Comparative Analysis And Evolutionary Study Of Plant TRNA

Transfer RNAs (tRNAs) are thought to be one of the most ancestral RNA molecules. The main function of tRNAs is to play an important role in biological synthesis of new proteins; besides, tRNAs are also involved in many other cellular metabolisms. In plants, tRNA genes reside in nucleus genome, mitochondrial(mt) genome and chloroplast(cp) genome and they could transfer from organellar genomes to the nucleus genome or between organellar genomes. The survey on distribution and transfer of tRNA genes may provide a clue to the study of structure evolution for plant genomes. Currently, there are only a few plants of which the nucleus genome was decoded; furthermore, the draft genome may lead to incomplete tRNA gene content, which can affect the final result for tRNA gene evolution. Compared to the nucleus genome, organellar genomes are much easier to assemble. Up to date, there are55Plantae species of which mitochondrion and chloroplast genomes are both sequenced. Here, we compare the tRNA gene content of organellar genomes and investigate the evolution of organellar tRNA genes.We reannotated tRNA genes in mitochondrial and chloroplast genomes of the55plants, and investigated the gene content variation, intron structure, conservation and transfer of tRNA genes in this study.(1) The variance of tRNA gene content between different plants is large in mitochondrial genome, while it is much less in chloroplast genome. The amino acid sets recognized by tRNA genes in mitochondrial genome vary greatly between different plants. Only9of the analyzed55plants, such as Micromonas sp. RCC299and Marchantia polymorpha, could recognize all20natural amino acids. The mitochondrial tRNA genes of Oryza rufipogon only recognize16natural amino acids, while that of Chlamydomonas reinhardtii only recognize3natural amino acids. As for chloroplast genomes, all plants recognize all20natural amino acids, except Micromonas sp. RCC299lacking tRNA genes corresponding to histidine and valine. According to the anticodon of tRNA genes, there are13anticodons, such as Ala-AGC and Ala-GGC, to which none of the55plant mitochondria contain corresponding tRNA genes; there are11anticodons, such as Ala-AGC and Ala-CGC, to which none of the55plant chloroplasts contain corresponding tRNA genes. There are15anticodons to which all of the55plant chloroplasts contain corresponding tRNA genes, while there is no anticodon to which all of the55plant mitochondria contain corresponding tRNA genes. The range of total number of tRNA genes for55plants is from3to41among mitochondrial genomes and is from26to77among chloroplast genomes. The number of tRNA genes for each amino acid ranges from0to8, and most amino acids have1or2tRNA genes. Chloroplast tRNA genes resided in the inverted repeats are duplicated once; other chloroplast tRNA genes and all mitochondrial tRNA genes are single copy genes.(2) Some mitochondrial native tRNA genes contain typical group II intron in lower plants, while none of mitochondrial native tRNA genes contains typical intron in higher plants. In chloroplasts, intron-containing tRNA genes distribute in all Streptophytina species, suggesting that chloroplast tRNA intron may arise after the emergence of Streptophytina. We compare the conservation of tRNA genes and conclude that tRNA genes tend to be unconserved between alages and much more conserved between Tracheophyta species; chloroplast tRNA genes are more conserved than mitochondrial tRNA genes. We further compare organellar tRNA genes to bacterial tRNA genes, and the results suggest that sequences of mitochondrial tRNA genes change rapidly while sequences of chloroplast tRNA genes change slowly. There are four chloroplast tRNA genes share≥95%sequence identity with cyanobacterial tRNA genes, i.e. tRNAIle(GAT), tRNALys(TTT), tRNAphe(GAA) and tRNAAsp(GTC), and these four tRNA genes may be the most ancient chloroplast tRNA genes.(3) We investigate the transfer of tRNA gene between organellar genomes detailedly. First, we identify the cp-derived DNA in each mitochondrial genome(MTPT), and the results show that frequent transfer events of cpDNA to mitochondrial genomes occurred in the common ancestor of Tracheophyta. The MTPT content shows no significant correlation to repeat content in mitochondrial genomes. Second, by analyzing the transfer and loss of tRNA genes in mitochondrial genomes, we find that mitochondria of all Tracheophyta species gained cp-derived tRNAMet(CAT) and tRNAHis(GTG); mitochondria of all angiosperms gained cp-derived tRNAAsn(GTT), tRNATrp(CCA) and tRNAPro(TGG); mitochondria of commelinids species gained cp-derived tRNACys(GCA) and tRNAphe(GAA). After transferred to mitochondrial genomes, cp-derived tRNA genes may be lost from mitochondrial genome, or kept in mitochondrial genome, either replacing mt-native tRNA genes or coexisting with mt-native tRNA genes. Finally, we infer when the cp-derived tRNA genes transferred to mitochondria. tRNAMet(CAT) was dated to the common ancestor of Tracheophyta; tRNAHis(GTG) was at least dated to the common ancestor of monocots and dicots; tRNAAsn(GTT) was dated to the common ancestor of angiosperms; tRNATrp(CCA) and tRNAPro(TGG) are included in a same MTPT which transferred to the mitochondrial genome of the common ancestor of angiosperms. We also discuss the mechanism of cpDNA transferring to mitochondrial genomes and suggest that the mechanism is similar to the way organellar DNA transferring to nucleus genomes.In sum, our results further support that in most plant mitochondria, tRNA genes are unable to recognize all20natural amino acids, by contrast, in almost all chloroplasts, tRNA genes can recognize all20natural amino acids. The great varying of recognized amino acid sets among different plants reveals that these species need to import different tRNAs from the cytoplasm into their mitochondria. During the evolution of organellar genomes, mitochondrial tRNA gene sequences tend to change rapidly while chloroplast tRNA gene sequences tend to change slowly. The investigation of MTPT and transferred tRNA genes supports that frequent transfer events of DNA between organellar genomes occurred in the common ancestor of Tracheophyta. The transfers of some tRNA genes were dated to the common ancestor of Tracheophyta or angiosperms.