The DEAD-box RNA helicase RhlE2 is a global regulator ofPseudomonas aeruginosalifestyle and pathogenesis

Abstract

RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The bacterial RhlE-like DEAD-box RNA helicases are among the least well studied of these enzymes. They are widespread especially among Proteobacteria, whose genomes often encode multiple homologs. The significance of the expansion and diversification of RhlE-like proteins for bacterial fitness has not yet been established. Here, we study the two RhlE homologs present in the opportunistic pathogen Pseudomonas aeruginosa. We show that, in the course of evolution, RhlE1 and RhlE2 have diverged in their biological functions, molecular partners and RNA-dependent enzymatic activities. Whereas RhlE1 is mainly needed for growth in the cold, RhlE2 also acts as global post-transcriptional regulator, affecting the level of hundreds of cellular transcripts indispensable for both environmental adaptation and virulence. The global impact of RhlE2 is mediated by its unique C-terminal extension, which supports the RNA unwinding activity of the N-terminal domain as well as an RNA-dependent interaction with the RNase E endonuclease and the cellular RNA degradation machinery. Overall, our work reveals how the functional and molecular divergence between two homologous RNA helicases can contribute to bacterial fitness and pathogenesis.

Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization

“…Beyond membrane-associated functions, our analysis also highlights regulatory genes such as SWI/SNF DEAD box helicases (K14440). Intriguingly, such genes have not only been shown to be involved in biofilm formation [41,[57][58][59][60], but also specifically drive expression of efflux pumps and LPS/EPS genes [57].…”

“…Beyond membrane-associated functions, our analysis also highlights regulatory genes such as SWI/SNF DEAD box helicases (K14440). Intriguingly, such genes have not only been shown to be involved in biofilm formation [41, 57–60], but also specifically drive expression of efflux pumps and LPS/EPS genes [57]. We speculate that in mucosa-associated taxa, key regulator genes act as master switches for a host of bacterial functions that alter outer membrane composition to enhance biophysical interactions with the mucosal surface and thus increase mucosal colonization fitness, leading to global spatial organization of these taxa towards the mucosa (Fig.…”

“…Intriguingly, LPS/EPS biosynthesis [39][40][41][42][43], membrane transporters/efflux pumps [44][45][46][47][48][49][50], membrane proteases [51][52][53][54][55][56], and DEAD box helicase gene regulators [41,[57][58][59][60] all have known links to biofilm formation and adhesion. Aggregating all 244 microcosm-associated KOs by KEGG BRITE gene categories, we identify several BRITE categories enriched for significant KOs, representing antibiotic resistance genes, glycosyltranferases (E.C.…”

A research program-linked, course-based undergraduate research experience that allows undergraduates to participate in current research on mycobacterial gene regulation

“…Some essential functions in M. smegmatis, like RNA helicase activity, may be fulfilled by redundant genes that are individually classified as non-essential. Three putative RNA helicases exist in M. smegmatis (helY, rhlE1, and rhlE2) (Uson et al, 2015;Khemici and Linder, 2016;Hausmann et al, 2021), and none of these genes are essential. The Shell lab previously constructed deletion mutations for each of these three genes, and in each case, the knockout has no or a very modest growth defect phenotype.…”

Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria

“…While RhlE1 primarily supports cold growth, RhlE2 has broader impacts on various phenotypes of P. aeruginosa , including virulence. Furthermore, RhlE2 interacts with the RNase E endonuclease, a major component of the RNA degradation machinery in many bacteria, and influences RNA stability [25, 29]. The interaction occurred via the RhlE2 C-terminal extension (CTE), and it is mediated or stabilized by RNA [25].…”