Identification and analysis of candidate fungal tRNA 3′-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2

Background: tRNase Z is the endonuclease that is responsible for the 3'-end processing of tRNA precursors, a process essential for tRNA 3'-CCA addition and subsequent tRNA aminoacylation. Based on their sizes, tRNase Zs can be divided into the long (tRNase Z(L)) and short (tRNase Z(S)) forms. tRNase Z(L) is thought to have arisen from a tandem gene duplication of tRNase Z(S) with further sequence divergence. The species distribution of tRNase Z is complex. Fungi represent an evolutionarily diverse group of eukaryotes. The recent proliferation of fungal genome sequences provides an opportunity to explore the structural and functional diversity of eukaryotic tRNase Zs. Results: We report a survey and analysis of candidate tRNase Zs in 84 completed fungal genomes, spanning a broad diversity of fungi. We find that tRNase Z(L) is present in all fungi we have examined, whereas tRNase Z(S) exists only in the fungal phyla Basidiomycota, Chytridiomycota and Zygomycota. Furthermore, we find that unlike the Pezizomycotina and Saccharomycotina, which contain a single tRNase Z(L), Schizosaccharomyces fission yeasts (Taphrinomycotina) contain two tRNase Z(L)s encoded by two different tRNase Z(L) genes. These two tRNase Z(L)s are most likely localized to the nucleus and mitochondria, respectively, suggesting partitioning of tRNase Z function between two different tRNase Z(L)s in fission yeasts. The fungal tRNase Z phylogeny suggests that tRNase Z(S)s are ancestral to tRNase Z(L)s. Additionally, the evolutionary relationship of fungal tRNase Z(L)s is generally consistent with known phylogenetic relationships among the fungal species and supports tRNase Z(L) gene duplication in certain fungal taxa, including Schizosaccharomyces fission yeasts. Analysis of tRNase Z protein sequences reveals putative atypical substrate binding domains in most fungal tRNase Z(S)s and in a subset of fungal tRNase Z(L)s. Finally, we demonstrate the presence of pseudo-substrate recognition and catalytic motifs at the N-terminal halves of tRNase Z(L)s. Conclusions: This study describes the first comprehensive identification and sequence analysis of candidate fungal tRNase Zs. Our results support the proposal that tRNase Z(L) has evolved as a result of duplication and diversification of the tRNase Z(S) gene.