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

Abstract

Small non-coding RNAs (sRNAs) are key regulators of post-transcriptional gene expression in bacteria. Despite the identification of hundreds of bacterial sRNAs, their roles on bacterial physiology and virulence remain largely unknown, as is the case of bacteria of the Burkholderia cepacia complex (Bcc). Bcc is a group of opportunistic pathogens with relatively large genomes that can cause lethal lung infections amongst cystic fibrosis (CF) patients. To characterise sRNAs expressed by Bcc bacteria when infecting a host, the nematode Caenorhabditis elegans was used as an infection model by the epidemic CF strain B. cenocepacia J2315. A total of 108 new and 31 previously described sRNAs with a predicted Rho independent terminator were identified, most of them located on chromosome 1. RIT11b, a sRNA downregulated under C. elegans infection conditions, was shown to directly affect B. cenocepacia virulence, biofilm formation, and swimming motility. RIT11b overexpression reduced the expression of the direct targets dusA and pyrC, involved in biofilm formation, epithelial cell adherence, and chronic infections in other organisms. The in vitro direct interaction of RIT11b with the dusA and pyrC messengers was demonstrated by electrophoretic mobility shift assays. To the best of our knowledge this is the first report on the functional characterization of a sRNA directly involved in B. cenocepacia virulence. Key points • 139 sRNAs expressed by B. cenocepacia during C. elegans infection were identified • The sRNA RIT11b affects B. cenocepacia virulence, biofilm formation, and motility • RIT11b directly binds to and regulates dusA and pyrC mRNAs

Non-coding regulatory sRNAs from bacteria of the Burkholderia cepacia complex

“…Aiming at the identification of sRNAs playing a role in B. cenocepacia virulence, Pita et al ( 2023 ) used the nematode Caenorhabditis elegans as an infection model and extracted total RNA from bacteria inside the nematode guts after 48 h of infection. The extracted RNA was analyzed by RNA-seq.…”

“…The differential expression of some sRNAs was assessed by qRT-PCR, and the results are indicated in parentheses (Biofilms) or in qRT-PCR columns (conditions of low iron concentration and low pH). Data was retrieved from 1 Pita et al ( 2023 ), 2 Pita et al ( 2018 ), 3 Sass et al ( 2013 ), and 4 Sass et al ( 2017 )…”