Domain combinations in archaeal, eubacterial and eukaryotic proteomes
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
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DOI：
10.1006/jmbi.2001.4776
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发表时间：
2001-07-06
影响因子：
5.6
通讯作者：
Teichmann, SA
中科院分区：
文献类型：
--
作者：
Apic, G;Gough, J;Teichmann, SA
有一组有限的结构域家族，它们以不同的方式复制和组合，形成基因组中的一组蛋白质。蛋白质是基因产物，在基因水平上，复制、重组、融合和裂变是产生新基因的过程。我们试图通过研究40个基因组的蛋白质序列中蛋白质、结构域和蛋白质序列中的进化单位来获得这些过程的概述。利用蛋白质结构分类数据库中的结构域和超家族的定义，我们可以根据它们的超家族组合来查看基因组序列中所有相邻的结构域对。我们在这些基因组中发现了SCOP中859个超家族中的783个，这783个家族出现在1307个成对组合中。大多数家系与一到两个家系组合在一起，少数家系的组合行为非常多样，209个家庭不与其他家系组合。这种模式可以被描述为无标度网络。我们还研究了结构域对和结构域重复的N到C末端的取向。调查了领域组合的系统发育分布，以确定共同的和特定领域的组合的程度。在特定王国的组合中，由所有三个王国的家庭组成的组合明显多于一个或两个王国的家庭组成的组合。因此，我们得出的结论是，与新家族的发明和这些家族之间的重组相比，共同家族之间的重组也是这三个王国生物特有和物种特有功能进化的主要贡献。最后，我们将基因组中的区域组合集合与RCSB蛋白质数据库中的区域组合进行比较，并讨论其对结构基因组学的影响。(C)2001年学术出版社。
There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour, 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics. (C) 2001 Academic Press.