Hayoun Karim, Geersens Emilie, Laczny Cédric C, Halder Rashi, Lázaro Sánchez Carmen, Manna Abhijit, Bringel Françoise, Ryckelynck Michaël, Wilmes Paul, Muller Emilie E L, Alpha-Bazin Béatrice, Armengaud Jean, Vuilleumier Stéphane
Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols-sur-Cèze, France.
Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, F-67000 Strasbourg, France.
Microorganisms. 2020 Nov 27;8(12):1876. doi: 10.3390/microorganisms8121876.
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of genes in this strain. This suggests that the enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.
几种细菌能够利用保守的脱卤酶DcmA降解主要的工业溶剂二氯甲烷（DCM），这是迄今为止在序列水平上表征的唯一的DCM降解系统。我们利用差异蛋白质组学快速鉴定了未测序的兼性甲基营养型DCM降解菌株sp. MC8b中DCM降解的关键决定因素。为此，我们设计了一个泛蛋白质组学数据库，该数据库包含13个不同菌株的注释基因组序列。与以甲醇为碳源的生长相比，以DCM为碳源的生长会引起菌株MC8b蛋白质组的剧烈变化。通过差异泛蛋白质组学检测到了二氯甲烷脱卤酶DcmA，但序列覆盖率很低，这表明该菌株中DCM脱卤系统具有非典型特征。通过容错搜索为DcmA分配了更多的肽段，这促使我们对菌株MC8b的基因组进行后续测序，结果显示该菌株中有一组高度分化的基因。这表明该酶系统的保守性不如之前认为的那么强，而且基因在细菌域中的水平转移之外还发生了大量的分子进化。我们的研究展示了泛蛋白质组学在快速表征生命之树中基因组密集测序分支的新菌株方面的强大作用。
