Evolution of the extracytoplasmic function σ factor protein family

NAR Genom Bioinform. 2020 Jan 13;2(1):lqz026. doi: 10.1093/nargab/lqz026. eCollection 2020 Mar.


Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF σ factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF σ factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF σ factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated σ factor. At last, we also demonstrate horizontal transfer of ECF σ factors between soil bacteria.