Ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are generally synthesized as larger precursors that require processing of both their 5′ and 3′ ends to become functional molecules, and there is significant overlap between the enzymes involved in mRNA degradation and stable RNA maturation.
The pathways for tRNA maturation are fairly well understood in E. coli. Processing at the 5′ side is catalyzed by the quasi-universal ribozyme RNase P (this enzyme has been found in every organism studied thus far but A. aeolicus).
The processing of 3' end of tRNAs in Escherichia coli is initiated by an endonucleolytic cleavage downstream of the CCA terminus followed by an exonucleolytic trimming reaction. Two enzymes, RNase E and RNase III, have so far been identified as being involved in the endonucleolytic cleavage. Both of these RNases (as well as RNase P) seem to be associated with the inner membrane and cleave RNA in the context of small primary or secondary structural elements rather than being specific for a particular type of RNA. RNase III has been found to recognize double-stranded RNA structures as substrates, while RNase E cleaves single-stranded AU-rich sequences.
Exonucleolytic processing at the 3′-extremity is catalyzed by any one of a number of redundant 3′-to-5′ exonucleases: six different enzymes (RNases II, BN, D, PH, PNPase, T) are able to catalyse this reaction in vitro and in vivo, although there seems to be a hierarchy of preferences for the use of these exonucleases (RNase T and RNase PH seem to be most effective). As is the case for the endonucleolytic cleavage, none of these is specific for tRNA maturation. (PMID: 11252717).
In E.coli all tRNAs have an encoded CCA motif.
Picture based on maturation of tRNAGlu2 from rrnC operon.