Ribonuclease J-Mediated mRNA Turnover Modulates Cell Shape, Metabolism and Virulence in Corynebacterium diphtheriae

Abstract

Controlled RNA degradation is a crucial process in bacterial cell biology for maintaining proper transcriptome homeostasis and adaptation to changing environments. mRNA turnover in many Gram-positive bacteria involves a specialized ribonuclease called RNase J (RnJ). To date, however, nothing is known about this process in the diphtheria-causative pathogen Corynebacterium diphtheriae, nor is known the identity of this ribonuclease in this organism. Here, we report that C. diphtheriae DIP1463 encodes a predicted RnJ homolog, comprised of a conserved N-terminal β-lactamase domain, followed by β-CASP and C-terminal domains. A recombinant protein encompassing the β-lactamase domain alone displays 5′-exoribonuclease activity, which is abolished by alanine-substitution of the conserved catalytic residues His186 and His188. Intriguingly, deletion of DIP1463/rnj in C. diphtheriae reduces bacterial growth and generates cell shape abnormality with markedly augmented cell width. Comparative RNA-seq analysis revealed that RnJ controls a large regulon encoding many factors predicted to be involved in biosynthesis, regulation, transport, and iron acquisition. One upregulated gene in the ∆rnj mutant is ftsH, coding for a membrane protease (FtsH) involved in cell division, whose overexpression in the wild-type strain also caused cell-width augmentation. Critically, the ∆rnj mutant is severely attenuated in virulence in a Caenorhabditis elegans model of infection, while the FtsH-overexpressing and toxin-less strains exhibit full virulence as the wild-type strain. Evidently, RNase J is a key ribonuclease in C. diphtheriae that post-transcriptionally influences the expression of numerous factors vital to corynebacterial cell physiology and virulence. Our findings have significant implications for basic biological processes and mechanisms of corynebacterial pathogenesis.

Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis

“…PCC6803, where the respective roles of the two nucleases have been investigated [26,71]. In contrast, RNase J plays a leading role in bulk mRNA degradation in several species that naturally lack RNase E, such as B. subtills, C. diphtheriae, S. aureus and H. pylori [72][73][74][75].…”

Stepwise metabolic engineering of <i>Corynebacterium glutamicum</i> for the production of phenylalanine

“…Focusing on the relationship between RNase J and amino acid metabolism, it has been reported that RNase J1 of two forms of RNase J in Bacillus subtilis and RNase J of Corynebacterium diphtheriae regulate the expression of trp operon (Deikus et al 2008;Luong et al 2021). However, the involvement of RNase J of C. glutamicum in amino acid metabolism has not been clarified although it was recently shown that RNase J of C. glutamicum regulates its own gene by degrading its mRNA and that its expression is induced by cold shock (Tanaka et al 2022).…”

Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis

“…PCC6803, where the respective roles of the two nucleases have been investigated (Rische-Grahl et al, 2014, Cavaiuolo et al, 2020. In contrast, RNase J plays a leading role in bulk mRNA degradation in several species that naturally lack RNase E, such as B. subtills, C. diphtheriae, S. aureus and H. pylori (Durand et al, 2012, Linder et al, 2014, Redko et al, 2016, Luong et al, 2021.…”