Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
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DOI：
10.1046/j.1365-2958.1997.4821861.x
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发表时间：
1997-08-01
影响因子：
3.6
通讯作者：
Walker, DR
中科院分区：
文献类型：
--
作者：
Koonin, EV;Mushegian, AR;Walker, DR
利用BLAST2算法和氨基酸基序检测方法，对流感嗜血杆菌、生殖支原体和集胞藻属的三个完整细菌基因组以及第一个可用的古菌基因组——詹氏甲烷球菌的基因组所编码的蛋白质序列进行了分析。在每个细菌基因组中预测的蛋白质有75% - 90%，詹氏甲烷球菌的蛋白质有73%与其他物种的蛋白质显示出显著的序列相似性。细菌和古菌蛋白质中含有在较长系统发育距离上保守区域的比例几乎相同，接近70%。以不同的精度预测了70 - 85%的细菌蛋白质和大约70%的古菌蛋白质的功能。这与之前的报道形成对比，之前报道称超过一半的古菌蛋白质没有同源物，并且表明，通过更灵敏的方法和对保守基序的详细分析，古菌基因组像细菌基因组一样易于通过计算机进行有意义的解读。对保守基序的分析导致对细菌和古菌蛋白质一些先前未检测到的功能进行了预测，并鉴定了新的蛋白质家族。尽管蛋白质序列通常具有高度保守性，但在每个单独的完全测序基因组中，仅检测到25%或更少的詹氏甲烷球菌基因的直系同源物，这支持了古菌作为一个独特生命域的独特性。大约53%的詹氏甲烷球菌蛋白质属于旁系同源物家族，这一比例与具有较大基因组的细菌（如集胞藻属和大肠杆菌）相似，但高于流感嗜血杆菌，流感嗜血杆菌的基因数量与詹氏甲烷球菌大致相同。某些蛋白质组，例如分子伴侣和DNA修复酶，被认为是普遍存在的，并在通过细菌基因组比较得出的最小基因集中有体现，但在詹氏甲烷球菌中缺失，这表明负责基本功能的基因发生了大量的非直系同源置换。詹氏甲烷球菌基因产物中出乎意料的大部分（44%）与细菌蛋白质的相似性显著高于与真核蛋白质的相似性，相比之下，有13%的蛋白质以真核蛋白质为其最接近的同源物（其余蛋白质与细菌和真核同源物的相似性水平大致相同或没有同源物）。参与翻译、转录、复制和蛋白质分泌的蛋白质与真核蛋白质关系最为密切，而代谢酶、代谢物摄取系统、细胞壁生物合成酶和许多未表征的蛋白质似乎是“细菌样的”。在来自远缘古菌属——硫化叶菌的当前可用序列中也观察到了明显源自细菌的蛋白质的类似普遍存在情况。古菌的进化很可能包括来自细菌谱系的祖先细胞和通向真核细胞核质的谱系之间至少一次重大融合。
Protein sequences encoded in three complete bacterial genomes, those of Haemophilus influenzae, Mycoplasma genitalium and Synechocystis sp., and the first available archaeal genome sequence, that of Methanococcus jannaschii, were analysed using the BLAST2 algorithm and methods for amino acid motif detection. Between 75% and 90% of the predicted proteins encoded in each of the bacterial genomes and 73% of the M, jannaschii proteins showed significant sequence similarity to proteins from other species. The fraction of bacterial and archaeal proteins containing regions conserved over long phylogenetic distances is nearly the same and close to 70%, Functions of 70-85% of the bacterial proteins and about 70% of the archaeal proteins were predicted with varying precision. This contrasts with the previous report that more than half of the archaeal proteins have no homologues and shows that, with more sensitive methods and detailed analysis of conserved motifs, archaeal genomes become as amenable to meaningful interpretation by computer as bacterial genomes. The analysis of conserved motifs resulted in the prediction of a number of previously undetected functions of bacterial and archaeal proteins and in the identification of novel protein families. In spite of the generally high conservation of protein sequences, orthologues of 25% or less of the IM. jannaschii genes were detected in each individual completely sequenced genome, supporting the uniqueness of archaea as a distinct domain of life. About 53% of the M. jannaschii proteins belong to families of paralogues, a fraction similar to that in bacteria with larger genomes, such as Synechocystis sp, and Escherichia coli, but higher than that in H. influenzae, which has approximately the same number of genes as M. jannaschii. Certain groups of proteins, e.g. molecular chaperones and DNA repair enzymes, thought to be ubiquitous and represented in the minimal gene set derived by bacterial genome comparison, are missing in M. jannaschii, indicating massive non-orthologous displacement of genes responsible for essential functions. An unexpectedly large fraction of the nn. jannaschii gene products, 44%, shows significantly higher similarity to bacterial than to eukaryotic proteins, compared with 13% that have eukaryotic proteins as their closest homologues (the rest of the proteins show approximately the same level of similarity to bacterial and eukaryotic homologues or have no homologues), Proteins involved in translation, transcription, replication and protein secretion are most closely related to eukaryotic proteins, whereas metabolic enzymes, metabolite uptake systems, enzymes for cell wall biosynthesis and many uncharacterized proteins appear to be 'bacterial'. A similar prevalence of proteins of apparent bacterial origin was observed among the currently available sequences from the distantly related archaeal genus, Sulfolobus. It is likely that the evolution of archaea included at least one major merger between ancestral cells from the bacterial lineage and the lineage leading to the eukaryotic nucleocytoplasm.