Comparative Analysis Of Completely Sequenced Genomes

细菌、古生物和真核生物全序列基因组数据库的快速增长(截至2004年底已有200多个基因组，还有更多基因组正在进行中)为基因组研究创造了新的机遇和挑战。在过去的一年里，我们进行了几项研究，利用基因组信息来建立基因组进化和功能的基本原则。通过比较人、小鼠和大鼠的同源基因序列，我们发现在哺乳动物cDNA的5‘-非翻译区(5’-UTRs)，而在3‘-UTRs或编码序列中，Aug的保守性明显高于其他63个核苷酸三联体中的任何一个。通过对酵母属不同物种的同源基因进行比较，得到了定性上相似的结果。再加上哺乳动物和酵母的5‘-UTRs的AUG总含量显著减少，这些发现表明，5’-UTRs中的AUG三联体受到两个相反方向的净化选择的压力：没有特定功能的uAUG往往是有害的，并在进化过程中被淘汰，而那些确实具有功能的uAUG是保守的。很可能，保守的uAUG的主要作用是在起始阶段减弱翻译，这通常受到哺乳动物5‘-UTRs选择性剪接的额外调节。在另一个项目中，我们评估了祖先类比的范围，这可以追溯到所有真核生物的最后一个共同祖先，并研究了祖先类比的起源及其在真核细胞复杂性出现中的潜在作用。对祖先基因库的简约重建表明，最后一个真核共同祖先(LECA)中的4137个同源基因集映射到假设的第一个真核共同祖先(FECA)中的2150个同源基因集[拟合商(PQ)为1.92]。类似的重建显示原核生物的同源水平显著降低，古生菌和细菌的同源性水平分别为1.19和1.25。真核生物蛋白质中唯一一类具有显著超过平均值的平行簇的功能类别包括分子伴侣和具有相关功能的蛋白质。在早期的真核生物进化中，几乎所有这类基因都经历了多次复制。在结构方面，最突出的一组平行基因是具有重复结构域的超结构形成蛋白，如WD-40和TPR。除了在真核生物进化之初通过复制进化的祖先类基因外，还检测到了大量的伪类基因，即显然是早期真核生物通过不同途径获得的同源基因，包括来自不同细菌的水平基因转移(HGT)。这项研究的结果表明，作为真核生物早期进化的标志，基因同源性水平显著增加。我们还研究了蛋白质氨基酸组成进化的普遍趋势。我们比较了由来自15个分类群的三元组紧密相关的基因组编码的一组同源蛋白质，这些基因组代表了生命的所有三个领域(细菌、古生菌和真核生物)，并使用系统发生学来极化氨基酸替代。Cys、Met、His、Ser和Phe在至少14个分类群中积累，而Pro、Ala、Glu和Gly持续丢失。对非同义单核苷酸多态的分析表明，这九种氨基酸目前在人类蛋白质中积累或丢失。所有频率下降的氨基酸都被认为是最早被纳入遗传密码的氨基酸之一；相反，除了Ser之外，所有频率增加的氨基酸可能都是较晚被招募的。因此，始于34亿多年前的最初代表不足的氨基酸的扩张显然延续到了今天。

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (over 200 genomes available by the end of 2004 and many more in progress) creates both new opportunities and new challenges for genome research. During the last year, we performed several studies that took advantage of the genomic information to establish fundamental principles of genome evolution and function. By comparing sequences of human, mouse and rat orthologous genes, we show that in 5'-untranslated regions (5'-UTRs) of mammalian cDNAs but not in 3'-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5'-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5'-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5'-UTRs. In another project, we assessed the extent of ancestral paralogy, which dates back to the last common ancestor of all eukaryotes, and examine the origins of the ancestral paralogs and their potential roles in the emergence of the eukaryotic cell complexity. A parsimonious reconstruction of ancestral gene repertoires shows that 4137 orthologous gene sets in the last eukaryotic common ancestor (LECA) map back to 2150 orthologous sets in the hypothetical first eukaryotic common ancestor (FECA) [paralogy quotient (PQ) of 1.92]. Analogous reconstructions show significantly lower levels of paralogy in prokaryotes, 1.19 for archaea and 1.25 for bacteria. The only functional class of eukaryotic proteins with a significant excess of paralogous clusters over the mean includes molecular chaperones and proteins with related functions. Almost all genes in this category underwent multiple duplications during early eukaryotic evolution. In structural terms, the most prominent sets of paralogs are superstructure-forming proteins with repetitive domains, such as WD-40 and TPR. In addition to the ancestral paralogs which evolved via duplication at the onset of eukaryotic evolution, numerous pseudoparalogs were detected, i.e. homologous genes that apparently were acquired by early eukaryotes via different routes, including horizontal gene transfer (HGT) from diverse bacteria. The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes. We also studied universal trends in the evolution of amino acid composition of proteins. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.