Abstract
The stationary-phase response mediated by the RpoS sigma factor (σS, σ38) has been widely studied as a general mechanism of activation of highly diverse genes that maintain cell viability. In bacteria, genes for diverse functions have been associated with this response, showing that bacteria use a large number of functions to contend with adverse conditions in their environment. However, little is known about how the genes have been functionally recruited in diverse organisms. In this work, we address the analysis of genes regulated by σS, based on a comparative genomic-scale analysis considering four versatile bacterial species that represent different lifestyles and taxonomic groups, Escherichia coli K-12, Geobacter sulfurreducens, Borrelia burgdorferi and Bacillus subtilis, as well as the extent of conservation in bacterial genomes, as a means of assessing the evolution of this sigmulon across all organisms completely sequenced. The analysis presented here shows that genes associated with the σS response have been recruited from diverse regulons to achieve a global response. In addition, and based on the distribution of orthologues, we show a group of genes that is highly conserved among all organisms, mainly associated with glycerol metabolism, as well as diverse functional genes recruited in a lineage-specific manner.
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A supplementary figure, showing a single linkage-clustering algorithm with none leaf order optimization applied with Manhattan distance as similarity measure, is available with the online version of this paper.
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Edited by: D. W. Ussery
- Abbreviations:
- TCA cycle
- tricarboxylic acid cycle
- TF
- transcription factor