Monloy Kim Carlo, Planta Jose
National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
Front Plant Sci. 2024 Dec 23;15:1486612. doi: 10.3389/fpls.2024.1486612. eCollection 2024.
Transfer RNAs (tRNAs) are noncoding RNAs involved in protein biosynthesis and have noncanonical roles in cellular metabolism, such as RNA silencing and the generation of transposable elements. Extensive tRNA gene duplications, modifications to mature tRNAs, and complex secondary and tertiary structures impede tRNA sequencing. As such, a comparative genomic analysis of complete tRNA sets is an alternative to understanding the evolutionary processes that gave rise to the extant tRNA sets. Although the tRNA gene (tDNA) structure and distribution in prokaryotes and eukaryotes, specifically in vertebrates, yeasts, and flies, are well understood, there is little information regarding plants. A detailed and comprehensive analysis and annotation of tDNAs from the genomes of 44 eudicots, 20 monocots, and five other non-eudicot and non-monocot species belonging to the Ceratophyllaceae and the ANA (Amborellales, Nymphaeales, and Austrobaileyales) clade will provide a global picture of plant tDNA structure and organization. Plant genomes exhibit varying numbers of nuclear tDNAs, with only the monocots showing a strong correlation between nuclear tDNA numbers and genome sizes. In contrast, organellar tDNA numbers varied little among the different lineages. A high degree of tDNA duplication in eudicots was detected, whereby most eudicot nuclear genomes (91%) and only a modest percentage of monocot (65%) and ANA nuclear genomes (25%) contained at least one tDNA cluster. Clusters of tRNA-tRNA and tRNA genes were found in eudicot and monocot genomes, respectively, while both eudicot and monocot genomes showed clusters of tRNA genes. All plant genomes had intron-containing tRNA and tRNA genes with modest sequence conservation and a strictly conserved tRNA species. Regulatory elements found upstream (TATA-box and CAA motifs) and downstream (poly(T) signals) of the tDNAs were present in only a fraction of the detected tDNAs. A and B boxes within the tDNA coding region show varying consensus sequences depending on the tRNA isotype and lineage. The chloroplast genomes, but not the mitogenomes, possess relatively conserved tRNA gene organization. These findings reveal differences and patterns acquired by plant genomes throughout evolution and can serve as a foundation for further studies on plant tRNA gene function and regulation.
转运RNA（tRNA）是参与蛋白质生物合成的非编码RNA，在细胞代谢中具有非经典作用，如RNA沉默和转座元件的产生。大量的tRNA基因重复、成熟tRNA的修饰以及复杂的二级和三级结构阻碍了tRNA测序。因此，对完整tRNA集进行比较基因组分析是理解导致现存tRNA集的进化过程的一种替代方法。尽管原核生物和真核生物，特别是脊椎动物、酵母和果蝇中的tRNA基因（tDNA）结构和分布已得到充分了解，但关于植物的信息却很少。对44种双子叶植物、20种单子叶植物以及属于金鱼藻科和ANA（无油樟目、睡莲目和木兰藤目）分支的其他5种非双子叶植物和非单子叶植物基因组中的tDNA进行详细而全面的分析和注释，将提供植物tDNA结构和组织的全局图景。植物基因组中核tDNA的数量各不相同，只有单子叶植物的核tDNA数量与基因组大小之间存在强相关性。相比之下，不同谱系中细胞器tDNA的数量变化不大。在双子叶植物中检测到高度的tDNA重复，其中大多数双子叶植物核基因组（91%）以及仅一小部分单子叶植物（65%）和ANA核基因组（25%）至少包含一个tDNA簇。在双子叶植物和单子叶植物基因组中分别发现了tRNA - tRNA和tRNA基因簇，而双子叶植物和单子叶植物基因组均显示出tRNA基因簇。所有植物基因组都有含内含子的tRNA和tRNA基因，序列保守性适中，且tRNA种类严格保守。在检测到的tDNA中，只有一小部分存在于tDNA上游（TATA盒和CAA基序）和下游（poly(T)信号）发现的调控元件。tDNA编码区内的A盒和B盒根据tRNA同型和谱系显示出不同的共有序列。叶绿体基因组而非线粒体基因组具有相对保守的tRNA基因组织。这些发现揭示了植物基因组在整个进化过程中获得的差异和模式，并可为进一步研究植物tRNA基因功能和调控奠定基础。
