Draft Genome Sequences of Seven Strains of Dickeya dadantii, a Quick Decline-Causing Pathogen in Fruit Trees, Isolated in Japan

Fujikawa, Takashi; Hatomi, Hiroe; Ota, Nobuyoshi

doi:10.1128/mra.00609-20

Cited by 4 publications

(4 citation statements)

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“…Extension of the host range of Dickeya spp. to trees is a relatively new observation, however, it does not appear to be a unique characteristic of D. fangzhongdai, since it was also reported for D. dadantii (Ogoshi et al, 2019;Fujikawa et al, 2020). Both species predominantly affect fruit trees such as pear, apple, peach, and jackfruit trees (Tian et al, 2016;Ogoshi et al, 2019;Chen et al, 2020;Fujikawa et al, 2020;Choi et al, 2021).…”

Section: Introductionmentioning

confidence: 86%

“…to trees is a relatively new observation, however, it does not appear to be a unique characteristic of D. fangzhongdai, since it was also reported for D. dadantii (Ogoshi et al, 2019;Fujikawa et al, 2020). Both species predominantly affect fruit trees such as pear, apple, peach, and jackfruit trees (Tian et al, 2016;Ogoshi et al, 2019;Chen et al, 2020;Fujikawa et al, 2020;Choi et al, 2021). Based on the literature, the majority of the reported D. fangzhongdai strains and all tree infections have been reported in Asian countries (Table 1).…”

Section: Introductionmentioning

confidence: 93%

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Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay

Alič,

Bačnik,

Dreo

2024

Front. Microbiol.

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Dickeya fangzhongdai, an aggressive plant pathogen, causes symptoms on a variety of crops and ornamental plants including bleeding canker of Asian pear trees. Historical findings stress the need for a specific detection tool for D. fangzhongdai to prevent overlooking the pathogen or assigning it to general Dickeya spp. Therefore, a qualitative real-time PCR for specific detection of D. fangzhongdai has been developed and validated. The developed assay shows selectivity of 100%, diagnostic sensitivity of 76% and limit of detection with 95% confidence interval in plant matrices ranging from 311 to 2,275 cells/mL of plant extracts. The assay was successfully used in a retrospective survey of selected host plants of relevance to Europe and environmental niches relevant to D. fangzhongdai. Samples of potato tubers and plants, plants from the Malinae subtribe (apple, pear, quince, and Asian pear tree) and fresh surface water from Slovenia were analyzed. D. fangzhongdai was not detected in any plant samples, however, 12% of surface water samples were found to be positive.

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Section: Introductionmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 93%

Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay

Alič,

Bačnik,

Dreo

2024

Front. Microbiol.

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“…Symptoms are usually soft rot but these bacteria can provoke blackleg or wilting on aerial parts of potato. Recently, diseases on woody plants caused by Dickeya have been reported [ 2 ]. There is no efficient way to fight these bacterial diseases.…”

Section: Introductionmentioning

confidence: 99%

Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system

Condemine

Derout

2022

PLoS ONE

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Dickeya are plant pathogenic bacteria able to provoke disease on a wide range of plants. A type 2 secretion system (T2SS) named Out is necessary for Dickeya virulence. Previous studies showed that the D. dadantii T2SS secretes a wide range of plant cell wall degrading enzymes, including pectinases and a cellulase. However, the full repertoire of exoproteins it can secrete has probably not yet been identified. Secreted proteins possess a signal peptide and are first addressed to the periplasm before their recruitment by Out. T2SS-specific secretion signals remain unknown which prevents in silico identification of T2SS substrates. To identify new Out substrates, we analyzed D. dadantii transcriptome data obtained in plant infection condition and searched for genes strongly induced and encoding proteins with a signal sequence. We identified four new Out-secreted proteins: the expansin YoaJ, the putative virulence factor VirK and two proteins of the DUF 4879 family, SvfA and SvfB. We showed that SvfA and SvfB are required for full virulence of D. dadantii and that svf genes are present in a variable number of copies in other Pectobacteriaceae, up to three in D. fanghzongdai. This work opens the way to the study of the role of non-pectinolytic proteins secreted by the Out pathway in Pectobacteriaceae.

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“…Recently, disease on woody plants caused by Dickeya have been reported (2). There is no efficient way to fight the disease.…”

Section: Introductionmentioning

confidence: 99%

Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system

Condemine

Derout

2021

Preprint

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Dickeya are plant pathogenic bacteria able to provoke disease on a wide range of plants. A type 2 secretion system named Out is necessary for bacterial virulence. Its study in D. dadantii showed that it secretes a wide range of pectinolytic enzymes. However, the full repertoire of exoproteins it can secrete has not been identified. No secretion signal present on the protein allows the identification of substrates of a type 2 secretion system. To identify new Out substrates, we analyzed D. dadantii transcriptome data obtained in plant infection condition and searched for genes strongly induced encoding a protein with a signal sequence. We identified four new Out-secreted proteins: the expansin YoaJ, VirK and two proteins of the DUF 4879 family, SvfA and SvfB. We showed that SvfA and SvfB are required for full virulence of D. dadantii and showed that Svf proteins are present with a variable number of copies, up to three in D. fanghzongdai, in other Pectobacteriaceae. This work opens the way to the study of the role in virulence of non-pectinolytic proteins secreted by the Out pathway in Pectobacteriaceae.IMPORTANCEThe plant pathogen Dickeya rely on a type 2 secretion system named Out for their pathogenicity. Importance of plant cell wall degrading enzymes secreted by this system has been well studied. However, existence and role of other Out-secreted proteins has barely been investigated. By mining D. dadantii transcriptome data, we identified four new Out-secreted proteins. We showed that two of them, SvfA and SvfB, are necessary for the full virulence of the bacteria. These findings show that identification of all the proteins secreted by the Dickeya Out system is necessary for a better knowledge of the virulence of these bacteria.

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Draft Genome Sequences of Seven Strains of Dickeya dadantii, a Quick Decline-Causing Pathogen in Fruit Trees, Isolated in Japan

Cited by 4 publications

References 4 publications

Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay

Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay

Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system

Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system

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