Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
Highlights
Introduction and Aim of this ReviewBacteria, like all other living organisms, have adapted and evolved to inhabit a specific environment, tuning their physiology and metabolism to the pervading conditions provided by their habitat
Oxidative stress can be overcome by expressing catalases or peroxiredoxins [3,4], which catalyze the conversion of ROS into harmless compounds before they can damage cell structures
This explains the reduced melting capacity and high promoter stringency of Extracytoplasmic function σ factors (ECFs), which prevents non-specific transcription initiation, in contrast to primary σ70 factors, characterized by a high promoter-melting capacity required to drive the bulk of bacterial transcription from promoters where A-11 and T-7, and G-6, are conserved [46,49]
Summary
Like all other living organisms, have adapted and evolved to inhabit a specific environment, tuning their physiology and metabolism to the pervading conditions provided by their habitat. In the early 1990s, certain representatives of this group caught the attention of molecular microbiologists (reviewed in [11]) because of their small size They comprise the essential domains allowing RNAP interaction, promoter-binding and initiation activity. Due to their diversity and the relative simplicity of their mechanism of action, they have stood out as a versatile and powerful bacterial tool to efficiently activate stress responses [12] Since their discovery, much effort has been focused on unraveling all biological aspects of ECFs. Since their discovery, much effort has been focused on unraveling all biological aspects of ECFs These include their role in bacterial physiology, their evolution and classification, the regulation of their production and activity, the stimuli that activate them and their target genes, their structural features and their transcription initiation mechanisms. In this review, we comprehensively cover the most prominent aspects of the biology of ECFs, such as their role in the response to stress, how they are regulated, their classification, their mechanism of action and the future perspectives we consider to be important in future research on these regulators
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