RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains

Abstract

RNase E of Escherichia coli is a membrane-associated endoribonuclease that has a major role in mRNA degradation. The enzyme has a large C-terminal noncatalytic region that is mostly intrinsically disordered (ID). Under standard growth conditions, RhlB, enolase and PNPase associate with the noncatalytic region to form the multienzyme RNA degradosome. To elucidate the origin and evolution of the RNA degradosome, we have identified and characterized orthologs of RNase E in the γ-Proteobacteria, a phylum of bacteria with diverse ecological niches and metabolic phenotypes and an ancient origin contemporary with the radiation of animals, plants and fungi. Intrinsic disorder, composition bias and tandem sequence repeats are conserved features of the noncatalytic region. Composition bias is bipartite with a catalytic domain proximal ANR-rich region and distal AEPV-rich region. Embedded in the noncatalytic region are microdomains (also known as MoRFs, MoREs or SLiMs), which are motifs that interact with protein and other ligands. Our results suggest that tandem repeat sequences are the progenitors of microdomains. We have identified 24 microdomains with phylogenetic signals that were acquired once with few losses. Microdomains involved in membrane association and RNA binding are universally conserved suggesting that they were present in ancestral RNase E. The RNA degradosome of E. coli arose in two steps with RhlB and PNPase acquisition early in a major subtree of the γ-Proteobacteria and enolase acquisition later. We propose a mechanism of microdomain acquisition and evolution and discuss implications of these results for the structure and function of the multienzyme RNA degradosome.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-014-0959-5) contains supplementary material, which is available to authorized users.

RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs

“…Although we have used the term microdomain to be consistent with previous work on RNase E, the sequences identified by Aït‐Bara et al . () are actually SLiMs since their identification does not rely on the detection of RISPs. It has recently been proposed that SLiMs in the human proteome represent a vast pool of peptide motifs involved in biomolecular interactions (Tompa et al ., ; Van Roey et al ., ).…”

“…The EBS was acquired in the ancestor of Vibrionales , Pasteurellales and Enterobacteriales (Aït‐Bara and Carpousis, ). The HBS and PBS were acquired together at the root of a large subtree of the γ‐proteobacteria (Aït‐Bara et al ., ), which is consistent with known functional interactions between RNase E, RhlB and PNPase (Py et al ., ; Vanzo et al ., ; Coburn et al ., ; Khemici and Carpousis, ; Khemici et al ., ). The RNA degradosome of γ‐proteobacteria distantly related to E. coli such as P. syringae Lz4W exhibits a distinct composition (Fig.…”

“…The noncatalytic region of Ps ‐RNase E has motifs that could be sites of interaction with RhlE and RNase R. The work of Aït‐Bara et al . () provides quantitative evidence that plasticity in composition of the RNA degradosome is the result of the acquisition and evolution of microdomains in the noncatalytic region of RNase E.…”

RNase E‐based degradosome modulates polyadenylation of mRNAs after Rho‐independent transcription terminators in Escherichia coli

“…Experiments using deletion mutants have identified association regions for the RhlB RNA helicase, enolase and PNPase to be at amino acids 719-731, 834-850 and 1021-1061 of the RNase E scaffold, respectively, ( Fig. 4) (Vanzo et al, 1998;Ait-Bara et al, 2015). Accordingly, we determined the polyadenylation profiles of the rpsQ and rplQ mRNAs in an rneD374 mutant, which is missing amino acids 689-1060 that contain the binding domains for RhlB, enolase, and PNPase ( Fig.…”

“…The catalytic region of amino acids 1-529 and the degradosome scaffold region of 530-1061 amino acids are shown. The degradosome scaffold region includes the binding sites for the RhlB RNA helicase, enolase, Hfq and PNPase (Vanzo et al, 1998;Ikeda et al, 2011;Ait-Bara et al, 2015).…”