Abstract
BackgroundtRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase ZS and eukaryotic-type tRNase ZL, and one minor type, Thermotoga maritima (TM)-type tRNase ZS. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. It is unknown whether multiple tRNase Zs found in A. thaliana is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom.ResultsWe report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase ZSs are present only in basal land plants and green algae, the TM-type tRNase ZSs are widespread in green plants. The protein sequences of the TM-type tRNase ZSs identified in green plants are similar to those of the bacterial-type tRNase ZSs but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase ZSs may not recognize the CCA sequence as an anti-determinant.ConclusionsOur findings substantially expand the current repertoire of the TM-type tRNase ZSs and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants.
Highlights
TRNase Z removes the 3’-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short and long forms
Our survey of current plant genome databases shows that green plants are represented by multiple tRNase Zs, which include one or two tRNase ZLs and two tRNase ZSs
One tRNase ZL is predicted to participate in 3’-end processing of nuclear and mitochondrial pre-tRNA, whereas the other is likely to provide a backup for mitochondrial pre-tRNA processing
Summary
TRNase Z removes the 3’-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. TRNase Z removes the 3’-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. TRNA 3’-end maturation is a process through which the 3’-trailer sequence of precursor tRNAs (pre-tRNAs) is removed, and processed tRNAs acquire the CCA end which is absolutely essential for tRNA aminoacylation and protein synthesis (for reviews, see [1,2,3]). Unlike prokaryotic pre-tRNAs, eukaryotic nuclear and organellar pre-tRNAs generally lack the 3’-CCA sequence (which is added post-transcriptionally) and their 3’-trailer sequences are removed by tRNase Z. In the absence of the yeast La protein, the 3’-trailer sequence of nuclear pre-tRNAs is trimmed by 3’-exoribonucleases including
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