Complete genome sequence of the cellulase-producing bacterium Clavibacter michiganensis PF008

Bae, Chungyun; Oh, Eom-Ji; Lee, Han-Beoyl; Kim, Byung-Yong; Oh, Chang‐Sik

doi:10.1016/j.jbiotec.2015.09.021

Cited by 8 publications

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“…The genome information of C. michiganensis ssp. capsici type strain PF008 available at GenBank database (accession numbers: for chromosome, for pCM1 Cmc , for pCM2 Cmc ) was used for further analysis (Bae et al ., ). Accession numbers for genome information of other C. michiganensis subspecies used in this study are listed in Supporting Information Table S1.…”

Section: Methodsmentioning

confidence: 97%

“…C. michiganensis ssp. capsici strain PF008 carries two plasmids, pCM1 Cmc (39-kb) and pCM2 Cmc (145-kb) (Bae et al, 2015). The celA gene was not identified from either C. michiganensis ssp.…”

Section: Introductionmentioning

confidence: 97%

“…Genome analyses of C. michiganensis subspecies have been performed since the first report of the genome sequence of C. michiganensis ssp. michiganensis strain NCPPB382 (Bentley et al, 2008;Gartemann et al, 2008;Bae et al, 2015;Lu et al, 2015b;Tambong et al, 2015;Tambong, 2017). Genomic analysis of NCPPB382 revealed that it has a 130 kb chromosomal pathogenicity island (PAI) consisting of chp and tomA subregions, which include multiple virulence genes mostly encoding enzymes such as pectate lyase, serine proteases, and tomatinase, and this PAI region has been shown to play an important role in invasion of the host plant (Eichenlaub & Gartemann, 2011;Jackson et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…nebraskensis or C. michiganensis ssp. capsici, but another cellulase gene, celB, was identified to encode cellulase without the expansin domain, although its virulence function has not been well studied (Eichenlaub & Gartemann, 2011;Bae et al, 2015). Whole genome sequences of nonpathogenic strains, such as C. michiganensis CF11 isolated from soil at a tomato-planting glasshouse and C. michiganensis LMG26808, have also been reported (Zaluga et al, 2014;Du et al, 2015), although there is little information on the biology of nonpathogenic C. michiganensis strains.…”

Section: Introductionmentioning

confidence: 99%

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Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

Hwang

Kim

et al. 2017

New Phytologist

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Clavibacter michiganensis ssp. capsici is a Gram-positive plant-pathogenic bacterium causing bacterial canker disease in pepper. Virulence genes and mechanisms of C. michiganensis ssp. capsici in pepper have not yet been studied. To identify virulence genes of C. michiganensis ssp. capsici, comparative genome analyses with C. michiganensis ssp. capsici and its related C. michiganensis subspecies, and functional analysis of its putative virulence genes during infection were performed. The C. michiganensis ssp. capsici type strain PF008 carries one chromosome (3.056 Mb) and two plasmids (39 kb pCM1 and 145 kb pCM2 ). The genome analyses showed that this bacterium lacks a chromosomal pathogenicity island and celA gene that are important for disease development by C. michiganensis ssp. michiganensis in tomato, but carries most putative virulence genes in both plasmids. Virulence of pCM1 -cured C. michiganensis ssp. capsici was greatly reduced compared with the wild-type strain in pepper. The complementation analysis with pCM1 -located putative virulence genes showed that at least five genes, chpE, chpG, ppaA1, ppaB1 and pelA1, encoding serine proteases or pectate lyase contribute to disease development in pepper. In conclusion, C. michiganensis ssp. capsici has a unique genome structure, and its multiple plasmid-borne genes play critical roles in virulence in pepper, either separately or together.

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Section: Methodsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

Hwang

Kim

et al. 2017

New Phytologist

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“…The complete chromosomal genome sequences of Cmn strain NCPPB 2581 (K.H. Gartemann, GenBank accession # HE614873), Cmi strain R1-1 [13] and Cmc strain PF008 [14] were published. The Cmi genome carries 3 plasmids while that of Cmc has two plasmids which might possess similar virulence factors.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Tambong

2017

PLoS ONE

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Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.

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Diversity and characterization of antagonistic bacteria against Pseudomonas syringae pv. actinidiae isolated from kiwifruit rhizosphere

Yan,

Fu,

Mir

et al. 2023

FEMS Microbiology Letters

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Kiwifruit bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) is a severe global disease. However, effective biological control agents for controlling Psa are currently unavailable. This study aimed to screen potential biological control agents against Psa from the kiwifruit rhizosphere. In this study, a total of 722 isolates of bacteria were isolated from the rhizosphere of kiwifruit orchards in five regions of China. Eighty-two strains of rhizosphere bacteria showed antagonistic effects against Psa on plates. Based on amplified ribosomal DNA restriction analysis (ARDRA), these antagonistic rhizosphere bacteria were grouped into 17 clusters. BLAST analyses based on 16S rRNA gene sequence revealed 95.44–100% sequence identity to recognized species. The isolated strains belonged to genus Acinetobacter, Bacillus, Chryseobacterium, Flavobacterium, Glutamicibacter, Lysinibacillus, Lyso-bacter, Pseudomonas, Pseudarthrobacter and Streptomyces, respectively. Four representative strains were selected to determine their extracellular metabolites and cell-free supernatant activity against Psa in vitro. They all produce protease and none of them produce glucanase. One strain of Pseudomonas sp. produces siderophore. Strains of Bacillus spp. and Flavobacteria sp. produce cellulase, and Flavobacteria sp. also produce chitinase. Our results suggested that the kiwifruit rhizosphere soils contain a variety of antagonistic bacteria that effectively inhibit the growth of Psa.

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Complete genome sequence of the cellulase-producing bacterium Clavibacter michiganensis PF008

Cited by 8 publications

References 11 publications

Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Diversity and characterization of antagonistic bacteria against Pseudomonas syringae pv. actinidiae isolated from kiwifruit rhizosphere

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