COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

快速增长的数据库， 细菌、古生菌和真核生物的基因组测序 （截至1998年底，大约有20个基因组可用， 创造新的机会， 挑战为了利用这些信息，我们 开发了一个保守的蛋白质家族系统， 正向同源蛋白（直接对应物）从8个完全 基因组测序将所有国家和国际组织 其余的基因组测序工作正在进行中。这 系统允许超过50%的几乎自动的功能注释 每种测试的细菌和古细菌中编码的蛋白质 基因组，虽然只有大约20%的真核蛋白适合 这些团体。除了功能预测，这种方法 系统地描绘了一套古老的， 保守的蛋白质家族在任何特定的 基因组研究进化模式（即表征 不同种类的（和系统发育谱系）在家庭的 直系同源物表明水平基因转移的主要作用， 原核生物进化中的谱系特异性基因丢失。更 具体地说，比较分析了第一个可用的基因组， 超嗜热菌（Aquifex aeolicus）和古细菌 基因组表明古细菌和 嗜热细菌比较基因组学现在已经成为 任何关于特定蛋白质家族进化的研究， 功能系统经常检查系统发育 结构域和具有特定结构域的蛋白质的分布 架构提供了详细重建的可能性， 进化的场景。这些分析是针对 细菌、古生菌和真核生物的DNA修复系统， 真核细胞程序性死亡系统。重要作用 水平基因转移和多结构域重排 这两个系统的演变被证明和一些新的 进行了功能预测。

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (approximately 20 genomes available by the end of 1998 and many more in progress) creates both new opportunities and new challenges. In order to take advantage of this information, we developed a system of conserved protein families that include likely orthologous proteins (direct counterparts) from 8 completely sequenced genomes. The process of incorporation of all the remaining completely sequenced genomes is in progress. This system allows nearly automatic functional annotation of more 50% of the proteins encoded in each of the tested bacterial and archaeal genomes, though only about 20% of the eukaryotic proteins fit into these groups. In addition to functional prediction, this approach provides for the systematic delineation of the set of ancient, conserved protein families that are missing in any particular genome. Examination of evolutionary patterns (i.e. representation of different species iand phylogenetic lineages) in the families of orthologs suggests a major role of horizontal gene transfer and lineage specific gene loss in the evolution of prokaryotes. More specifically, comparative analysis of the first available genome of hyperthermophilic bacterium (Aquifex aeolicus) and archaeal genomes indicates massive gene exchange between archaeal and bacterial thermophiles. Comparative genomics has now become a part of any study on the evolution of a particular protein family or a functional system. Frequently examination of the phylogenetic distribution of structural domains and proteins with specific domain architectures provides for the possibility of detailed reconstructions of evolutionary scenarios. Such analyses were performed for the DNA repair systems of bacteria, archaea and eukaryotes and for the eukaryotic programmed cell death systems. Significant roles of horizontal gene transfer and multiple domain rearrangements in the evolution of both systems were demonstrated and a number of new functional predictions were made.