Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis

• Published in: RNA (Cambridge) Vol. 28; no. 2; pp. 227 - 238
• Main Authors: Ingle, Shakti, Chhabra, Shivani, Chen, Jiandong, Lazarus, Michael B., Luo, Xing, Bechhofer, David H.
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.02.2022
• Subjects: Bacillus subtilis; Bacillus subtilis - enzymology; Bacillus subtilis - genetics; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Endoribonucleases - chemistry; Endoribonucleases - genetics; Endoribonucleases - metabolism; Enzymatic activity; Enzymes; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Gene Expression Regulation, Bacterial; Genomes; Microorganisms, Genetically-Modified; Mutation; Ribonuclease; Ribonucleases - genetics; Ribonucleases - metabolism; Ribonucleic acid; RNA; RNA Stability; RNA, Bacterial - chemistry; RNA, Bacterial - metabolism; Substrate Specificity; Viral Nonstructural Proteins - metabolism; oligomer; endoribonuclease; bacteria; Bacillus; small RNA processing
• ISSN: 1355-8382; 1469-9001; 1469-9001
• DOI: 10.1261/rna.078962.121

The Bacillus subtilis genome is predicted to encode numerous ribonucleases, including four 3′ exoribonucleases that have been characterized to some extent. A strain containing gene knockouts of all four known 3′ exoribonucleases is viable, suggesting that one or more additional RNases remain to be discovered. A protein extract from the quadruple RNase mutant strain was fractionated and RNase activity was followed, resulting in the identification of an enzyme activity catalyzed by the YloC protein. YloC is an endoribonuclease and is a member of the highly conserved “YicC family” of proteins that is widespread in bacteria. YloC is a metal-dependent enzyme that catalyzes the cleavage of single-stranded RNA, preferentially at U residues, and exists in an oligomeric form, most likely a hexamer. As such, YloC shares some characteristics with the SARS-CoV Nsp15 endoribonuclease. While the in vivo function of YloC in B. subtilis is yet to be determined, YloC was found to act similarly to YicC in an Escherichia coli in vivo assay that assesses decay of the small RNA, RyhB. Thus, YloC may play a role in small RNA regulation.