Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors

  • Davi R. Ortega
  • Igor B. Zhulin
Part of the Methods in Molecular Biology book series (MIMB, volume 1729)


Identifying chemoreceptors in sequenced bacterial genomes, revealing their domain architecture, inferring their evolutionary relationships, and comparing them to chemoreceptors of known function become important steps in genome annotation and chemotaxis research. Here, we describe bioinformatics procedures that enable such analyses, using two closely related bacterial genomes as examples.


Chemotaxis Chemoreceptors Sequence analysis Phylogenetic analysis Protein domains Rhizobia 



This work was supported by NIH grant R35 GM122588 to D.R.O and R01 GM072285 to I.B.Z.


  1. 1.
    Hazelbauer GL, Falke JJ, Parkinson JS (2008) Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci 33:9–19CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Wuichet K, Zhulin IB (2010) Origins and diversification of a complex signal transduction system in prokaryotes. Sci Signal 3:ra50CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Adebali O, Zhulin IB (2017) Aquerium: a web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. Proteins 85:72–77CrossRefPubMedGoogle Scholar
  4. 4.
    Wuichet K, Alexander RP, Zhulin IB (2007) Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods Enzymol 422:1–31PubMedPubMedCentralGoogle Scholar
  5. 5.
    Alexander RP, Zhulin IB (2007) Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proc Natl Acad Sci U S A 104:2885–2890CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Borziak K, Fleetwood AD, Zhulin IB (2013) Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli. J Bacteriol 195:3596–3602CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Day CJ, King RM, Shewell LK, Tram G, Najnin T et al (2016) A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni. Nat Commun 7:13206CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB (2016) Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes. PLoS Comput Biol 12:e1004862CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Meier VM, Scharf BE (2009) Cellular localization of predicted transmembrane and soluble chemoreceptors in Sinorhizobium meliloti. J Bacteriol 191:5724–5733CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Webb BA, Hildreth S, Helm RF, Scharf BE (2014) Sinorhizobium meliloti chemoreceptor McpU mediates chemotaxis toward host plant exudates through direct proline sensing. Appl Environ Microbiol 80:3404–3415CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Webb BA, Helm RF, Scharf BE (2016) Contribution of individual chemoreceptors to Sinorhizobium meliloti chemotaxis towards amino acids of host and nonhost seed exudates. Mol Plant-Microbe Interact 29:231–239CrossRefPubMedGoogle Scholar
  12. 12.
    Webb BA, Karl Compton K, Castañeda Saldaña R, Arapov TD, Keith Ray W et al (2017) Sinorhizobium meliloti chemotaxis to quaternary ammonium compounds is mediated by the chemoreceptor McpX. Mol Microbiol 103:333–346CrossRefGoogle Scholar
  13. 13.
    O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44:D733–D745CrossRefPubMedGoogle Scholar
  14. 14.
    Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285CrossRefPubMedGoogle Scholar
  15. 15.
    Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7(10):e1002195CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Huson DH, Scornavacca C (2012) Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 61:1061–1067CrossRefPubMedGoogle Scholar
  21. 21.
    Adebali O, Ortega DR, Zhulin IB (2015) CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 31:1475–1477CrossRefPubMedGoogle Scholar
  22. 22.
    Letunic I, Doerks T, Bork P (2015) SMART: recent updates, new developments and status in 2015. Nucleic Acids Res 43:D257–D260CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA
  2. 2.Computer Science and Mathematics DivisionOak Ridge National LaboratoryOak RidgeUSA
  3. 3.Department of MicrobiologyUniversity of TennesseeKnoxvilleUSA

Personalised recommendations