Rawlings Timothy A, Collins Timothy M, Bieler Rudiger
Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15700-5. doi: 10.1073/pnas.2535036100. Epub 2003 Dec 12.
Although the majority of metazoan mitochondrial genomes (mtDNAs) contain the same 37 genes, including 22 encoding transfer RNAs (tRNAs), the recognition of orthologs is not always straightforward. Here we demonstrate that inferring tRNA orthologs among taxa by using anticodon triplets and deduced secondary structure can be misleading: through a process of tRNA duplication and mutation in the anticodon triplet, remolded leucine (LUUR) tRNA genes have repeatedly taken over the role of isoaccepting LCUN leucine tRNAs within metazoan mtDNA. In the present work, data from within the gastropods and a broad survey of metazoan mtDNA suggest that tRNA leucine duplication and remolding events have occurred independently at least seven times within three major animal lineages. In all cases where the mechanism of gene remolding can be inferred with confidence, the direction is the same: from LUUR to LCUN. Gene remolding and its apparent asymmetry have significant implications for the use of mitochondrial tRNA gene orders as phylogenetic markers. Remolding complicates the identification of orthologs and can result in convergence in gene order. Careful sequence-based analysis of tRNAs can help to recognize this homoplasy, improving gene-order-based phylogenetic hypotheses and underscoring the importance of careful homology assessment. tRNA remolding also provides an additional mechanism by which gene order changes can occur within mtDNA: through the changing identity of tRNA genes themselves. Recognition of these remolding events can lead to new interpretations of gene order changes, as well as the discovery of phylogenetically relevant gene dynamics that are hidden at the level of gene order alone.
尽管大多数后生动物的线粒体基因组（mtDNA）都包含相同的37个基因，其中包括22个编码转运RNA（tRNA）的基因，但直系同源物的识别并非总是一目了然。在这里，我们证明，通过使用反密码子三联体和推导的二级结构来推断不同分类群之间的tRNA直系同源物可能会产生误导：通过tRNA复制和反密码子三联体中的突变过程，重塑的亮氨酸（LUUR）tRNA基因在多细胞动物mtDNA中多次取代了同功接受的LCUN亮氨酸tRNA的作用。在目前的工作中，腹足动物内部的数据以及对后生动物mtDNA的广泛调查表明，tRNA亮氨酸的复制和重塑事件在三个主要动物谱系中至少独立发生了七次。在所有能够可靠推断基因重塑机制的情况下，其方向都是相同的：从LUUR到LCUN。基因重塑及其明显的不对称性对将线粒体tRNA基因顺序用作系统发育标记具有重要意义。重塑使直系同源物的识别变得复杂，并可能导致基因顺序趋同。基于tRNA序列的仔细分析有助于识别这种同塑性，改进基于基因顺序的系统发育假设，并强调仔细进行同源性评估的重要性。tRNA重塑还提供了一种额外的机制，通过这种机制，mtDNA内的基因顺序可以发生变化：通过tRNA基因本身身份的改变。识别这些重塑事件可以导致对基因顺序变化的新解释，以及发现仅在基因顺序水平上隐藏的系统发育相关基因动态。
