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Title: Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling

Abstract

We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The model indicated that over 90 percent of the acetate wascompletely oxidized to CO2 via a complete tricarboxylic acid (TCA) cyclewhile reducing iron. Pyruvate carboxylase and phosphoenolpyruvatecarboxykinase were present under these conditions, but enzymes in theglyoxylate shunt and malic enzyme were absent. Gluconeogenesis and thepentose phosphate pathway were mainly employed for biosynthesis andaccounted for less than 3 percent of total carbon consumption. The modelalso indicated surprisingly high reversibility in the reaction betweenoxoglutarate and succinate. This step operates close to the thermodynamicequilibrium possibly because succinate is synthesized via a transferasereaction, and its product, acetyl-CoA, inhibits the conversion ofoxoglutarate to succinate. These findings enable a better understandingof the relationship between genome annotation and extant metabolicpathways in G. metallireducens.

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Director. Office of Science. Biological andEnvironmental Research
OSTI Identifier:
925527
Report Number(s):
LBNL-62247
Journal ID: ISSN 0099-2240; R&D Project: GTL2KK; BnR: KP1102010; TRN: US200809%%786
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Applied Environmental Microtiology
Additional Journal Information:
Journal Volume: 73; Journal Issue: 12; Related Information: Journal Publication Date: June 2007; Journal ID: ISSN 0099-2240
Country of Publication:
United States
Language:
English
Subject:
60; ACETATES; AMINO ACIDS; BINDING ENERGY; BIOLOGICAL PATHWAYS; BIOSYNTHESIS; BYPASSES; CARBON; CARBON SOURCES; CARBOXYLASE; ELECTRONS; ENZYMES; IN VIVO; IRON; METABOLISM; PENTOSES; PHOSPHATES; REACTION KINETICS; STRAINS; THERMODYNAMICS; TRANSFERASES; VALENCE; labeled acetate electron acceptor minimal medium TCA cycleacetyl-CoA transferase

Citation Formats

Tang, Yinjie J, Chakraborty, Romy, Martin, Hector Garcia, Chu, Jeannie, Hazen, Terry C, and Keasling, Jay D. Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling. United States: N. p., 2007. Web. doi:10.1128/AEM.02986-06.
Tang, Yinjie J, Chakraborty, Romy, Martin, Hector Garcia, Chu, Jeannie, Hazen, Terry C, & Keasling, Jay D. Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling. United States. https://doi.org/10.1128/AEM.02986-06
Tang, Yinjie J, Chakraborty, Romy, Martin, Hector Garcia, Chu, Jeannie, Hazen, Terry C, and Keasling, Jay D. 2007. "Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling". United States. https://doi.org/10.1128/AEM.02986-06. https://www.osti.gov/servlets/purl/925527.
@article{osti_925527,
title = {Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling},
author = {Tang, Yinjie J and Chakraborty, Romy and Martin, Hector Garcia and Chu, Jeannie and Hazen, Terry C and Keasling, Jay D},
abstractNote = {We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The model indicated that over 90 percent of the acetate wascompletely oxidized to CO2 via a complete tricarboxylic acid (TCA) cyclewhile reducing iron. Pyruvate carboxylase and phosphoenolpyruvatecarboxykinase were present under these conditions, but enzymes in theglyoxylate shunt and malic enzyme were absent. Gluconeogenesis and thepentose phosphate pathway were mainly employed for biosynthesis andaccounted for less than 3 percent of total carbon consumption. The modelalso indicated surprisingly high reversibility in the reaction betweenoxoglutarate and succinate. This step operates close to the thermodynamicequilibrium possibly because succinate is synthesized via a transferasereaction, and its product, acetyl-CoA, inhibits the conversion ofoxoglutarate to succinate. These findings enable a better understandingof the relationship between genome annotation and extant metabolicpathways in G. metallireducens.},
doi = {10.1128/AEM.02986-06},
url = {https://www.osti.gov/biblio/925527}, journal = {Applied Environmental Microtiology},
issn = {0099-2240},
number = 12,
volume = 73,
place = {United States},
year = {2007},
month = {8}
}