The role of lineage-specific gene family expansion in the evolution of eukaryotes
The role of lineage-specific gene family expansion in the evolution of eukaryotes
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DOI：
10.1101/gr.174302
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发表时间：
2002-07-01
期刊：
影响因子：
7
通讯作者：
Aravind, L
中科院分区：
文献类型：
--
作者：
Lespinet, O;Wolf, YI;Aravind, L
建立了一种系统地检测测序基因组中蛋白质家族谱系特异性扩展(LSE)的计算程序，并应用于5个真核物种的LSE的普查，这些真核物种是酿酒酵母和裂殖酵母、线虫秀丽线虫、果蝇黑腹果蝇和绿色植物拟南芥。在这些基因组中编码的蛋白质中，有相当一部分属于LSE，在Athailana中高达80%。在每个被分析的物种中，许多相似的基因家族几乎全部由LSE组成，这表明它们的多样性发生在真核冠群的主要谱系分化之后。LSE显示了蛋白质功能的明显模式。最容易发生LSE的功能类别是结构蛋白、参与所有生物体对病原体和环境应激反应的酶以及负责特异性的信号通路的各种组成部分，包括泛素连接酶E3亚基和转录因子。通过深入的蛋白质序列分析，预测了几个以前未描述的、大量扩展的蛋白质家族的功能，例如在苍蝇体内和线虫中独立扩展的小分子激酶和甲基酶。其他几个主要的LSE的功能仍然是神秘的；这些蛋白质家族是真核生物中新的、谱系特有的功能的实验发现的有吸引力的目标。LSE似乎是适应的主要手段之一，也是冠群真核生物组织和调控多样性的最重要来源之一。
A computational procedure was developed for systematic detection of lineage-specific expansions (LSEs) of protein families in sequenced genomes and applied to obtain a census of LSEs in five eukaryotic species, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the green plant Arabidopsis thaliana. A significant fraction of the proteins encoded in each of these genomes, up to 80% in A thailana, belong to LSEs. Many paralogous gene families in each of the analyzed species are almost entirely comprised of LSEs, indicating that their diversification occurred after the divergence of the major lineages of the eukaryotic crown group. The LSEs show readily discernible patterns of protein functions. The functional categories most prone to LSE are structural proteins, enzymes involved in ail organism's response to pathogens and environmental stress, and various components of signaling pathways responsible for specificity, including ubiquitin ligase E3 subunits and transcription factors. The functions of several previously uncharacterized, vastly expanded protein families were predicted through in-depth protein sequence analysis, for example, small-molecule kinases and methylases that are expanded independently ill the fly and in the nematode. The functions of several other major LSEs remain mysterious; these protein families are attractive targets for experimental discovery of novel, lineage-specific functions in eukaryotes. LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes.