Diverse primary and secondary structural features are associated with Y complex-dependent mRNA maturation in B. subtilis

Abstract

In Bacillus subtilis, mRNA processing and decay are primarily initiated by the endonuclease RNase Y. Recent work by our group discovered a set of auxiliary factors called the Y complex that is required for the mRNA maturation of 21 operons. It is unclear, however, how these operons specifically are targeted by RNase Y and the Y complex. Here we use in silico sequence motif searches, kmer analysis and secondary structure prediction to analyze these 21 cleavage sites and their surrounding regions. We find enrichment for a guanine immediately preceding the cleavage site. Such enrichment has been previously observed in Staphylococcus aureus RNase Y cleavage sites, indicating a role for the Y complex in processing those sites as well. Surprisingly, there are no other detectable sequence or structural motifs in the regions around the 21 B. subtilis sites. This suggests that Y complex-dependent processing and, more broadly, mRNA processing in B. subtilis, is more complicated than previously anticipated.