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Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.

Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM - BMC Genomics (2008)

Bottom Line: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important.The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively).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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA. htt@chem.umass.edu

ABSTRACT

Background: Geobacter species are delta-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 (approximately 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 sigma28 and sigma54 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.

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Putative σ28 and σ54 promoter elements. (A) Putative σ28 promoter regulation sites found upstream of G. sulfurreducens che cluster 1 and the fliC genes of G. sulfurreducens (gsu3038), G. metallireducens (gsu0442), and G. uraniireducens (gsu4096) [97]. 125, 160, 127, and 152 nucleotide bases separate the predicted transcription start sites from the start codons, respectively. (B) Putative σ54 promoter elements upstream of the Geobacter major che gene clusters [51]. For G. metallireducens clusters 1 and 6, G. uraniireducens cluster 3, and G. sulfurreducens cluster 6, the predicted transcription start sites are 50, 33, 24 and 16 nucleotide bases upstream of predicted operon ATG start codons, respectively.
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Figure 4: Putative σ28 and σ54 promoter elements. (A) Putative σ28 promoter regulation sites found upstream of G. sulfurreducens che cluster 1 and the fliC genes of G. sulfurreducens (gsu3038), G. metallireducens (gsu0442), and G. uraniireducens (gsu4096) [97]. 125, 160, 127, and 152 nucleotide bases separate the predicted transcription start sites from the start codons, respectively. (B) Putative σ54 promoter elements upstream of the Geobacter major che gene clusters [51]. For G. metallireducens clusters 1 and 6, G. uraniireducens cluster 3, and G. sulfurreducens cluster 6, the predicted transcription start sites are 50, 33, 24 and 16 nucleotide bases upstream of predicted operon ATG start codons, respectively.

Mentions: We searched upstream of the major Geobacter che operons and fliC loci for evidence of σ28-regulated expression. As Figure 4A shows, σ28 binding sites were identified upstream of fliC in G. metallireducens, G. sulfurreducens and G. uraniireducens, but only one major che cluster, the G. sulfurreducens group α cluster (cluster 1, Figure 1), had a recognizable σ28 binding site. Therefore, it seems that the specific mechanisms of regulation for most of the Geobacter che clusters will be different from E. coli (and Salmonella).


Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.

Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM - BMC Genomics (2008)

Putative σ28 and σ54 promoter elements. (A) Putative σ28 promoter regulation sites found upstream of G. sulfurreducens che cluster 1 and the fliC genes of G. sulfurreducens (gsu3038), G. metallireducens (gsu0442), and G. uraniireducens (gsu4096) [97]. 125, 160, 127, and 152 nucleotide bases separate the predicted transcription start sites from the start codons, respectively. (B) Putative σ54 promoter elements upstream of the Geobacter major che gene clusters [51]. For G. metallireducens clusters 1 and 6, G. uraniireducens cluster 3, and G. sulfurreducens cluster 6, the predicted transcription start sites are 50, 33, 24 and 16 nucleotide bases upstream of predicted operon ATG start codons, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2577667&req=5

Figure 4: Putative σ28 and σ54 promoter elements. (A) Putative σ28 promoter regulation sites found upstream of G. sulfurreducens che cluster 1 and the fliC genes of G. sulfurreducens (gsu3038), G. metallireducens (gsu0442), and G. uraniireducens (gsu4096) [97]. 125, 160, 127, and 152 nucleotide bases separate the predicted transcription start sites from the start codons, respectively. (B) Putative σ54 promoter elements upstream of the Geobacter major che gene clusters [51]. For G. metallireducens clusters 1 and 6, G. uraniireducens cluster 3, and G. sulfurreducens cluster 6, the predicted transcription start sites are 50, 33, 24 and 16 nucleotide bases upstream of predicted operon ATG start codons, respectively.
Mentions: We searched upstream of the major Geobacter che operons and fliC loci for evidence of σ28-regulated expression. As Figure 4A shows, σ28 binding sites were identified upstream of fliC in G. metallireducens, G. sulfurreducens and G. uraniireducens, but only one major che cluster, the G. sulfurreducens group α cluster (cluster 1, Figure 1), had a recognizable σ28 binding site. Therefore, it seems that the specific mechanisms of regulation for most of the Geobacter che clusters will be different from E. coli (and Salmonella).

Bottom Line: Geobacter species are delta-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important.The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively).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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA. htt@chem.umass.edu

ABSTRACT

Background: Geobacter species are delta-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 (approximately 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 sigma28 and sigma54 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.

Show MeSH
Related in: MedlinePlus