Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy
Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy
复制标题
植物中 KCS 基因家族的进化：基因复制、亚/新功能化和冗余的历史
DOI：
10.1007/s00438-015-1142-3
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发表时间：
2016-04-01
影响因子：
3.1
通讯作者：
Xue, Jia-Yu
中科院分区：
文献类型：
--
作者：
Guo, Hai-Song;Zhang, Yan-Mei;Xue, Jia-Yu
甚长链脂肪酸(VLCFA)在植物的生存和发育中起着重要的作用，VLCFA的合成受β-酮酰辅酶A合成酶(KCSs)的调控，KCSs催化酰辅酶A与丙二酰辅酶A的缩合。在这里，我们对编码这些酶的基因，KCS基因，在28个物种(26个基因组和2个转录本)进行了全基因组调查，这代表了一个较大的系统发育规模，并重建了这个基因家族的进化史。KCS基因最初在绿色植物谱系中是单拷贝基因；在陆地植物中复制导致了5个祖先拷贝，形成了系统发育树中的5个基本单系类群。随后，KCS基因复制产生11个被子植物起源的基因，在进一步分化的被子植物物种中扩展到20-30个成员。在这个过程中，串联复制只起到了很小的作用，而多倍体事件和大规模的片段复制似乎是主要的驱动力。伴随这种扩展的是导致不同成员的亚功能和新功能的变异，导致可能由三维蛋白质结构决定的特异性。参与其他生理过程的新功能也出现了，尽管也观察到了冗余，主要是在最近的复制中。统计分析还确定了KCS蛋白的保守区和变异区。可变位点可能参与了产物特异性和催化能力的产生，而保守位点可能负责基本功能的保存。
Very long-chain fatty acids (VLCFAs) play an important role in the survival and development of plants, and VLCFA synthesis is regulated by beta-ketoacyl-CoA synthases (KCSs), which catalyze the condensation of an acyl-CoA with malonyl-CoA. Here, we present a genome-wide survey of the genes encoding these enzymes, KCS genes, in 28 species (26 genomes and two transcriptomes), which represents a large phylogenetic scale, and also reconstruct the evolutionary history of this gene family. KCS genes were initially single-copy genes in the green plant lineage; duplication resulted in five ancestral copies in land plants, forming five fundamental monophyletic groups in the phylogenetic tree. Subsequently, KCS genes duplicated to generate 11 genes of angiosperm origin, expanding up to 20-30 members in further-diverged angiosperm species. During this process, tandem duplications had only a small contribution, whereas polyploidy events and large-scale segmental duplications appear to be the main driving force. Accompanying this expansion were variations that led to the sub- and neofunctionalization of different members, resulting in specificity that is likely determined by the 3-D protein structure. Novel functions involved in other physiological processes emerged as well, though redundancy is also observed, largely among recent duplications. Conserved sites and variable sites of KCS proteins are also identified by statistical analysis. The variable sites are likely to be involved in the emergence of product specificity and catalytic power, and conserved sites are possibly responsible for the preservation of fundamental function.