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Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

(2013) MOLECULAR BIOLOGY AND EVOLUTION. 30(6). p.1302-1314
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically, and they share a large amount of their genetic material, which is commonly termed the "core genome." Despite their shared core genome, both species display very different lifestyles, and it is unclear to what extent the core genome, apart from the species-specific genes, plays a role in this lifestyle divergence. In this study, we focus on the differences in expression domains for the orthologous genes in E. coli and S. Typhimurium. The iterative comparison of coexpression methodology was used on large expression compendia of both species to uncover the conservation and divergence of gene expression. We found that gene expression conservation occurs mostly independently from amino acid similarity. According to our estimates, at least more than one quarter of the orthologous genes has a different expression domain in E. coli than in S. Typhimurium. Genes involved with key cellular processes are most likely to have conserved their expression domains, whereas genes showing diverged expression are associated with metabolic processes that, although present in both species, are regulated differently. The expression domains of the shared "core" genome of E. coli and S. Typhimurium, consisting of highly conserved orthologs, have been tuned to help accommodate the differences in lifestyle and the pathogenic potential of Salmonella.
Keywords
ELECTRON-ACCEPTOR, TRANSCRIPTIONAL REGULATION, Escherichia coli, pathogenesis, Salmonella, expression conservation, expression divergence, gene expression, GENE-EXPRESSION, EVOLUTION, IDENTIFICATION, SEQUENCE, GENOMES, HOST, ENVIRONMENTS, ADAPTATION

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Citation

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MLA
Meysman, Pieter, Aminael Sánchez-Rodríguez, Qiang Fu, et al. “Expression Divergence Between Escherichia Coli and Salmonella Enterica Serovar Typhimurium Reflects Their Lifestyles.” MOLECULAR BIOLOGY AND EVOLUTION 30.6 (2013): 1302–1314. Print.
APA
Meysman, P., Sánchez-Rodríguez, A., Fu, Q., Marchal, K., & Engelen, K. (2013). Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. MOLECULAR BIOLOGY AND EVOLUTION, 30(6), 1302–1314.
Chicago author-date
Meysman, Pieter, Aminael Sánchez-Rodríguez, Qiang Fu, Kathleen Marchal, and Kristof Engelen. 2013. “Expression Divergence Between Escherichia Coli and Salmonella Enterica Serovar Typhimurium Reflects Their Lifestyles.” Molecular Biology and Evolution 30 (6): 1302–1314.
Chicago author-date (all authors)
Meysman, Pieter, Aminael Sánchez-Rodríguez, Qiang Fu, Kathleen Marchal, and Kristof Engelen. 2013. “Expression Divergence Between Escherichia Coli and Salmonella Enterica Serovar Typhimurium Reflects Their Lifestyles.” Molecular Biology and Evolution 30 (6): 1302–1314.
Vancouver
1.
Meysman P, Sánchez-Rodríguez A, Fu Q, Marchal K, Engelen K. Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. MOLECULAR BIOLOGY AND EVOLUTION. 2013;30(6):1302–14.
IEEE
[1]
P. Meysman, A. Sánchez-Rodríguez, Q. Fu, K. Marchal, and K. Engelen, “Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles,” MOLECULAR BIOLOGY AND EVOLUTION, vol. 30, no. 6, pp. 1302–1314, 2013.
@article{4098785,
  abstract     = {Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically, and they share a large amount of their genetic material, which is commonly termed the "core genome." Despite their shared core genome, both species display very different lifestyles, and it is unclear to what extent the core genome, apart from the species-specific genes, plays a role in this lifestyle divergence. In this study, we focus on the differences in expression domains for the orthologous genes in E. coli and S. Typhimurium. The iterative comparison of coexpression methodology was used on large expression compendia of both species to uncover the conservation and divergence of gene expression. We found that gene expression conservation occurs mostly independently from amino acid similarity. According to our estimates, at least more than one quarter of the orthologous genes has a different expression domain in E. coli than in S. Typhimurium. Genes involved with key cellular processes are most likely to have conserved their expression domains, whereas genes showing diverged expression are associated with metabolic processes that, although present in both species, are regulated differently. The expression domains of the shared "core" genome of E. coli and S. Typhimurium, consisting of highly conserved orthologs, have been tuned to help accommodate the differences in lifestyle and the pathogenic potential of Salmonella.},
  author       = {Meysman, Pieter and Sánchez-Rodríguez, Aminael and Fu, Qiang and Marchal, Kathleen and Engelen, Kristof},
  issn         = {0737-4038},
  journal      = {MOLECULAR BIOLOGY AND EVOLUTION},
  keywords     = {ELECTRON-ACCEPTOR,TRANSCRIPTIONAL REGULATION,Escherichia coli,pathogenesis,Salmonella,expression conservation,expression divergence,gene expression,GENE-EXPRESSION,EVOLUTION,IDENTIFICATION,SEQUENCE,GENOMES,HOST,ENVIRONMENTS,ADAPTATION},
  language     = {eng},
  number       = {6},
  pages        = {1302--1314},
  title        = {Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles},
  url          = {http://dx.doi.org/10.1093/molbev/mst029},
  volume       = {30},
  year         = {2013},
}

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