Charkowski A, Blanco C, Condemine G, Expert D, Franza T, Hayes C, Hugouvieux-Cotte-Pattat N, López Solanilla E, Low D, Moleleki L, Pirhonen M, Pitman A, Perna N, Reverchon S, Rodríguez Palenzuela P, San Francisco M, Toth I, Tsuyumu S, van der Waals J, van der Wolf J, Van Gijsegem F, Yang CH, Yedidia I: The role of secretion systems and small molecules in soft-rot enterobacteriaceae pathogenicity. Annu Rev Phytopathol. 2012, 50: 425-449. 10.1146/annurev-phyto-081211-173013.
Article
CAS
PubMed
Google Scholar
Toth IK, van der Wolf JM, Saddler G, Lojkowska E, Hélias V, Pirhonen M, Tsror (Lahkim) L, Elphinstone JG: Dickeya species: an emerging problem for potato production in Europe. Plant Pathol. 2011, 60: 385-399. 10.1111/j.1365-3059.2011.02427.x.
Article
Google Scholar
van der Wolf JM, Nijhuis EH, Kowalewska MJ, Saddler GS, Parkinson N, Elphinstone JG, Pritchard L, Toth JK, Lojkowska E, Potrykus M, Waleron M, de Vos P, Cleenwerck I, Pirhonen M, Garlant L, Hélias V, Pothier JF, Pflüger V, Duffy B, Tsror L, Manulis S: Dickeya solani sp. nov., a pectinolytic plant pathogenic bacterium isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol. 2013, doi:10.1099/ijs.0.052944-0
Google Scholar
Laurila J, Ahola V, Lehtinen A, Joutsjoki T, Hannukkala A, Rahkonen A, Pirhonen M: Characterization of Dickeya strains isolated from potato and river water samples in Finland. Eur J Plant Pathol. 2008, 122: 213-225. 10.1007/s10658-008-9274-5.
Article
CAS
Google Scholar
Slawiak M, van Beckhoven JRCM, Speksnijder AGCL, Czajkowski RL, Grabe G, van der Wolf JM: Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe. Eur Plant Pathol. 2009, 125: 245-261. 10.1007/s10658-009-9479-2.
Article
Google Scholar
Van Vaerenbergh J, Baeyen S, De Vos P, Maes M: Sequence diversity in the Dickeya fliC gene: phylogeny of the Dickeya genus and TaqMan® PCR for ‘D. solani’, new biovar 3 variant on potato in Europe. PLoS ONE. 2012, 7: e35738-10.1371/journal.pone.0035738.
Article
CAS
PubMed Central
PubMed
Google Scholar
Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, Gardan L: Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov as Dickeya chrysanthemi comb. nov and Dickeya paradisiaca comb. nov and delineation of four novel species, Dickeya dadantii sp nov., Dickeya dianthicola sp nov., Dickeya dieffenbachiae sp nov and Dickeya zeae sp nov. Int J Syst Evol Microbiol. 2005, 55: 1415-1427. 10.1099/ijs.0.02791-0.
Article
CAS
PubMed
Google Scholar
Tsror (Lahkim) L, Erlich O, Lebiush S, Hazanovsky M, Zig U, Slawiak M, Grabe G, van der Wolf JM, van de Haar JJ: Assessment of recent outbreaks of Dickeya sp. (syn. Erwinia chrysanthemi) slow wilt in potato crops in Israel. Eur J Plant Pathol. 2009, 123: 311-320. 10.1007/s10658-008-9368-0.
Article
Google Scholar
Czajkowski R, de Boer WJ, van Veen JA, van der Wolf JM: Downward vascular translocation of a green fluorescent protein-tagged strain of Dickeya sp. (Biovar 3) from stem and leaf inoculation sites on potato. Phytopathol. 2010, 100: 1128-1137. 10.1094/PHYTO-03-10-0093.
Article
Google Scholar
Czajkowski R, de Boer WJ, van der Zouwen PS, Kastelein P, Jafra S, de Haan EG, van den Bovenkamp GW, van der Wolf JM: Virulence of ‘Dickeya solani’ and Dickeya dianthicola biovar-1 and -7 strains on potato (Solanum tuberosum). Plant Pathol. 2013, 62: 597-610. 10.1111/j.1365-3059.2012.02664.x.
Article
CAS
Google Scholar
Reverchon S, Nasser W: Dickeya ecology, environment sensing and regulation of virulence programme. Env Microbiol Rep. 2013, 5: 622-636.
Google Scholar
Glasner JD, Yang CH, Reverchon S, Hugouvieux-Cotte-Pattat N, Condemine G, Bohin JP, Van Gijsegem F, Yang S, Franza T, Expert D, Plunkett G, San Francisco MJ, Charkowski AO, Py B, Bell K, Rauscher L, Rodriguez-Palenzuela P, Toussaint A, Holeva MC, He SY, Douet V, Boccara M, Blanco C, Toth I, Anderson BD, Biehl BS, Mau B, Flynn SM, Barras F, Lindeberg M, et al: Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937. J Bacteriol. 2011, 193: 2076-2077. 10.1128/JB.01513-10.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hélias V: Jambe noire: evolution des souches et risques associés. La pomme de terre française. 2012, 580: 48-49.
Google Scholar
Crépin A, Beury-Cirou A, Barbey C, Farmer C, Hélias V, Burini J-F, Faure D, Latour X: N-Acyl Homoserine lactones in diverse Pectobacterium and Dickeya plant pathogens: diversity, abundance, and involvement in virulence. Sensors. 2012, 12: 3484-3497.
Article
PubMed Central
PubMed
Google Scholar
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011, 27: 578-579. 10.1093/bioinformatics/btq683.
Article
CAS
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008, 9: 75-10.1186/1471-2164-9-75.
Article
PubMed Central
PubMed
Google Scholar
Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007, 23: 673-679. 10.1093/bioinformatics/btm009.
Article
CAS
PubMed Central
PubMed
Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14: 1394-1403. 10.1101/gr.2289704.
Article
CAS
PubMed Central
PubMed
Google Scholar
Richter M, Rossello-Mora R: Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009, 106: 19126-19131. 10.1073/pnas.0906412106.
Article
CAS
PubMed Central
PubMed
Google Scholar
Richter DC, Ott F, Auch AF, Schmid R, Huson DH: MetaSim—a sequencing simulator for genomics and metagenomics. PLoS ONE. 2008, 3: e3373-10.1371/journal.pone.0003373.
Article
PubMed Central
PubMed
Google Scholar
Pritchard L, Humphris S, Saddler GS, Parkinson NM, Bertrand V, Elphinstone JG: Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathol. 2012, 62: 587-596.
Article
Google Scholar
Brunner J, Wittink FR, Jonker MJ, de Jong M, Breit TM, Laine ML, de Soet JJ, Crielaard W: The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis. BMC Microbiol. 2010, 10: 252-10.1186/1471-2180-10-252.
Article
PubMed Central
PubMed
Google Scholar
Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Mitchell TJ, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol. 2010, 11: R107-10.1186/gb-2010-11-10-r107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Chiapello H, Cruveiller S, Danchin A, Diard M, Dossat C, El Karoui M, Ghigo JM, Gilles AM, Johnson J, Le Bouguenec C, Lescat M, Mangenot S, Martinez-Jehanne V, Matic I, Nassif X, Petit MA, Pichon C, Rouy Z, Saint Ruf C, Schneider D, et al: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009, 5: e1000344-10.1371/journal.pgen.1000344.
Article
PubMed Central
PubMed
Google Scholar
Barras F, Van Gijsegem F, Chatterjee AK: Extracellular enzymes and pathogenesis of soft-rot Erwinia. Ann Rev Phytopathol. 1994, 32: 201-234. 10.1146/annurev.py.32.090194.001221.
Article
CAS
Google Scholar
Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S: Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol. 1996, 50: 213-257. 10.1146/annurev.micro.50.1.213.
Article
CAS
PubMed
Google Scholar
Perombelon MCM: Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol. 2002, 51: 1-12. 10.1046/j.0032-0862.2001.Short title.doc.x.
Article
Google Scholar
Gloux K, Touze T, Pagot Y, Jouan B, Blanco C: Mutations of ousA alter the virulence of Erwinia chrysanthemi. Mol Plant Microbe Interact. 2005, 18: 150-157. 10.1094/MPMI-18-0150.
Article
CAS
PubMed
Google Scholar
Ferrandez Y, Condemine G: Novel mechanism of outer membrane targeting of proteins in gram negative bacteria. Mol Microbiol. 2008, 69: 1349-1357. 10.1111/j.1365-2958.2008.06366.x.
Article
CAS
PubMed
Google Scholar
Aoki SK, Diner EJ, de Roodenbeke C, Burgess BR, Poole SJ, Jones AM, Webb JS, Hayes CS, Cotter PA: A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria. Nature. 2010, 468: 439-442. 10.1038/nature09490.
Article
CAS
PubMed Central
PubMed
Google Scholar
Koskiniemi S, Lamoureux JG, Nikolakakis K, t’Kint de Roodenbeeke C, Kaplan MD, Low DA, Hayes SH: Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A. 2013, 110: 7032-7037. 10.1073/pnas.1300627110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Poole SJ, Diner EJ, Aoki SK, Braaten BA, t’Kint de Roodenbeke C, Hayes CS: Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet. 2011, 7: e10017-
Google Scholar
Bingle LEH, Bailey CM, Pallen MJ: Type VI secretion: a beginner’s guide. Curr Opin Microbiol. 2008, 11: 3-8. 10.1016/j.mib.2008.01.006.
Article
CAS
PubMed
Google Scholar
Crepin A, Barbey C, Beury-Cirou A, Hélias V, Taupin L, Reverchon S, Nasser W, Faure D, Dufour A, Orange N, Feuilloley M, Heurlier K, Burini J-F, Latour X: Quorum sensing signalling molecules produced by reference and emerging soft-rot bacteria (Dickeya and Pectobacterium spp.). PLoS ONE. 2012, 7: e35176-10.1371/journal.pone.0035176.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lebeau A, Reverchon S, Gaubert S, Kraepiel Y, Simond-Côte E, Nasser W, Van Gijsegem F: The GacA global regulator is required for the appropriate expressionof Erwinia chrysanthemi 3937 pathogenicity genes during plant infection. Environ Microbiol. 2008, 10: 545-559. 10.1111/j.1462-2920.2007.01473.x.
Article
CAS
PubMed
Google Scholar
Mhedbi-Hajri N, Malfatti P, Pédron J, Gaubert S, Reverchon S, Van Gijsegem F: PecS is an important player in the regulatory network governing the coordinated expression of virulence genes during the interaction between Dickeya dadantii 3937 and plants. Environ Microbiol. 2011, 13: 2901-2914. 10.1111/j.1462-2920.2011.02566.x.
Article
CAS
PubMed
Google Scholar
Reverchon S, Van Gijsegem F, Effantin G, Zghidi-Abouzid O, Nasser W: Systematic targeted mutagenesis of the MarR/SlyA family members of Dickeya dadantii 3937 reveals a role for MfbR in the modulation of virulence gene expression in response to acidic pH. Mol Microbiol. 2010, 78: 1018-1037. 10.1111/j.1365-2958.2010.07388.x.
Article
CAS
PubMed
Google Scholar
Nasser W, Dorel C, Wawrzyniak J, Van Gijsegem F, Groleau M-C, Déziel E, Reverchon S: Vfm a new quorum sensing system controls the virulence of Dickeya dadantii. Environ Microbiol. 2013, 15: 865-880. 10.1111/1462-2920.12049.
Article
CAS
PubMed
Google Scholar
Van Gijsegem F, Wlodarczyk A, Cornu A, Reverchon S, Hugouvieux-Cotte-Pattat N: Analysis of the LacI family regulators of Erwinia chrysanthemi 3937, involvement in the bacterial phytopathogenicity. Mol Plant Microbe Interact. 2008, 21: 1471-1481. 10.1094/MPMI-21-11-1471.
Article
CAS
PubMed
Google Scholar
Babujee L, Apodaca J, Balakrishnan V, Liss P, Kiley PJ, Charkowski AO, Glasner JD, Perna NT: Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria. BMC Genomics. 2012, 13: 110-10.1186/1471-2164-13-110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Arber W: Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev. 2000, 24: 1-7. 10.1111/j.1574-6976.2000.tb00529.x.
Article
CAS
PubMed
Google Scholar
Van Houdt R, Toussaint A, Ryan MP, Pembroke JT, Mergeay M, Adley CC: Tn4731 ICE family of bacterial mobile genetic elements. Bacterial Integrative Mobile Genetic Elements. Edited by: Roberts AP, Mullany P. 2011, Landes Biosciences, 1-22.
Google Scholar
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007, 315: 1709-1712. 10.1126/science.1138140.
Article
CAS
PubMed
Google Scholar
Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T: antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 2013, 41: W204-W212. 10.1093/nar/gkt449.
Article
PubMed Central
PubMed
Google Scholar
Minowa Y, Araki M, Kanehisa M: Comprehensive analysis of distinctive polyketide and non ribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol. 2007, 368: 1500-1517. 10.1016/j.jmb.2007.02.099.
Article
CAS
PubMed
Google Scholar
Zhou J, Zhang H, WU J, Liu Q, XI P, Lee J, LIAO J, Jiang Z, Zhang L-H: A novel multi domain polyketide synthase is essential for zeamine production and the virulence of Dickeya zeae. Mol Plant Microbe Interact. 2011, 24: 1156-1164. 10.1094/MPMI-04-11-0087.
Article
CAS
PubMed
Google Scholar
Garlant L, Koshinen P, Rouhiainene L, Laine P, Paulin L, Auvinene P, Holm L, Pirhonen M: Genome sequence of Dickeya solani, a new soft rot pathogen of potato, suggests its emergence may be related to a novel combination of non-ribosomal peptide/polyketide synthase clusters. Diversity. 2013, 5: 824-842. 10.3390/d5040824.
Article
Google Scholar