Abstract
tRNase Z is the endonuclease responsible for removing the 3'-trailer sequences from precursor tRNAs, a prerequisite for the addition of the CCA sequence. It occurs in the short (tRNase ZS) and long (tRNase ZL) forms. Here we report the identification and sequence analysis of candidate tRNase Zs from 81 metazoan species. We found that the vast majority of deuterostomes, lophotrochozoans and lower metazoans have one tRNase ZS and one tRNase ZL genes, whereas ecdysozoans possess only a single tRNase ZL gene. Sequence analysis revealed that in metazoans, a single nuclear tRNase ZL gene is likely to encode both the nuclear and mitochondrial forms of tRNA 3′-end processing enzyme through mechanisms that include alternative translation initiation from two in-frame start codons and alternative splicing. Sequence conservation analysis revealed a variant PxKxRN motif, PxPxRG, which is located in the N-terminal region of tRNase ZSs. We also identified a previously unappreciated motif, AxDx, present in the C-terminal region of both tRNase ZSs and tRNase ZLs. The AxDx motif consisting mainly of a very short loop is potentially close enough to form hydrogen bonds with the loop containing the PxKxRN or PxPxRG motif. Through complementation analysis, we demonstrated the likely functional importance of the AxDx motif. In conclusion, our analysis supports the notion that in metazoans a single tRNase ZL has evolved to participate in both nuclear and mitochondrial tRNA 3′-end processing, whereas tRNase ZS may have evolved new functions. Our analysis also unveils new evolutionarily conserved motifs in tRNase Zs, including the C-terminal AxDx motif, which may have functional significance.
Highlights
TRNA 39-processing enzyme tRNase Z is an endonuclease involved in tRNA 39-end maturation
It should be noted that tRNase ZL was identified in all metazoan species examined, the protein sequences of some tRNase ZLs could not be accurately predicted due to gaps in their nucleotide sequences
The number of basal metazoan and protozoan species that have had their complete genome sequences reported is very limited, the inclusion of these species in our analysis would enable us to have a better understanding of the origin and evolution of metazoan tRNase Zs
Summary
TRNA 39-processing enzyme tRNase Z ( termed RNase Z or 39-tRNase) is an endonuclease involved in tRNA 39-end maturation (for reviews see [1,2,3,4]). It cleaves tRNA precursors (pretRNAs) after the discriminator nucleotide (the first nucleotide after the acceptor stem) to generate the tRNA 39-end suitable for CCA addition, which is essential for tRNA aminoacylation. Plants are represented by multiple genes for tRNase Zs including two tRNase ZSs and one to two tRNase ZLs [5]. These plant proteins seem to have different subcellular localization. In A. thaliana, the two tRNase ZSs are localized in the cytosol and chloroplast, respectively, whereas the two tRNase ZLs are targeted to both the nucleus and mitochondria and to the mitochondria, respectively [8]
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