Genome duplication and gene-family evolution: The case of three OXPHOS gene families
Genome duplication and gene-family evolution: The case of three OXPHOS gene families
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DOI：
10.1016/j.gene.2008.05.011
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发表时间：
2008-09-15
期刊：
影响因子：
3.5
通讯作者：
Saccone, Cecilia
中科院分区：
文献类型：
--
作者：
De Grassi, Anna;Lanave, Cecilia;Saccone, Cecilia
DNA复制是影响生物进化的主要力量之一，因为它创造了自然选择随后可以修改的原始遗传物质。重复区域主要是由于减数分裂不同阶段的“错误”，但DNA转座因子和逆转录也有助于扩增和移动基因组物质到不同的基因组位置。因此，冗余对基因组的影响程度各不相同：从单个基因到整个基因组（WGD）。基因家族是由重复产生的基因簇，其大小反映了每个物种中重复基因的数量，称为旁系同源物，本文的目的是描述真核生物基因家族的鉴定和分析的最新进展，特别关注脊椎动物中由古代大规模事件（WGD或大片段重复）产生的基因家族。作为案例研究。我们报告了我们对编码五个OXPHOS（氧化磷酸化）复合物亚基的基因家族的进化的工作，这些复合物在所有呼吸细胞中是基本的和高度保守的。虽然OXPHOS基因家族比核基因家族的总体趋势小，但也观察到一些例外，例如在脊椎动物中有三个基因家族至少有两个旁系同源物。这些基因家族编码细胞色素c（Cyt c，复合体fit和IV之间的电子穿梭蛋白），脂质结合蛋白（LBP，复合物V的通道蛋白，其通过线粒体内膜转移质子）和MLRQ亚基（MLRQ，大复合体1的一个额外亚基，功能未知）。我们提供了一个两步的方法，基于结构基因组数据，证明这些基因家族应该是在脊椎动物起源时通过WGD（或大片段复制）事件出现的，并且仅在之后才经历进一步基因复制和丢失的物种特异性事件。总之，这篇评论反映了需要应用基因组比较的方法，从“经典”的分子系统发育分析和“新”的基因组图谱分析，成功地定义基因家族成员之间的复杂的进化关系，反过来，是必不可少的，以获得任何其他比较系统发育或功能的结果。(c)2008 Elsevier B.V.保留所有权利。
DNA duplication is one of the main forces acting on the evolution of organisms because it creates the raw genetic material that natural selection can subsequently modify. Duplicated regions are mainly due to "errors" in different phases of meiosis, but DNA transposable elements and reverse transcription also contribute to amplify and move the genomic material to different genomic locations. As a result, redundancy affects genomes to variable degrees: from the single gene to the whole genome (WGD). Gene families are clusters of genes created by duplication and their size reflects the number of duplicated genes, called paralogs, in each species.The aim of this review is to describe the state of the art in the identification and analysis of gene families in eukaryotes, with specific attention to those generated by ancient large scale events in vertebrates (WGD or large segmental duplications). As a case study. we report our work on the evolution of gene families encoding subunits of the five OXPHOS (oxidative phosphorylation) complexes, fundamental and highly conserved in all respiring cells. Although OXPHOS gene families are smaller than the general trend in nuclear gene families, some exceptions are observed, such as three gene families with at least two paralogs in vertebrates. These gene families encode cytochrome c (Cyt c, the electron shuttle protein between complex fit and IV), Lipid Binding Protein (LBP, the channel protein of complex V which transfers protons through the inner mitochondrial membrane) and the MLRQ subunit (MLRQ, a supernumerary subunit of the large complex 1, with unknown function).We provide a two-step approach, based on structural genomic data, to demonstrate that these gene families should have arisen through WGD (or large segmental duplication) events at the origin of vertebrates and, only afterwards, underwent species-specific events of further gene duplications and loss. In summary, this review reflects the need to apply genome comparative approaches, deriving from both "classical" molecular phylogenetic analysis and "new" genome map analysis, to successfully define the complex evolutionary relations between gene family members which, in turn, are essential to obtain any other comparative phylogenetic or functional results. (c) 2008 Elsevier B.V. All rights reserved.