Lespinet Olivier, Wolf Yuri I, Koonin Eugene V, Aravind L
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
Genome Res. 2002 Jul;12(7):1048-59. doi: 10.1101/gr.174302.
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. thaliana, 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 an 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 in 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.
开发了一种计算程序，用于系统检测已测序基因组中蛋白质家族的谱系特异性扩增（LSE），并将其应用于获取五种真核生物物种中的LSE普查数据，这五种物种分别是酵母酿酒酵母和粟酒裂殖酵母、线虫秀丽隐杆线虫、果蝇黑腹果蝇以及绿色植物拟南芥。这些基因组中编码的很大一部分蛋白质（拟南芥中高达80%）属于LSE。每个被分析物种中的许多旁系同源基因家族几乎完全由LSE组成，这表明它们的多样化发生在真核冠群主要谱系分化之后。LSE呈现出易于识别的蛋白质功能模式。最容易发生LSE的功能类别是结构蛋白、参与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先前未表征、大量扩增的蛋白质家族的功能，例如在果蝇和线虫中独立扩增的小分子激酶和甲基化酶。其他几个主要LSE的功能仍然未知；这些蛋白质家族是在真核生物中通过实验发现新的谱系特异性功能的有吸引力的目标。LSE似乎是冠群真核生物适应的主要手段之一，也是组织和调节多样性的最重要来源之一。
