Degradation of RNA in bacteria: comparison of mRNA and stable RNA

Abstract

Degradation of RNA plays a central role in RNA metabolism. In recent years, our knowledge of the mechanisms of RNA degradation has increased considerably with discovery of the participating RNases and analysis of mutants affected in the various degradative pathways. Among these processes, mRNA decay and stable RNA degradation generally have been considered distinct, and also separate from RNA maturation. In this review, each of these processes is described, as it is currently understood in bacteria. The picture that emerges is that decay of mRNA and degradation of stable RNA share many common features, and that their initial steps also overlap with those of RNA maturation. Thus, bacterial cells do not contain dedicated machinery for degradation of different classes of RNA or for different processes. Rather, only the specificity of the RNase and the accessibility of the substrate determine whether or not a particular RNA will be acted upon.

Figure 1

Maturation of the 3′ ends of tRNA precursors. In E.coli, where the –CCA sequence is encoded, primarily the exoribonucleases, RNase T and RNase PH, remove the extra 3′ residues. In B.subtilis, precursors containing the –CCA sequence are processed as in E.coli, using RNase PH. Precursors lacking the –CCA sequence are first cleaved by the endoribonuclease, RNase Z, followed by addition of the –CCA sequence by tRNA nucleotidyltransferase (TNT). However, a few CCA-less precursors also use RNase PH (47). X represents precursor-specific residues.

Figure 2

Comparison of mRNA and stable RNA degradation and RNA maturation in E.coli. Initial cleavages during mRNA decay or maturation of rRNA and tRNA are carried out by the endoribonucleases, RNases E, G, III and P, although depending on the process, a different enzyme may serve the primary role. The enzyme(s) responsible for generating fragments of stable RNA is (are) not known. Terminal degradation of mRNA decay intermediates utilizes the processive exoribonucleases, RNases II, R or PNPase, followed by oligoribonuclease (ORN) to remove 5′ terminal oligonucleotides. Stable RNA degradation also utilizes RNase R or PNPase, but roles for RNase II and ORN have not yet been shown. Where known, maturation of the 3′ termini of tRNAs and some rRNAs uses RNases T or PH, but for 16S rRNA, the 3′ maturase has not been identified.