Role of RNase Y in Clostridium perfringens mRNA Decay and Processing

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 pathogenClostridium 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 inC. perfringens and involved thevirR-virS two-component system. We also observe evidence that RNase Y is indispensable for processing and stabilizing the transcripts ofcolA (encoding a major toxin collagenase) andpilA2 (encoding a major pilin component of the type IV pili). Posttranscriptional regulation ofcolA is known to be mediated by cleavage in the 5′ untranslated region (5′UTR), and we observe that RNase Y depletion diminishescolA 5′UTR processing. We show that RNase Y is also involved in the posttranscriptional stabilization ofpilA2 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 understandingC. perfringens specifically and RNases generally. Moreover, RNase Y is involved in processing specific transcripts, and we observed that this processing inC. 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 ofC. perfringens .