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

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.

Thermal acclimation of methanotrophs from the genusMethylobacter

“…Ribosomal proteins that are colored purple in the visualization of the ribosomal proteins on the right of the heatmaps indicate that the genes encoding these proteins are significantly higher expressed at 15 °C than at two or three of the other temperatures. The ribosomal protein overview is modified from [ 74 ]. All adjusted p values, normalized counts, genome IDs (a unique identifier that allows tracking of each gene to the genome annotation available in https://mage.genoscope.cns.fr/microscope ) and full protein names are given in SD C: Table C 4 .…”

The intracellular phase of extracellular respiratory tract bacterial pathogens and its role on pathogen-host interactions during infection

“…A confirmatory infection experiment with lung macrophages showed a clear survival advantage of the wildtype strain compared to an isogenic Δ hfq mutant after 24 h of infection but not in the early (3 h) time frame post infection [9 ▪ ]. For B. cenocepacia the impact of two Hfq proteins, similar regulators, and their controlled small RNAs during iron limitation and oxidative stress as well as virulence modulation is known as well, but the impact during internalization needs to be investigated further [63 ▪ ,64]. The small RNA Hrrf of H. influenzae is independent of Hfq but controlled by Fur and also responses to iron limitation [65].…”

Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection

“…The post-transcriptional regulation mediated by sRNAs is particularly important for bacterial pathogens, since these RNA molecules can modulate their target gene expression allowing a fast response towards an efficient adaptation to a challenging and dynamic host environment. The stability and function of these regulatory RNAs often require RNA chaperones, like the proteins Hfq and ProQ (Feliciano et al 2020;Djapgne and Oglesby 2021). Pseudomonas aeruginosa, an organism that is also responsible for severe infections amongst CF patients, possesses several characterised sRNAs involved in regulating key mechanisms for its virulence and pathogenicity, including quorum sensing, iron homeostasis, biofilm formation, response to stress, and host cell invasion (Pusic et al 2021).…”