An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

Pep Charusanti, Sadhana Chauhan, Kathleen McAteer, Joshua A. Lerman, Daniel R. Hyduke, Vladimir Motin, Charles Ansong, Joshua N. Adkins, Bernhard O. Palsson

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Background: Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas.Results: Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain.Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.

Original languageEnglish (US)
Article number163
JournalBMC Systems Biology
Volume5
DOIs
StatePublished - Oct 13 2011

Fingerprint

Yersinia pestis
Metabolic Network
Metabolic Networks and Pathways
Metabolism
Genome
Genes
Metabolites
Bacteria
Plague
Pathogens
Phenotype
Insect Vectors
Pathway
Carbon
Health
Continue
Siphonaptera
Nutritional Requirements
Flexibility
Experimental Data

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Applied Mathematics
  • Modeling and Simulation
  • Computer Science Applications

Cite this

Charusanti, P., Chauhan, S., McAteer, K., Lerman, J. A., Hyduke, D. R., Motin, V., ... Palsson, B. O. (2011). An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. BMC Systems Biology, 5, [163]. https://doi.org/10.1186/1752-0509-5-163

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. / Charusanti, Pep; Chauhan, Sadhana; McAteer, Kathleen; Lerman, Joshua A.; Hyduke, Daniel R.; Motin, Vladimir; Ansong, Charles; Adkins, Joshua N.; Palsson, Bernhard O.

In: BMC Systems Biology, Vol. 5, 163, 13.10.2011.

Research output: Contribution to journalArticle

Charusanti, P, Chauhan, S, McAteer, K, Lerman, JA, Hyduke, DR, Motin, V, Ansong, C, Adkins, JN & Palsson, BO 2011, 'An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92', BMC Systems Biology, vol. 5, 163. https://doi.org/10.1186/1752-0509-5-163
Charusanti, Pep ; Chauhan, Sadhana ; McAteer, Kathleen ; Lerman, Joshua A. ; Hyduke, Daniel R. ; Motin, Vladimir ; Ansong, Charles ; Adkins, Joshua N. ; Palsson, Bernhard O. / An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. In: BMC Systems Biology. 2011 ; Vol. 5.
@article{c77695f89f754c969951cc98ba7ba844,
title = "An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92",
abstract = "Background: Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas.Results: Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain.Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.",
author = "Pep Charusanti and Sadhana Chauhan and Kathleen McAteer and Lerman, {Joshua A.} and Hyduke, {Daniel R.} and Vladimir Motin and Charles Ansong and Adkins, {Joshua N.} and Palsson, {Bernhard O.}",
year = "2011",
month = "10",
day = "13",
doi = "10.1186/1752-0509-5-163",
language = "English (US)",
volume = "5",
journal = "BMC Systems Biology",
issn = "1752-0509",
publisher = "BioMed Central",

}

TY - JOUR

T1 - An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

AU - Charusanti, Pep

AU - Chauhan, Sadhana

AU - McAteer, Kathleen

AU - Lerman, Joshua A.

AU - Hyduke, Daniel R.

AU - Motin, Vladimir

AU - Ansong, Charles

AU - Adkins, Joshua N.

AU - Palsson, Bernhard O.

PY - 2011/10/13

Y1 - 2011/10/13

N2 - Background: Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas.Results: Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain.Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.

AB - Background: Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas.Results: Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain.Conclusions: Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.

UR - http://www.scopus.com/inward/record.url?scp=80053918943&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80053918943&partnerID=8YFLogxK

U2 - 10.1186/1752-0509-5-163

DO - 10.1186/1752-0509-5-163

M3 - Article

C2 - 21995956

AN - SCOPUS:80053918943

VL - 5

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

M1 - 163

ER -