Dec 12, 2019

Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family

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

Abstract

Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As result, we identified ∼10 ECFs per bacterial genome on average and classified them into 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands the number of unique ECF sequences ∼50-fold relative to previous classification efforts, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences, enables th...Continue Reading

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Mentioned in this Paper

Description
Ncbi Taxonomy
Subgroup
Cell Growth
Research
Classification
Phylogenetic Analysis
Signal Transduction
Genome
Biological Factors

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