Proteome Profile and Genome Refinement of the Tomato-Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis

Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species

Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.

Bacterial Canker of Tomato: Revisiting a Global and Economically Damaging Seedborne Pathogen

The gram-positive actinobacterium Clavibacter michiganensis is the causal agent of bacterial canker of tomato, an economically impactful disease with a worldwide distribution. This seedborne pathogen systemically colonizes tomato xylem leading to unilateral leaflet wilt, marginal leaf necrosis, stem and petiole cankers, and plant death. Additionally, splash dispersal of the bacterium onto fruit exteriors causes bird's-eye lesions, which are characterized as necrotic centers surrounded by white halos. The pathogen can colonize developing seeds systemically through xylem and through penetration of fruit tissues from the exterior. There are currently no commercially available resistant cultivars, and bactericidal sprays have limited efficacy for managing the disease once the pathogen is in the vascular system. In this review, we summarize research on epidemiology, host colonization, the bacterial genetics underlying virulence, and management of bacterial canker. Finally, we highlight important areas of research into this pathosystem that have the potential to generate new strategies for prevention and mitigation of bacterial canker.

Secretome Analysis of Clavibacter nebraskensis Strains Treated with Natural Xylem Sap In Vitro Predicts Involvement of Glycosyl Hydrolases and Proteases in Bacterial Aggressiveness

The Gram-positive bacterium Clavibacter nebraskensis (Cn) causes Goss's wilt and leaf blight on corn in the North American Central Plains with yield losses as high as 30%. Cn strains vary in aggressiveness on corn, with highly aggressive strains causing much more serious symptoms and damage to crops. Since Cn inhabits the host xylem, we investigated differences in the secreted proteomes of Cn strains to determine whether these could account for phenotypic differences in aggressiveness. Highly and a weakly aggressive Cn strains (Cn14-15-1 and DOAB232, respectively) were cultured, in vitro, in the xylem sap of corn (CXS; host) and tomato (TXS; non-host). The secretome of the Cn strains were extracted and processed, and a comparative bottom-up proteomics approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine their identities and concentration. Relative quantitation of peptides was based on precursor ion intensities to measure protein abundances. In total, 745 proteins were identified in xylem sap media. In CXS, a total of 658 and 396 proteins were identified in strains Cn14-5-1 and DOAB232, respectively. The unique and the differentially abundant proteins in the secretome of strain Cn14-5-1 were higher in either sap medium compared to DOAB232. These proteins were sorted using BLAST2GO and assigned to 12 cellular functional processes. Virulence factors, e.g., cellulase, β-glucosidase, β-galactosidase, chitinase, β-1,4-xylanase, and proteases were generally higher in abundance in the aggressive Cn isolate. This was corroborated by enzymatic activity assays of cellulase and protease in CXS. These proteins were either not detected or detected at significantly lower abundance levels in Cn strains grown in non-host xylem sap (tomato), suggesting potential factors involved in Cn-host (corn) interactions.

Characterizing Colonization Patterns of Clavibacter michiganensis During Infection of Tolerant Wild Solanum Species

Clavibacter michiganensis is the Gram-positive causal agent of bacterial canker of tomato, an economically devastating disease with a worldwide distribution. C. michiganensis colonizes the xylem, leading to unilateral wilt, stem canker, and plant death. C. michiganensis can also infect developing tomato fruit through splash dispersal, forming exterior bird's eye lesions. There are no documented sources of qualitative resistance in Solanum spp.; however, quantitative trait loci conferring tolerance in Solanum arcanum and Solanum habrochaites have been identified. Mechanisms of tolerance and C. michiganensis colonization patterns in wild tomato species remain poorly understood. This study describes differences in symptom development and colonization patterns of the wild type (WT) and a hypervirulent bacterial expansin knockout (ΔCmEXLX2) in wild and cultivated tomato genotypes. Overall, WT and ΔCmEXLX2 cause less severe symptoms in wild tomato species and are impeded in spread and colonization of the vascular system. Laser scanning confocal microscopy and scanning electron microscopy were used to observe preferential colonization of protoxylem vessels and reduced intravascular spread in wild tomatoes. Differences in C. michiganensis in vitro growth and aggregation were determined in xylem sap, which may suggest that responses to pathogen colonization are occurring, leading to reduced colonization density in wild tomato species. Finally, wild tomato fruit was determined to be susceptible to C. michiganensis through in vivo inoculations and assessing lesion numbers and size. Fruit symptom severity was in some cases unrelated to severity of symptoms during vascular infection, suggesting different mechanisms for colonization of different tissues.

Refining a Pathogen's Genome to Know the Enemy Better for the Winning Battles

Clavibacter michiganensis, subsp. michiganens is a gram positive bacterial pathogen infecting tomato, resulting in the great losses of yield and quality worldwide. Despite its great impact on economics, we do not fully understand the virulence factors from its genome probably due to imperfect genome annotation. Peritore-Galve et al. utilized proteogenomic approach to identify 26 novel protein-coding regions, to extend 59 annotated open reading frames and to confirm protein expression for ≈70% of predicted gene models of Clavibacter michiganensis subsp. michiganensis. New findings by the proteogenomics technique were further confirmed using reverse transcription-polymerase chain reaction. To win battles with pathogens, it is advantageous to know about our enemies accurately which can be achieved by mass spectrometry-based identifications of novel protein-coding regions in genomes.