Department of Microbiology and Immunology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73117 USA.
BMC Genomics. 2011 Aug 24;12:430. doi: 10.1186/1471-2164-12-430.
The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing suggests that these organisms should be classified as a single species (thus, we will refer to these organisms collectively as the Bc species-group). How do we account for the underlying similarity of these phenotypically diverse microbes? It has been established for some time that the most rapidly evolving and evolutionarily flexible portions of the bacterial genome are regulatory sequences and transcriptional networks. Other studies have suggested that the sigma factor gene family of these organisms has diverged and expanded significantly relative to their ancestors; sigma factors are those portions of the bacterial transcriptional apparatus that control RNA polymerase recognition for promoter selection. Thus, examining sigma factor divergence in these organisms would concurrently examine both regulatory sequences and transcriptional networks important for divergence. We began this examination by comparison to the sigma factor gene set of B. subtilis.
Phylogenetic analysis of the Bc species-group utilizing 157 single-copy genes of the family Bacillaceae suggests that several taxonomic revisions of the genus Bacillus should be considered. Within the Bc species-group there is little indication that the currently recognized species form related sub-groupings, suggesting that they are members of the same species. The sigma factor gene family encoded by the Bc species-group appears to be the result of a dynamic gene-duplication and gene-loss process that in previous analyses underestimated the true heterogeneity of the sigma factor content in the Bc species-group.
Expansion of the sigma factor gene family appears to have preferentially occurred within the extracytoplasmic function (ECF) sigma factor genes, while the primary alternative (PA) sigma factor genes are, in general, highly conserved with those found in B. subtilis. Divergence of the sigma-controlled transcriptional regulons among various members of the Bc species-group likely has a major role in explaining the diversity of phenotypic characteristics seen in members of the Bc species-group.
芽孢杆菌属感观组包括六个种（炭疽芽孢杆菌、蜡状芽孢杆菌、蕈状芽孢杆菌、类蕈状芽孢杆菌、苏云金芽孢杆菌和魏氏芽孢杆菌）。虽然经典微生物分类学将这些生物体视为不同的物种，但较新的分子系统发育和比较基因组测序表明，这些生物体应被归类为一个单一的物种（因此，我们将这些生物体统称为 Bc 种组）。我们如何解释这些表型差异很大的微生物之间的潜在相似性？一段时间以来，人们已经确定细菌基因组中进化最快和最具进化灵活性的部分是调控序列和转录网络。其他研究表明，这些生物体的σ因子基因家族相对于其祖先已经显著分化和扩张；σ因子是细菌转录装置的一部分，控制 RNA 聚合酶识别启动子选择。因此，检查这些生物体中的σ因子分化将同时检查对于分化很重要的调控序列和转录网络。我们通过与芽孢杆菌属的σ因子基因集进行比较开始了这项检查。
利用芽孢杆菌科的 157 个单拷贝基因对 Bc 种组进行系统发育分析表明，应该考虑对芽孢杆菌属的几个分类修订。在 Bc 种组内，目前公认的种形成相关亚群的迹象很少，这表明它们是同一物种的成员。Bc 种组编码的σ因子基因家族似乎是基因复制和基因丢失过程的动态结果，在以前的分析中低估了 Bc 种组中 σ 因子含量的真实异质性。
σ 因子基因家族的扩张似乎主要发生在外质功能（ECF）σ 因子基因中，而主要的替代（PA）σ 因子基因通常与枯草芽孢杆菌中的那些高度保守。Bc 种组中各种成员之间的 σ 控制转录调控子的分化可能在解释 Bc 种组成员中看到的表型特征多样性方面起着主要作用。
