Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of Bacillus subtilis mRNAs

Sylvain Durand,Ciarán Condon,Philippe Bessières,Pierre Nicolas,Laetitia Gilet,Shoshy Altuvia

doi:10.1371/journal.pgen.1002520

Abstract

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.

Highlights

The amount of a particular mRNA in the cell is a function of the equilibrium between its synthesis and degradation
While the characterization of the pathways and enzymes for RNA degradation are well-advanced in Escherichia coli and yeast, studies in Gram-positive bacteria have lagged behind
This tiling array study shows that two essential enzymes, the single-strand specific endonuclease RNase Y and the 59–39 exoribonuclease RNase J1, play central roles in the degradation of mRNAs in Bacillus subtilis

Summary

Introduction

The amount of a particular mRNA in the cell is a function of the equilibrium between its synthesis and degradation. The pathways of RNA degradation are fairly well defined in the Gram-negative model bacterium Escherichia coli and in the eukaryotic paradigm Saccharyomyces cerevisiae. In E. coli, degradation of RNA is primarily dependent on the single-strand specific endonuclease RNase E, followed by degradation of the resulting fragments by 39-59 exoribonucleases (for recent review, see [1]). RNase E can either attack primary transcripts directly [2] or, in a more efficient reaction, following conversion of the 59 triphosphate moiety to a monophosphate group by the RNA pyrophosphohydrolase RppH [3]. MRNA is primarily degraded by exonucleases following removal of the methylguanosine ‘cap’ from the 59 end (for recent review see [4]). The exoribonuclease Xrn operates in the 59-39 orientation, while the exosome complex degrades RNA from the 39 end. Recent evidence has indicated a role for endonucleolytic cleavages in the decay of some yeast mRNAs (for recent review see [5])

Methods

Results

Discussion

Conclusion