Research Article: The Highly Conserved Bacterial RNase YbeY Is Essential in Vibrio cholerae, Playing a Critical Role in Virulence, Stress Regulation, and RNA Processing

Date Published: June 5, 2014

Publisher: Public Library of Science

Author(s): Maarten Vercruysse, Caroline Köhrer, Bryan W. Davies, Markus F. F. Arnold, John J. Mekalanos, Uttam L. RajBhandary, Graham C. Walker, Karl E. Klose.


YbeY, a highly conserved protein, is an RNase in E. coli and plays key roles in both processing of the critical 3′ end of 16 S rRNA and in 70 S ribosome quality control under stress. These central roles account for YbeY’s inclusion in the postulated minimal bacterial genome. However, YbeY is not essential in E. coli although loss of ybeY severely sensitizes it to multiple physiological stresses. Here, we show that YbeY is an essential endoribonuclease in Vibrio cholerae and is crucial for virulence, stress regulation, RNA processing and ribosome quality control, and is part of a core set of RNases essential in most representative pathogens. To understand its function, we analyzed the rRNA and ribosome profiles of a V. cholerae strain partially depleted for YbeY and other RNase mutants associated with 16 S rRNA processing; our results demonstrate that YbeY is also crucial for 16 S rRNA 3′ end maturation in V. cholerae and that its depletion impedes subunit assembly into 70 S ribosomes. YbeY’s importance to V. cholerae pathogenesis was demonstrated by the complete loss of mice colonization and biofilm formation, reduced cholera toxin production, and altered expression levels of virulence-associated small RNAs of a V. cholerae strain partially depleted for YbeY. Notably, the ybeY genes of several distantly related pathogens can fully complement an E. coli ΔybeY strain under various stress conditions, demonstrating the high conservation of YbeY’s activity in stress regulation. Taken together, this work provides the first comprehensive exploration of YbeY’s physiological role in a human pathogen, showing its conserved function across species in essential cellular processes.

Partial Text

To thrive in diverse and changing environments, bacteria have to quickly sense and respond to a broad range of stimuli and signals. The ability to adapt to environmental changes is particularly important for pathogens during invasion of the host. Bacterial adaptation is often mediated through modulation of gene expression at the post-transcriptional level. A common mechanism for post-transcriptional control of gene expression is global mRNA stability, which in term is regulated by ribonucleases (RNases) that act either directly on their target mRNAs or in conjunction with regulatory RNAs [1]–[6].

We have shown that YbeY is an essential RNase in the pathogen V. cholerae. Depletion of YbeY: i) results in severe defects in 16 S rRNA maturation, ribosome assembly, and stress regulation, ii) affects regulation of virulence-associated sRNAs, and iii) reduces overall pathogenesis (Figure 10). Moreover, we found that key functions of YbeY’s multifaceted activity are highly conserved among pathogens.




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