pFiD188, the linear virulence plasmid of Rhodococcus fascians D188

Molecular Plant-Microbe Interactions

Volumn 25, Issue 5, 2012, Pages 637-647

  Francis, Isolde ^a,d   De Keyser, Annick ^a   De Backer, Philippe ^a,e   Simón Mateo, Carmen ^a,f   Kalkus, Jutta ^a   Pertry, Ine ^a   Ardiles Diaz, Wilson ^a   De Rycke, Riet ^a   Vandeputte, Olivier M ^b   Jaziri, Mondher El ^b   Holsters, Marcelle ^a   Vereecke, Danny ^c  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c UNIVERSITY COLLEGE GHENT   (Belgium)

^d UNIVERSITY OF FLORIDA   (United States)

^e LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^f CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIUM CONJUGATION; BIOFILM; CHEMISTRY; DNA SEQUENCE; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PATHOGENICITY; PLANT DISEASE; PLANT LEAF; PLASMID; REPLICON; RHODOCOCCUS; SEQUENCE ALIGNMENT; TELOMERE; TOBACCO; ULTRASTRUCTURE; VIRULENCE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BIOFILMS; CONJUGATION, GENETIC; DNA MUTATIONAL ANALYSIS; DNA, BACTERIAL; GENE EXPRESSION REGULATION; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; OPERON; PLANT DISEASES; PLANT LEAVES; PLASMIDS; REPLICON; RHODOCOCCUS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TELOMERE; TOBACCO; VIRULENCE;

ACTINOBACTERIA; RHODOCOCCUS; RHODOCOCCUS ERYTHROPOLIS; RHODOCOCCUS FASCIANS; RHODOCOCCUS JOSTII; RHODOCOCCUS OPACUS;

EID: 84860427406     PISSN: 08940282     EISSN: None     Source Type: Journal    
DOI: 10.1094/MPMI-08-11-0215     Document Type: Article

References (79)

1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
2. Arnold, C., and Hodgson, I. J. 1991. Vectorette PCR: A novel approach to genomic walking. PCR Methods Appl. 1:39-42.
3. Bao, K., and Cohen, S. N. 2003. Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev. 17:774-785. (Pubitemid 36359195)
4. Barash, I., and Manulis-Sasson, S. 2009. Recent evolution of bacterial pathogens: The gall-forming Pantoea agglomerans case. Annu. Rev. Phytopathol. 47:133-152.
5. Barre, F.-X. 2007. FtsK and SpoIIIE: The tale of the conserved tails. Mol. Microbiol. 66:1051-1055. (Pubitemid 350115019)
6. Bentley, S. D., Corton, C., Brown, S. E., Barron, A., Clark, L., Doggett, J., Harris, B., Ormond, D., Quail, M. A., May, G., Francis, D., Knudson, D., Parkhill, J., and Ishimaru, C. A. 2008. Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J. Bacteriol. 190:2150-2160. (Pubitemid 351355338)
7. Bignell, D. R. D., Huguet-Tapia, J. C., Joshi, M. V., Pettis, G. S., and Loria, R. 2010. What does it take to be a plant pathogen: Genomic insights from Streptomyces species. Antonie Van Leeuwenhoek 98:179-194.
8. Carvalho, C. M. L., Aires-Barros, M. R., and Cabral, J. M. S. 1999. Cutinase: From molecular level to bioprocess development. Biotechnol. Bioeng. 66:17-34.
9. Carver, T. J., Rutherford, K. M., Berriman, M., Rajandream, M.-A., Barrell, B. G., and Parkhill, J. 2005. ACT: The Artemis comparison tool. Bioinformatics 21:3422-3423. (Pubitemid 41222448)
10. Chen, C. W. 2007. Streptomyces linear plasmids: Replication and telomeres. Pages 33-61 in: Microbial Linear Plasmids, Microbiology Monographs, Vol. 7. F. Meinhardt and R. Klassen, eds. Springer-Verlag, Berlin.
11. Cornelis, K., Ritsema, T., Nijsse, J., Holsters, M., Goethals, K., and Jaziri, M. 2001. The plant pathogen Rhodococcus fascians colonizes the exterior and interior of the aerial parts of plants. Mol. Plant-Microbe Interact. 14:599-608. (Pubitemid 32333381)
12. Crespi, M., Messens, E., Caplan, A. B., Van Montagu, M., and Desomer, J. 1992. Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene. EMBO (Eur. Mol. Biol. Organ.) J. 11:795-804.
13. Crespi, M., Vereecke, D., Temmerman, W., Van Montagu, M., and Desomer, J. 1994. The fas operon of Rhodococcus fascians encodes new genes required for efficient fasciation of host plants. J. Bacteriol. 176:2492-2501. (Pubitemid 24139025)
14. Danhorn, T., and Fuqua, C. 2007. Biofilm formation by plant-associated bacteria. Annu. Rev. Microbiol. 61:401-422. (Pubitemid 350058215)
15. Delcher, A. L., Bratke, K. A., Powers, E. C, and Salzberg, S. L. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679. (Pubitemid 46554717)
16. Depuydt, S., Doležal, K., Van Lijsebettens, M., Moritz, T., Holsters, M., and Vereecke, D. 2008. Modulation of the hormone setting by Rhodococcus fascians results in ectopic KNOX activation in Arabidopsis. Plant Physiol. 146:1267-1281. (Pubitemid 352844146)
17. Desomer, J., Dhaese, P., and Van Montagu, M. 1988. Conjugative transfer of cadmium resistance plasmids in Rhodococcus fascians strains. J. Bacteriol. 170:2401-2405.
18. Desomer, J., Dhaese, P., and Van Montagu, M. 1990. Transformation of Rhodococcus fascians by high-voltage electroporation and development of R. fascians cloning vectors. Appl. Environ. Microbiol. 56:2818-2825. (Pubitemid 20273118)
19. Desomer, J., Crespi, M., and Van Montagu, M. 1991. Illegitimate integration of non-replicative vectors in the genome of Rhodococcus fascians upon electrotransformation as an insertional mutagenesis system. Mol. Microbiol. 5:2115-2124. (Pubitemid 21896244)
20. Desomer, J., Vereecke, D., Crespi, M., and Van Montagu, M. 1992. The plasmid-encoded chloramphenicol resistance protein of Rhodococcus fascians is homologous to the transmembrane tetracycline efflux proteins. Mol. Microbiol. 6:2377-2385.
21. Finking, R., and Marahiel, M. A. 2004. Biosynthesis of nonribosomal peptides. Annu. Rev. Microbiol. 58:453-488. (Pubitemid 39551994)
22. Flärdh, K. 2010. Cell polarity and the control of apical growth in Streptomyces. Curr. Opin. Microbiol. 13:758-765.
23. Francis, I., Gevers, D., Karimi, M., Holsters, M., and Vereecke, D. 2007. Linear plasmids and phytopathogenicity. Pages 99-115 in: Microbial Linear Plasmids, Microbiology Monographs, Vol. 7. F. Meinhardt and R. Klassen, eds. Springer-Verlag, Berlin.
24. Gal-Mor, O., and Finlay, B. B. 2006. Pathogenicity islands: A molecular toolbox for bacterial virulence. Cell. Microbiol. 8:1707-1719. (Pubitemid 44530664)
25. Grohmann, E., Muth, G., and Espinosa, M. 2003. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67:277-301. (Pubitemid 36693475)
26. Gröning, J. A. D., Tischler, D., Kaschabek, S. R., and Schlömann, M. 2010. Optimization of a genome-walking method to suit GC-rich template DNA from biotechnological relevant Actinobacteria. J. Basic Microbiol. 50:499-502.
27. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580. (Pubitemid 13027898)
28. Hayes, C. S., and Low, D. A. 2009. Signals of growth regulation in bacteria. Curr. Opin. Microbiol. 12:667-673.
29. Jin, H., and Pancholi, V 2006. Identification and biochemical characterization of a eukaryotic-type serine/threonine kinase and its cognate phosphatase in Streptococcus pyogenes: Their biological functions and substrate identification. J. Mol. Biol. 357:1351-1372.
30. Jones, G., and Dyson, P. 2006. Evolution of transmembrane protein kinases implicated in coordinating remodeling of gram-positive peptidoglycan: Inside versus outside. J. Bacteriol. 188:7470-7476. (Pubitemid 44646246)
31. Joshi, M., and Loria, R. 2007. Streptomyces turgidiscabies possesses a functional cytokinin biosynthetic pathway and produces leafy galls. Mol. Plant-Microbe Interact. 20:751-758. (Pubitemid 46944969)
32. Kalkus, J., Menne, R., Reh, M., and Schlegel, H. G. 1998. The terminal structures of linear plasmids from Rhodococcus opacus. Microbiology 144:1271-1279. (Pubitemid 28233831)
33. Kato, J.-y, Funa, N., Watanabe, H., Ohnishi, Y., and Horinouchi, S. 2007. Biosynthesis of γ-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc. Natl. Acad. Sci. U.S.A. 104:2378-2383. (Pubitemid 46391405)
34. Konz, D., and Marahiel, M. A. 1999. How do peptide synthetases generate structural diversity? Chem. Biol. 6:R39-R48. (Pubitemid 29363156)
35. Lacey, M. S. 1961. The development of filter-passing organisms in Corynebacterium fascians cultures. Ann. Appl. Biol. 49:634-644.
36. Larkin, M. J., Kulakov, L. A., and Allen, C. C. R. 2005. Biodegradation and Rhodococcus - masters of catabolic versatility. Curr. Opin. Biotechnol. 16:282-290. (Pubitemid 40806465)
37. Lawson, E. N., Gantotti, B. V, and Starr, M. P. 1982. A 78-megadalton plasmid occurs in avirulent strains as well as virulent strains of Corynebacterium fascians. Curr. Microbiol. 7:327-332. (Pubitemid 13154318)
38. LeChevalier, H. A. 1986. Nocardioforms. Pages 1458-1506 in: Bergey's Manual of Systematic Bacteriology, Vol. 2. P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt, eds. Williams & Wilkins, Baltimore.
39. Letek, M., Fiuza, M., Ordóñez, E., Villadangos, A. F, Ramos, A., Mateos, L. M., and Gil, J. A. 2008. Cell growth and cell division in the rodshaped actinomycete Corynebacterium glutamicum. Antonie Van Leeuwenhoek 94:99-109.
40. Letek, M., González, P., MacArthur, I., Rodríguez, H., Freeman, T. C., Valero-Rello, A., Blanco, M., Buckley, T., Cherevach, I., Fahey, R., Hapeshi, A., Holdstock, J., Leadon, D., Navas, J., Ocampo, A., Quail, M. A., Sanders, M., Scortti, M. M., Prescott, J. F., Fogarty, U., Meijer, W. G., Parkhill, J., Bentley, S. D., and Vázquez-Boland, J. A. 2010. The genome of a pathogenic Rhodococcus: Cooptive virulence underpinned by key gene acquisitions. PLoS Genet. 6:e1001145.
41. Liang, X., and Van Doren, S. R. 2008. Mechanistic insights into phosphoprotein-binding FHA domains. Accounts Chem. Res. 41:991-999.
42. Maes, T., Vereecke, D., Ritsema, T., Cornelis, K., Ngo Thi Thu, H., Van Montagu, M., Holsters, M., and Goethals, K. 2001. The att locus of Rhodococcus fascians strain D188 is essential for full virulence on tobacco through the production of an autoregulatory compound. Mol. Microbiol. 42:13-28. (Pubitemid 34212157)
43. McLeod, M. P., Warren, R. L., Hsiao, W. W. L., Araki, N., Myhre, M., Fernandes, C., Miyazawa, D., Wong, W., Lillquist, A. L., Wang, D., Dosanjh, M., Hara, H., Petrescu, A., Morin, R. D., Yang, G., Stott, J. M., Schein, J. E., Shin, H., Smailus, D., Siddiqui, A. S., Marra, M. A., Jones, S. J. M., Holt, R., Brinkman, F. S. L., Miyauchi, K., Fukuda, M., Davies, J. E., Mohn, W. W., and Eltis, L. D. 2006. The complete genome of Rhodococcus sp. RHA1 provides insight into a catabolic powerhouse. Proc. Natl. Acad. Sci. U.S.A. 103:15582-15587. (Pubitemid 44625635)
44. Meinhardt, F., and Klassen, R., eds. 2007. Microbial Linear Plasmids, Microbiology Monographs, Vol. 7. Springer-Verlag, Berlin.
45. Molle, V., and Kremer, L. 2010. Division and cell envelope regulation by Ser/Thr phosphorylation: Mycobacterium shows the way. Mol. Microbiol. 75:1064-1077.
46. Mortier-Barrière, I., Velten, M., Dupaigne, P., Mirouze, N., Piétrement, O., McGovern, S., Fichant, G., Martin, B., Noirot, P., Le Cam, E., Polard, P., and Claverys, J.-P. 2007. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell 130:824-836. (Pubitemid 47337112)
47. Ochman, H., Gerber, A. S., and Hartl, D. L. 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120:621-623. (Pubitemid 18260496)
48. Parschat, K., Overhage, J., Strittmatter, A. W., Henne, A., Gottschalk, G., and Fetzner, S. 2007. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J. Bacteriol. 189:3855-3867. (Pubitemid 46740183)
49. Pertry, I. 2009. How the fas locus contributes to R. fascians cytokinin production: An in-depth molecular and biochemical analysis. Ph.D. thesis, Ghent University, Belgium.
50. Pertry, I., Václavíková, K., Depuydt, S., Galuszka, P., Spíchal, L., Temmerman, W., Stes, E., Schmülling, T., Kakimoto, T., Van Montagu, M., Strnad, M., Holsters, M., Tarkowski, P., and Vereecke, D. 2009. Identification of Rhodococcus fascians cytokinins and their modus operandi to reshape the plant. Proc. Natl. Acad. Sci. U.S.A. 106:929-934.
51. Pertry, I., Václavíková, K., Gemrotová, M., Spíchal, L., Galuszka, P., Depuydt, S., Temmerman, W., Stes, E., De Keyser, A., Riefler, M., Biondi, S., Novák, O., Schmülling, T., Strnad, M., Tarkowski, P., Holsters, M., and Vereecke, D. 2010. Rhodococcus fascians impacts plant development through the dynamic Fas-mediated production of a cytokinin mix. Mol. Plant-Microbe Interact. 23:1164-1174.
52. Pisabarro, A., Correia, A., and Martín, J. F. 1998. Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fascians: Genome size and linear and circular replicon composition in virulent and avirulent strains. Curr. Microbiol. 36:302-308. (Pubitemid 28182913)
53. Rajaonson, S., Vandeputte, O. M., Vereecke, D., Kiendrebeogo, M., Ralambofetra, E., Stévigny, C., Duez, P., Rabemanantsoa, C., Mol, A., Diallo, B., Baucher, M., and El Jaziri, M. 2011. Virulence quenching with a prenylated isoflavanone renders the Malagasy legume Dalbergia pervillei resistant to Rhodococcus fascians. Environ. Microbiol. 13:1236-1252.
54. Riggs, P. 2000. Expression and purification of recombinant proteins by fusion to maltose-binding protein. Mol. Biotechnol. 15:51-62.
55. Sambrook, J., and Russell, D. W., eds. 2001. Molecular Cloning, a Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, U.S.A.
56. SantaLucia, J., Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95:1460-1465.
57. Sauvage, E., Kerff, F., Terrak, M., Ayala, J. A., and Charlier, P. 2008. The penicillin-binding proteins: Structure and role in peptidoglycan biosynthesis. FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Rev. 32:234-258. (Pubitemid 351257821)
58. Schäfer, W. 1993. The role of cutinase in fungal pathogenicity. Trends Microbiol. 1:69-71. (Pubitemid 23187167)
59. Sekine, M., Tanikawa, S., Omata, S., Saito, M., Fujisawa, T., Tsukatani, N, Tajima, T., Sekigawa, T., Kosugi, H., Matsuo, Y, Nishiko, R., Imamura, K., Ito, M., Narita, H., Tago, S., Fujita, N., and Harayama, S. 2006. Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ. Microbiol. 8:334-346.
60. Simón-Mateo, C, Depuydt, S., de Oliveira Manes, C. L., Cnudde, F., Holsters, M., Goethals, K., and Vereecke, D. 2006. The phytopathogen Rhodococcus fascians breaks apical dominance and activates axillary meristems by inducing plant genes involved in hormone metabolism. Mol. Plant Pathol. 7:103-112.
61. Stange, R. R., Jeffares, D., Young, C, Scott, D. B., Eason, J. R., and Jameson, P. E. 1996. PCR amplification of the fas-1 gene for detection of virulent strains of Rhodococcus fascians. Plant Pathol. 45:407-417. (Pubitemid 126448056)
62. Stecker, C, Johann, A., Herzberg, C, Averhoff, B., and Gottschalk, G. 2003. Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J. Bacteriol. 185:5269-5274. (Pubitemid 37021988)
63. Stes, E., Vandeputte, O., El Jaziri, M., Holsters, M., and Vereecke, D. 2011. A successful bacterial coup d'état: How Rhodococcus fascians redirects plant development. Annu. Rev. Phytopathol. 49:69-86.
64. Surtees, J. A., and Funnell, B. E. 2003. Plasmid and chromosome traffic control: How ParA and ParB drive partition. Curr. Topics Dev. Biol. 56:145-180. (Pubitemid 137640965)
65. Taylor, L. A., and Rose, R. E. 1988. A correction in the nucleotide sequence of the Tn903 kanamycin resistance determinant in pUC4K. Nucleic Acids Res. 16:358.
66. Temmerman, W., Vereecke, D., Dreesen, R., Van Montagu, M., Holsters, M., and Goethals, K. 2000. Leafy gall formation is controlled by fasR, an AraC-type regulatory gene in Rhodococcus fascians. J. Bacteriol. 182:5832-5840.
67. Tomich, M., Planet, P. J., and Figurski, D. H. 2007. The tad locus: Postcards from the widespread colonization island. Nat. Rev. Microbiol. 5:363-375. (Pubitemid 46605490)
68. Vandeputte, O., Öden, S., Mol, A., Vereecke, D., Goethals, K., El Jaziri, M., and Prinsen, E. 2005. Biosynthesis of auxin by the gram-positive phytopathogen Rhodococcus fascians is controlled by compounds specific to infected plant tissues. Appl. Environ. Microbiol. 71:1169-1177. (Pubitemid 40396652)
69. van der Geize, R., and Dijkhuizen, L. 2004. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 7:255-261. (Pubitemid 38758066)
70. Van Melderen, L., and Saavedra De Bast, M. 2009. Bacterial toxin-antitoxin systems: More than selfish entities? PLoS Genet. 5:e1000437.
71. Vereecke, D., Burssens, S., Simón-Mateo, C, Inzé, D., Van Montagu, M., Goethals, K., and Jaziri, M. 2000. The Rhodococcus fascians-plant interaction: Morphological traits and biotechnological applications. Planta 210:241-251. (Pubitemid 30067888)
72. Vereecke, D., Cornelis, K., Temmerman, W., Jaziri, M., Van Montagu, M., Holsters, M., and Goethals, K. 2002. Chromosomal locus that affects the pathogenicity of Rhodococcus fascians. J. Bacteriol. 184:1112-1120. (Pubitemid 34113380)
73. Vernikos, G. S., and Parkhill, J. 2006. Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands. Bioinformatics 22:2196-2203. (Pubitemid 44390872)
74. Vivian, A., Murillo, J., and Jackson, R. W. 2001. The roles of plasmids in phytopathogenic bacteria: Mobile arsenals? Microbiology 147:763-780. (Pubitemid 32401317)
75. West, N. P., Chow, F. M. E., Randall, E. J., Wu, J., Chen, J., Ribeiro, J. M. C, and Britton, W. J. 2009. Cutinase-like protein of Mycobacterium tuberculosis: Characterization of their variable enzymatic functions and active site identification. FASEB (Fed. Am. Soc. Exp. Biol.) J. 23:1694-1704.
76. Wu, L. J., and Errington, J. 2003. RacA and the Soj-Spo0J system combine to effect polar chromosome segregation in sporulating Bacillus subtilis. Mol. Microbiol. 49:1463-1475. (Pubitemid 37153510)
77. Yeats, C, Finn, R. D., and Bateman, A. 2002. The PASTA domain: A β-lactam-binding domain. Trends Biochem. Sci. 27:438-440.
78. Zhang, W, and Shi, L. 2004. Evolution of the PPM-family protein phosphatases in Streptomyces: Duplication of catalytic domain and lateral recruitment of additional sensory domains. Microbiology 150:4189-4197. (Pubitemid 40045347)
79. Zhu, L., Zhang, Y, Teh, J.-S., Zhang, J., Connell, N., Rubin, H., and Inouye, M. 2006. Characterization of mRNA interferases from Mycobacterium tuberculosis. J. Biol. Chem. 281:18638-18643. (Pubitemid 44035523)