Modeling the evolution of protein domain architectures using maximum parsimony
Modeling the evolution of protein domain architectures using maximum parsimony
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DOI：
10.1016/j.jmb.2006.11.017
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发表时间：
2007-02-09
影响因子：
5.6
通讯作者：
Bryant, Stephen H.
中科院分区：
文献类型：
--
作者：
Fong, Jessica H.;Geer, Lewis Y.;Bryant, Stephen H.
结构域是蛋白质的基本进化单位，大多数蛋白质具有多个结构域。结构域建模和收集的进展使得通过结构域的线性排序来注释大部分已知蛋白质序列成为可能，从而产生它们的结构。蛋白质结构域结构将进化上相关的蛋白质联系起来，并强调它们的共同功能。在这里，我们试图更好地理解这种关联，通过识别现存的架构可能已经演变的进化途径。我们提出了一个模型的演变，在该架构中出现的推断前体架构和收购新的域的重排。这些途径的排名使用简约原则，从而需要最少数量的独立重组事件，即裂变和聚变操作的情况下，被认为是更有可能的。使用159个蛋白质组中存在的结构域架构的数据集，这些蛋白质组代表生命树的所有三个主要分支，使我们能够估计序列数据库中超过85%的所有架构的历史。我们发现，重排类的分布是强大的替代简约规则推断祖先物种的前体架构的存在。分析最简约的途径，我们发现87%的架构通过简单的变化随着时间的推移而变得复杂，其中融合事件占架构数量的5.6倍。我们的研究结果可用于计算域架构的相似性，例如，基于分离它们的历史重组事件的数量。以这种方式确定的结构域结构“邻居”可能会导致对蛋白质功能进化的新见解。出版社：Elsevier Ltd
Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function. Published by Elsevier Ltd.