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Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5585-E5594. doi: 10.1073/pnas.1803283115. Epub 2018 May 24.

Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex in Bacillus subtilis.

Author information

1
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
2
Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139.
3
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.
4
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; gwli@mit.edu.

Abstract

Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability, and thus discordant abundance, among cotranscribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity toward the cggR-gapA operon, an event that differentiates the synthesis of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified as also being required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. However, whether the Y-complex is broadly required for RNase Y activity is unknown. Here, we used end-enrichment RNA sequencing (Rend-seq) to globally identify operon mRNAs that undergo maturation posttranscriptionally by RNase Y and the Y-complex. We found that the Y-complex is required for the majority of RNase Y-mediated mRNA maturation events and also affects riboswitch abundance in B. subtilis In contrast, noncoding RNA maturation by RNase Y often does not require the Y-complex. Furthermore, deletion of RNase Y has more pleiotropic effects on the transcriptome and cell growth than deletions of the Y-complex. We propose that the Y-complex is a specificity factor for RNase Y, with evidence that its role is conserved in Staphylococcus aureus.

KEYWORDS:

Bacillus subtilis; RNase Y; Y-complex; mRNA degradation; mRNA processing

PMID:
29794222
DOI:
10.1073/pnas.1803283115
[Indexed for MEDLINE]
Free PMC Article

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