Ottawa Research and Development Centre, Ottawa, ON, Canada.
Institut des sciences de santé et de la vie, Collège La Cité, Ottawa, ON, Canada.
Microbiologyopen. 2018 Apr;7(2):e00553. doi: 10.1002/mbo3.553. Epub 2018 Feb 21.
Multilocus sequence analysis (MLSA) of two new biological control strains (S1E40 and S3E12) of Pseudomonas was performed to assess their taxonomic position relative to close lineages, and comparative genomics employed to investigate whether these strains differ in key genetic features involved in hypersensitivity responses (HRs). Strain S3E12, at high concentration, incites HRs on tobacco and corn plantlets while S1E40 does not. Phylogenies based on individual genes and 16S rRNA-gyrB-rpoB-rpoD concatenated sequence data show strains S1E40 and S3E12 clustering in distinct groups. Strain S3E12 consistently clustered with Pseudomonas marginalis, a bacterium causing soft rots on plant tissues. MLSA data suggest that strains S1E40 and S3E12 are novel genotypes. This is consistent with the data of genome-based DNA-DNA homology values that are below the proposed cutoff species boundary. Comparative genomics analysis of the two strains revealed major differences in the type III secretion systems (T3SS) as well as the predicted T3SS secreted effector proteins (T3Es). One nonflagellar (NF-T3SS) and two flagellar T3SSs (F-T3SS) clusters were identified in both strains. While F-T3SS clusters in both strains were relatively conserved, the NF-T3SS clusters differed in the number of core components present. The predicted T3Es also differed in the type and number of CDSs with both strains having unique predicted protease-related effectors. In addition, the T1SS organization of the S3E12 genome has protein-coding sequences (CDSs) encoding for key factors such as T1SS secreted agglutinin repeats-toxins (a group of cytolysins and cytotoxins), a membrane fusion protein (LapC), a T1SS ATPase of LssB family (LapB), and T1SS-associated transglutaminase-like cysteine proteinase (LapP). In contrast, strain S1E40 has all CDSs for the seven-gene operon (pelA-pelG) required for Pel biosynthesis but not S3E12, suggesting that biofilm formation in these strains is modulated differently. The data presented here provide an insight of the genome organization of these two phytobacterial strains.
对 2 株新的 Pseudomonas 生物防治菌株（S1E40 和 S3E12）进行了多位点序列分析（MLSA），以评估它们与近亲谱系的分类地位，并进行比较基因组学研究，以调查这些菌株在参与过敏反应（HRs）的关键遗传特征上是否存在差异。在高浓度下，菌株 S3E12 会引起烟草和玉米幼苗的 HR，而 S1E40 则不会。基于单个基因和 16S rRNA-gyrB-rpoB-rpoD 串联序列数据构建的系统发育树显示，菌株 S1E40 和 S3E12 聚类在不同的群组中。菌株 S3E12 始终与 Pseudomonas marginalis 聚类，后者是一种导致植物组织软腐病的细菌。MLSA 数据表明，菌株 S1E40 和 S3E12 是新型基因型。这与基于基因组的 DNA-DNA 同源性值数据一致，该数据低于提议的种间界限。对这两个菌株的比较基因组学分析表明，它们在 III 型分泌系统（T3SS）以及预测的 T3SS 分泌效应蛋白（T3E）方面存在主要差异。在两个菌株中均鉴定出一个非鞭毛（NF-T3SS）和两个鞭毛 T3SS（F-T3SS）簇。虽然两个菌株的 F-T3SS 簇相对保守，但 NF-T3SS 簇在存在的核心组件数量上存在差异。预测的 T3E 在 CDS 类型和数量上也存在差异，两个菌株都具有独特的预测蛋白酶相关效应子。此外，S3E12 基因组的 T1SS 组织具有编码 T1SS 分泌凝集素重复毒素（一组细胞溶解素和细胞毒素）、膜融合蛋白（LapC）、LssB 家族 T1SS ATPase（LapB）和 T1SS 相关转谷氨酰胺酶样半胱氨酸蛋白酶（LapP）的关键因子的蛋白编码序列（CDS）。相比之下，菌株 S1E40 具有 Pel 生物合成所需的七个基因操纵子（pelA-pelG）的所有 CDS，但 S3E12 没有，这表明这些菌株中的生物膜形成受到不同的调节。本研究提供了这两个植物病原菌菌株基因组组织的见解。
