Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
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DOI：
10.1073/pnas.182432999
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发表时间：
2002-09-17
影响因子：
11.1
通讯作者：
Penny, D
中科院分区：
文献类型：
--
作者：
Martin, W;Rujan, T;Penny, D
叶绿体曾经是自由生活的蓝细菌，成为内共生体，但当代质体的基因组编码的基因只有它们自由生活的表亲的基因组的大约5 -10%，这表明在植物进化过程中，许多基因要么从质体丢失，要么转移到细胞核。以前的估计表明，拟南芥基因组中有800到2,000个基因可能来自蓝藻，但缺乏全基因组系统发育调查，可以直接估计这个数字。我们将拟南芥基因组中编码的24，990种蛋白质与来自三种蓝藻基因组、16种其他原核参考基因组和酵母的蛋白质进行了比较。在9，368个足够保守的拟南芥蛋白质中，866个仅在蓝藻中检测到同源物，834个在系统发育树中与蓝藻同源物分支。从这些保守的蛋白质外推到整个基因组，数据表明大约4,500个拟南芥蛋白质编码基因（约占总数的18%）是从质体的蓝藻祖先获得的。这些蛋白质包括所有的功能类别，并且它们中的大多数被靶向到细胞隔室而不是叶绿体。对15个已测序的叶绿体基因组的分析揭示了117个核编码的蛋白质，这些蛋白质仍然存在于至少一个叶绿体基因组中。从41个蛋白质和8,303个氨基酸位点推断的叶绿体基因组的同源性表明，至少发生了两个独立的二级内共生事件涉及红藻和叶绿体蛋白质中的氨基酸组成的偏见强烈影响质体基因组同源性。
Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only approximate to5-10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that approximate to4,500 of Arabidopsis protein-coding genes (approximate to18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.