Structure, function and metabolic stability of antisense RNAs

Abstract: Antisense RNAs usually are small, highly structured, unstable RNAs that control a varietyof different biological processes. They exert their effect by binding to complementarytarget RNAs and thereby inhibit their functions.This thesis is concerned with the main features that determine the efficiency of antisense RNAs: their metabolic stability, the binding rate between antisense and target RNA, and the structure of the antisense RNA itself. Three different plasmid-encoded antisense RNAs were studied.RNA decay in bacteria is complex: a large number of proteins are involved in processing and degradation. My results show that mutations in an Escherichia coli gene, pcnB, encoding a poly(A)polymerase, exert an effect on the replication of antisense RNA-regulated plasmids. PcnB aids in the degradation of the inhibitors of replication, the antisense RNAs. This enzyme can polyadenylate both CopA and RNAI, the antisense RNAs controlling the replication of plasmids R1 and ColE1, respectively. Accelerated pcnB dependent decay of CopA requires processing by an endoribonuclease, RNase E. This cleavage step appears to initiate decay of both CopA and RNA I. In addition, the 3'-5' exoribonucleases PNPase and RNase II can independently degrade RNase E-cleaved CopA.Other ribonucleases are involved in the pcnB dependent degradation since CopA decay is shown (although at lower rates) in the absence of these enzymes.Analysis of FinP, an antisense RNA controlling plasmid conjugation, indicates astructure consisting of two stem-loops. Stem-loops are preferred motifs in most antisenseRNAs. The binding rate between FinP and its target RNA is in the same range as in otherwell-characterized systems. Upon binding, the target RNA (traJ mRNA) is renderedunstable, probably due to RNase III-dependent cleavages. This destabilization requiresthe presence of the helper protein FinO.