Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens

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.

Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up

“…The acetate imported by G. sulfurreducens can be activated via ligation with coenzyme A (CoA) through two main pathways (70). The first of these pathways involves the oxidation of acetate through the conversion of succinyl-CoA to succinate via the activity of the succinyl-CoA:acetate CoA-transferase enzyme (EC 2.8.3.18) (Fig.…”

“…7, yellow arrow). Acetyl-CoA produced via this pathway is directed toward the citrate synthase reaction in the tricarboxylic acid (TCA) cycle (70). The second pathway involves the phosphorylation of acetate via acetate kinase (EC 2.7.2.1) followed by a second reaction involving phosphotransacetylase (EC 2.3.1.8) converting acetylphosphate to acetyl-CoA (Fig.…”

“…The second pathway involves the phosphorylation of acetate via acetate kinase (EC 2.7.2.1) followed by a second reaction involving phosphotransacetylase (EC 2.3.1.8) converting acetylphosphate to acetyl-CoA (Fig. 7, purple arrows) (70,71). The acetyl-CoA produced via this pathway is converted to pyruvate via the activity of pyruvate oxidoreductase (EC 1.2.7.1) operating in the reverse direction (Fig.…”

In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions

“…While animal studies are the ultimate cornerstone against which new hypotheses should be tested, computer simulations, or in-silico experiments, constitute a powerful tool in preclinical research. In-silico experiments could be used to: (i) gather preliminary evidence in favour or against a specific hypothesis through systematic pilot trials on the computer2; (ii) achieve statistical power in an animal study via careful selection of the number of trials, independent and dependent variables, and frequency of measurement3; and (iii) reinforce the scientific merit of existing observations through comparison against synthetic data and statistical analysis informed by modelling insight4567.…”

Shewanella spp. Use Acetate as an Electron Donor for Denitrification but Not Ferric Iron or Fumarate Reduction

“…(26)(27)(28). The most prominent difference is that these acetate oxidizers activate acetate to acetyl coenzyme A (CoA) by using a succinyl-CoA:acetate-CoA transferase through direct transfer of CoA from succinyl-CoA to acetate, thus eliminating the ATP requirement to activate acetate (28)(29)(30).…”