Metabolic pathways in the post-genome era

Papin, Jason A.; Price, Nathan D.; Wiback, Sharon J.; Fell, David A.; Palsson, Bernhard Ø.

doi:10.1016/s0968-0004(03)00064-1

Cited by 325 publications

(164 citation statements)

References 47 publications

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“…50) that connects the fundamental metabolic processes of catabolism and anabolism, the results presented here are also important for faithful modeling of E. coli metabolism (1,(51)(52)(53), in particular for the generation of a whole-cell model (54). More generally, the apparent flexibility of E. coli NADPH metabolism provokes a question: why are the Enterobacteriaceae the only known group that contains both transhydrogenase isoforms?…”

Section: Discussionmentioning

confidence: 99%

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli

Sauer

Canonaco

Heri

et al. 2004

Journal of Biological Chemistry

530

526

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Pentose phosphate pathway and isocitrate dehydrogenase are generally considered to be the major sources of the anabolic reductant NADPH. As one of very few microbes, Escherichia coli contains two transhydrogenase isoforms with unknown physiological function that could potentially transfer electrons directly from NADH to NADP ؉ and vice versa. Using defined mutants and metabolic flux analysis, we identified the proton-translocating transhydrogenase PntAB as a major source of NADPH in E. coli. During standard aerobic batch growth on glucose, 35-45% of the NADPH that is required for biosynthesis was produced via PntAB, whereas pentose phosphate pathway and isocitrate dehydrogenase contributed 35-45% and 20 -25%, respectively. The energy-independent transhydrogenase UdhA, in contrast, was essential for growth under metabolic conditions with excess NADPH formation, i.e. growth on acetate or in a phosphoglucose isomerase mutant that catabolized glucose through the pentose phosphate pathway. Thus, both isoforms have divergent physiological functions: energy-dependent reduction of NADP ؉ with NADH by PntAB and reoxidation of NADPH by UdhA. Expression appeared to be modulated by the redox state of cellular metabolism, because genetic and environmental manipulations that increased or decreased NADPH formation down-regulated pntA or udhA transcription, respectively. The two transhydrogenase isoforms provide E. coli primary metabolism with an extraordinary flexibility to cope with varying catabolic and anabolic demands, which raises two general questions: why do only a few bacteria contain both isoforms, and how do other organisms manage NADPH metabolism?About 1,000 anabolic reactions synthesize the macromolecular components that make up functional cells (1, 2), but only 11 intermediates of central carbon metabolism and the cofactors ATP, NADH, and NADPH constitute the core of this intricate biochemical network (3, 4). These intermediates and cofactors must be supplied through the catabolism of different substrates at appropriate rates and stoichiometries for balanced growth; hence, anabolism and catabolism are delicately balanced and regulated to enable growth under fluctuating environmental conditions. Although chemically very similar, the redox cofactors NADH and NADPH serve distinct biochemical functions and participate in more than 100 enzymatic reactions (5). The electrons of the main respiratory cofactor NADH are transferred primarily to oxygen, thereby driving oxidative phosphorylation of ADP to ATP (3,4,6). NADPH, in contrast, exclusively drives anabolic reduction reactions. Despite the important role in linking the fundamental processes of catabolism and anabolism, however, even a qualitative understanding of NADPH metabolism is still missing for most organisms.The primary NADPH-generating reactions are considered to be the oxidative pentose phosphate (PP) 1 pathway and the NADPH-dependent isocitrate dehydrogenase in the TCA cycle (Fig.

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Section: Discussionmentioning

confidence: 99%

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli

Sauer

Canonaco

Heri

et al. 2004

Journal of Biological Chemistry

530

526

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“…The ability of existing model pathways to portray flux through complex metabolic networks, however, is an open question that is just beginning to be addressed theoretically (1)(2)(3) and experimentally (4,5). Microbial growth on the most abundant carbon-source glucose represses transcription of metabolic functions that are required on alternative carbon sources.…”

mentioning

confidence: 99%

A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli

Fischer

Sauer

2003

Journal of Biological Chemistry

182

172

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Complete oxidation of carbohydrates to CO 2 is considered to be the exclusive property of the ubiquitous tricarboxylic acid cycle, the central process in cellular energy metabolism of aerobic organisms. Based on metabolism-wide in vivo quantification of intracellular carbon fluxes, we describe here complete oxidation of carbohydrates via the novel P-enolpyruvate (PEP)-glyoxylate cycle, in which two PEP molecules are oxidized by means of acetyl coenzyme A, citrate, glyoxylate, and oxaloacetate to CO 2 , and one PEP is regenerated. Key reactions are the constituents of the glyoxylate shunt and PEP carboxykinase, whose conjoint operation in this bi-functional catabolic and anabolic cycle is in sharp contrast to their generally recognized functions in anaplerosis and gluconeogenesis, respectively. Parallel operation of the PEP-glyoxylate cycle and the tricarboxylic acid cycle was identified in the bacterium Escherichia coli under conditions of glucose hunger in a slow-growing continuous culture. Because the PEPglyoxylate cycle was also active in glucose excess batch cultures of an NADPH-overproducing phosphoglucose isomerase mutant, one function of this new central pathway may be the decoupling of catabolism from NADPH formation that would otherwise occur in the tricarboxylic acid cycle.Structuring of cellular networks into pathways with distinct functions is pivotal for comprehension of "textbook" biochemistry. The ability of existing model pathways to portray flux through complex metabolic networks, however, is an open question that is just beginning to be addressed theoretically (1-3) and experimentally (4, 5). Microbial growth on the most abundant carbon-source glucose represses transcription of metabolic functions that are required on alternative carbon sources. This universal phenomenon is referred to as catabolite repression and includes a number of mechanistically distinguishable but physiologically related regulation mechanisms (6, 7). Although catabolite repression is strong under conditions of feast with excess glucose, microbes typically thrive under conditions of starvation (absence of nutrients) or hunger (suboptimal supply of nutrients) in their natural environments (8,9). This metabolic state of hunger, between optimal growth and starvation, can be studied in glucose-limited continuous (chemostat) cultures with very low glucose concentrations at a rate of growth that is controlled by the experimenter. Catabolite repression is absent under the severe glucose limitation in slow growing chemostat cultures (9 -11), and, as a consequence, increased in vivo activity of repressed metabolic enzymes is often observed with advanced methods of metabolic flux analyses based on 13 C-labeling experiments (4, 5, 12, 13).Here we elucidate metabolic impacts of severe and absent catabolite repression during growth of Escherichia coli in glucose-excess batch cultures and glucose-limited chemostat cultures. Direct analytical interpretation of 13 C-labeling patterns in proteinogenic amino acids was used to establish the ...

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“…In the past decade, a significant amount of research has been done to understand and describe a metabolic system using extreme pathway analysis, see Papin et al (2002bPapin et al ( , 2003Papin et al ( , 2004; ; Schilling & Palsson (1998). Similar to the flux balance analysis, the extreme pathways analysis imposes a steady state condition, but instead of a single optimal solution, it produces a set of feasible solutions in finite dimensional space.…”

Section: Linear Programming Solutionmentioning

confidence: 99%

“…Since the number of extreme pathways can be very large for large-scale metabolic network systems (Papin et al, 2002a(Papin et al, , 2003, a set of improved tools was developed to solve these problems (Barrett et al, 2006;Price et al, 2003b;Wiback et al, 2003).…”

Section: Linear Programming Solutionmentioning

confidence: 99%

Bayesian flux balance analysis applied to a skeletal muscle metabolic model

Heino

Tunyan

Calvetti

et al. 2007

Journal of Theoretical Biology

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In this article, the steady state condition for the multi-compartment models for cellular metabolism is considered. The problem is to estimate the reaction and transport fluxes, as well as the concentrations in venous blood when the stoichiometry and bound constraints for the fluxes and the concentrations are given. The problem has been addressed previously by a number of authors, and optimization based approaches as well as extreme pathway analysis have been proposed. These approaches are briefly discussed here. The main emphasis of this work is a Bayesian statistical approach to the flux balance analysis (FBA). We show how the bound constraints and optimality conditions such as maximizing the oxidative phosphorylation flux can be incorporated into the model in the Bayesian framework by proper construction of the prior densities. We propose an effective Markov Chain Monte Carlo (MCMC) scheme to explore the posterior densities, and compare the results with those obtained via the previously studied Linear Programming (LP) approach. The proposed methodology, which is applied here to a two-compartment model for skeletal muscle metabolism, can be extended to more complex models.

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Metabolic pathways in the post-genome era

Cited by 325 publications

References 47 publications

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli

The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli

A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli

Bayesian flux balance analysis applied to a skeletal muscle metabolic model

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