Factors involved in the 3' processing of M1 RNA and the role of the processing

Abstract

M1 RNA, the catalytic component of Escherichia coli RNase P, is derived by 3` processing from pM1 RNA, a major transcript of the rnpB gene. This 3` processing occurs by two pathways involving multiple steps. The pM1 RNA molecule has an rne-dependent site downstream of the processing site, GAUUU, whose sequence variation affects the processing efficiency. In this thesis, first, roles of the sequence of the rne-dependent site on the pathways of 3` processing of M1 RNA were examined. The results showed that the primary sequence itself of the rne-dependent site possessed the ability to determine the processing pathways. Therefore, the sequence of the rne-dependent site seems not only to affect the processing efficiency, but also to guide the RNA metabolic pathway. The sequence of the rne-dependent site also affected the substrate specificity by generating the processing products at one nucleotide upstream or downstream from the normal cleavage sites. Interestingly, in case of the variants involving both pathways, the same 3`-ends were generated by either pathway, suggesting that the substrate specificity by both pathways is same. These results may provide a mechanistic basis for the role of the rne-dependent site in control of biosynthesis of M1 RNA in E. coli. Although this 3` processing of M1 RNA has been known to be carried out by RNase E, no one has shown the direct involvement of RNase E in the processing. RNase E is an essential endonuclease, which was initially characterized as an enzyme responsible for the generation of 5S rRNA from a 9S RNA precursor. RNase E is also the main component of an mRNA degradation complex, the degradosome. The N-terminal half of RNase E containing the ribonucleolytic site is sufficient for the cleavage of 9S RNA. In this thesis, whether or not RNase E is directly involved in 3` processing of M1 RNA was examined by using the N-terminal half of RNase E. Indeed, the N-terminal half of RNase E cleaved pM1 RNA endonucleolytically. H...