Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
Antonie Van Leeuwenhoek. 2012 Jan;101(1):105-24. doi: 10.1007/s10482-011-9628-4. Epub 2011 Aug 10.
The members of the order Pasteurellales are currently distinguished primarily on the basis of their branching in the rRNA trees and no convincing biochemical or molecular markers are known that distinguish them from all other bacteria. The genome sequences for 20 Pasteurellaceae species/strains are now publicly available. We report here detailed analyses of protein sequences from these genomes to identify conserved signature indels (CSIs) that are specific for either all Pasteurellales or its major clades. We describe more than 23 CSIs in widely distributed genes/proteins that are uniquely shared by all sequenced Pasteurellaceae species/strains but are not found in any other bacteria. Twenty-one additional CSIs are also specific for the Pasteurellales except in some of these cases homologues were not detected in a few species or the CSI was also present in an isolated non-Pasteurellaceae species. The sequenced Pasteurellaceae species formed two distinct clades in a phylogenetic tree based upon concatenated sequences for 10 conserved proteins. The first of these clades consisting of Aggregatibacter, Pasteurella, Actinobacillus succinogenes, Mannheimia succiniciproducens, Haemophilus influenzae and Haemophilus somnus was also independently supported by 13 uniquely shared CSIs that are not present in other Pasteurellaceae species or other bacteria. Another clade consisting of the remaining Pasteurellaceae species (viz. Actinobacillus pleuropneumoniae, Actinobacillus minor, Haemophilus ducryi, Mannheimia haemolytica and Haemophilus parasuis) was also strongly and independently supported by nine CSIs that are uniquely present in these bacteria. The order Pasteurellales is presently made up of a single family, Pasteurellaceae, that encompasses all of its genera. In this context, our identification of two distinct clades within the Pasteurellales, which are supported by both phylogenetic analyses and by multiple highly specific molecular markers, strongly argues for and provides potential means for the division of various genera from this order into a minimum of two families. The genetic changes responsible for these CSIs were likely introduced in the common ancestors of either all Pasteurellales or of these two specific clades. These CSIs provide novel means for the identification and circumscription of these groups of Pasteurellales in molecular terms.
巴氏杆菌目成员目前主要根据 rRNA 树的分支进行区分，并且没有令人信服的生化或分子标记可将其与所有其他细菌区分开来。现在已经公开了 20 种巴斯德氏菌科种/株的基因组序列。我们在此报告了对这些基因组中蛋白质序列的详细分析，以鉴定特定于巴氏杆菌目或其主要分支的保守特征插入缺失（CSI）。我们描述了在广泛分布的基因/蛋白质中存在的 23 多个 CSI，这些基因/蛋白质被所有测序的巴斯德氏菌科种/株共同拥有，但在任何其他细菌中都没有发现。另外 21 个 CSI 也特异性存在于巴氏杆菌目中，但在某些情况下，某些种中未检测到同源物，或者 CSI 也存在于孤立的非巴氏杆菌科种中。基于 10 种保守蛋白的串联序列构建的系统发育树中，测序的巴氏杆菌科种形成了两个不同的分支。第一个分支由Aggregatibacter、Pasteurella、Actinobacillus succinogenes、Mannheimia succiniciproducens、Haemophilus influenzae 和 Haemophilus somnus 组成，也得到了 13 个独特的 CSI 的独立支持，这些 CSI 不存在于其他巴氏杆菌科种或其他细菌中。另一个分支由其余的巴氏杆菌科种（即 Actinobacillus pleuropneumoniae、Actinobacillus minor、Haemophilus ducryi、Mannheimia haemolytica 和 Haemophilus parasuis）组成，也得到了存在于这些细菌中的 9 个独特 CSI 的强烈和独立支持。巴氏杆菌目目前由一个单一家族巴斯德氏菌科组成，该科包含其所有属。在这种情况下，我们在巴氏杆菌目中鉴定出两个不同的分支，这两个分支得到了系统发育分析和多个高度特异性分子标记的支持，强烈支持并提供了将该目中的各种属划分为至少两个科的可能性。这些 CSI 所涉及的遗传变化可能发生在所有巴氏杆菌目或这两个特定分支的共同祖先中。这些 CSI 为从分子角度鉴定和定义这些巴氏杆菌目群体提供了新的手段。
