Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia.
Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia.
Int J Mol Sci. 2021 Feb 24;22(5):2244. doi: 10.3390/ijms22052244.
, commonly referred to as , is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make a prominent source of biologicals. To categorize the exuberance of strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of strains' phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the -attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the strain were also compared to the spores of strains belonging to two other major serovars, namely and . The identified proteins were analyzed regarding the presence of the respective genes in the 104 genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains' phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains.
, 通常被称为, 由于其高效的杀虫特性，成为微生物学家长期关注的对象，使其成为生物制品的重要来源。为了对发现的 菌株进行分类，人们利用血清型分析方法，其中鞭毛蛋白作为主要的血清反应分子。尽管这种方法很方便，但它既不能说明 菌株的表型，也不能反映该物种内的实际系统发育关系。在这方面，比较基因组学和蛋白质组学技术似乎更具信息性，但它们在 菌株分类中的应用仍然有限。在本工作中，我们使用了一种基于荧光二维差异凝胶电泳（2D-DIGE）结合液相色谱/串联质谱（LC-MS/MS）蛋白质鉴定的自下而上的蛋白质组学方法，以评估培养物的哪个阶段，营养期或孢子期，对菌株特征描述更有信息。为此，评估了与 - 相关的菌株的蛋白质组差异，以比较毒力衍生菌株的孢子形成培养物与无毒菌株以及营养期细菌的差异。使用相同的方法，还将 菌株的毒力孢子与属于另外两个主要 血清型，即 和 的菌株的孢子进行了比较。对鉴定的蛋白质进行了分析，根据在开放获取的 104 个基因组组装中存在的相应基因，这些基因组组装指定了血清型归属。在鉴定的 21 种蛋白质中，有 15 种在所有现有组装中以 67%的同一性阈值被发现编码，其中包括几种毒力因子。值得注意的是，这些核心基因的个体系统发育既没有赋予血清型分类，也没有赋予鞭毛蛋白系统发育，但在树拓扑相似性方面支持基于系统发育基因组学方法的重建。另一方面，辅助蛋白基因的分布不限于现有的血清型。获得的结果表明，基因的存在或核心基因序列都不能作为血清型归属的独特基础，这削弱了血清型分类系统反映菌株表型或遗传相似性的观点。我们还提供了一组与系统发育基因组学数据相符的基因座，这些基因座可能用于新菌株的草案系统发育估计。
