Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.
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DOI：
10.1093/nar/gkr1131
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Stadler PF
中科院分区：
文献类型：
--
作者：
Jühling F;Pütz J;Bernt M;Donath A;Middendorf M;Florentz C;Stadler PF
转移RNA(TRNA)存在于所有类型的细胞和细胞器中。动物线粒体tRNA的一级序列保守性较低，二级结构奇特，缺乏普通三叶草的完整结构域。这样的序列很难被检测到，因此在计算分析和线粒体基因组注释中经常被遗漏。在这里，我们介绍了一种后生动物线粒体tRNA基因的自动注释程序，该程序基于人工管理的协方差模型中的序列和结构信息。该方法被应用于重新注释1876个可用后生动物线粒体RefSeq基因组，允许区分剩余的功能基因和退化的假基因，即使在分歧的早期阶段也是如此。随后对一组全面的线粒体tRNA基因的分析为线粒体tRNA序列结构的进化以及基因组重排的机制提供了新的见解。我们发现tRNA基因的频繁丢失集中在基础后生动物，tRNA基因的个别部分经常独立丢失，特别是在节肢动物中，tRNA在相反的阅读方向上存在广泛的保守重叠。获得了最近几个串联复制-随机丢失事件的直接证据，表明这种机制对新的线粒体基因序列的出现有影响。
Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.
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影响因子：
3.1
作者：
Fahrein, Kathrin;Masta, Susan E.;Podsiadlowski, Lars
通讯作者：
Podsiadlowski, Lars
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
DOI：
10.1073/pnas.0400941101
发表时间：
2004-07-20
影响因子：
11.1
作者：
Helfenbein, KG;Fourcade, HM;Boore, JL
通讯作者：
Boore, JL
影响因子：
4.1
作者：
Braband, Anke;Cameron, Stephen L.;Mayer, Georg
通讯作者：
Mayer, Georg
影响因子：
3.9
作者：
Higgs, PG;Jameson, D;Rattray, M
通讯作者：
Rattray, M