the second model, aberrant monoubiquitination or K63-linked polyubiquitination resulting from impaired E3s or DUBs alters crucial non-proteasomal functions, such as gene transcription and protein trafficking, thereby causing neurodegeneration without protein aggregation.

These two models are not mutually exclusive because a single E3 or DUB enzyme, such as parkin or UCH-L1, could regulate more than one type of ubiquitination. In addition, abnormal ubiquitination and neurodegeneration could also result from mutation or oxidative stress-induced structural changes in the protein substrates that alter their recognition and degradation by the UPS.

Lian Li and Chin LS. IMPAIRMENT OF THE UBIQUITIN-PROTEASOME SYSTEM: A COMMON PATHOGENIC MECHANISM IN NEURODEGENERATIVE DISORDERS. In The Ubiquitin Proteasome System…Chapter 23. (Eds: Eds: Mario Di Napoli and Cezary Wojcik) 553-577 © 2007 Nova Science Publishers, Inc. ISBN 978-1-60021-749-4.

filedesc Schematic diagram of the ubiquitylati...

filedesc Schematic diagram of the ubiquitylation system. Created by Roger B. Dodd (Photo credit: Wikipedia)


Current Noteworthy Work

Nassif M and Hetz C.  Autophagy impairment: a crossroad between neurodegeneration and tauopathies.  BMC Biology 2012; 10:78.

Impairment of protein degradation pathways such as autophagy is emerging as a consistent and transversal pathological phenomenon in neurodegenerative diseases, including Alzheimer´s, Huntington´s, and Parkinson´s disease. Genetic inactivation of autophagy in mice has demonstrated a key role of the pathway in maintaining protein homeostasis in the brain, triggering massive neuronal loss and the accumulation of abnormal protein inclusions.  A paper in Molecular Neurodegeneration from Abeliovich´s group now suggests a role for phosphorylation of Tau and the activation of glycogen synthase kinase 3β (GSK3β) in driving neurodegeneration in autophagy-deficient neurons. We discuss the implications of this study for understanding the factors driving neurofibrillary tangle formation in Alzheimer´s disease and tauopathies.

Cajee UF, Hull R and Ntwasa M. Modification by Ubiquitin-Like Proteins: Significance in Apoptosis and Autophagy Pathways. Int. J. Mol. Sci. 2012, 13, 11804-11831; doi:10.3390/ijms130911804

Ubiquitin-like proteins (Ubls) confer diverse functions on their target proteins. The modified proteins are involved in various biological processes, including DNA replication, signal transduction, cell cycle control, embryogenesis, cytoskeletal regulation,
metabolism, stress response, homeostasis and mRNA processing. Modifiers such as SUMO, ATG12, ISG15, FAT10, URM1, and UFM have been shown to modify proteins thus conferring functions related to programmed cell death, autophagy and regulation of
the immune system. Putative modifiers such as Domain With No Name (DWNN) have been identified in recent times but not fully characterized. In this review, we focus on cellular processes involving human Ubls and their targets.

Aloy P. Shaping the future of interactome networks. (A report of the third Interactome Networks Conference, Hinxton, UK, 29 August-1 September 2007). Genome Biology 2007; 8:316 (doi:10.1186/gb-2007-8-10-316)

Complex systems are often networked, and biology is no exception. Following on from the genome sequencing projects,
experiments show that proteins in living organisms are highly connected, which helps to explain how such great complexity
can be achieved by a comparatively small set of gene products. At a recent conference on interactome networks held outside
Cambridge, UK, the most recent advances in research on cellular networks were discussed. This year’s conference focused on
identifying the strengths and weaknesses of currently resolved interaction networks and the techniques used to determine
them – reflecting the fact that the field of mapping interaction networks is maturing.

Peroutka RJ, Orcutt SJ, Strickler JE, and Butt TR. SUMO Fusion Technology for Enhanced Protein Expression and Purification in Prokaryotes and Eukaryotes. Chapter 2. in T.C. Evans, M.-Q. Xu (eds.), Heterologous Gene Expression in E. coli, Methods in Molecular Biology 705:15-29. DOI 10.1007/978-1-61737-967-3_2, © Springer Science+Business Media, LLC 2011

The preparation of sufficient amounts of high-quality protein samples is the major bottleneck for structural proteomics. The use of recombinant proteins has increased significantly during the past decades. The most commonly used host, Escherichia coli, presents many challenges including protein misfolding, protein degradation, and low solubility. A novel SUMO fusion technology appears to enhance protein expression and solubility ( Efficient removal of the SUMO tag by SUMO protease in vitro facilitates the generation of target protein with a native N-terminus. In addition to its physiological relevance in eukaryotes, SUMO can be used as a powerful biotechnology tool for enhanced functional protein expression in prokaryotes and eukaryotes.

Juang YC, Landry MC, et al. OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function. Molecular Cell 2012; 45: 384–397. DOI 10.1016/j.molcel.2012.01.011

Ubiquitylation entails the concerted action of E1, E2, and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response.

Hunter T. The Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond. Molecular Cell  2007; 28:730-738. DOI 10.1016/ j.molcel.2007.11.019.

Crosstalk between different types of posttranslational modification is an emerging theme in eukaryotic biology. Particularly prominent are the multiple connections between phosphorylation and ubiquitination, which act either positively or negatively in both directions to regulate these processes.

Tu Y, Chen C, et al. The Ubiquitin Proteasome Pathway (UPP) in the regulation of cell cycle control and DNA damage repair and its implication in tumorigenesis. Int J Clin Exp Pathol 2012;5(8):726-738. /ISSN:1936-2625/IJCEP1208018

Accumulated evidence supports that the ubiquitin proteasome pathway (UPP) plays a crucial role in protein
metabolism implicated in the regulation of many biological processes such as cell cycle control, DNA damage
response, apoptosis, and so on. Therefore, alterations for the ubiquitin proteasome signaling or functional impairments
for the ubiquitin proteasome components are involved in the etiology of many diseases, particularly in cancer
development.The authors discuss the ubiquitin proteasome pathway in the regulation of cell cycle control and DNA
damage response, the relevance for the altered regulation of these signaling pathways in tumorigenesis, and finally
assess and summarize the advancement for targeting the ubiquitin proteasome pathway in cancer therapy.

Cebollero E , Reggiori F  and Kraft C.  Ribophagy: Regulated Degradation of Protein Production Factories. Int J Cell Biol. 2012; 2012: 182834. doi:  10.1155/2012/182834 (online).

During autophagy, cytosol, protein aggregates, and organelles are sequestered into double-membrane vesicles called autophagosomes and delivered to the lysosome/vacuole for breakdown and recycling of their basic components. In all eukaryotes this pathway is important for adaptation to stress conditions such as nutrient deprivation, as well as to regulate intracellular homeostasis by adjusting organelle number and clearing damaged structures. For a long time, starvation-induced autophagy has been viewed as a nonselective transport pathway; however, recent studies have revealed that autophagy is able to selectively engulf specific structures, ranging from proteins to entire organelles. In this paper, we discuss recent findings on the mechanisms and physiological implications of two selective types of autophagy: ribophagy, the specific degradation of ribosomes, and reticulophagy, the selective elimination of portions of the ER.

Lee JH, Yu WH,…, Nixon RA.  Lysosomal Proteolysis and Autophagy Require Presenilin 1 and Are Disrupted by Alzheimer-Related PS1 Mutations. Cell 2010; 141, 1146–1158. DOI 10.1016/j.cell.2010.05.008.

Macroautophagy is a lysosomal degradative pathway essential for neuron survival. Here, we show that macroautophagy requires the Alzheimer’s disease (AD)-related protein presenilin-1 (PS1). In PS1 null blastocysts, neurons from mice hypomorphic for PS1 or
conditionally depleted of PS1, substrate proteolysis and autophagosome clearance during macroautophagy are prevented as a result of a selective impairment of autolysosome acidification and cathepsin activation. These deficits are caused by failed PS1-dependent
targeting of the v-ATPase V0a1 subunit to lysosomes. N-glycosylation of the V0a1 subunit, essential for its efficient ER-to-lysosome delivery, requires the selective binding of PS1 holoprotein to the unglycosylated subunit and the  sec61alpha/ oligosaccharyltransferase complex. PS1 mutations causing early-onset AD produce a similar lysosomal/autophagy phenotype in
fibroblasts from AD patients. PS1 is therefore essential for v-ATPase targeting to lysosomes, lysosome acidification, and proteolysis during autophagy. Defective lysosomal proteolysis represents a basis for pathogenic protein accumulations and neuronal cell death in AD and suggests previously unidentified therapeutic targets.

Pohl C and Jentsch S. Midbody ring disposal by autophagy is a post-abscission event of cytokinesis. nature cell biology 2009; 11 (1): 65-70.  DOI: 10.1038/ncb1813.

At the end of cytokinesis, the dividing cells are connected by an intercellular bridge, containing the midbody along with a single,
densely ubiquitylated, circular structure called the midbody ring (MR). Recent studies revealed that the MR serves as a target
site for membrane delivery and as a physical barrier between the prospective daughter cells. The MR materializes in telophase,
localizes to the intercellular bridge during cytokinesis, and moves asymmetrically into one cell after abscission. Daughter
cells rarely accumulate MRs of previous divisions, but how these large structures finally disappear remains unknown.
Here, we show that MRs are discarded by autophagy, which involves their sequestration into autophagosomes and delivery to
lysosomes for degradation. Notably, autophagy factors, such as the ubiquitin adaptor p62 and the ubiquitin-related protein Atg8 , associate with the MR during abscission, suggesting that autophagy is coupled to cytokinesis. Moreover, MRs accumulate in cells of patients with lysosomal storage disorders, indicating that defective MR disposal is characteristic of these diseases. Thus our findings suggest that autophagy has a broader role than previously assumed, and that cell renovation by clearing from superfluous large macromolecular assemblies, such as MRs, is an important autophagic function.


Hanai JI, Cao P, Tanksale P, Imamura S, et al. The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity. The Journal of Clinical Investigation  2007; 117(12):3930-3951.

Statins inhibit HMG-CoA reductase, a key enzyme in cholesterol synthesis, and are widely used to treat hypercholesterolemia.
These drugs can lead to a number of side effects in muscle, including muscle fiber breakdown; however, the mechanisms of muscle injury by statins are poorly understood. We report that lovastatin induced the expression of atrogin-1, a key gene involved in skeletal muscle atrophy, in humans with statin myopathy, in zebrafish embryos, and in vitro in murine skeletal muscle cells. In cultured mouse myotubes, atrogin-1 induction following lovastatin treatment was accompanied by distinct morphological changes, largely absent in
atrogin-1 null cells. In zebrafish embryos, lovastatin promoted muscle fiber damage, an effect that was closely mimicked by knockdown of zebrafish HMG-CoA reductase. Moreover, atrogin-1 knockdown in zebrafish embryos prevented lovastatin-induced muscle injury. Finally, overexpression of PGC-1α, a transcriptional coactivator that induces mitochondrial biogenesis and protects against the development of muscle atrophy, dramatically prevented lovastatin-induced muscle damage and abrogated atrogin-1 induction both in fish and in cultured mouse myotubes. Collectively, our human, animal, and in vitro findings shed light on the molecular mechanism of statin-induced myopathy and suggest that atrogin-1 may be a critical mediator of the muscle
damage induced by statins.

Inami Y, Waguri S, Sakamoto A, Kouno T, et al.  Persistent activation of Nrf2 through p62 in hepatocellular carcinoma cells. J. Cell Biol. 2011; 193(2): 275–284.

Macroautophagy (hereafter referred to as autophagy) is a cellular degradation system in which cytoplasmic components, including
organelles, are sequestered by double membrane structures called autophagosomes and the sequestered materials are
degraded by lysosomal hydrolases for supply of amino acids and for cellular homeostasis. Although autophagy has generally been considered nonselective, recent studies have shed light on another indispensable role for basal autophagy in cellular homeostasis, which is mediated by selective degradation of a specific substrate(s).  p62 is a ubiquitously expressed cellular protein that is conserved in metazoa but not in plants and fungi, and recently it has been known as one of the selective substrates for autophagy.
This protein is localized at the autophagosome formation site  and directly interacts with LC3, an autophagosome localizing protein . Subsequently, the p62 is incorporated into the autophagosome and then degraded. Therefore, impaired autophagy is accompanied by
accumulation of p62 followed by the formation of p62 and ubiquitinated protein aggregates because of the nature of both self- oligomerization and ubiquitin binding of p62.


Kima K, Khayrutdinov BI, Leeb CK, et al. Solution structure of the Zβ domain of human DNA-dependent activator of IFN-regulatory factors and its binding modes to B- and Z-DNAs. PNAS 2010; Early Edition ∣ pp 6.

The DNA-dependent activator of IFN-regulatory factors (DAI), also known as DLM-1/ZBP1, initiates an innate immune response by binding to foreign DNAs in the cytosol. For full activation of the immune response, three DNA binding domains at the N terminus are required: two Z-DNA binding domains (ZBDs), Zα and Zβ, and an adjacent putative B-DNA binding domain. The crystal structure of the Zβ domain of human DAI (hZβDAI) in complex with Z-DNA revealed structural features distinct from other known Z-DNA binding proteins, and it was classified as a group II ZBD. To gain structural insights into the DNA binding mechanism of hZβDAI, the solution structure of the free hZβDAI was solved, and its bindings to B- and Z-DNAs were analyzed by NMR spectroscopy. Compared to the Z-DNA–bound structure, the conformation of free hZβDAI has notable alterations in the α3 recognition helix, the “wing,” and Y145, which are critical in Z-DNA recognition. Unlike some other Zα domains, hZβDAI appears to have conformational flexibility, and structural adaptation is required for Z-DNA binding. Chemical-shift perturbation experiments revealed that hZβDAI also binds weakly to B-DNA via a different binding mode. The C-terminal domain of DAI is reported to undergo a conformational change on B-DNA binding; thus, it is possible that these changes are correlated. During the innate immune response, hZβDAI is likely to play an active role in binding to DNAs in both B and Z conformations in the recognition of foreign DNAs.



This extensive review leaves little left unopened. We have seen the central role that the UPS system plays in normal organelle proteolysis in concert with autophagy. Impaired ubiquitination occurs from aging, and/or toxins, under oxidative stress involving E3s or DUBs.

This leads to altered gene transcripton, altered protein trafficking, and plays a role in neurodegenative disease, muscle malfunction, and cancer as well.

English: A cartoon representation of a lysine ...

English: A cartoon representation of a lysine 48-linked diubiquitin molecule. The two ubiquitin chains are shown as green cartoons with each chain labelled. The components of the linkage are indicated and shown as orange sticks. Image was created using PyMOL from PDB id 1aar. (Photo credit: Wikipedia)

Different forms of protein ubiquitylation

Different forms of protein ubiquitylation (Photo credit: Wikipedia)

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