Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group

Abstract

Chemotaxis is a process in which bacteria sense their chemical environment and move towards more favorable conditions. Since plant colonization by bacteria is a multifaceted process which requires a response to the complex chemical environment, a finely tuned and sensitive chemotaxis system is needed. Members of the Bacillus subtilis group including Bacillus amyloliquefaciens are industrially important, for example, as bio-pesticides. The group exhibits plant growth-promoting characteristics, with different specificity towards certain host plants. Therefore, we hypothesize that while the principal molecular mechanisms of bacterial chemotaxis may be conserved, the bacterial chemotaxis system may need an evolutionary tweaking to adapt it to specific requirements, particularly in the process of evolution of free-living soil organisms, towards plant colonization behaviour. To date, almost nothing is known about what parts of the chemotaxis proteins are subjected to positive amino acid substitutions, involved in adjusting the chemotaxis system of bacteria during speciation. In this novel study, positively selected and purified sites of chemotaxis proteins were calculated, and these residues were mapped onto homology models that were built for the chemotaxis proteins, in an attempt to understand the spatial evolution of the chemotaxis proteins. Various positively selected amino acids were identified in semi-conserved regions of the proteins away from the known active sites.

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Acknowledgements

AY thanks Rhodes University and National Research Foundation (NRF) of South Africa for financial support, OR's work was funded by the NRF grant 71261. We thank Prof. R. Borriss (Humboldt University, Berlin) for providing us with newly sequenced B. amyloliquefaciens genomes. We also thank Prof. N. Bishop and Dr. T. Bray for kindly proofreading the manuscript. AY and OTB started this work at the Bioinformatics and Computational Biology Unit, University of Pretoria; then continued at Rhodes University, Grahamstown.

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Correspondence to Ozlem Tastan Bishop.

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Yssel, A., Reva, O. & Tastan Bishop, O. Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group. Appl Microbiol Biotechnol 92, 997–1008 (2011). https://doi.org/10.1007/s00253-011-3582-y

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Keywords

  • Homology modeling
  • Chemotaxis receptor
  • Positive selection
  • Purifying selection