Interaction of structured RNAs with the N-terminal half of RNase E

RNase E, an endoribonuclease found in many bacteria, undertakes roles in the processing and degradation of RNA. Previous work on RNase E from Escherichia coli, has suggested that tRNA processing requires RNase E to interact with structured as well as single-stranded regions via a site on RNase E that had not yet been identified. Recently, X-ray crystallography by others revealed an interaction between a groove, distal to the site of catalysis, and a duplex region of an sRNA. Here the role of this RNA-binding groove in RNase E is explored using a combination of genetics, molecular and structural biology. It is shown that this groove is the site that contacts tRNA and is essential for efficient cleavage of tRNA precursors. However, contrary to current thinking, the groove appears not to be specific for double-stranded RNA. It may also be involved in allosteric regulation. The RNA-binding groove does not appear to be crucial for autoregulation of RNase E despite the cis-acting factor being a highly structured 5´ untranslated region. This may suggest the existence of redundancy, a possibility open to functional analysis in vivo. However, any approach has to consider another key finding of this study, namely the RNA-binding groove is essential for E. coli viability. The RNA-binding groove is absent from a paralogue of RNase E called RNase G. This may be one reason why RNase G is unable to compensate for the loss of RNase E in E. coli. To provide a better platform for further functional analysis it is clear that further structural understanding of the interactions described here is required. To this end, study by electron microscopy was initiated. Discussed are the ramifications of insight gained here, direction of future structural studies, and the potential of new sequencing approaches to facilitate transcriptome-wide analyses.