Effect ofEscherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model

Pramanik, J.; Keasling, Jay D.

doi:10.1002/(sici)1097-0290(19981020)60:2<230::aid-bit10>3.0.co;2-q

Cited by 92 publications

(80 citation statements)

References 26 publications

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“…By comparison, a change in electron acceptor from fumarate to Fe(III) citrate caused threefold differences in yield or respiration rates (29). This revealed that the model predictions were robust to changes in biomass composition and nutrient availability, which was consistent with other work showing that variations in biomass composition produce only subtle effects on predicted growth yields or fluxes through central metabolic pathways (23,74,75). Hence, it is possible to assume that even significant changes (10 to 20%) in biomass composition would not affect the nature of metabolic predictions.…”

Section: Resultssupporting

confidence: 82%

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling

Mahadevan

Bond

Butler

et al. 2006

Appl Environ Microbiol

289

304

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Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttleproducing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.

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Section: Resultssupporting

confidence: 82%

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling

Mahadevan

Bond

Butler

et al. 2006

Appl Environ Microbiol

289

304

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“…To test the hypothesis that variations in availability of amino acids for import and/or variations in growth rates may affect amino acid ratios within cells (32), the proteinogenic amino acids in strain 195 were analyzed in AA0, AA4, and AA20. In each condition, overall amino acid composition of stain 195 exhibited negligible differences (see Table S4 in the supple- .…”

Section: Incorporation Of Amino Acids By Strain 195mentioning

confidence: 99%

Selective Utilization of Exogenous Amino Acids by Dehalococcoides ethenogenes Strain 195 and Its Effects on Growth and Dechlorination Activity

Zhuang

Feng

et al. 2011

Appl Environ Microbiol

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Bacteria of the genus Dehalococcoides are important members of bioremediation communities because of their ability to detoxify chloroethenes to the benign end product ethene. Genome-enabled studies conducted with Dehalococcoides ethenogenes 195 have revealed that two ATP-binding cassette (ABC)-type amino acid transporters are expressed during its exponential growth stages. In light of previous findings that Casamino Acids enhanced its dechlorination activity, we hypothesized that strain 195 is capable of importing amino acids from its environment to facilitate dechlorination and growth. To test this hypothesis, we applied isotopomerbased dilution analysis with 13 C-labeled acetate to differentiate the amino acids that were taken up by strain 195 from those synthesized de novo and to determine the physiological changes caused by the significantly incorporated amino acids. Our results showed that glutamate/glutamine and aspartate/asparagine were almost exclusively synthesized by strain 195, even when provided in excess in the medium. In contrast, phenylalanine, isoleucine, leucine, and methionine were identified as the four most highly incorporated amino acids, at levels >30% of respective proteinogenic amino acids. When either phenylalanine or all four highly incorporated amino acids were added to the defined mineral medium, the growth rates, dechlorination activities, and yields of strain 195 were enhanced to levels similar to those observed with supplementation with 20 amino acids. However, genes for the putative ABC-type amino acids transporters and phenylalanine biosynthesis exhibited insignificant regulation in response to the imported amino acids. This study also demonstrates that using isotopomer-based metabolite analysis can be an efficient strategy for optimizing nutritional conditions for slow-growing microorganisms.

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“…2), has culminated in a network containing a total number of 1,260 ORF metabolic functions [12][13][14][15][16][17][18][19] . This reconstruction represents 48% of the total experimentally annotated ORF functions in the E. coli genome (Table 1).…”

Section: The E Coli Metabolic Reconstructionmentioning

confidence: 99%

“…Shown are six milestone efforts contributing to the reconstruction of the E. coli metabolic network. For each of the six reconstructions [12][13][14][15][16][17][18][19] , the number of included reactions (blue diamonds), genes (green triangles) and metabolites (purple squares) are displayed. Also listed are noteworthy properties that each successive reconstruction provided over previous efforts.…”

Section: Supplementary Materialsmentioning

confidence: 99%

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

2008

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The number and scope of methods developed to interrogate and use metabolic network reconstructions has significantly expanded since the first review of the use of constraint-based analysis in Nature Biotechnology some 14 years ago. In particular, the Escherichia coli metabolic network reconstruction has reached the genome-scale and has been broadly adapted. Specifically, it has been used to address a broad spectrum of basic and practical applications, falling into five main categories: 1) metabolic engineering, 2) model-directed discovery, 3) interpretations of phenotypic screens, 4) analysis of network properties, and 5) studies of evolutionary processes. With these accomplishments in hand, the field is expected to move forward and seek to further, i) broaden the scope and content of network reconstructions, ii) develop new and novel in silico analysis tools, and iii) expand in adaptation to uses of proximal and distal causation in biology. Taken together, these efforts will solidify a mechanistic genotype-phenotype relationship for microbial metabolism.The availability of reconstructed metabolic networks for microorganisms has increased rapidly in recent years, and a growing number of research groups are reconstructing metabolic networks for organisms of interest 1 . A network reconstruction represents a highly curated set of primary biological information for a particular organism and thus can be considered a biochemically, genetically and genomically structured (BiGG) data base 1, 2 . A curated BiGG data base (de facto a knowledge base) can be converted into a mathematical format (i.e., an in silico model), and used to computationally assess phenotypic properties using a variety of computational methods 2,3 . Genome-scale reconstructions are thus, a key step in quantifying the genotype-phenotype relationship and can be used to 'bring genomes to life' 4 . The purpose of this review is to summarize and classify applications utilizing the E. coli reconstruction to answer a broad spectrum of biological questions. These studies provide both an up to date review of the applications of constraint-based analysis and a guide to similar applications for the growing number of organisms for which genome-scale reconstructions are becoming available. The Key Steps in the Formulation of Genome-scale Metabolic Network ModelsThe four key steps in the formulation and use of genome-scale models are illustrated in Fig. 1. Foundational to the process is the generation of global, or genome-scale, omics data. Omics data, along with legacy information (i.e., the 'bibliome') and small-scale detailed experiments, can be used to define the interactions amongst the biological components that are used to reconstruct organism-specific networks 1 . Network reconstruction is also an iterative, on-going process that continually integrates data in a formal fashion as it becomes available 5 . As a result, a current and well curated genome-scale network reconstruction is a common denominator for those studying systems biology of an or...

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Effect ofEscherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model

Cited by 92 publications

References 26 publications

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling

Selective Utilization of Exogenous Amino Acids by Dehalococcoides ethenogenes Strain 195 and Its Effects on Growth and Dechlorination Activity

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

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