The Third Pillar of Bacterial Signal Transduction: Signaling Diversity and Evolution of Extracytoplasmic Function (ECF) Sigma Factors

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Adaptation of a bacterium to environmental conditions necessitates transmembrane signaltransduction to orchestrate adequate cellular responses. The promoter determines the specificity and efficiency of transcriptional initiation, and is therefore an important regulatory switchboard to coordinate differential gene expression. Extracytoplasmic function (ECF) σ factors, the largest and most diverse group of alternative σ factors, respond to environmental stimuli through a second, normally membraneanchored sensor protein, the corresponding anti-σ factor. Despite their abundance and overall importance, only a very limited number of these systems have been experimentally studied to date. Here we propose the analysis of members of three novel and unusual groups of conserved ECF σ factors that were identified during comprehensive comparative genomics and transcriptomics studies, (i) ECF σ factors involved in the cell envelope stress response of Bacillus licheniformis. (ii) ECF σ factors that are functionally linked to response regulators, but lack an anti-σ factor, indicative for a novel mechanism of signal transduction. (iii) ECF σ factors implicated to be involved in oxidative stress response. These proteins are functionally linked to carboxymuconolactone decarboxylase homologs instead of a standard anti-σ factor. Our analyses (ongoing and proposed) will be embedded in a comparative genomics database and used to establish bioinformatics tools to reconstruct and predict ECF σ factor-dependent regulatory networks in microbial genomes.