Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex.

Joana R Feliciano,Jorge H Leitão,Tiago Pita,António M M Seixas

doi:10.3390/genes11020231

Joana R Feliciano, Jorge H Leitão + Show 2 more

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https://doi.org/10.3390/genes11020231

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Abstract

RNA-binding proteins (RBPs) are important regulators of cellular functions, playing critical roles on the survival of bacteria and in the case of pathogens, on their interaction with the host. RBPs are involved in transcriptional, post-transcriptional, and translational processes. However, except for model organisms like Escherichia coli, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the Burkholderia cepacia complex (Bcc). Bcc is a group of bacterial species associated with a poor clinical prognosis in cystic fibrosis patients. These species have some of the largest bacterial genomes, and except for the presence of two-distinct Hfq-like proteins, their RBP repertoire has not been analyzed so far. Using in silico approaches, we identified 186 conventional putative RBPs in Burkholderia cenocepacia J2315, an epidemic and multidrug resistant pathogen of cystic fibrosis patients. Here we describe the comparative genomics and phylogenetic analysis of RBPs present in multiple copies and predicted to play a role in transcription, protein synthesis, and RNA decay in Bcc bacteria. In addition to the two different Hfq chaperones, five cold shock proteins phylogenetically close to E. coli CspD protein and three distinct RhlE-like helicases could be found in the B. cenocepacia J2315 genome. No RhlB, SrmB, or DeaD helicases could be found in the genomes of these bacteria. These results, together with the multiple copies of other proteins generally involved in RNA degradation, suggest the existence, in B. cenocepacia and in other Bcc bacteria, of some extra and unexplored functions for the mentioned RBPs, as well as of alternative mechanisms involved in RNA regulation and metabolism in these bacteria.

Highlights

RNA-binding proteins (RBPs) are found in all domains of life, playing a critical role in the stabilization, protection, processing, and transport of RNA, as well as in the posttranscriptional control of gene expression [1,2]
Except for an RNase, the SpoU protein, and proteins containing the ANTAR domain, homologs genes of putative RBPs identified in B. cenocepacia J2315 are encoded in the E. coli genome
RBPs play vital roles in regulating gene expression and cell physiology, the study of these proteins remains scarce in Burkholderia cepacia complex (Bcc) bacteria

Summary

Introduction

RNA-binding proteins (RBPs) are found in all domains of life, playing a critical role in the stabilization, protection, processing, and transport of RNA, as well as in the posttranscriptional control of gene expression [1,2]. The classical bacterial RBDs include the S1 domain, the cold-shock domain, the Sm and Sm-like domains, the double-stranded RNA binding domain, the K-homology domain, the DEAD motif, and the ANTAR domain. Ribosomal proteins (r-proteins) are the most abundant and best characterized RBPs that have been identified and annotated in bacterial genomes [5,8] These proteins, together with other RBP major classes such as tRNA synthetases, RNA helicases, and ribonucleases, are critical for many cellular processes. In addition to their involvement in processes associated with RNA metabolism and protein synthesis, the importance of bacterial RBPs in the extensive control of gene expression at the posttranscriptional level has been highlighted over the past two decades. While some RBPs can regulate transcription termination via attenuation

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