Role of RNase Y in Clostridium perfringens mRNA Decay and Processing

Abstract

RNase Y is a major endoribonuclease that plays a crucial role in mRNA degradation and processing. We study the role of RNase Y in the Gram-positive anaerobic pathogen Clostridium perfringens, which until now has not been well understood. Our study implies an important role for RNase Y-mediated RNA degradation and processing in virulence gene expression and the physiological development of the organism. We began by constructing an RNase Y conditional knockdown strain in order to observe the importance of RNase Y on growth and virulence. Our resulting transcriptome analysis shows that RNase Y affects the expression of many genes, including toxin-producing genes. We provide data to show that RNase Y depletion repressed several toxin genes in C. perfringens and involved the virR-virS twocomponent system. We also observe evidence that RNase Y is indispensable for processing and stabilizing the transcripts of colA (encoding a major toxin collagenase) and pilA2 (encoding a major pilin component of the type IV pili). Posttranscriptional regulation of colA is known to be mediated by cleavage in the 5= untranslated region (5=UTR), and we observe that RNase Y depletion diminishes colA 5=UTR processing. We show that RNase Y is also involved in the posttranscriptional stabilization of pilA2 mRNA, which is thought to be important for host cell adherence and biofilm formation.IMPORTANCE RNases have important roles in RNA degradation and turnover in all organisms. C. perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen that produces numerous extracellular enzymes and toxins, and it is linked to digestive disorders and disease. A highly conserved endoribonuclease, RNase Y, affects the expression of hundreds of genes, including toxin genes, and studying these effects is useful for understanding C. perfringens specifically and RNases generally. Moreover, RNase Y is involved in processing specific transcripts, and we observed that this processing in C. perfringens results in the stabilization of mRNAs encoding a toxin and bacterial extracellular apparatus pili. Our study shows that RNase activity is associated with gene expression, helping to determine the growth, proliferation, and virulence of C. perfringens.

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

“…Another possibility is that the speB mRNA 5′ UTR is targeted by a sRNA regulating speB expression, which in turn would trigger the processing of the targeted transcript. This is the case in C. perfringens , where VR-RNA binds to the 5′ UTR of colA mRNA, resulting in the processing of this transcript by RNase Y and an increase in its stability [9,38]. …”

“…Ribonucleases (RNases) play a critical role in RNA metabolism and have been largely associated with the regulation of factors involved in bacterial pathogenicity [3,4]. In particular, the single-stranded specific endoribonuclease Y (RNase Y) is crucial for the virulence of Gram-positive pathogens such as Staphyloccocus aureus, Clostridium perfringens and Streptococcus pyogenes [5–9]. In S. aureus , RNase Y stabilizes the mRNA coding for the two-component system SaeRS, which acts as a general regulator of virulence [8,10].…”

“…In C. perfringens , RNase Y regulates the expression of multiple virulence proteins. For example, upon binding of the sRNA VR-RNA, RNase Y processes the transcript coding for the collagenase toxin (ColA), resulting in increased stability of this transcript [9]. In S. pyogenes , RNase Y affects the expression of numerous virulence genes during the stationary growth phase [7].…”

Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces

“…There is a promoter upstream of the pilB2 gene and an intragenic terminator in the pilC2 gene A promoter has been predicted to be located upstream of the pilD gene [3,9,14,16], and this is supported by the increased transcript levels between the pilA1 and pilD genes ( Fig. 4).…”

Genome‐wide screening of potential RNase Y‐processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131

“…The importance of RNase Y targets ropB and speB for S. pyogenes virulence is well established (Carroll & Musser, 2011). Interestingly, a recent study of RNase Y-dependent mRNA decay and processing in pathogenic Clostridium perfringens demonstrated a similar effect on global mRNA stability, but similarly identified only two transcripts stabilized by RNase Y processing (Obana, Nakamura, & Nomura, 2017).…”