Insertions and deletions trigger adaptive walks in Drosophila proteins.
Insertions and deletions trigger adaptive walks in Drosophila proteins.
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DOI：
10.1098/rspb.2011.2571
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发表时间：
2012-08-07
期刊：
影响因子：
--
通讯作者：
Kondrashov AS
中科院分区：
文献类型：
--
作者：
Leushkin EV;Bazykin GA;Kondrashov AS
将所有可能的基因型或表型与适合度相关联的图谱是生命进化的核心，但仍然知之甚少。一个或几个氨基酸的插入或缺失（indel）构成了蛋白质在氨基酸序列空间内的实质性跳跃，并且在这样的跳跃之后，新序列不太可能精确地对应于适合度峰值。因此，人们可以预期在群体中固定的蛋白质编码序列中的插入缺失之后会有一定数量的适应性氨基酸取代，这将新序列移向附近的适应性峰值。在这里，我们研究了果蝇蛋白质进化过程中的框架保留插入缺失后发生的替换。插入在以插入位点为中心的蛋白质区域内触发1.03 ± 0.75个氨基酸取代，并且缺失在这样的区域内触发4.77 ± 1.03个取代。这些值之间的差异可能是由于较高比例的有效中性插入。几乎所有触发的氨基酸取代都可以归因于正选择，并且它们中的大多数在触发indel之后相对很快地发生并且发生在其位点的上游。插入缺失之后的大部分取代发生在先前保守的位点，这表明插入缺失实质上改变了塑造其周围蛋白质区域的选择。因此，插入缺失之后通常是长度的适应性行走，这与分子适应理论一致。
Maps that relate all possible genotypes or phenotypes to fitness—fitness landscapes—are central to the evolution of life, but remain poorly known. An insertion or a deletion (indel) of one or several amino acids constitutes a substantial leap of a protein within the space of amino acid sequences, and it is unlikely that after such a leap the new sequence corresponds precisely to a fitness peak. Thus, one can expect an indel in the protein-coding sequence that gets fixed in a population to be followed by some number of adaptive amino acid substitutions, which move the new sequence towards a nearby fitness peak. Here, we study substitutions that occur after a frame-preserving indel in evolving proteins of Drosophila. An insertion triggers 1.03 ± 0.75 amino acid substitutions within the protein region centred at the site of insertion, and a deletion triggers 4.77 ± 1.03 substitutions within such a region. The difference between these values is probably owing to a higher fraction of effectively neutral insertions. Almost all of the triggered amino acid substitutions can be attributed to positive selection, and most of them occur relatively soon after the triggering indel and take place upstream of its site. A high fraction of substitutions that follow an indel occur at previously conserved sites, suggesting that an indel substantially changes selection that shapes the protein region around it. Thus, an indel is often followed by an adaptive walk of length that is in agreement with the theory of molecular adaptation.
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影响因子：
7
作者：
Heger, Andreas;Ponting, Chris P.
通讯作者：
Ponting, Chris P.
影响因子：
64.8
作者：
Smith, NGC;Eyre-Walker, A
通讯作者：
Eyre-Walker, A
影响因子：
64.8
作者：
Meer, Margarita V.;Kondrashov, Alexey S.;Kondrashov, Fyodor A.
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Kondrashov, Fyodor A.
影响因子：
64.8
作者：
MCDONALD, JH;KREITMAN, M
通讯作者：
KREITMAN, M
影响因子：
64.8
作者：
Mackay, Trudy F. C.;Richards, Stephen;Stone, Eric A.;Barbadilla, Antonio;Ayroles, Julien F.;Zhu, Dianhui;Casillas, Sonia;Han, Yi;Magwire, Michael M.;Cridland, Julie M.;Richardson, Mark F.;Anholt, Robert R. H.;Barron, Maite;Bess, Crystal;Blankenburg, Kerstin Petra;Carbone, Mary Anna;Castellano, David;Chaboub, Lesley;Duncan, Laura;Harris, Zeke;Javaid, Mehwish;Jayaseelan, Joy Christina;Jhangiani, Shalini N.;Jordan, Katherine W.;Lara, Fremiet;Lawrence, Faye;Lee, Sandra L.;Librado, Pablo;Linheiro, Raquel S.;Lyman, Richard F.;Mackey, Aaron J.;Munidasa, Mala;Muzny, Donna Marie;Nazareth, Lynne;Newsham, Irene;Perales, Lora;Pu, Ling-Ling;Qu, Carson;Ramia, Miquel;Reid, Jeffrey G.;Rollmann, Stephanie M.;Rozas, Julio;Saada, Nehad;Turlapati, Lavanya;Worley, Kim C.;Wu, Yuan-Qing;Yamamoto, Akihiko;Zhu, Yiming;Bergman, Casey M.;Thornton, Kevin R.;Mittelman, David;Gibbs, Richard A.
通讯作者：
Gibbs, Richard A.