He Xionglei, Zhang Jianzhi
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor 48109, USA.
Curr Biol. 2005 Jun 7;15(11):1016-21. doi: 10.1016/j.cub.2005.04.035.
Eukaryotic genes are on average more complex than prokaryotic genes in terms of expression regulation, protein length, and protein-domain structure [1-5]. Eukaryotes are also known to have a higher rate of gene duplication than prokaryotes do [6, 7]. Because gene duplication is the primary source of new genes [], the average gene complexity in a genome may have been increased by gene duplication if complex genes are preferentially duplicated. Here, we test this "gene complexity and gene duplicability" hypothesis with yeast genomic data. We show that, on average, duplicate genes from either whole-genome or individual-gene duplication have longer protein sequences, more functional domains, and more cis-regulatory motifs than singleton genes. This phenomenon is not a by-product of previously known mechanisms, such as protein function [10-13], evolutionary rate [14, 15], dosage [11], and dosage balance [16], that influence gene duplicability. Rather, it appears to have resulted from the sub-neo-functionalization process in duplicate-gene evolution [11]. Under this process, complex genes are more likely to be retained after duplication because they are prone to subfunctionalization, and gene complexity is regained via subsequent neofunctionalization. Thus, gene duplication increases both gene number and gene complexity, two important factors in the origin of genomic and organismal complexity.
就表达调控、蛋白质长度和蛋白质结构域结构而言，真核基因平均比原核基因更复杂[1 - 5]。已知真核生物的基因复制率也高于原核生物[6, 7]。由于基因复制是新基因的主要来源[]，如果复杂基因被优先复制，那么基因组中平均基因复杂性可能会因基因复制而增加。在此，我们用酵母基因组数据检验这一“基因复杂性与基因可复制性”假说。我们发现，平均而言，全基因组复制或单个基因复制产生的重复基因比单拷贝基因具有更长的蛋白质序列、更多的功能结构域和更多的顺式调控基序。这种现象并非先前已知的影响基因可复制性的机制的副产物，比如蛋白质功能[10 - 13]、进化速率[14, 15]、剂量[11]和剂量平衡[16]。相反，它似乎是重复基因进化中的亚新功能化过程导致的[11]。在这个过程中，复杂基因在复制后更有可能被保留，因为它们易于发生亚功能化，并且基因复杂性会通过随后的新功能化得以恢复。因此，基因复制增加了基因数量和基因复杂性，这是基因组和生物复杂性起源中的两个重要因素。
