Genetic and biochemical studies on the differential modulation of RNA decay and processing by inhibitory proteins in Escherichia coli

The regulation of mRNA decay is a critical post-transcriptional step in the control of gene expression. In E. coli, RNase E carries out the first and rate-limiting step in the decay of most mRNAs, as well as in the processing of ribosomal, transfer RNAs and small regulatory RNAs. The RNase E protein has two domains: the catalytic N-terminal half and the C-terminal half containing the scaffold region for the assembly of an RNA degrading machine termed the degradosome. Earlier studies in our lab identified the trans-acting proteins, RraA and RraB, which inhibit RNase E activity through direct-interaction with the enzyme. The present work explores several mechanistic, physiological and biotechnology-related aspects of the modulation of E. coli RNA decay and processing by inhibitory proteins. We found that, in contrast to RraA, RraB interacts with a different site on RNase E, results in distinct changes in degradosome composition, and interferes with cleavage of a different set of transcripts. Therefore, our results revealed a novel