Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): Identification of the "missing" ATPase 8 gene
Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): Identification of the "missing" ATPase 8 gene
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DOI：
10.1016/j.margen.2010.01.001
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发表时间：
2010-03-01
期刊：
影响因子：
1.9
通讯作者：
Hoeh, Walter R.
中科院分区：
文献类型：
--
作者：
Breton, Sophie;Stewart, Donald T.;Hoeh, Walter R.
双壳类物种在线粒体（mt）基因组大小、基因排列和tRNA基因数量方面具有非凡的可变性。许多物种被认为缺乏线粒体蛋白编码基因atp8。在这些物种中，Mytilidae似乎是唯一已知的双单代遗传mtDNA的分类单元，不拥有atp8基因。这就提出了一个问题，即myliids是否已经完全失去了ATP8蛋白，该基因是否已经转移到细胞核中，或者它们是否拥有导致其缺乏注释的基因/蛋白质的高度修饰版本。在本研究中，我们重新研究了之前测序的所有完整（或接近完整）的F和M myliid mt基因组，因为它们存在保守的开放阅读框（orf），这些orf可能编码ATP8和/或在这些双壳类动物中具有其他重要的功能。我们还修改了所有已知的双壳类动物和线虫缺乏atp8的完整线粒体基因组的注释，试图检测它。我们的研究结果表明，一个新的myliid ORF具有显著的长度（即ORF长度为bb1085个氨基酸），具有完整的开始和停止密码子。是atp8基因的候选基因：(1)它具有纯化选择下蛋白质编码基因进化的模式（即第3 >第1 >第2密码子进化模式），(2)它在贻贝螺物种中活跃转录，(3)它有一个预测的跨膜螺旋（与其他后生动物的ATP8蛋白一样），(4)它具有保守的功能基序，(5)它的氨基酸序列与其他软体动物或双壳类动物的ATP8序列的比较揭示了类似的亲水特征。此外，我们修订的注释也证实了atp8在几乎所有双壳类物种和一种线虫物种中都存在。因此，我们的结果支持在大多数双壳类动物mt基因组（如果不是全部）中识别atp酶8的存在，而不是继续表征这些基因组缺乏该基因。(C) 2010 Elsevier B.V.版权所有
Bivalve species are characterized by extraordinary variability in terms of mitochondrial (mt) genome size, gene arrangement and tRNA gene number. Many species are thought to lack the mitochondrial protein-coding gene atp8. Of these species, the Mytilidae appears to be the only known taxon with doubly uniparental inheritance of mtDNA that does not possess the atp8 gene. This raises the question as to whether mytilids have completely lost the ATP8 protein, whether the gene has been transferred to the nucleus or whether they possess a highly modified version of the gene/protein that has led to its lack of annotation. In the present study, we re-investigated all complete (or nearly complete) F and M mytilid mt genomes previously sequenced for the presence of conserved open reading frames (ORFs) that might code for ATP8 and/or have other functional importance in these bivalves. We also revised the annotations of all available complete mitochondrial genomes of bivalves and nematodes that are thought to lack atp8 in an attempt to detect it. Our results indicate that a novel mytilid ORF of significant length (i.e., the ORF is > 85 amino acids in length), with complete start and stop codons. is a candidate for the atp8 gene: (1) it possesses a pattern of evolution expected for a protein-coding gene evolving under purifying selection (i.e., the 3rd > 1st > 2nd codon pattern of evolution), (2) it is actively transcribed in Mytilus species, (3) it has one predicted transmembrane helix (as do other metazoan ATP8 proteins), (4) it has conserved functional motifs and (5). comparisons of its amino acid sequence with ATP8 sequences of other molluscan or bivalve species reveal similar hydropathy profiles. Furthermore, our revised annotations also confirmed the mt presence of atp8 in almost all bivalve species and in one nematode species. Our results thus support recognizing the presence of ATPase 8 in most bivalves mt genomes (if not all) rather than the continued characterization of these genomes as lacking this gene. (C) 2010 Elsevier B.V. All rights reserved.