Genome analysis of two novel Pseudomonas strains exhibiting differential hypersensitivity reactions on tobacco seedlings reveals differences in nonflagellar T3SS organization and predicted effector proteins

Abstract

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.

Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov.

“…Up to four, morphologically-unique colonies were picked from each plate onto fresh NA plates using a sterile needle and incubated for 48 h. A total of 42 cultures were sent to the Ottawa Molecular Bacteriology Laboratory of Agriculture and Agri-Food Canada for identification. After repeated streaking ( Tambong et al, 2017 ; Tchagang et al, 2018 ), 49 single colonies were obtained and preserved at −80°C in LB medium with 30% glycerol (v/v) for long-term storage. Gram-reaction of the strains was determined using the 3% KOH assay ( Ryu, 1940 ).…”

An Environmental Escherichia coli Strain Is Naturally Competent to Acquire Exogenous DNA

“…Genomic analysis allowed to identify a larger number of genes encoding for metabolic pathways in ED1 genome rather than in the one of K12 NEB DH5α strain, e.g., we found in ED1 genome the propanediol utilization pathway, which allows E. coli to grow in anaerobic conditions using rhamnose as carbon source ( Liu et al, 2007 ) and the genes of methilcytrate cycle, which allows microorganisms to use propionate as a carbon/energy sources, being especially useful in the propionate-rich environments such as the gastrointestinal tract ( Upton and McKinney, 2007 ). Furthermore, we found several genes that may help ED1 to thrive in different habitats, i.e., genes encoding for proteins related to the osmotic stress (involved in the synthesis and uptake of compatible solutes; Sim et al, 2014 ); genes involved in cell to cell aggregation and biofilm production, such as RTX that seems to be responsible for cell-surface adhesions, cells’ aggregation and production of biofilm ( Tchagang et al, 2018 ); CFA/I pili-related genes implicated in the bacterial adhesion through the production of fimbriae; and genes encoding the type III secretion injectosome ( Diepold et al, 2011 ; Zheng et al, 2019 ; Table 1 ). Therefore, strain ED1 has different traits that may help it to thrive in the environment and that might be related to a high transformation rate success.…”

PRRs and NB-LRRs: From Signal Perception to Activation of Plant Innate Immunity

“…Collectively, 565 and 567 effector proteins were identified in the S1E40 and S3E12 strains, respectively. Genomic analysis revealed one nonflagellar and two flagellar-based T3SS clusters in the genomes of both strains [93]. A large number of existing studies in the broader literature revealed that 20–30 effectors can be injected by means of T3SS, e.g., P. syringae [94,95].…”