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Conservation of Two-Component Signal Transduction Systems in E. coli, Salmonella, and Across 100,000 Bacteria of Various Bacterial Phyla

  • Trudy M. Wassenaar
  • Visanu Wanchai
  • Duah Alkam
  • Intawat Nookaew
  • David W. Ussery
Chapter
Part of the Grand Challenges in Biology and Biotechnology book series (GCBB)

Abstract

The number of publicly available bacterial genome sequences has reached 100,000 and continues to increase rapidly. Mining such a large dataset for gene content requires proper strategies, both in terms of quality control and finding functionally related genes that may share little sequence similarity. This is demonstrated here by comparison of bacterial two-component signal transduction systems (2CSTS), which mediate the environmental adaptability of bacteria. These systems typically consist of a sensor histidine kinase (HK) and a response regulator (RR). The HK detects environmental cues and transmits a signal to the intracellular RR, which mediates the cell’s response by changes in gene expression. Since members of a bacterial species usually thrive in similar environments, we hypothesized that the number and nature of HKs and RRs would be conserved across all members within a species, while species living under different conditions would contain different sets of 2CSTS. To test this, we compared the HKs and RRs across approximately 6000 E. coli, 7000 Salmonella, and 87,000 other bacterial genomes. The proteins were identified by the presence of telltale protein family domains. The number of HKs and RRs across E. coli and Salmonella varied some, but these species share a conserved set of around 28 2CSTS, with most genomes containing an additional two to five highly variable 2CSTS. E. coli and Salmonella contain slightly more RRs than HKs, and this is also observed in many other bacteria, but in some species HKs are in excess, in particular in species that contain high numbers of both. The number of 2CSTS generally increases with the size of the genome. Soil bacteria have either large genomes (>10 Mb) and thus many 2CSTS, or they have more of these per 1000 kb DNA. Corrected for genome size, the highest relative numbers of 2CSTS were recorded for soil bacteria of various phyla. At the other extreme, endosymbionts completely lack 2CSTS. The method applied here can swiftly and accurately compare the content of thousands of genomes by using protein functional domains.

Notes

Acknowledgments

This research was funded in part by the College of Medicine and the Department of Biomedical Informatics at UAMS, the Helen Adams & Arkansas Research Alliance Endowment, and by discretionary funding from the Joint Institute of Computational Sciences (JICS), and Oak Ridge National Laboratory sponsored laboratory director’s research and development project 7899 and by US DOE Office of Biological and Environmental Research, Genomic Science Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US Department of Energy under Contract no. DEAC05-00OR22725.

Supplementary material

371824_1_En_7_MOESM1_ESM.xlsx (70 kb)
Table S1 (XLSX 70 kb)

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Trudy M. Wassenaar
    • 1
  • Visanu Wanchai
    • 2
  • Duah Alkam
    • 2
  • Intawat Nookaew
    • 2
  • David W. Ussery
    • 2
  1. 1.Molecular Microbiology and Genomics ConsultantsZotzenheimGermany
  2. 2.Department of BioMedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockUSA

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