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The susceptibility of an RNA to different RNases can be affected by structural features of the RNA. RNA 3′ ends generated by termination of transcription at a factorindependent terminator contain an RNA hairpin, which inhibits binding of 3′-5′ exoribonucleases (Figure 2.18). Degradation of RNAs of this type is often initiated by endonucleolytic cleavage, which removes the 3′ end of the RNA and allows the 5′ region of the molecule to be degraded. Degradation of the 3′ fragment can be initiated by polyadenylation of the 3′ end of the RNA by polyadenylate [poly(A)] polymerase, encoded by the pcnB gene. Addition of the poly(A) tail provides a “landing zone” for 3′-5′ exoribonucleases, which can initiate degradation of the poly(A) sequence and then continue to move through the terminator hairpin. This may be facilitated by colocalization of poly(A) polymerase and polynucleotide phosphorylase (PNPase; Table 2.1), one of the major 3′-5′ exonucleases, with other RNases into a complex called the degradosome. Note that polyadenylation of an mRNA in eukaryotes generally results in stabilization of the mRNA, while polyadenylation of an RNA in bacteria results in rapid degradation. Degradation of the 3′ fragment generated by endonucleolytic cleavage can also be directed by 5′-3′ exoribonucleases in organisms like B. subtilis that have this activity (see Condon, Suggested Reading). It is interesting to note that the 5′ ends of transcripts newly synthesized by RNA polymerase contain a triphosphate (from the initiating nucleotide), whereas the 5′ ends of RNAs generated by endonuclease cleavage contain monophosphates. The presence of a triphosphate protects the RNA, and this triphosphate can be removed by a dedicated enzyme, designated RppH, which enhances susceptibility to degradation by 5′-3′ exonucleases (see Hui et al., Suggested Reading).

Susceptibility to degradation can be used as a mechanism to regulate gene expression, because rapid degradation of an mRNA results in reduced synthesis of its protein product. Modulation of RNA stability can occur through changes in the RNA structure that affect RNase binding by binding of a regulatory protein to the RNA or by binding of a regulatory RNA. Mechanisms of this type are discussed in chapter 11.

Table 2.1 Enzymes involved in mRNA processing and degradation

Enzyme	Substrate(s)	Description
RNase E	mRNA, rRNA, tRNA	Endonuclease, highly conserved in all Proteobacteria and some Firmicutes (not B. subtilis)
RNase III	rRNA, polycistronic mRNA	Endonuclease, cleaves double-stranded RNA in some stem-loops; found in most bacteria
RNase P	Polycistronic mRNA, tRNA precursors	Ribozyme, necessary to process 5′ ends of tRNAs
RNase G	5′ end of 16S rRNA, mRNA	Endonuclease, replaces RNase E in some bacteria
RNases J1 and J2	mRNA, rRNA	5′-3′ exonuclease, endonuclease; found in most Firmicutes and some Proteobacteria bacteria (not E. coli)
Poly(A) polymerase	mRNA	Found in most bacteria
PNPase	mRNA, poly(A) tails	3′-5′ exonuclease, found in all bacteria

Figure 2.18 Pathways for RNA degradation. RNA transcripts that are generated by termination at a factor-independent terminator contain a hairpin at the 3′ end, which inhibits degradation by 3′-5′ exoribonucleases. Degradation is often initiated by cleavage by an endonuclease, followed by rapid exonucleolytic digestion from the new 3′ end. The stable 3′ fragment (which retains the terminator hairpin) can be cleaved again by an endoribonuclease or can be degraded by a 5′-3′ exoribonuclease in organisms that have this class of enzyme. Alternatively, poly(A) polymerase can add a poly(A) tail to the 3′ end of the RNA, which allows binding of a 3′-5′ exoribonuclease and degradation.