InterPro domain: IPR013471

This entry includes ribonuclease Z (RNase Z) and its orthologues, such as RNase BN (also known as elaC) from E.coli. They are ribonucleases that have functions in tRNA-3' processing. RNase Z orthologues are present in all eukaryotes and archaea sequenced so far, and are widely distributed in bacteria [ 1 , 2 ].

All tRNAs are synthesized as precursor molecules and their maturation to functional tRNAs requires several processing steps. First, the removal of the 5'-leader is catalysed by the endonucleolytic ribozyme RNase P. Second, the removal of the 3'-trailer sequences, which is either a single-step endonucleolytic process or a two-step process involving downstream cleavage by an endonuclease followed by exonucleolytic trimming to generate the mature 3'-end [ 3 ].

The first evidence for the maturation of tRNA 3'-ends by a single endonucleolytic cleavage reaction came from eukaryotes. In these cases, the cleavage of the 3'-end is carried out by RNase Z. In most cases, RNase Z removes the 3'-trailer sequence by cleaving directly after the discriminator nucleotide. Interestingly, the CCA motif present in all mature tRNAs is a general anti-determinant for RNase Z activity. The activity of some RNase Z homologues found in bacterial and archaea have also been shown to be inhibited by the presence of a CCA motif [ 3 ].

For some bacteria and archaea, such as B. subtilis, RNase Z is essential for their viability [ 3 ]. However, in E. coli, a different pathway has been used for tRNA 3'-ends processing. The early studies showed that the E. coli pre-tRNA 3'-end processing is catalysed by an exonucleolytic. However, later studies showed that the pre-tRNA 3'-end maturation is generally initiated by a downstream endonucleolytic cleavage reaction followed by exonucleolytic trimming of the remaining nucleotides by any one of several redundant 3'-to-5'-exonucleases [ 4 ]. The RNase Z homologue in E. coli, RNase BN, has been identified. Despite RNase Z is thought to be less important than the other ribonucleases in E. coli tRNA maturation, E. coli cells lacking the four main enzymes of the exonucleolytic pathway (RNases T, PH, D and II) are viable, whereas further mutation of RNase BN/Z in this genetic context causes an unviable phenotype [ 4 ].

1. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 21, 2769-77
2. When all's zed and done: the structure and function of RNase Z in prokaryotes. Nat. Rev. Microbiol. 5, 278-86
3. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 22, 4534-43
4. Multiple exoribonucleases are required for the 3' processing of Escherichia coli tRNA precursors in vivo. FASEB J. 7, 143-8