Comparative Analysis Of Completely Sequenced Genomes

细菌、古细菌和真核生物基因组完全测序数据库的迅速增长（到2004年底，大约有200个基因组可用，还有更多正在进行中）为基因组研究创造了新的机会和新的挑战。为了利用这些信息，我们从30个完全测序的基因组中开发了一个同源蛋白群（COGs）集群系统。这个数据库正在不断更新，以纳入新出现的基因组。COG方法允许对每个测试细菌和古细菌基因组中编码的60-80%的蛋白质进行几乎自动的功能注释。在去年，COG分析被大大扩展到包括真核生物基因组。本文详细研究了最近从7个真核生物基因组中构建的5,873个预测同源群（真核同源群或KOGs）的功能和进化模式：秀丽隐索线虫、黑腹果蝇、智人、拟南芥、酿酒酵母、pombe Schizosaccharomyces和cuniculi脑囊虫。真核生物中KOGs的保存与它们的功能以及基因敲除对生物生存能力的影响密切相关。在6到7个物种中，大约40%的kog富含负责家政功能的蛋白质，特别是翻译和RNA加工。这些保守的KOGs通常是生存所必需的，可能近似于真核生物必需基因的最小集合。我们对鉴定的131个单成员泛真核kog进行了详细检查。对于大约20个尚未确定的基因，通过深入的序列分析和基因组背景检查来预测其功能。这些蛋白质几乎都是已知或预测的多蛋白复合物的亚基，符合基因拷贝数进化的平衡假说。其他KOGs显示出各种各样的种系模式，这指出了谱系特异性基因丢失和真核生物进化新基因的“发明”的主要贡献。对单个谱系中丢失的KOGs组的检查揭示了功能相关基因的共同消除。重建了真核生物基因组进化的简约场景和祖先真核生物形式的基因集。冠群最后的共同祖先的基因集由3,413个KOGs组成，主要包括参与基因组复制和表达以及中枢代谢的蛋白质。只有44%的KOGs在原核生物中有可检测到的同源物，这些KOGs主要来自冠群最后共同祖先的重建基因集；其余的显然是通过复制、分化和新基因的发明而进化的。结论：KOG分析揭示了与真核生物基因组进化相关的大部分重要真核基因的保守核心以及主要的多样化和创新。这些结果为以前在定性水平上注意到的真核生物进化的主要趋势提供了定量支持，并为真核生物基因组进化和祖先形态生物学的详细重建奠定了基础。

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (approximately 200 genomes available by the end of 2004 and many more in progress) creates both new opportunities and new challenges for genome research. In order to take advantage of this information, we developed a system of Clusters of Orthologous Groups of proteins (COGs) from 30 completely sequenced genomes. This database is being continuously updated to incorporate newly appearing genomes. The COG approach allows nearly automatic functional annotation of 60-80% of the proteins encoded in each of the tested bacterial and archaeal genomes. During last year, the COG analysis was substantially expanded to include euakryotic genomes. Functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs (eukaryotic orthologous groups or KOGs) from seven eukaryotic genomes: Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Encephalitozoon cuniculi, were examined in detail. Conservation of KOGs through the phyletic range of eukaryotes strongly correlates with their functions and with the effect of gene knockout on the organism's viability. The approximately 40% of KOGs that are represented in six or seven species are enriched in proteins responsible for housekeeping functions, particularly translation and RNA processing. These conserved KOGs are often essential for survival and might approximate the minimal set of essential eukaryotic genes. The 131 single-member, pan-eukaryotic KOGs we identified were examined in detail. For around 20 that remained uncharacterized, functions were predicted by in-depth sequence analysis and examination of genomic context. Nearly all these proteins are subunits of known or predicted multiprotein complexes, in agreement with the balance hypothesis of evolution of gene copy number. Other KOGs show a variety of phyletic patterns, which points to major contributions of lineage-specific gene loss and the 'invention' of genes new to eukaryotic evolution. Examination of the sets of KOGs lost in individual lineages reveals co-elimination of functionally connected genes. Parsimonious scenarios of eukaryotic genome evolution and gene sets for ancestral eukaryotic forms were reconstructed. The gene set of the last common ancestor of the crown group consists of 3,413 KOGs and largely includes proteins involved in genome replication and expression, and central metabolism. Only 44% of the KOGs, mostly from the reconstructed gene set of the last common ancestor of the crown group, have detectable homologs in prokaryotes; the remainder apparently evolved via duplication with divergence and invention of new genes. CONCLUSIONS: The KOG analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. The results provide quantitative support for major trends of eukaryotic evolution noticed previously at the qualitative level and a basis for detailed reconstruction of evolution of eukaryotic genomes and biology of ancestral forms.