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

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. © 2012 durand et al.