Apr 10, 2020

Co-evolutionary analysis reveals a conserved dual binding interface between extracytoplasmic function (ECF) σ factors and class I anti-σ factors

BioRxiv : the Preprint Server for Biology
Delia Casas-PastorGeorg Fritz

Abstract

Extracytoplasmic function {sigma} factors (ECFs) belong to the most abundant signal transduction mechanisms in bacteria. Amongst the diverse regulators of ECF activity, class I anti-{sigma} factors are the most important signal transducers in response to internal and external stress conditions. Despite the conserved secondary structure of the class I anti-{sigma} factor domain (ASDI) that binds and inhibits the ECF under non-inducing conditions, the binding interface between ECFs and ASDIs is surprisingly variable between the published co-crystal structures. In this work, we provide a comprehensive computational analysis of the ASDI protein family and study the different contact themes between ECFs and ASDIs. To this end, we harness the co-evolution of these diverse protein families and predict covarying amino acid residues as likely candidates of an interaction interface. As a result, we find two common binding interfaces linking the first -helix of the ASDI to the DNA binding region in the {sigma}4 domain of the ECF, and the fourth -helix of the ASDI to the RNA polymerase (RNAP) binding region of the {sigma}2 domain. The conservation of these two binding interfaces contrasts with the apparent quaternary structure diversity of...Continue Reading

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Sample Fixation
Site
Species
Alleles
Fixation - Action
Mutation Abnormality
Population Group

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