ArticlePLoS computational biology2008
Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 80 citations in OpenAlex.
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- Cytochromes in Extracellular Electron Transfer inApplied and environmental microbiology · 2021Review
- Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens.Applied and environmental microbiology · 2021Article
- Proteomic Analysis of a Syntrophic Coculture ofFrontiers in microbiology · 2021Article
- Comparative proteomics of Geobacter sulfurreducens PCAEnvironmental microbiology · 2021Article
- The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate.The ISME journal · 2020Article
- Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.Microbial ecology · 2019Article
- Long-Term Behavior of Defined Mixed Cultures ofFrontiers in bioengineering and biotechnology · 2019Article
- Silica immobilization of Geobacter sulfurreducens for constructing ready-to-use artificial bioelectrodes.Microbial biotechnology · 2018Article
- Genome Scale Mutational Analysis of Geobacter sulfurreducens Reveals Distinct Molecular Mechanisms for Respiration and Sensing of Poised Electrodes versus Fe(III) Oxides.Journal of bacteriology · 2017Article
- In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions.Scientific reports · 2017Article
- Anodic electro-fermentation of 3-hydroxypropionic acid from glycerol by recombinantBiotechnology for biofuels · 2017Article
- Genetic switches and related tools for controlling gene expression and electrical outputs of Geobacter sulfurreducens.Journal of industrial microbiology & biotechnology · 2016Article
- Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up.Applied and environmental microbiology · 2015Article
- Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T).Standards in genomic sciences · 2015Article
- Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.PloS one · 2014Article
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Previous model-based analysis of the metabolic network of Geobacter sulfurreducens suggested the existence of several redundant pathways. Here, we identified eight sets of redundant pathways that included redundancy for the assimilation of acetate, and for the conversion of pyruvate into acetyl-CoA. These equivalent pathways and two other sub-optimal pathways were studied using 5 single-gene deletion mutants in those pathways for the evaluation of the predictive capacity of the model. The growth phenotypes of these mutants were studied under 12 different conditions of electron donor and acceptor availability. The comparison of the model predictions with the resulting experimental phenotypes indicated that pyruvate ferredoxin oxidoreductase is the only activity able to convert pyruvate into acetyl-CoA. However, the results and the modeling showed that the two acetate activation pathways present are not only active, but needed due to the additional role of the acetyl-CoA transferase in the TCA cycle, probably reflecting the adaptation of these bacteria to acetate utilization. In other cases, the data reconciliation suggested additional capacity constraints that were confirmed with biochemical assays. The results demonstrate the need to experimentally verify the activity of key enzymes when developing in silico models of microbial physiology based on sequence-based reconstruction of metabolic networks.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.