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Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function
BMC Genomics (2008)
  • Hoa T Tran
  • Julia Krushkal
  • Frances M Antommattei
  • Derek R Lovley
  • Robert Weis, University of Massachusetts - Amherst

Background Geobacter species are δ-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells. Results The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (~70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors σ28 and σ54 play a role in regulating the Geobacter chemotaxis gene expression. Conclusion The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.

Publication Date
October 9, 2008
Publisher Statement
This article was harvested from BioMed Central. doi:10.1186/1471-2164-9-471 The electronic version of this article is the complete one and can be found online at: Attribution CC BY
Citation Information
Hoa T Tran, Julia Krushkal, Frances M Antommattei, Derek R Lovley, et al.. "Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function" BMC Genomics Vol. 9 Iss. 471 (2008)
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