YbeY Controls the Type III and Type VI Secretion Systems and Biofilm Formation through RetS in Pseudomonas aeruginosa

Abstract

YbeY is a highly conserved RNase in bacteria and plays essential roles in the maturation of 16S rRNA, regulation of small RNAs (sRNAs) and bacterial responses to environmental stresses. Previously, we verified the role of YbeY in rRNA processing and ribosome maturation in Pseudomonas aeruginosa and demonstrated YbeY-mediated regulation of rpoS through a sRNA ReaL. In this study, we demonstrate that mutation of the ybeY gene results in upregulation of the type III secretion system (T3SS) genes as well as downregulation of the type VI secretion system (T6SS) genes and reduction of biofilm formation. By examining the expression of the known sRNAs in P. aeruginosa, we found that mutation of the ybeY gene leads to downregulation of the small RNAs RsmY/Z that control the T3SS, the T6SS and biofilm formation. Further studies revealed that the reduced levels of RsmY/Z are due to upregulation of retS. Taken together, our results reveal the pleiotropic functions of YbeY and provide detailed mechanisms of YbeY-mediated regulation in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa causes a variety of acute and chronic infections in humans. The type III secretion system (T3SS) plays an important role in acute infection and the type VI secretion system (T6SS) and biofilm formation are associated with chronic infections. Understanding of the mechanisms that control the virulence determinants involved in acute and chronic infections will provide clues for the development of effective treatment strategies. Our results reveal a novel RNase mediated regulation on the T3SS, T6SS and biofilm formation in P. aeruginosa.

Purification and preliminary X-ray analysis of YbeY from Staphylococcus aureus

“…Transcriptomic analyses in the opportunistic bacteria Pseudomonas aeruginosa revealed that the deletion of ybeY gives rise to downregulation of catalase genes with increased susceptibility to oxidative stress (Xia et al, 2020a). A subsequent study further revealed the pleiotropic roles of YbeY and YbeYmediated regulation in adapting to environmental stress, which was found to be associated with bacterial virulence (Xia et al, 2020b). In P. aeruginosa, E. coli, and S. aureus, the ybe operon contains the ybeY and ybeZ genes with ATP binding and a nucleoside triphosphate hydrolase domain (Butland et al, 2005;Vercruysse et al, 2016;Wood et al, 2019).…”

YbeY, éminence grise of ribosome biogenesis

“…Indeed, while the interactions of YbeY with ribosomal components are extensively characterised across various species (see below), there is little evidence of its direct association with protein-coding or regulatory RNAs [33,34]. Instead, a few studies exposed amazingly complex and meandering regulatory cascades underlying some of ΔybeY phenotypes [19,32,35]. Pervasive gene expression changes often arise when regulators, such as transcription factors or sRNAs, get involved.…”

“…In Pseudomonas aeruginosa, YbeY loss curtails the production of the key σ-factor RpoS, which is responsible for the expression of virulence and stress response genes [19]. In the same organism, a complex cascade involving the posttranscriptional regulators of the Rsm system mediates the upregulation of the type 3 and the downregulation of the type 6 secretion system upon ybeY deletion, resulting in high cytotoxicity and low biofilm formation [35]. Thus, by affecting the levels of just a few positive and negative regulators, YbeY deficiency can lead to impressive genome-wide gene expression changes and pleiotropic phenotypes (Fig.…”

“…For example, the putative ATPase YbeZ/PhoL, found in many bacterial clades and often encoded in one operon with YbeY (Fig. 6), interacts with the latter physically and shows similar phenotypes upon deletion [19,35,53,65]. The functional significance of this highly conserved association is currently unknown.…”

“…Pervasive gene expression changes; decreased catalase activity; low σ S transcription and translation; deregulated Rsm system; upregulated type 3 secretion system genes; downregulated type 6 secretion system genes; 70S ribosome assembly defect (paralleled by increased free subunits); accumulation of a 16S rRNA precursor; decrease of mature 16S rRNA. [19,35] Firmicutes Bacillus subtilis Essential. Depletion causes growth arrest, which can be rescued by deletion of RNase R.…”