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首页> 外文期刊>PLoS Genetics >Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis
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Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis

机译：多种机制促进四倍体青蛙非洲爪蟾中基因重复表达的保留表达。

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Gene duplication provides a window of opportunity for biological variants to persist under the protection of a co-expressed copy with similar or redundant function. Duplication catalyzes innovation (neofunctionalization), subfunction degeneration (subfunctionalization), and genetic buffering (redundancy), and the genetic survival of each paralog is triggered by mechanisms that add, compromise, or do not alter protein function. We tested the applicability of three types of mechanisms for promoting the retained expression of duplicated genes in 290 expressed paralogs of the tetraploid clawed frog, Xenopus laevis. Tests were based on explicit expectations concerning the ka/ks ratio, and the number and location of nonsynonymous substitutions after duplication. Functional constraints on the majority of paralogs are not significantly different from a singleton ortholog. However, we recover strong support that some of them have an asymmetric rate of nonsynonymous substitution: 6% match predictions of the neofunctionalization hypothesis in that (1) each paralog accumulated nonsynonymous substitutions at a significantly different rate and (2) the one that evolves faster has a higher ka/ks ratio than the other paralog and than a singleton ortholog. Fewer paralogs (3%) exhibit a complementary pattern of substitution at the protein level that is predicted by enhancement or degradation of different functional domains, and the remaining 13% have a higher average ka/ks ratio in both paralogs that is consistent with altered functional constraints, diversifying selection, or activity-reducing mutations after duplication. We estimate that these paralogs have been retained since they originated by genome duplication between 21 and 41 million years ago. Multiple mechanisms operate to promote the retained expression of duplicates in the same genome, in genes in the same functional class, over the same period of time following duplication, and sometimes in the same pair of paralogs. None of these paralogs are superfluous; degradation or enhancement of different protein subfunctions and neofunctionalization are plausible hypotheses for the retained expression of some of them. Evolution of most X. laevis paralogs, however, is consistent with retained expression via mechanisms that do not radically alter functional constraints, such as selection to preserve post-duplication stoichiometry or temporal, quantitative, or spatial subfunctionalization.
机译：基因复制为生物学变异在具有相似或冗余功能的共表达拷贝的保护下持久存在提供了机会。复制会催化创新（新功能化），亚功能变性（亚功能化）和遗传缓冲（冗余），并且每个旁系同源物的遗传存活都由增加，损害或不改变蛋白质功能的机制触发。我们测试了三种类型的机制在四倍体爪蛙Xenopus laevis的290个表达的旁系同源物中促进重复基因的保留表达的适用性。测试基于对ka / ks比率以及复制后非同义替换的数量和位置的明确期望。大多数旁系同源物的功能限制与单例直系同源物没有显着差异。但是，我们获得了强有力的支持，其中有些具有非对称替换的不对称率：新功能假设的6％匹配预测，因为（1）每个旁系同源物以不同的速率积累了非同义词替换，以及（2）进化的速率与其他旁系同源物和单例直系同源物相比，速度更快的ka / ks比率更高。较少的旁系同源物（3％）在蛋白质水平上表现出互补的取代模式，这是通过不同功能域的增强或降解来预测的，其余13％在两个旁系同源物中均具有较高的平均ka / ks比，与复制后改变了功能限制，选择多样化或活动减少的突变。我们估计，这些旁系同源物自21至4100万年前之间因基因组复制而起源以来一直被保留。在复制后的相同时间段内，有时在同一对旁系同源物中，多种机制起作用以促进相同基因组中，相同功能类别的基因中重复物的保留表达。这些旁系同源物中没有一个是多余的。不同蛋白质亚功能的降解或增强以及新功能化是其中某些保留表达的合理假说。然而，大多数X. laevis旁系同源物的进化与通过根本不改变功能限制的机制（例如选择保留复制后化学计量或时间，定量或空间亚功能化机制）的保留表达相一致。

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