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Title: Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment

Abstract

Biomass and shotgun global proteomics data that reflected relative protein abundances from samples collected during the 2008 experiment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge site in Rifle, Colorado, provided an unprecedented opportunity to validate a genome-scale metabolic model of Geobacter metallireducens and assess its performance with respect to prediction of metal reduction, biomass yield, and growth rate under dynamic field conditions. Reconstructed from annotated genomic sequence, biochemical, and physiological data, the constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, suchmore » as the relatively low fluxes through amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1083417
Report Number(s):
PNNL-SA-88037
830403000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology, 78(24):8735 - 8742
Additional Journal Information:
Journal Name: Applied and Environmental Microbiology, 78(24):8735 - 8742
Country of Publication:
United States
Language:
English

Citation Formats

Fang, Yilin, Wilkins, Michael J., Yabusaki, Steven B., Lipton, Mary S., and Long, Philip E. Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment. United States: N. p., 2012. Web. doi:10.1128/AEM.01795-12.
Fang, Yilin, Wilkins, Michael J., Yabusaki, Steven B., Lipton, Mary S., & Long, Philip E. Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment. United States. doi:10.1128/AEM.01795-12.
Fang, Yilin, Wilkins, Michael J., Yabusaki, Steven B., Lipton, Mary S., and Long, Philip E. Wed . "Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment". United States. doi:10.1128/AEM.01795-12.
@article{osti_1083417,
title = {Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment},
author = {Fang, Yilin and Wilkins, Michael J. and Yabusaki, Steven B. and Lipton, Mary S. and Long, Philip E.},
abstractNote = {Biomass and shotgun global proteomics data that reflected relative protein abundances from samples collected during the 2008 experiment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge site in Rifle, Colorado, provided an unprecedented opportunity to validate a genome-scale metabolic model of Geobacter metallireducens and assess its performance with respect to prediction of metal reduction, biomass yield, and growth rate under dynamic field conditions. Reconstructed from annotated genomic sequence, biochemical, and physiological data, the constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low fluxes through amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.},
doi = {10.1128/AEM.01795-12},
journal = {Applied and Environmental Microbiology, 78(24):8735 - 8742},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {12}
}