Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs

• Published in: PLoS genetics 2012-03, Vol.8 (3), p.e1002520-e1002520
• Main Authors: Durand, Sylvain, Gilet, Laetitia, Bessières, Philippe, Nicolas, Pierre, Condon, Ciarán
• Format: Article
• Language: English
• Subjects: Bacillus subtilis; Bacillus subtilis - enzymology; Bacterial genetics; Bacteriology; Biology; Computer Science; E coli; Escherichia coli; Experiments; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genetic aspects; Genome, Bacterial; Hypotheses; Life Sciences; Mathematics; Messenger RNA; Microbiology; Nucleases; Physiological aspects; Ribonuclease III - antagonists & inhibitors; Ribonuclease III - genetics; RNA Stability - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; Yeast
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1002520

Bacillus subtilis possesses three essential enzymes thought to be involved in mRNA decay to varying degrees, namely RNase Y, RNase J1, and RNase III. Using recently developed high-resolution tiling arrays, we examined the effect of depletion of each of these enzymes on RNA abundance over the whole genome. The data are consistent with a model in which the degradation of a significant number of transcripts is dependent on endonucleolytic cleavage by RNase Y, followed by degradation of the downstream fragment by the 5'-3' exoribonuclease RNase J1. However, many full-size transcripts also accumulate under conditions of RNase J1 insufficiency, compatible with a model whereby RNase J1 degrades transcripts either directly from the 5' end or very close to it. Although the abundance of a large number of transcripts was altered by depletion of RNase III, this appears to result primarily from indirect transcriptional effects. Lastly, RNase depletion led to the stabilization of many low-abundance potential regulatory RNAs, both in intergenic regions and in the antisense orientation to known transcripts.