Journal of Molecular Evolution

, Volume 70, Issue 2, pp 167–180

Comparative Genomic and Phylogenetic Analyses Reveal the Evolution of the Core Two-Component Signal Transduction Systems in Enterobacteria

  • Mingsheng Qi
  • Feng-Jie Sun
  • Gustavo Caetano-Anollés
  • Youfu Zhao

DOI: 10.1007/s00239-009-9318-2

Cite this article as:
Qi, M., Sun, FJ., Caetano-Anollés, G. et al. J Mol Evol (2010) 70: 167. doi:10.1007/s00239-009-9318-2


The two-component signal transduction system (TCST) consists of a histidine kinase (HK) and a response regulator (RR). TCSTs play important roles in sensing and reacting to environmental changes, and in bacterial pathogenesis. Previously, we have identified and characterized TCSTs in Erwinia amylovora, a severe plant enterobacterial pathogen, at genome-wide level. Here we conducted a comparative genomic analysis of TCSTs in 53 genomes of 16 enterobacterial species. These species include important plant, animal, human, and insect pathogenic, saprophytic or symbiotic microorganisms. Comparative genomic analysis revealed that enterobacteria contain eight pairs of core TCSTs. Phylogenetic trees reconstructed from a concatenation of the core set of TCSTs from enterobacteria and for individual TCST proteins from species in Proteobacteria showed that most TCST protein trees in the Enterobacteriaceae or in species of the γ-Proteobacteria agreed well with that of the corresponding 16S rRNA gene. It also showed that co-evolutionary relationships existed between cognate partners of the HKs and RRs. Several core TCSTs were quite ancient and universal based on phylogenomic analysis of protein structures. These results indicate that the core TCSTs are relatively conserved, and suggest that these enterobacteria may have maintained their ancient core TCSTs and might acquire specific new TCSTs for their survival in different environments or hosts, or may have evolved new functionalities of the core TCSTs for adaptation to different ecological niches.


Two-component regulatory system Enterobacteria Gene regulation Phylogenomics Classification 

Supplementary material

239_2009_9318_MOESM1_ESM.pdf (24 kb)
Supplementary material 1 (PDF 24 kb)
239_2009_9318_MOESM2_ESM.docx (12 kb)
(DOCX 12 kb)
239_2009_9318_MOESM3_ESM.pdf (80 kb)
Supplementary material 3 (PDF 80 kb)

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Mingsheng Qi
    • 1
  • Feng-Jie Sun
    • 2
  • Gustavo Caetano-Anollés
    • 1
  • Youfu Zhao
    • 1
  1. 1.Department of Crop SciencesUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Bioinformatics Unit, W.M. Keck Center for Comparative and Functional Genomics, Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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