Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex
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 fo...
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doaj-37c6f68b0d9e463cb2ec6764a33826ba2020-11-25T02:39:26ZengMDPI AGGenes2073-44252020-02-0111223110.3390/genes11020231genes11020231Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> ComplexJoana R. Feliciano0António M. M. Seixas1Tiago Pita2Jorge H. Leitão3iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, PortugaliBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, PortugaliBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, PortugaliBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, PortugalRNA-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 <i>Escherichia coli</i>, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the <i>Burkholderia cepacia</i> 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 <i>Burkholderia cenocepacia</i> 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 <i>E. coli</i> CspD protein and three distinct RhlE-like helicases could be found in the <i>B. cenocepacia</i> 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 <i>B. cenocepacia</i> 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.https://www.mdpi.com/2073-4425/11/2/231<i>burkholderia cepacia</i> complexrna-binding proteinscomparative genomicshfqcold shock proteinsrhle helicase |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Joana R. Feliciano António M. M. Seixas Tiago Pita Jorge H. Leitão |
spellingShingle |
Joana R. Feliciano António M. M. Seixas Tiago Pita Jorge H. Leitão Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex Genes <i>burkholderia cepacia</i> complex rna-binding proteins comparative genomics hfq cold shock proteins rhle helicase |
author_facet |
Joana R. Feliciano António M. M. Seixas Tiago Pita Jorge H. Leitão |
author_sort |
Joana R. Feliciano |
title |
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex |
title_short |
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex |
title_full |
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex |
title_fullStr |
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex |
title_full_unstemmed |
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of <i>Burkholderia cenocepacia</i> J2315 and Other Members of the <i>B. cepacia</i> Complex |
title_sort |
comparative genomics and evolutionary analysis of rna-binding proteins of <i>burkholderia cenocepacia</i> j2315 and other members of the <i>b. cepacia</i> complex |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2020-02-01 |
description |
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 <i>Escherichia coli</i>, there is little information about the identification or characterization of RBPs in other bacteria, namely in members of the <i>Burkholderia cepacia</i> 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 <i>Burkholderia cenocepacia</i> 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 <i>E. coli</i> CspD protein and three distinct RhlE-like helicases could be found in the <i>B. cenocepacia</i> 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 <i>B. cenocepacia</i> 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. |
topic |
<i>burkholderia cepacia</i> complex rna-binding proteins comparative genomics hfq cold shock proteins rhle helicase |
url |
https://www.mdpi.com/2073-4425/11/2/231 |
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