COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

全测序基因组的比较分析

• 批准号: 6111075
• 负责人: Eugene V Koonin
• 金额: --
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6111075
• 关键词: Escherichia coli; Haemophilus influenzae; Mycoplasma; bacterial genetics; biochemical evolution; computer assisted sequence analysis; genome

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.

快速增长的数据库完全 细菌、古细菌和真核生物的基因组测序 （到 1998 年底大约有 20 个基因组可用，其中许多 更多进展）创造了新的机遇和新的 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，其中可能包括 来自 8 个完全的直系同源蛋白质（直接对应物） 测序的基因组。所有公司合并的过程 剩余的完整基因组测序正在进行中。这 系统允许近乎自动的功能注释超过 50% 每种测试的细菌和古细菌编码的蛋白质 基因组，尽管只有大约 20% 的真核蛋白质适合 这些群体。除了功能预测之外，这种方法 系统地描述了一组古代、 任何特定区域中缺失的保守蛋白质家族 基因组。进化模式的检查（即表征 不同物种和系统发育谱系）的科 直向同源物表明水平基因转移的主要作用和 原核生物进化中谱系特异性基因的丢失。更多的 具体来说，对第一个可用基因组进行比较分析 超嗜热细菌（Aquifex aeolicus）和古细菌 基因组表明古菌和古菌之间存在大量基因交换 嗜热细菌。比较基因组学现已成为一门 任何关于特定蛋白质家族或蛋白质进化的研究的一部分 功能系统。经常检查系统发育 结构域和具有特定域的蛋白质的分布 架构提供了详细重建的可能性 的进化情景。进行此类分析是为了 细菌、古细菌和真核生物的 DNA 修复系统 真核程序性细胞死亡系统。的重要作用 水平基因转移和多结构域重排 两个系统的演变都得到了展示，并且出现了一些新的 进行了功能预测。