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Extracellular evaluation of intracellular flux in yeast cells

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

Leaders in Pharmaceutical Intelligence

This is the fourth article in a series on metabolomics, which is a major development in -omics, integrating transcriptomics, proteomics,  genomics, metabolic pathways analysis, metabolic and genomic regulatory control using computational mapping.  In the previous two part presentation, flux analysis was not a topic for evaluation, but here it is the major focus.  It is a study of yeast cells, and bears some relationship to the comparison of glycemia, oxidative phosphorylation, TCA cycle, and ETC in leukemia cell lines.  In the previous study – system flux was beyond the scope of analysis, and explicitly stated.  The inferences made in comparing the two lymphocytic leukemia cells was of intracellular metabolism from extracellular measurements.  The study of yeast cells is aimed at looking at cellular effluxes, which is also an important method for studying pharmacological effects and drug resistance.

Metabolomic series

1.  Metabolomics, Metabonomics and Functional Nutrition: the next step in nutritional metabolism and biotherapeutics

https://pharmaceuticalintelligence.com/2014/08/22/metabolomics-metabonomics-and-functional-nutrition-the-next-step-in-nutritional-metabolism-and-biotherapeutics/

2.  Metabolomic analysis of two leukemia cell lines. I

https://pharmaceuticalintelligence.com/2014/08/23/metabolomic-analysis-of-two-leukemia-cell-lines-_i/

3.  Metabolomic analysis of two leukemia cell lines. II.

 https://pharmaceuticalintelligence.com/2014/08/24/metabolomic-analysis-of-two-leukemia-cell-lines-ii/

4.  Extracellular evaluation of intracellular flux in yeast cells

Q1. What is efflux?

Q2. What measurements were excluded from the previous study that would not allow inference about fluxes?

Q3. Would this study bear any relationship to the Pasteur effect?

Q4 What is a genome scale network reconstruction?

Q5 What type of information is required for a network prediction model?

Q6. Is there a difference between the metabolites profiles for yeast grown under aerobic and anaerobuc conditions – under the constrainsts?

Q7.  If there is a difference in the S metabolism, would there be an effect on ATP production?

 

 

Connecting extracellular metabolomic measurements to intracellular flux
states in yeast

Monica L Mo1Bernhard Ø Palsson1 and Markus J Herrgård12*

Author Affiliations

1 Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA

2 Current address: Synthetic Genomics, Inc, 11149 N Torrey Pines Rd, La Jolla, CA 92037, USA

For all author emails, please log on.

BMC Systems Biology 2009, 3:37  doi:10.1186/1752-0509-3-37

 

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1752-0509/3/37

 

Received: 15 December 2008
Accepted: 25 March 2009
Published: 25 March 2009

© 2009 Mo et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Metabolomics has emerged as a powerful tool in the

  • quantitative identification of physiological and disease-induced biological states.

Extracellular metabolome or metabolic profiling data, in particular,

  • can provide an insightful view of intracellular physiological states in a noninvasive manner.

Results

We used an updated genome-scale

  • metabolic network model of Saccharomyces cerevisiae, iMM904, to investigate
  1. how changes in the extracellular metabolome can be used
  2. to study systemic changes in intracellular metabolic states.

The iMM904 metabolic network was reconstructed based on

  • an existing genome-scale network, iND750,
  • and includes 904 genes and 1,412 reactions.

The network model was first validated by

  • comparing 2,888 in silico single-gene deletion strain growth phenotype predictions
  • to published experimental data.

Extracellular metabolome data measured

  • of ammonium assimilation pathways 
  • in response to environmental and genetic perturbations

was then integrated with the iMM904 network

  • in the form of relative overflow secretion constraints and
  • a flux sampling approach was used to characterize candidate flux distributions allowed by these constraints.

Predicted intracellular flux changes were

  • consistent with published measurements
  • on intracellular metabolite levels and fluxes.

Patterns of predicted intracellular flux changes

  • could also be used to correctly identify the regions of
  • the metabolic network that were perturbed.

Conclusion

Our results indicate that

  • integrating quantitative extracellular metabolomic profiles
  • in a constraint-based framework
  • enables inferring changes in intracellular metabolic flux states.

Similar methods could potentially be applied

  • towards analyzing biofluid metabolome variations
  • related to human physiological and disease states.

Background

“Omics” technologies are rapidly generating high amounts of data

  • at varying levels of biological detail.

In addition, there is a rapidly growing literature and

  • accompanying databases that compile this information.

This has provided the basis for the assembly of

  • genome-scale metabolic networks for various microbial and eukaryotic organisms [111].

These network reconstructions serve

  • as manually curated knowledge bases of
  • biological information as well as
  • mathematical representations of biochemical components and
  • interactions specific to each organism.

genome-scale network reconstruction is

  • structured collection of genes, proteins, biochemical reactions, and metabolites
  • determined to exist and operate within a particular organism.

This network can be converted into a predictive model

  • that enables in silico simulations of allowable network states based on
  • governing physico-chemical and genetic constraints [12,13].

A wide range of constraint-based methods have been developed and applied

  • to analyze network metabolic capabilities under
  • different environmental and genetic conditions [13].

These methods have been extensively used to

  • study genome-scale metabolic networks and have successfully predicted, for example,
  1. optimal metabolic states,
  2. gene deletion lethality, and
  3. adaptive evolutionary endpoints [1416].

Most of these applications utilize

  • optimization-based methods such as flux balance analysis (FBA)
  • to explore the metabolic flux space.

However, the behavior of genome-scale metabolic networks can also be studied

  • using unbiased approaches such as
  • uniform random sampling of steady-state flux distributions [17].

Instead of identifying a single optimal flux distribution based on

  • a given optimization criterion (e.g. biomass production),

these methods allow statistical analysis of

  • a large range of possible alternative flux solutions determined by
  • constraints imposed on the network.

Sampling methods have been previously used to study

  1. global organization of E. coli metabolism [18] as well as
  2. to identify candidate disease states in the cardiomyocyte mitochondria [19].

Network reconstructions provide a structured framework

  • to systematically integrate and analyze disparate datasets
  • including transcriptomic, proteomic, metabolomic, and fluxomic data.

Metabolomic data is one of the more relevant data types for this type of analysis as

  1. network reconstructions define the biochemical links between metabolites, and
  2. recent advancements in analytical technologies have allowed increasingly comprehensive
  • intracellular and extracellular metabolite level measurements [20,21].

The metabolome is

  1. the set of metabolites present under a given physiological condition
  2. at a particular time and is the culminating phenotype resulting from
  • various “upstream” control mechanisms of metabolic processes.

Of particular interest to this present study are

  • the quantitative profiles of metabolites that are secreted into the extracellular environment
  • by cells under different conditions.

Recent advances in profiling the extracellular metabolome (EM) have allowed

  • obtaining insightful biological information on cellular metabolism
  • without disrupting the cell itself.

This information can be obtained through various

  • analytical detection,
  • identification, and
  • quantization techniques

for a variety of systems ranging from

  • unicellular model organisms to human biofluids [2023].

Metabolite secretion by a cell reflects its internal metabolic state, and

  • its composition varies in response to
  • genetic or experimental perturbations
  • due to changes in intracellular pathway activities
  • involved in the production and utilization of extracellular metabolites [21].

Variations in metabolic fluxes can be reflected in EM changes which can

  • provide insight into the intracellular pathway activities related to metabolite secretion.

The extracellular metabolomic approach has already shown promise

  • in a variety of applications, including
  1. capturing detailed metabolite biomarker variations related to disease and
  2. drug-induced states and
  3. characterizing gene functions in yeast [2427].

However, interpreting changes in the extracellular metabolome can be challenging

  • due to the indirect relationship between the proximal cause of the change
    (e.g. a mutation)
  • and metabolite secretion.

Since metabolic networks describe

  • mechanistic,
  • biochemical links between metabolites,

integrating such data can allow a systematic approach

  • to identifying altered pathways linked to
  • quantitative changes in secretion profiles.

Measured secretion rates of major byproduct metabolites

  • can be applied as additional exchange flux constraints
  • that define observed metabolic behavior.

For example, a recent study integrating small-scale EM data

  • with a genome-scale yeast model
  • correctly predicted oxygen consumption and ethanol production capacities
  • in mutant strains with respiratory deficiencies [28].

The respiratory deficient mutant study

  • used high accuracy measurements for a small number of
  • major byproduct secretion rates
  • together with an optimization-based method well suited for such data.

Here, we expand the application range of the model-based method used in [28]

  • to extracellular metabolome profiles,
  • which represent a temporal snapshot of the relative abundance
  • for a larger number of secreted metabolites.

Our approach is complementary to

  • statistical (i.e. “top-down”) approaches to metabolome analysis [29]
  • and can potentially be used in applications such as biofluid-based diagnostics or
  • large-scale characterization of mutants strains using metabolite profiles.

This study implements a constraint-based sampling approach on

  • an updated genome-scale network of yeast metabolism
  • to systematically determine how EM level variations

are linked to global changes in intracellular metabolic flux states.

By using a sampling-based network approach and statistical methods (Figure 1),

  • EM changes were linked to systemic intracellular flux perturbations
    in an unbiased manner
  • without relying on defining single optimal flux distributions
  • used in the previously mentioned study [28].

The inferred perturbations in intracellular reaction fluxes were further analyzed

  • using reporter metabolite and subsystem (i.e., metabolic pathway) approaches [30]
  • in order to identify dominant metabolic features that are collectively perturbed (Figure 2).

The sampling-based approach also has the additional benefit of

  • being less sensitive to inaccuracies in metabolite secretion profiles than
  • optimization-based methods and can effectively be used – in biofluid metabolome analysis.
integration of exometabolomic (EM) data

integration of exometabolomic (EM) data

Figure 1. Schematic illustrating the integration of exometabolomic (EM) data with the constraint-based framework.

(A) Cells are subjected to genetic and/or environmental perturbations to secrete metabolite patterns unique to that condition.
(B) EM is detected, identified, and quantified.
(C) EM data is integrated as required secretion flux constraints to define allowable solution space.
(D) Random sampling of solution space yields the range of feasible flux distributions for intracellular reactions.
(E) Sampled fluxes were compared to sampled fluxes of another condition to determine

  • which metabolic regions were altered between the two conditions (see Figure 2).

(F) Significantly altered metabolic regions were identified.

http://www.biomedcentral.com/content/figures/1752-0509-3-37-1.jpg

 

sampling and scoring analysis to determine intracellular flux changes

sampling and scoring analysis to determine intracellular flux changes

Figure 2. Schematic of sampling and scoring analysis to determine intracellular flux changes.

(A) Reaction fluxes are sampled for two conditions.
(B & C) Sample of flux differences is calculated by selecting random flux values from each condition

  • to obtain a distribution of flux differences for each reaction.

(D) Standardized reaction Z-scores are determined, which represent

  • how far the sampled flux differences deviates from a zero flux change.

Reaction scores can be used in

  1. visualizing perturbation subnetworks and
  2. analyzing reporter metabolites and subsystems.

http://www.biomedcentral.com/content/figures/1752-0509-3-37-2.jpg

This study was divided into two parts and describes:

(i) the reconstruction and validation of an expanded S. cerevisiae metabolic network, iMM904; and
(ii) the systematic inference of intracellular metabolic states from

  • two yeast EM data sets using a constraint-based sampling approach.

The first EM data set compares wild type yeast to the gdh1/GDH2 (glutamate dehydrogenase) strain [31],

  • which indicated good agreement between predicted metabolic changes
  • of intracellular metabolite levels and fluxes [31,32].

The second EM data set focused on secreted amino acid measurements

  • from a separate study of yeast cultured in different
    ammonium and potassium concentrations [33].

We analyzed the EM data to gain further insight into

  • perturbed ammonium assimilation processes as well as
  1. metabolic states relating potassium limitation and
  2. ammonium excess conditions to one another.

The model-based analysis of both

  • separately published extracellular metabolome datasets
  • suggests a relationship between
  1. glutamate,
  2. threonine and
  3. folate metabolism,
  • which are collectively perturbed when
    ammonium assimilation processes are broadly disrupted
  1. either by environmental (excess ammonia) or
  2. genetic (gene deletion/overexpression) perturbations.

The methods herein present an approach to

  • interpreting extracellular metabolome data and
  • associating these measured secreted metabolite variations
  • to changes in intracellular metabolic network states.

Additional file 1. iMM904 network content.

The data provided represent the content description of the iMM904 metabolic network and
detailed information on the expanded content.

Format: XLS Size: 2.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2. iMM904 model files.

The data provided are the model text files of the iMM904 metabolic network
that is compatible with the available COBRA Toolbox [13]. The model structure
can be loaded into Matlab using the ‘SimPhenyPlus’ format with GPR and compound information.

Format: ZIP Size: 163KB Download file

Conversion of the network to a predictive model

The network reconstruction was converted to a constraint-based model using established procedures [13].

Network reactions and metabolites were assembled into a stoichiometric matrix 

  • containing the stoichiometric coefficients of the reactions in the network.

The steady-state solution space containing possible flux distributions

  • is determined by calculating the null space of S= 0,

where is the reaction flux vector.

Minimal media conditions were set through constraints on exchange fluxes

  • corresponding to the experimental measured substrate uptake rates.

All the model-based calculations were done using the Matlab COBRA Toolbox [13]

  • utilizing the glpk or Tomlab/CPLEX (Tomopt, Inc.) optimization solvers.

Chemostat growth simulations

The iMM904 model was initially validated by

  1. simulating wild type yeast growth in aerobic and anaerobic
    carbon-limited chemostat conditions
  2. and comparing the simulation results to published experimental data

on substrate uptake and byproduct secretion in these conditions [34].

The study was performed following the approach taken to validate the iFF708 model in a previous study [35].

The predicted glucose uptake rates were determined

  1. by setting the in silico growth rate to the measured dilution rate,
    – equivalent under continuous culture growth,
  2. and minimizing the glucose uptake rate.

The accuracy of in silico predictions of

  • substrate uptake and byproduct secretion by the iMM904 model
  • was similar to the accuracy obtained using the iFF708 model
  • and results are shown in Figure S1 [see Additional file 3].

Additional file 3. Supplemental figures. 

The file provides the supplemental figures and descriptions of S1, S2, S3, and S4.

Format: PDF Size: 513KB Download file

This file can be viewed with: Adobe Acrobat Reader

Genome-scale gene deletion phenotype predictions

The iMM904 network was further validated by

  • performing genome-scale gene lethality computations
  • following established procedures to determine growth phenotypes
  1. under minimal medium conditions and
  2. compared to published data.

A modified version of the biomass function used in previous iND750 studies

  1. was set as the objective to be maximized and
  2. gene deletions were simulated by

setting the flux through the corresponding reaction(s) to zero.

The biomass function was based on the experimentally measured

  1. composition of major cellular constituents
  2. during exponential growth of yeast cells and
  3. was reformulated to include trace amounts of
  4. additional cofactors and metabolites
  5. with the assumed fractional contribution of 10-.

These additional biomass compounds were included

according to the biomass formulation used in the iLL672 study

  • to improve lethality predictions through
  • the inclusion of additional essential biomass components [3].

The model was constrained by limiting

  1. the carbon source uptake to 10 mmol/h/gDW
  2. and oxygen uptake to 2 mmol/h/gDW.

Ammonia, phosphate, and sulfate were assumed to be non-limiting.

The experimental phenotyping data was obtained

  • using strains that were auxotrophic for
  1. methionine,
  2. leucine,
  3. histidine, and
  4. uracil.

These auxotrophies were simulated

  1. by deleting the appropriate genes from the model and
  2. supplementing the in silico strain with the appropriate supplements
  3. at non-limiting, but low levels.

Furthermore, trace amounts of essential nutrients that are present

  • in the experimental minimal media formulation
  1. 4-aminobenzoate,
  2. biotin,
  3. inositol,
  4. nicotinate,
  5. panthothenate,
  6. thiamin)
  • were supplied in the simulations [3].

Three distinct methods to simulate the outcome of gene deletions were utilized:

  1. Flux-balance analysis (FBA) [36-38],
  2. Minimization of Metabolic Adjustment (MoMA) [39], and
  3. a linear version of MoMA (linearMoMA).

In the linearMoMA method, minimization of the quadratic objective function
of the original MoMA algorithm

  • was replaced by minimization of the corresponding 1-norm objective function
    (i.e. sum of the absolute values of the differences of wild type FBA solution
    and the knockout strain flux solution).

The computed results were then compared to growth phenotype data
(viable/lethal) from a previously published experimental gene deletion study [3].

The comparison between experimental and in silico deletion phenotypes involved

  • choosing a threshold for the predicted relative growth rate of
  • a deletion strain that is considered to be viable.

We used standard ROC curve analysis

  • to assess the accuracy of different prediction methods and models
  • across the full range of the viability threshold parameter,
    results shown in Figure S2 [see Additional file 3].

The ROC curve plots the true viable rate against the false viable rate

  • allowing comparison of different models and methods
  • without requiring arbitrarily choosing this parameter a priori [40].

The optimal prediction performance corresponds to

  • the point closest to the top left corner of the ROC plot
    (i.e. 100% true viable rate, 0% false viable rate).

Table 1

Table 1 Comparison of iMM904 and iLL672 gene deletion predictions and experimental data under minimal media conditions
Media Model Method True viable False viable False lethal True lethal True viable % False viable % MCC
Glucose iMM904 full FBA 647 10 32 33 95.29 23.26 0.6
iMM904 full linMOMA 644 10 35 33 94.85 23.26 0.58
iMM904 full MOMA 644 10 35 33 94.85 23.26 0.58
iMM904 red FBA 440 9 28 33 94.02 21.43 0.61
iMM904 red linMOMA 437 9 31 33 93.38 21.43 0.6
iMM904 red MOMA 437 9 31 33 93.38 21.43 0.6
iLL672 full MOMA 433 9 35 33 92.52 21.43 0.57
Galactose iMM904 full FBA 595 32 36 59 94.29 35.16 0.58
iMM904 full linMOMA 595 32 36 59 94.29 35.16 0.58
iMM904 full MOMA 595 32 36 59 94.29 35.16 0.58
iMM904 red FBA 409 12 33 56 92.53 17.65 0.67
iMM904 red linMOMA 409 12 33 56 92.53 17.65 0.67
iMM904 red MOMA 409 12 33 56 92.53 17.65 0.67
iLL672 full MOMA 411 19 31 49 92.99 27.94 0.61
Glycerol iMM904 full FBA 596 43 36 47 94.3 47.78 0.48
iMM904 full linMOMA 595 44 37 46 94.15 48.89 0.47
iMM904 full MOMA 598 44 34 46 94.62 48.89 0.48
iMM904 red FBA 410 20 34 46 92.34 30.3 0.57
iMM904 red linMOMA 409 21 35 45 92.12 31.82 0.56
iMM904 red MOMA 412 21 32 45 92.79 31.82 0.57
iLL672 full MOMA 406 20 38 46 91.44 30.3 0.55
Ethanol iMM904 full FBA 593 45 29 55 95.34 45 0.54
iMM904 full linMOMA 592 45 30 55 95.18 45 0.54
iMM904 full MOMA 592 44 30 56 95.18 44 0.55
iMM904 red FBA 408 21 27 54 93.79 28 0.64
iMM904 red linMOMA 407 21 28 54 93.56 28 0.63
iMM904 red MOMA 407 20 28 55 93.56 26.67 0.64
iLL672 full MOMA 401 13 34 62 92.18 17.33 0.68
MCC, Matthews correlation coefficient (see Methods). Note that the iLL672 predictions were obtained directly from [3] and thus the viability threshold was not optimized using the maximum MCC approach.
Mo et al. BMC Systems Biology 2009 3:37  http://dx.doi.org:/10.1186/1752-0509-3-37

 

The values reported in Table 1 correspond to selecting

  • the optimal viability threshold based on this criterion.

We summarized the overall prediction accuracy of a model and method

  • using the Matthews Correlation Coefficient (MCC) [40].

The MCC ranges from -1 (all predictions incorrect) to +1 (all predictions correct) and

  • is suitable for summarizing overall prediction performance

in our case where there are substantially more viable than lethal gene deletions.

ROC plots were produced in Matlab (Mathworks, Inc.).

 

Table 1. Comparison of iMM904 and iLL672

  • gene deletion predictions and
  • experimental data

Inferring perturbed metabolic regions based on EM profiles

The method implemented in this study is shown schematically in Figures 1 and 2

Constraining the iMM904 network 

Relative levels of quantitative EM data were incorporated into the constraint-based framework

  • as overflow secretion exchange fluxes to simulate the required low-level production of
  • experimentally observed excreted metabolites.

The primary objective of this study is to associate

  • relative metabolite levels that are generally measured for metabonomic or biofluid analyses
  • to the quantitative ranges of intracellular reaction fluxes required to produce them.

However, without detailed kinetic information or dynamic metabolite measurements available,

  • we approximated EM datasets of relative quantitative metabolite levels
  • to be proportional to the rate in which they are secreted and detected
  • (at a steady state) – into the extracellular media.

This approach is analogous to approximating uptake rates based

  • on metabolite concentrations from a previous study performing sampling analysis
  • on a cardiomyocyte mitochondrial network
  • to identify differential flux distribution ranges

for various environmental (i.e. substrate uptake) conditions [19].

The raw data was normalized by the raw maximum value of the dataset
(thus the maximum secretion flux was 1 mmol/hr/gDW) with

  • an assumed error of 10%
  • to set the lower and upper bounds and thus
  • inherently accounting for sampling calculation sensitivity.

The gdh1/GDH2 strains were flask cultured under minimal glucose media conditions; thus,

  • glucose and oxygen uptake rates were set at 15 and 2 mmol/hr/gDW, respectively,
  • for the gdh1/GDH2 strain study.

In the anaerobic case the oxygen uptake rate was set to zero, and

  • sterols and fatty acids were provided as in silico supplements as described in [35].

For the potassium limitation/ammonium toxicity study

  • the growth rate was set at 0.17 1/h, and
  • the glucose uptake rate was minimized
  • to mimic experimental chemostat cultivation conditions.

These input constraints were constant for each perturbation and comparative wild-type condition

  • such that the calculated solution spaces between the conditions
  • differed based only on variations in the output secretion constraints.

FBA optimization of EM-constrained networks

A modified FBA method with minimization of the 1-norm objective function

  • between two optimal flux distributions was used
  • to determine optimal intracellular fluxes
  • based on the EM-constrained metabolic models.

This method determines two optimal flux distributions simultaneously

  • for two differently constrained models (e.g. wild type vs. mutant) –
  • these flux distributions maximize biomass production in each case and
  • the 1-norm distance between the distributions is as small as possible
  • given the two sets of constraints.

This approach avoids problems with

  • alternative optimal solutions when comparing two FBA-computed flux distributions
  • by assuming minimal rerouting of flux distibution between a perturbed network and its reference network.

Reaction flux changes from the FBA optimization results were determined

  • by computing the relative percentage fold change for each reaction
  • between the mutant and wild-type flux distributions.

Random sampling of the steady-state solution space

We utilized artificial centering hit-and-run (ACHR) Monte Carlo sampling [19,41]

  • to uniformly sample the metabolic flux solution space
  • defined by the constraints described above.

Reactions, and their participating metabolites, found to participate in intracellular loops [42]

  • were discarded from further analysis as these reactions can have arbitrary flux values.

The following sections describe the approaches used for the analysis of the different datasets.

Sampling approach used in the gdh1/GDH2 study

Due to the overall shape of the metabolic flux solution space,

  • most of the sampled flux distributions resided close to the minimally allowed growth rate
    (i.e. biomass production) and
  • corresponded to various futile cycles that utilized substrates but
  • did not produce significant biomass.

In order to study more physiologically relevant portions of the flux space

  • we restricted the sampling to the part of the solution space
  • where the growth rate was at least 50% of the maximum growth rate
  • for the condition as determined by FBA.

This assumes that cellular growth remains an important overall objective by the yeast cells

  • even in batch cultivation conditions, but
  • that the intracellular flux distributions
  • may not correspond to maximum biomass production [43].

To test the sensitivity of the results to the minimum growth rate threshold,

  • separate Monte Carlo samples were created for each minimum threshold
  • ranging from 50% to 100% at 5% increments.

We also tested the sensitivity of the results

  • to the relative magnitude of the extracellular metabolite secretion rates
  • by performing the sampling at three different relative levels

(0 corresponding to no extracellular metabolite secretion, maximum rate of 0.5 mmol/hr/gDW,
and maximum rate of 1.0 mmol/hr/gDW).

For each minimum growth rate threshold and extracellular metabolite secretion rate,

  • the ACHR sampler was run for 5 million steps and
  • a flux distribution was stored every 5000 steps.

The sensitivity analysis results are presented in Figures S3 and S4 [see Additional File 3], and

  • the results indicate that the reaction Z-scores (see below) are not significantly affected by
  1. either the portion of the solution space sampled or
  2. the exact scaling of secretion rates.

The final overall sample used was created by combining the samples for all minimum growth rate thresholds

  • for the highest extracellular metabolite secretion rate (maximum 1 mmol/hr/gDW).

This approach allowed biasing the sampling towards

  • physiologically relevant parts of the solution space
  • without imposing the requirement of strictly maximizing a predetermined objective function.

The samples obtained with no EM data were used as control samples

  • to filter reporter metabolites/subsystems whose scores were significantly high
  • due to only random differences between sampling runs.

Sampling approach used in the potassium limitation/ammonium toxicity study

Since the experimental data used in this study was generated in chemostat conditions, and

  • previous studies have indicated that chemostat flux patterns predicted by FBA are
  • close to the experimentally measured ones [43],
  • we assumed that sampling of the optimal solution space was appropriate for this study.

In order to sample a physiologically reasonable range of flux distributions,

  • samples for four different oxygen uptake rates
    (1, 2, 3, and 4 mmol/hr/gDW with 5 million steps each)
  • were combined in the final analysis.

Standardized scoring of flux differences between perturbation and control conditions

Z-score based approach was implemented to quantify differences in flux samples between two conditions (Figure 2).
First, two flux vectors were chosen randomly,

  • one from each of the two samples to be compared and
  • the difference between the flux vectors was computed.

This approach was repeated to create a sample of 10,000 (n) flux difference vectors

  • for each pair of conditions considered (e.g. mutant or perturbed environment vs. wild type).

Based on this flux difference sample, the sample mean (μdiff,i) and standard deviation (σdiff,i)

  • between the two conditions was calculated for each reaction i. The reaction Z-score was calculated as:

 

reaction Z-score

reaction Z-score

which describes the sampled mean difference deviation

  • from a population mean change of zero (i.e. no flux difference
    between perturbation and wild type).

Note that this approach allows accounting for uncertainty in the

  • flux distributions inferred based on the extracellular metabolite secretion constraints.

This is in contrast to approaches such as FBA or MoMA that would predict

  • a single flux distribution for each condition and thus potentially
  • overestimate differences between conditions.

The reaction Z-scores can then be further used in analysis

  • to identify significantly perturbed regions of the metabolic network
  • based on reporter metabolite [44] or subsystem [30] Z-scores.

These reporter regions indicate, or “report”, dominant perturbation features

  • at the metabolite and pathway levels for a particular condition.

The reporter metabolite Z-score for any metabolite can be derived from the reaction Z-scores

  • of the reactions consuming or producing j (set of reactions denoted as Rj) as:

 

reporter z-score for any metabolite j

reporter z-score for any metabolite j

where Nis the number of reactions in Rand mmet,is calculated as

 

distributional correction for m_met,j SQRT

distributional correction for m_met,j SQRT

To account and correct for background distribution, the metabolite Z-score was normalized

  • by computing μmet,Nj and σmet,,Nj corresponding to the mean mmet and
  • its standard deviation for 1,000 randomly generated reaction sets of size Nj.

Z-scores for subsystems were calculated similarly by considering the set of reactions R

  • that belongs to each subsystem k.

Hence, positive metabolite and subsystem scores indicate a significantly perturbed metabolic region

  • relative to other regions, whereas
  • a negative score indicate regions that are not perturbed
  • more significantly than what is expected by random chance.

Perturbation subnetworks of reactions and connecting metabolites were visualized using Cytoscape [45].

Results and discussion

  1. Reconstruction and validation of iMM904 network iMM904 network content 

A previously reconstructed S. cerevisiae network, iND750,

  • was used as the basis for the construction of the expanded iMM904 network.
  • Prior to its presentation here, the
    iMM904 network content was the basis for a consensus jamboree network that was recently published
  • but has not yet been adapted for FBA calculations [46].

The majority of iND750 content was carried over and

  • further expanded on to construct iMM904, which accounts for
  1. 904 genes,
  2. 1,228 individual metabolites, and
  3. 1,412 reactions of which
  •                       395 are transport reactions.

Both the number of gene-associated reactions and the number of metabolites

  • increased in iMM904 compared with the iND750 network.

Additional genes and reactions included in the network primarily expanded the

  • lipid,
  • transport, and
  • carbohydrate subsystems.

The lipid subsystem includes

  • new genes and
  • reactions involving the degradation of sphingolipids and glycerolipids.

Sterol metabolism was also expanded to include

  • the formation and degradation of steryl esters, the
  •                      storage form of sterols.

The majority of the new transport reactions were added

  • to connect network gaps between intracellular compartments
  • to enable the completion of known physiological functions.

We also added a number of new secretion pathways

  • based on experimentally observed secreted metabolites [31].

A number of gene-protein-reaction (GPR) relationships were modified

  • to include additional gene products that are required to catalyze a reaction.

For example, the protein compounds

  • thioredoxin and
  • ferricytochrome C

were explicitly represented as compounds in iND750 reactions, but

  • the genes encoding these proteins were not associated with their corresponding GPRs.

Other examples include glycogenin and NADPH cytochrome p450 reductases (CPRs),

  1. which are required in the assembly of glycogen and
  2. to sustain catalytic activity in cytochromes p450, respectively.

These additional proteins were included in iMM904 as

  • part of protein complexes to provide a more complete
  • representation of the genes and
  • their corresponding products necessary for a catalytic activity to occur.

Major modifications to existing reactions were in cofactor biosynthesis, namely in

  • quinone,
  • beta-alanine, and
  • riboflavin biosynthetic pathways.

Reactions from previous S. cerevisiae networks associated with

  • quinone,
  • beta-alanine, and
  • riboflavin biosynthetic pathways

were essentially inferred from known reaction mechanisms based on

  • reactions in previous network reconstructions of E. coli [2,47].

These pathways were manually reviewed

  • based on current literature and subsequently replaced by
  • reactions and metabolites specific to yeast.

Additional changes in other subsystems were also made, such as

  1. changes to the compartmental location of a gene and
  2. its corresponding reaction(s),
  3. changes in reaction reversibility and cofactor specificity, and
  4. the elucidation of particular transport mechanisms.

A comprehensive listing of iMM904 network contents as well as

  • a detailed list of changes between iND750 and iMM904 is included
    [see Additional file 1].

Predicting deletion growth phenotypes

The updated genome-scale iMM904 metabolic network was validated

  • by comparing in silico single-gene deletion predictions to
  • in vivo results from a previous study used
  • to analyze another S. cerevisiae metabolic model, iLL672 [3].

This network was constructed based on the iFF708 network [22],

  • which was also the starting point for
  • reconstructing the iND750 network [2].

The experimental data used to validate the iLL672 model consisted of

3,360 single-gene knockout strain phenotypes evaluated

  • under minimal media growth conditions with
  1. glucose,
  2. galactose,
  3. glycerol, and
  4. ethanol

as sole carbon sources. Growth phenotypes for the iMM904 network were predictedusing

  1. FBA [3234],
  2. MoMA [35], and
  3. linear MoMA methods

as described in Methods and subsequently compared to the experimental data (Table 1).

Each deleted gene growth prediction comparison was classified as

  1. true lethal,
  2. true viable,
  3. false lethal, or
  4. false viable.

The growth rate threshold for considering a prediction viable was chosen

  • for each condition and method separately
  • to optimize the tradeoff between true viable and false viable predictions
    (maximum Matthews correlation coefficient, see Methods).

Since iMM904 has 212 more genes than iLL672 with experimental data, we also present results

  • for the subset of iMM904 predictions with genes included in iLL672 (reduced iMM904 set).

When the same gene sets are compared, iMM904 improves gene lethality predictions under

  • glucose,
  • galactose, and
  • glycerol conditions

over iLL672 somewhat, but is less accurate

  • at predicting growth phenotypes under the ethanol condition.

It should be noted that the iLL672 predictions were obtained directly from [3]

  • thus the growth rate threshold was not optimized similarly to iMM904 predictions.

Overall, when viability cutoff is chosen

  • as indicated above for each method separately,
  • the three prediction methods perform similarly
  1. FBA,
  2. MOMA, and
  3. linear MOMA) .

While the full gene complement in iMM904 greatly increased

  • the number of true viable predictions,
  • the full model also made significantly more false viable predictions
  • compared with reduced iMM904 and iLL672 predictions.

However, it is important to note that 143 reactions involved in dead-end biosynthetic pathways were actually

  • removed from iFF708 to build the iLL672 reconstruction [3].

These dead-ends are considered “knowledge gaps” in pathways

  • that have not been fully characterized and, as a result,
  • lead to false viable predictions when determining gene essentiality
  • if the pathway is in fact required for growth under a certain condition [2,26].

As more of these pathways are elucidated and

  • included in the model to
  • fill in existing network gaps,
  • we can expect false viable prediction rates to consequently decrease.

Thus, while a larger network has a temporarily reduced capacity to accurately predict gene deletion phenotypes,

  • it captures a more complete picture of currently known metabolic functions and
  • provides a framework for network expansion as new pathways are elucidated [48].

 

Inferring intracellular perturbation states from metabolic profiles – Aerobic and anaerobic gdh1/GDH2 mutant behavior

The gdh1/GDH2 mutant strain was previously developed [49,50]

  • to lower NADPH consumption in ammonia assimilation, which would
  • favor the NADPH-dependent fermentation of xylose.

In this strain, the NADPH-dependent glutamate dehydrogenase, Gdh1, was

  • deleted and the NADH-dependent form of the enzyme, Gdh2,
  •                     was overexpressed.

The net effect is to allow efficient assimilation of ammonia

  • into glutamate using NADH instead of NADPH as a cofactor.

While growth characteristics remained unaffected,

  • relative quantities of secreted metabolites differed between the wild-type and mutant strain
  • under aerobic and anaerobic conditions.

We analyzed EM data for the gdh1/GDH2 and wild-type strains reported

  • in [31] under aerobic and anaerobic conditions separately using
  • both FBA optimization and
  • sampling-based approaches as described in Methods.

43 measured extracellular and intracellular metabolites from the original dataset [31],

  • primarily of central carbon and amino acid metabolism,
  • were explicitly represented in the iMM904 network [see Additional file 4].

Extracellular metabolite levels were used

  • to formulate secretion constraints and
  • differential intracellular metabolites were used
  • to compare and validate the intracellular flux predictions.

Perturbed reactions from the FBA results were

  • determined by calculating relative flux changes, and
  • reaction Z-scores were calculated from the sampling analysis
  • to quantify flux changes between the mutant and wild-type strains,
  • with Z reaction > 1.96 corresponding to a two-tailed p-value < 0.05 and
  • considered to be significantly perturbed [see Additional file 4].

Additional file 4. Gdh mutant aerobic and anaerobic analysis results. 

The data provided are the full results for the exometabolomic analysis of aerobic and anerobic gdh1/GDH2 mutant.

Format: XLS Size: 669KB Download file

This file can be viewed with: Microsoft Excel Viewer

To validate the predicted results, reaction flux changes from both FBA and sampling methods were compared to differential intracellular metabolite level data measured from the same study. Intracellular metabolites involved in highly perturbed reactions (i.e. reactants and products) predicted from FBA and sampling analyses were identified and
compared to metabolites that were experimentally identified as significantly changed (< 0.05) between mutant and wild-type. Statistical measures of recall, accuracy, and
precision were calculated and represent the predictive sensitivity, exactness, and reproducibility respectively. From the sampling analysis, a considerably larger number of
significantly perturbed reactions are predicted in the anaerobic case (505 reactions, or 70.7% of active reactions) than in aerobic (394 reactions, or 49.8% of active reactions). The top percentile of FBA flux changes equivalent to the percentage of significantly perturbed sampling reactions were compared to the intracellular data. Results from both analyses are summarized in Table 2. Sampling predictions were considerably higher in recall than FBA predictions for both conditions, with respective ranges of 0.83–1
compared to 0.48–0.96. Accuracy was also higher in sampling predictions; however, precision was slightly better in the FBA predictions as expected due to the smaller
number of predicted changes. Overall, the sampling predictions of perturbed intracellular metabolites are strongly consistent with the experimental data and significantly
outperforms that of FBA optimization predictions in accurately predicting differential metabolites involved in perturbed intracellular fluxes.

Table 2. Statistical comparison of the differential intracellular metabolite data set (< 0.05) with metabolites involved in perturbed reactions predicted by FBA optimization and sampling analyses for aerobic and anaerobic gdh1/GDH2 mutant.

 

Table 2 Statistical comparison of the differential intracellular metabolite data set (p < 0.05)
with metabolites involved in perturbed reactions predicted by FBA optimization and
sampling analyses for aerobic and anaerobic gdh1/GDH2 mutant.
                           Aerobic                         Anaerobic                             Overall
FBA Sampling FBA Sampling FBA
Recall 0.48 0.83 0.96 1 0.71 0.91
Accuracy 0.55 0.62 0.64 0.64 0.6 0.63
Precision 0.78 0.69 0.64 0.63 0.68 0.66
Overall statistics indicate combined results of both conditions.
Mo et al. BMC Systems Biology 2009 3:37   http://dx.doi.org:/10.1186/1752-0509-3-37


Figure 3.
 Perturbation reaction subnetwork of gdh1/GDH2 mutant under aerobic conditions.

The network illustrates a simplified subset of highly perturbedPerturbation subnetworks can be drawn to visualize predicted significantly perturbed intracellular reactions and illustrate their connection to the observed secreted metabolites in the aerobic and anaerobic gdh1/GDH2 mutants.

Perturbation reaction subnetwork of gdh1.GDH2 mutant under aerobic conditions.

Perturbation reaction subnetwork of gdh1.GDH2 mutant under aerobic conditions.

Figure 3 shows an example of a simplified aerobic perturbation subnetwork consisting primarily of proximal pathways connected directly to a subset of major secreted
metabolites

  • glutamate,
  • proline,
  • D-lactate, and
  • 2-hydroxybuturate.

Figure 4 displays anaerobic reactions with Z-scores of similar magnitude to the perturbed reactions in Figure 3. The same subset of metabolites is also present in the
larger anaerobic perturbation network and indicates that the NADPH/NADH balance perturbation induced by the gdh1/GDH2 manipulation has widespread effects
beyond just altering glutamate metabolism anaerobically.

Interestingly, it is clear that the majority of the secreted metabolite pathways involve connected perturbed reactions that broadly converge on glutamate.

Note that Figures 3 and 4 only show the subnetworks that consisted of two or more connected reactions  for a number of secreted metabolites no contiguous perturbed pathway could be identified by the sampling approach. This indicates that the secreted metabolite pattern alone is not sufficient to determine which specific
production and secretion pathways are used by the cell for these metabolites.

Reactions connected to aerobically-secreted metabolites predicted from the sampling analysis of the gdh1/GDH2 mutant strain.
The major secreted metabolites

  • glutamate,
  • proline,
  • D-lactate, and
  • 2-hydroxybuturate

were also detected in the anaerobic condition. Metabolite abbreviations are found in Additional file 1.

Figure 4.

Perturbation reaction subnetwork of gdh1/GDH2 mutant under anaerobic conditions.

Perturbation reaction subnetwork of gdh1.GDH2 mutant under anaerobic conditions

Perturbation reaction subnetwork of gdh1.GDH2 mutant under anaerobic conditions

Subnetwork illustrates the highly perturbed anaerobic reactions of similar Z-reaction magnitude to the reactions in Figure 3.

A significantly larger number of reactions indicates mutant metabolic effects are more widespread in the anaerobic environment.
The network shows that perturbed pathways converge on glutamate, the main site in which the gdh1/GDH2 modification was introduced, which
suggests that the direct genetic perturbation effects are amplified under this environment. Metabolite abbreviations are found in Additional file 1.

To further highlight metabolic regions that have been systemically affected by the gdh1/GDH2 modification, reporter metabolite and subsystem methods [30] were used to
summarize reaction scores around specific metabolites and in specific metabolic subsystems. The top ten significant scores for metabolites/subsystems associated with more
than three reactions are summarized in Tables 3 (aerobic) and 4 (anaerobic), with Z > 1.64 corresponding to < 0.05 for a one-tailed distribution. Full data for all reactions,
reporter metabolites, and reporter subsystems is included [see Additional file 4].

Table 3. List of the top ten significant reporter metabolite and subsystem scores for the gdh1/GDH2 vs. wild type comparison in aerobic conditions.

Table 3
List of the top ten significant reporter metabolite and subsystem scores for the gdh1/GDH2 vs. wild type comparison in aerobic conditions.
Reporter metabolite Z-score No of reactions*
L-proline [c] 2.71 4
Carbon dioxide [m] 2.51 15
Proton [m] 2.19 51
Glyceraldehyde 3-phosphate [c] 1.93 7
Ubiquinone-6 [m] 1.82 5
Ubiquinol-6 [m] 1.82 5
Ribulose-5-phosphate [c] 1.8 4
Uracil [c] 1.74 4
L-homoserine [c] 1.72 4
Alpha-ketoglutarate [m] 1.71 8
Reporter subsystem Z-score No of reactions
Citric Acid Cycle 4.58 7
Pentose Phosphate Pathway 3.29 12
Glycine and Serine Metabolism 2.69 17
Alanine and Aspartate Metabolism 2.65 6
Oxidative Phosphorylation 1.79 8
Thiamine Metabolism 1.54 8
Arginine and Proline Metabolism 1.44 20
Other Amino Acid Metabolism 1.28 5
Glycolysis/Gluconeogenesis 0.58 14
Anaplerotic reactions 0.19 9
*Number of reactions categorized in a subsystem or found to be neighboring each metabolite
Mo et al. BMC Systems Biology 2009 3:37   http://dx.doi.org:/10.1186/1752-0509-3-37

Table 4. List of top ten significant reporter metabolite and subsystem scores for the gdh1/GDH2 vs. wild type comparison in anaerobic conditions.

 

Table 4
List of top ten significant reporter metabolite and subsystem scores for the gdh1/GDH2 vs. wild type comparison in anaerobic conditions.
Reporter metabolite Z-score No of reactions
Glutamate [c] 4.52 35
Aspartate [c] 3.21 11
Alpha-ketoglutarate [c] 2.66 17
Glycine [c] 2.65 7
Pyruvate [m] 2.56 7
Ribulose-5-phosphate [c] 2.43 4
Threonine [c] 2.28 6
10-formyltetrahydrofolate [c] 2.27 5
Fumarate [c] 2.27 5
L-proline [c] 2.04 4
Reporter subsystem Z-score No of reactions
Valine, Leucine, and Isoleucine Metabolism 3.97 15
Tyrosine, Tryptophan, and Phenylalanine Metabolism 3.39 23
Pentose Phosphate Pathway 3.29 11
Purine and Pyrimidine Biosynthesis 3.08 40
Arginine and Proline Metabolism 2.96 19
Threonine and Lysine Metabolism 2.74 14
NAD Biosynthesis 2.66 7
Alanine and Aspartate Metabolism 2.65 6
Histidine Metabolism 2.24 10
Cysteine Metabolism 1.85 10
Mo et al. BMC Systems Biology 2009 3:37   http://dx.doi.org:/10.1186/1752-0509-3-37
Open Data

Perturbations under aerobic conditions largely consisted of pathways involved in mediating the NADH and NADPH balance. Among the highest scoring aerobic subsystems
are TCA cycle and pentose phosphate pathway – key pathways directly involved in the generation of NADH and NADPH. Reporter metabolites involved in these
subsystems –

  • glyceraldehyde-3-phosphate,
  • ribulose-5-phosphate, and
  • alpha-ketoglutarate – were also identified.

These results are consistent with flux and enzyme activity measurements

  • of the gdh1/GDH2 strain under aerobic conditions [32],
  1. which reported significant reduction in the pentose phosphate pathway flux
  2. with concomitant changes in other central metabolic pathways.

Levels of several TCA cycle intermediates (e.g. fumarate, succinate, malate) were also elevated

  • in the gdh1/GDH2 mutant according to the differential intracellular metabolite data.

Altered energy metabolism, as indicated by

  • reporter metabolites (i.e. ubiquinone- , ubiquinol, mitochondrial proton)
  • and subsystem (oxidative phosphorylation),

is certainly feasible as NADH is a primary reducing agent for ATP production.

Pentose phosphate pathway and NAD biosynthesis also appears

  • among the most perturbed anaerobic subsystems, further suggesting
  • perturbed cofactor balance as a common, dominant effect under both conditions.

Glutamate dehydrogenase is a critical enzyme of amino acid biosynthesis as it acts as

  • the entry point for ammonium assimilation via glutamate.

Consequently, metabolic subsystems involved in amino acid biosynthesis were broadly perturbed

  • as a result of the gdh1/GDH2 modification in both aerobic and anaerobic conditions.

For example, the proline biosynthesis pathway that uses glutamate as a precursor

  • was significantly perturbed in both conditions,
  • with significantly changed intracellular and extracellular levels.

There were differences, however, in that more amino acid related subsystems were

  • significantly affected in the anaerobic case (Table 4),
  • further highlighting that altered ammonium assimilation in the mutant
  • has a more widespread effect under anaerobic conditions.

This effect is especially pronounced for

  • threonine and nucleotide metabolism,
  • which were predicted to be significantly perturbed only in anaerobic conditions.

Intracellular threonine levels were amongst the most significantly reduced

  • relative to other differential intracellular metabolites in the anaerobically grown gdh1/GDH2 strain
    (see [31] and Additional file 4), and
  • the relationship between threonine and nucleotide biosynthesis is further supported

by threonine’s recently discovered role as a key precursor in yeast nucleotide biosynthesis [51].

Other key anaerobic reporter metabolites are

  • glycine and 10-formyltetrahydrofolate,
  • both of which are involved in the cytosolic folate cycle (one-carbon metabolism).

Folate is intimately linked to biosynthetic pathways of

  • glycine (with threonine as its precursor) and purines
  • by mediating one-carbon reaction transfers necessary in their metabolism and
  • is a key cofactor in cellular growth [52].

Thus, the anaerobic perturbations identified in the analysis emphasize the close relationship

  • between threonine, folate, and nucleotide metabolic pathways as well as
  • their potential connection to perturbed ammonium assimilation processes.

Interestingly, this association has been previously demonstrated at the transcriptional level

  • as yeast ammonium assimilation (via glutamine synthesis) was found to be
  • co-regulated with genes involved in glycine, folate, and purine synthesis [53].

In summary, the overall differences in predicted gdh1/GDH2 mutant behavior

  • under aerobic and anaerobic conditions show that changes in flux states
  • directly related to modified ammonium assimilation pathway
  1. are amplified anaerobically whereas the
  2. indirect effects through NADH/NADPH balance are more significant aerobically.

Perturbed metabolic regions under aerobic conditions were predominantly

  • in central metabolic pathways involved in responding to the changed NADH/NADPH demand
  • and did not necessarily emphasize that glutamate dehydrogenase was the site of the genetic modification.

The majority of affected anaerobic pathways were involved directly

  • in modified ammonium assimilation as evidenced by

1) significantly perturbed amino acid subsystems,

2) a broad perturbation subnetwork converging on glutamate (Figure 4), and

3) glutamate as the most significant reporter metabolite (Table 4).

Potassium-limited and excess ammonium environments

A recent study reported that potassium limitation resulted in significant

  • growth retardation effect in yeast due to excess ammonium uptake
  • when ammonium was provided as the sole nitrogen source [33].

The proposed mechanism for this effect was that ammonium

  • could to be freely transported through potassium channels
  • when potassium concentrations were low in the media environment, thereby
  • resulting in excess ammonium uptake [33].

As a result, yeast incurred a significant metabolic cost

  • in assimilating ammonia to glutamate and
  • secreting significant amounts of glutamate and other amino acids
  • in potassium-limited conditions as a means to detoxify the excess ammonium.

A similar effect was observed when yeast was grown

  • with no potassium limitation,
  • but with excess ammonia in the environment.

While the observed effect of both environments (low potassium or excess ammonia) was similar,

  • quantitatively unique amino acid secretion profiles suggested that
  • internal metabolic states in these conditions are potentially different.

In order to elucidate the differences in internal metabolic states, we utilized

  • the iMM904 model and the EM profile analysis method to analyze amino acid secretion profiles
  • for a range of low potassium and high ammonia conditions reported in [33].

As before, we utilized amino acid secretion patterns as constraints to the iMM904 model,

  1. sampled the allowable solution space,
  2. computed reaction Z-scores for changes from a reference condition (normal potassium and ammonia), and
  3. finally summarized the resulting changes using reporter metabolites.

Figure 5 shows a clustering of the most significant reporter metabolites (Z ≥ 1.96 in any of the four conditions studied)

  • obtained from this analysis across the four conditions studied.

Interestingly, the potassium-limited environment perturbed only a subset of

  • the significant reporter metabolites identified in the high ammonia environments.

Both low potassium environments shared a consistent pattern of

  • highly perturbed amino acids and related precursor biosynthesis metabolites
    (e.g. pyruvate, PRPP, alpha-ketoglutarate)
  • with high ammonium environments.

The amino acid perturbation pattern (indicated by red labels in Figure 5) was present in

  • the ammonium-toxic environments, although the pattern was
  • slightly weaker for the lower ammonium concentration.

Nevertheless, the results clearly indicate that a similar

  • ammonium detoxifying mechanism that primarily perturbs pathways
  • directly related to amino acid metabolism
  • exists under both types of media conditions.

Figure 5.

Clustergram of top reporter metabolites - y in ammonium-toxic and potassium-limited conditions

Clustergram of top reporter metabolites – y in ammonium-toxic and potassium-limited conditions

Clustergram of top reporter metabolites (i.e. in yellow) in ammonium-toxic and potassium-limited conditions.

Amino acid perturbation patterns (shown in red) were shown to be consistently scored across conditions, indicating that potassium-limited environments K1 (lowest
concentration) and K2 (low concentration) elicited a similar ammonium detoxification response as ammonium-toxic environments N1 (high concentration) and N2
(highest concentration). Metabolites associated with folate metabolism (highlighted in green) are also highly perturbed in ammonium-toxic conditions. Metabolite
abbreviations are found in Additional file 1.

In addition to perturbed amino acids, a secondary effect notably appears at high ammonia levels in which metabolic regions related to folate metabolism are significantly affected. As highlighted in green in Figure 3, we predicted significantly perturbed key metabolites involved in the cytosolic folate cycle. These include tetrahydrofolate derivatives and other metabolites connected to the folate pathway, namely glycine and the methionine-derived methylation cofactors S-adenosylmethionine and S-adenosyl-homocysteine. Additionally, threonine was identified to be a key perturbed metabolite in excess ammonium conditions. These results further illustrate the close
connection between threonine biosynthesis, folate metabolism involving glycine derived from its threonine precursor, and nucleotide biosynthesis [51] that was discussed in
conjunction with the gdh1/GDH2 strain data. Taken together with the anaerobic gdh1/GDH2 data, the results consistently suggest highly perturbed threonine and folate
metabolism when amino acid-related pathways are broadly affected.

In both ammonium-toxic and potassium-limited environments, impaired cellular growth was observed, which can be attributed to high energetic costs of increased
ammonium assimilation to synthesize and excrete amino acids. However, under high ammonium environments, reporter metabolites related to threonine and folate
metabolism indicated that their perturbation, and thus purine supply, may be an additional factor in decreasing cellular viability as there is a direct relationship between
intracellular folate levels and growth rate [54]. Based on these results, we concluded that while potassiumlimited growth in yeast indeed shares physiological features with
growth in ammonium excess, its effects are not as detrimental as actual ammonium excess. The effects on proximal amino acid metabolic pathways are similar in both
environments as indicated by the secretion of the majority of amino acids. However, when our method was applied to analyze the physiological basis behind differences in
secretion profiles between low potassium and high ammonium conditions, ammonium excess was predicted to likely disrupt physiological ammonium assimilation processes,
which in turn potentially impacts folate metabolism and associated cellular growth.

Conclusion

The method presented in this study presents an approach to connecting intracellular flux states to metabolites that are excreted under various physiological conditions. We
showed that well-curated genome-scale metabolic networks can be used to integrate and analyze quantitative EM data by systematically identifying altered intracellular
pathways related to measured changes in the extracellular metabolome. We were able to identify statistically significant metabolic regions that were altered as a result of
genetic (gdh1/GD2 mutant) and environmental (excess ammonium and limited potassium) perturbations, and the predicted intracellular metabolic changes were consistent
with previously published experimental data including measurements of intracellular metabolite levels and metabolic fluxes. Our reanalysis of previously published EM data
on ammonium assimilation-related genetic and environmental perturbations also resulted in testable hypotheses about the role of threonine and folate pathways in mediating
broad responses to changes in ammonium utilization. These studies also demonstrated that the samplingbased method can be readily applied when only partial secreted
metabolite profiles (e.g. only amino acids) are available.

With the emergence of metabolite biofluid biomarkers as a diagnostic tool in human disease [55,56] and the availability of genome-scale human metabolic networks [1],
extensions of the present method would allow identifying potential pathway changes linked to these biomarkers. Employing such a method for studying yeast metabolism was possible as the metabolomic data was measured under controllable environmental conditions where the inputs and outputs of the system were defined. Measured metabolite biomarkers in a clinical setting, however, is far from a controlled environment with significant variations in genetic, nutritional, and environmental factors between different
patients. While there are certainly limitations for clinical applications, the method introduced here is a progressive step towards applying genome-scale metabolic networks
towards analyzing biofluid metabolome data as it 1) avoids the need to only study optimal metabolic states based on a predetermined objective function, 2) allows dealing with noisy experimental data through the sampling approach, and 3) enables analysis even with limited identification of metabolites in the data. The ability to establish potential
connections between extracellular markers and intracellular pathways would be valuable in delineating the genetic and environmental factors associated with a particular
disease.

Authors’ contributions

Conceived and designed the experiments: MLM MJH BOP. Performed experiments: MLM MJH. Analyzed the data: MLM MJH. Wrote the paper: MLM MJH BOP. All authors have read and approved the final manuscript.

Acknowledgements

We thank Jens Nielsen for providing the raw metabolome data for the mutant strain, and Jan Schellenberger and Ines Thiele for valuable discussions. This work was supported by NIH grant R01 GM071808. BOP serves on the scientific advisory board of Genomatica Inc.

 

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Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation


 

English: A diagram of cellular respiration inc...

English: A diagram of cellular respiration including glycolysis, Krebs cycle, citric acid cycle, and the electron transport chain (Photo credit: Wikipedia)

English: Figure from Journal publication of sc...

English: Diagram showing regulation of the enz...

Reporter and Curator: Larry H Bernstein, MD, FACP

Introduction

Mitochondria are essential for life, and are critical for the generation of ATP. Otto Warburg won the Nobel Prize in 1918 for his studies of respiration and he described a situation of impaired respiration in cancer cells causing them to produce lactic acid, like bacteria. This has been termed facultative anaerobic glycolysis. The metabolic explanation for mitochondrial respiration had to await the Nobel discoveries of the Krebs cycle and high energy ~P in acetyl CoA by Fritz Lippman. The Krebs cycle generates 16 ATPs I respiration compared to 2 ATPs through glycolysis. The discovery of the genetic code with the “Watson-Crick” model and the identification of DNA polymerase opened a window for contuing discovery leading to the human genome project at 20th century end that has now been followed by “ENCODE” in the 21st century. This review opens a rediscovery of the metabolic function of mitochondria and adaptive functions with respect to cancer and other diseases.

Function in aerobic and anaerobic metabolism

Two-carbon compounds – the TCA, the pentose phosphate pathway, together with gluconeogenesis and the glyoxylate cycle are essential for the provision of anabolic precursors. Yeast environmental diversity mostly leads to a vast metabolic complexity driven by carbon and the energy available in environmental habitats. This resulted in much early research on analysis of yeast metabolism associated with glucose catabolism in Saccharomyces cerevisiae, under both aerobic and anaerobic environments. Yeasts may be physiologically classified with respect to the type of energy-generating process involved in sugar metabolism, namely non-, facultative- or obligate fermentative. The nonfermentative yeasts have exclusively a respiratory metabolism and are not capable of alcoholic fermentation from glucose, while the obligate-fermentative yeasts – “natural respiratory mutants” – are only capable of metabolizing glucose through alcoholic fermentation. Most of the yeasts identified are facultative-fermentative ones, and depending on the growth conditions, the type and concentration of sugars and/or oxygen availability, may display either a fully respiratory or a fermentative metabolism or even both in a mixed respiratory-fermentative metabolism (e.g., S. cerevisiae). The sugar composition of the media and oxygen availability are the two main environmental conditions that have a strong impact on yeast metabolic physiology, and three frequently observed effects associated with the type of energy-generating processes involved in sugar metabolism and/or oxygen availability are Pasteur, Crabtree and Custer. In modern terms the Pasteur effect refers to an activation of anaerobic glycolysis in order to meet cellular ATP demands owing to the lower efficiency of ATP production by fermentation compared with respiration. In 1861 Pasteur observed that S. cerevisiae consume much more glucose in the absence of oxygen than in its presence. S. cerevisiae only shows a Pasteur at low growth rates and at resting-cell conditions, where a high contribution of respiration to sugar catabolism occurs owing to the loss of fermentative capacity. The Crabtree effect is defined as the occurrence of alcoholic fermentation under aerobic conditions, explained by a theory involving “limited respiratory capacities” in the branching point of pyruvate metabolism. The Custer effect is known as the inhibition of alcoholic fermentation by the absence of oxygen. It is thought that the Custer effect is caused by reductive stress.

Glycolysis

Once inside the cell, glucose is phosphorylated by kinases to glucose 6-phosphate and then isomerized to fructose 6-phosphate, by phosphoglucose isomerase. The next enzyme is phospho-fructokinase, which is subject to regulation by several metabolites, and further phosphorylates fructose 6-phosphate to fructose 1,6-bisphosphate. These steps of glycolysis require energy in the form of ATP. Glycolysis leads to pyruvate formation associated with a net production of energy and reducing equivalents. Approximately 50% of glucose 6-phosphate is metabolized via glycolysis and 30% via the pentose phosphate pathway in Crabtree negative yeasts. However, about 90% of the carbon going through the pentose phosphate pathway reentered glycolysis at the level of fructose 6-phosphate or glyceraldehyde 3-phosphate. The pentose phosphate pathway in Crabtree positive yeasts (S. cerevisiae) is predominantly used for NADPH production but not for biomass production or catabolic reactions.
Pyruvate branch point. At the pyruvate (the end product of glycolysis) branching point, pyruvate can follow three different metabolic fates depending on the yeast species and the environmental conditions. On the other hand, the carbon flux may be distributed between the respiratory and fermentative pathways. Pyruvate might be directly converted to acetyl–cofactor A (CoA) by the mitochondrial multienzyme complex pyruvate dehydrogenase (PDH) after its transport into the mitochondria by the mitochondrial pyruvate carrier. Alternatively, pyruvate can also be converted to acetyl–CoA in the cytosol via acetaldehyde and to acetate by the so-called PDH-bypass pathway. Compared with cytosolic pyruvate decarboxylase, the mitochondrial PDH complex has a higher affinity for pyruvate and therefore most of the pyruvate will flow through the PDH complex at low glycolytic rates. However, at increasing glucose concentrations, the glycolytic rate will increase and more pyruvate is formed, saturating the PDH bypass and shifting the carbon flux through ethanol production. In the yeast S. cerevisiae, the external glucose level controls the switch between respiration and fermentation.

Rodrigues F, Ludovico P and Leão C. Sugar Metabolism in Yeasts: an Overview of Aerobic and Anaerobic Glucose Catabolism. In Molecular and Structural Biology. Chapter 6. qxd 07/23/05 P117
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Biogenesis of mitochondrial structures from aerobically grown S. cerevisiae

Under aerobic conditions S. cerevisiae forms mitochondria which are classical in their properties,
but the number, morphology, and enzyme activity of these mitochondria are also affected by catabolite repression, but it cannot respire under anaerobic conditions and lacks cytochromes. These structures were isolated from anaerobically grown yeast cells and contain malate and succinate dehydrogenases, ATPase, and DNA characteristic of yeast mitochondria. These lipid-complete structures consist predominantly of double-membrane vesicles enclosing a dense matrix which contains a folded inner membrane system bordering electron-transparent regions similar to the cristae of mitochondria.

  • The morphology of the structures is critically dependent on their lipid composition
  • Their unsaturated fatty acid content is similar to that of mitochondria from aerobically grown cells
  • The structures from cells grown without lipid supplements have simpler morphology – a dense granular matrix surrounded by a double membrane but have no obvious folded inner membrane system within the matrix
  • The lipid-depleted structures are only isolated in intact form from protoplasts
  • The synthesis of ergosterol and unsaturated fatty acids is oxygen-dependent and anaerobically grown cells may be depleted of these lipid components
  • The cytology of anaerobically grown yeast cells is profoundly affected by both lipid-depletion and catabolite repression
  • Lipid-depleted anaerobic cells, membranous mitochondrial profiles were not demonstrable
  • The structures from the aerobically and anaerobically grown cells are markedly different in morphology and fatty acid composition, but both contain mitochondrial DNA and a number of mitochondrial enzymes

The phospholipid composition of various strains of Saccharomyces cerevisiae, wild type and petite (cytoplasmic respiratory deficient) yeasts and derived mitochondrial mutants grown under conditions designed to induce variations in the complement of mitochondrial were fractionated into various subcellular fractions and analyzed for cytochrome oxidase (in wild type) and phospholipid composition . 90% or more of the phospholipid, cardiolipin was found in the mitochondrial membranes of wild type and petite yeast . Cardiolipin content differed markedly under various growth conditions .

  • Stationary yeast grown in glucose had better developed mitochondria and more cardiolipin than repressed log phase yeast .
  • Aerobic yeast contained more cardiolipin than anaerobic yeast .
  • Respiration-deficient cytoplasmic mitochondrial mutants, both suppressive and neutral, contained less cardiolipin than corresponding wild types .
  • A chromosomal mutant lacking respiratory function had normal cardiolipin content .
  • Log phase cells grown in galactose and lactate, which do not readily repress the development of mitochondrial membranes, contained as much cardiolipin as stationary phase cells grown in glucose .
  • Cytoplasmic mitochondrial mutants respond to changes in the glucose concentration of the growth medium by variations in their cardiolipin content in the same way as wild type yeast does under similar growth conditions.
  • It is of interest that the chromosomal petite, which as far as can be ascertained has qualitatively normal mitochondrial DNA and a normal cardiolipin content when grown under maximally derepressed conditions .

Thus, the genetic defect in this case probably does not diminish the mass of inner mitochondrial membrane under appropriate conditions . This suggests the cardiolipin content of yeast is a good indicator of the state of development of mitochondrial membrane.
Jakovcic S, Getz Gs, Rabinowitz M, Jakob H, Swift H. Cardiolipin Content Of Wild Type and Mutant Yeasts in Relation to Mitochondrial Function and Development. JCB 1971. jcb.rupress.org
Jakovcic S, Haddock J, Getz GS, Rabinowitz M, Swift H. Biochem J. 1971; 121 :341 .
EPHRUSSI, B . 1953 . Nucleocytoplasmic Relations in Microorganisms . Clarendon Press, Oxford.

Mitochondria, hydrogenosomes and mitosomes

Before and after the publication of an unnoticed article in 1905 by Mereschkowsky there were many publications dealing with plant “chimera’s” and cytoplasmic inheritance in plants, which should have favoured the interpretation of plastids as “semi-autonomous” symbiotic entities in the cytoplasm of the eukaryotic plant cell. Twenty years after Mereschkowsky’s plea for an endosymbiotic origin of plastids, Wallin (1925, 1927) postulated the “bacterial nature of mitochondria”. And so it is one of the mysteries of the 20th century that an endosymbiotic origin of plastids had not been generally accepted before the 1970s, primarily because one cannot experience the consequences of mutations in the mitochondrial genome by naked eye.

  • Mitochondrial DNA is usually present in multiple copies in one and the same mitochondrion and those in the hundreds to thousands of mitochondria in a single cell are not necessarily identical.
  • The random partitioning of the mitochondria in mitosis (and meiosis) frequently results in a more or less biased distribution of the diverent mitochondria in the daughter cells, eventually causing diverent phenotypes in different tissues obscuring the maternal inheritance
  • It was not until the 1990s that certain diseases—which had been interpreted as being X-chromosomal with incomplete penetrance—eventually turned out to be

Lastly, the vast majority of mitochondrial proteins are encoded in the nucleus and, consequently, mutations in the corresponding genes exhibit a Mendelian, and not a cytoplasmic, maternal inheritance
In the 1970s and 1980s the unequivocal demonstration of mitochondrial DNA occurred
and mitochondrial mutations at the DNA level provided the final proof for the role of such mutations in a wealth of hereditary diseases in man.

  • The genomics era provided the tools to prove the endosymbiont-hypothesis for the origin of the eukaryotic cell

Since DNA does not arise de novo, the genomes of organisms and organelles provide a historical record for the evolution of the eukaryotic cell and its organelles. The DNA sequences of two to three genomes of the eukaryotic cell turned out to be a record of the evolution of the eukaryotic life on earth. The analysis of organelle genomes unequivocally revealed a cyanobacterial origin for plastids and an -proteobacterial origin for mitochondria. Both plastids and mitochondria appear to be monophyletic, i.e. plastids derived from one and the same cyanobacterial ancestor, and mitochondria from one and the same -proteobacterial ancestor.
The evolution of the eukaryotic cell appears to have involved one (in the case of animals) or two (in the case of plants) events that took place 1.5 to 2 billion years ago. However, it appears that symbioses involving one or the other eubacterium arose repeatedly during the billions of years available. For example, photosynthetic algae by phagotrophic eukaryotes, negating the hypothesis of a single eukaryotic event, rather than stringent selection shaping the diversity of present-day life. Recent hypotheses for the origin of the nucleus have postulated that introns, which could be acquired by the uptake of the -proteobacterial endosymbiont, forced the nucleus-cytosol compartmentalization. Lateral gene transfer among eukaryotes is more frequent than was assumed earlier, and “mitochondrial genes” in the nuclear genomes of amitochondrial organisms are not necessarily the consequence of a transient presence of a DNA-containing mitochondrial-like organelle.
To cope with the obvious ubiquity of “mitochondrial” genes and the chimerism of the DNA of present day eukaryotes, the hydrogen hypothesis postulates that an archaeal host took up a eubacterial symbiont that became the ancestor of mitochondria and hydrogenosomes. The hydrogen hypothesis has the potential to explain both the monophyly of the mitochondria, and the existence of “anaerobic” and “aerobic” variants of one and the same original organelle. Based on these observations we have only the terms “mitochondrion”, “hydrogenosome” and “mitosome” to classify the various variants of the mitochondrial family.
Hackstein JHP, Joachim Tjaden J , Huynen M. Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering! Curr Genet (2006) 50:225–245. DOI 10.1007/s00294-006-0088-8.

Lineages

A look at the phylogenetic distribution of characterized anaerobic mitochondria among animal lineages shows that these are not clustered but spread across metazoan phylogeny. The biochemistry and the enzyme equipment used in the facultatively anaerobic mitochondria of metazoans is nearly identical across lineages, strongly indicating a common origin from an archaic metazoan ancestor. The organelles look like hydrogenosomes – anaerobic forms of mitochondria that generate H2 and adenosine triphosphate (ATP) from pyruvateoxidation and which were previously found only in unicellular eukaryotes. The animals harbor structures resembling prokaryotic endosymbionts, reminiscent of the methanogenic endosymbionts found in some hydrogenosome-bearing protists; fluorescence of F420, a typical methanogen cofactor, or lack thereof, will bring more insights as to what these structures are. If we follow the anaerobic lifestyle further back into evolutionary history, beyond the origin of the metazoans, we see that the phylogenetic distribution of eukaryotes with facultative anaerobic mitochondria, eukaryotes with hydrogenosomes and eukaryotes that possess mitosomes (reduced forms of mitochondria with no direct role in ATP synthesis) the picture is similar to that seen for animals. In all six of the major lineages (or supergroups) of eukaryotes that are currently recognized, forms with anaerobic mitochondria have been found. The newest additions to the growing collection of anaerobic mitochondrial metabolisms are the denitrifying foraminiferans. A handful of about a dozen enzymes make the difference between a ‘normal’ O2-respiring mitochondrion found in mammals, and the energy metabolism of eukaryotes with anaerobic mitochondria, hydrogenosomes or mitosomes. Notably, the full complement of those enzymes, once thought to be specific to eukaryotic anaerobes, surprisingly turned up in the green alga Chlamydomonas reinhardtii , which produces O2 in the light, has typical O2-respiring mitochondria but, within about 30 min of exposure to heterotrophic, anoxic and dark conditions, expresses its anaerobic biochemistry to make H2 in the same way as trichomonads, the group in which hydrogenosomes were discovered. Chlamydomonas provides evidence which indicates that the ability to inhabit oxygen-harbouring, as well as anoxic environments, is an ancestral feature of eukaryotes and their mitochondria. The prokaryote inhabitants have existed for well over a billion years, and have reached this new habitat by dispersal, not by adaptive evolution de novo and in situ. Indeed, geochemical evidence has shown that methanogenesis and sulphate reduction, and the niches in which they occur, are truly ancient.
Mentel and Martin. Anaerobic mitochondria: more common all the time. BMC Biology 2010; 8:32. BioMed Central Ltd. http://www.biomedcentral.com/1741-7007/8/32.

Anaerobic mitochondrial enzymes

Mitochondria from the muscle of the parasitic nematode Ascaris lumbricoides var. suum function anaerobically in electron transport-associated phosphorylations under physiological conditions. These helminth organelles have been fractionated into inner and outer membrane, matrix, and inter-membrane space fractions. The distributions of enzyme systems were determined and compared with corresponding distributions reported in mammalian mitochondria. Succinate and pyruvate dehydrogenases as well as NADH oxidase, Mg++-dependent ATPase, adenylate kinase, citrate synthase, and cytochrome c reductases were determined to be distributed as in mammalian mitochondria. In contrast with the mammalian systems, fumarase and NAD-linked “malic” enzyme were isolated primarily from the intermembrane space fraction of the worm mitochondria. These enzymes are required for the anaerobic energy-generating system in Ascaris and would be expected to give rise to NADH in the intermembrane space.
Pyruvate kinase activity is barely detectable in Ascaris muscle. Therefore, rather than giving rise to cytoplasmic pyruvate, CO2 is fixed into phosphoenolpyruvate, resulting in the formation of oxalacetate which, in turn, is reduced by NADH to form malate regenerating glycolytic NAD . Ascaris muscle mitochondria utilize malate anaerobically as their major substrate by means of a dismutation reaction. The “malic” enzyme in the mitochondrion catalyzes theoxidation of malate to form pyruvate, CO2, and NADH. This reaction serves to generate intramitochondrial reducing power in the form of NADH. Concomitantly, fumarase catalyzes thedehydration of an equivalent amount of malate to form fumarate which, in turn, is reduced by an NADH-linked fumarate reductase to succinate. The flavin-linked fumarate reductase reaction results in a site I electron transport-associated phosphorylation of ADP, giving rise to ATP. This identifies a proton translocation system to obtain energy generation.
Rew RS, Saz HJ. Enzyme Localization in the Anaerobic Mitochondria Of Ascaris Lumbricoides. The Journal Of Cell Biology 1974; 63: 125-135. jcb.rupress.org

Mitochondrial redox status

Tumor cells are characterized by accelerated growth usually accompanied by up-regulated pathways that ultimately increase the rate of ATP production. These cells can suffer metabolic reprogramming, resulting in distinct bioenergetic phenotypes, generally enhancing glycolysis channeled to lactate production. These investigators showed metabolic reprogramming by means of inhibitors of histone deacetylase (HDACis), sodium butyrate and trichostatin. This treatment was able to shift energy metabolism by activating mitochondrial systems such as the respiratory chain and oxidative phosphorylation that were largely repressed in the untreated controls.
Amoêdo ND, Rodrigues MF, Pezzuto P, Galina A, et al. Energy Metabolism in H460 Lung Cancer Cells: Effects of Histone Deacetylase Inhibitors. PLoS ONE 2011; 6(7): e22264. doi:10.1371/ journal.pone.0022264
Antioxidant pathways that rely on NADPH are needed for the reduction of glutathione and maintenance of proper redox status. The mitochondrial matrix protein isocitrate dehydrogenase 2 (IDH2) is a major source of NADPH. NAD+-dependent deacetylase SIRT3 is essential for the prevention of age related hearing loss of caloric restricted mice. Oxidative stress resistance by SIRT3 was mediated through IDH2. Inserting SIRT3 Nε-acetyl-lysine into position 413 of IDH2 and has an activity loss by as much as 44-fold. Deacetylation by SIRT3 fully restored maximum IDH2 activity. The ability of SIRT3 to protect cells from oxidative stress was dependent on IDH2, and the deacetylated mimic, IDH2K413R variant was able to protect Sirt3-/- MEFs from oxidative stress through increased reduced glutathione levels. The increased SIRT3 expression protects cells from oxidative stress through IDH2 activation. Together these results uncover a previously unknown mechanism by which SIRT3 regulates IDH2 under dietary restriction. Recent findings demonstrate that IDH2 activities are a major factor in cancer, and as such, these results implicate SIRT3 as a potential regulator of IDH2-dependent functions in cancer cell metabolism.
Wei Yu, Dittenhafer-Reed KE and JM Denu. SIRT3 Deacetylates Isocitrate Dehydrogenase 2 (IDH2) and Regulates Mitochondrial Redox Status. JBC Papers in Press. Published on March 13, 2012 as Manuscript M112.355206. http://www.jbc.org
Computationally designed drug small molecules targeted for metabolic processes: a bridge from the genome to repair of dysmetabolism
New druglike small molecules with possible anticancer applications were computationally designed. The molecules formed stable complexes with antiapoptotic BCL-2, BCL-W, and BFL-1 proteins. These findings are novel because, to the best of the author’s knowledge, molecules that bind all three of these proteins are not known. A drug based on them should be more economical and better tolerated by patients than a combination of drugs, each targeting a single protein. The calculated drug-related properties of the molecules were similar to those found in most commercial drugs. The molecules were designed and evaluated following a simple, yet effective procedure. The procedure can be used efficiently in the early phases of drug discovery to evaluate promising lead compounds in time- and cost-effective ways.
Keywords: small molecule mimetics, antiapoptotic proteins, computational drug design.

Tardigrades

Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.
Keywords: RNA, expressed sequence tag, cluster, protein family, adaptation, tardigrada, transcriptome

Epicrisis

This discussion has disparate pieces that are tied together by dysfunctional changes that are

  • adaptations from metabolic process in the channeling of energy dependent of mitochondrial enzymes in interaction with three to 6 carbon carbohydrates, high energy phosphate, oxygen and membrane lipid structures, as well as
  • proteins rich or poor in sulfur linked with genome specific targets, and semisynthetic modifications, oxidative stress
  • leading to a new approach to pharmaceutical targeted drug design.

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