Phylogeny of genes for secretion NTPases:: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification
Phylogeny of genes for secretion NTPases:: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification
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DOI：
10.1073/pnas.051436598
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发表时间：
2001-02-27
影响因子：
11.1
通讯作者：
Figurski, DH
中科院分区：
文献类型：
--
作者：
Planet, PJ;Kachlany, SC;Figurski, DH
目前，细菌中的大分子转运系统根据功能和序列比较分为五种基本类型。在这个分类系统中，II 型和 IV 型分泌系统都拥有假定的 NTP 水解酶 (NTPase) 蛋白基因超家族的成员，它们在结构、功能和序列上惊人地相似。其中包括 VirB11、TrbB、TraG、GspE、PiIB、PiIT 和 ComG1。 tadA 是最近发现的伴放线放线杆菌顽强粘附所需的基因，其预测的蛋白质产物也与该超家族的成员以及古细菌和细菌的几种未分类和未表征的基因产物具有显着的序列相似性。为了了解tadA和tadA样基因与编码II/IV型分泌的推定NTPase的基因的关系，我们使用系统发育方法获得了148个NTPase基因的谱系并重建了基因超家族进化的场景。在这个系统发育史中，II 型和 IV 型家族及其组成亚科之间可以做出明确的区分。此外，包含tadA的亚组构成了该家族中一个新颖且极其广泛的亚家族，涵盖了IV型分泌系统的所有推定的NTPase。我们报告了系统发育树中每个主要单系家族和亚家族的诊断性氨基酸残基位置，并提出了一种基于系统发育对假定的 NTPase 基因进行精确分类和命名的简单方法。这种基于分子密钥的方法可应用于其他基因超家族，是基因组分析的宝贵工具。
Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PiIB, PiIT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.