The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Pieretti, Isabelle ^a   Royer, Monique ^a   Barbe, Valérie ^b   Carrere, Sébastien ^c   Koebnik, Ralf ^d   Cociancich, Stéphane ^a   Couloux, Arnaud ^b   Darrasse, Armelle ^e   Gouzy, Jérôme ^c   Jacques, Marie Agnès ^e   Lauber, Emmanuelle ^c   Manceau, Charles ^e   Mangenot, Sophie ^b   Poussier, Stéphane ^f   Segurens, Béatrice ^b   Szurek, Boris ^d   Verdier, Valérie ^d   Arlat, Matthieu ^g   Rott, Philippe ^a  

^a CIRAD   (France)

^b DIF   (France)

^c LABORATOIRE DES INTERACTIONS PLANTES MICROORGANISMES LIPM   (France)

^d UNIVERSITÉ DE PERPIGNAN   (France)

^e CEMAGREF   (France)

^f AGROCAMPUS OUEST   (France)

^g UNIVERSITÉ DE TOULOUSE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALBICIDIN; BACTERIAL TOXIN; UNCLASSIFIED DRUG; BACTERIAL RNA; RIBOSOME RNA;

ADAPTATION; ARTICLE; CONTROLLED STUDY; CONVERGENT EVOLUTION; GENOME ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; SYMBIONT; TOXIN SYNTHESIS; XANTHOMONADACEAE; XANTHOMONAS; XANTHOMONAS ALBILINEANS; XANTHOMONAS FASTIDIOSA; XYLEM; BACTERIAL GENOME; BIOLOGICAL MODEL; CLASSIFICATION; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

ANIMALIA; BACTERIA (MICROORGANISMS); HEXAPODA; XANTHOMONADACEAE; XANTHOMONAS; XANTHOMONAS ALBILINEANS; XYLELLA FASTIDIOSA;

EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL; XANTHOMONADACEAE; XANTHOMONAS; XYLEM;

EID: 75449104484     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-616     Document Type: Article

References (53)

1. Saddler GS, Bradbury JF. The Proteobacteria. Bergey's Manual of Systematic Bacteriology 2005, 63. New York: Springer, Brenner DJ, Krieg NR, Staley JT, Garrity GM.
2. Meyer DF, Bogdanove AJ. Genomics-driven advances in Xanthomonas biology. Plant Pathogenic Bacteria: Genomics and Molecular Biology 2009, 147-161. Norfolk: Caister Academic Press, Jackson RW.
3. Simpson AJG, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LMC, Araya JE, Bala GS, Baptista CS, et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 2000, 406:151-157. 10.1038/35018003, 10910347.
4. Nesme X, Vaneechoutte M, Orso S, Hoste B, Swings J. Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR-amplified 16S rRNA gene. Syst Appl Microbiol 1995, 18:127-135.
5. Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, et al. Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in Xanthomonas. PLoS ONE 2008, 3:e3828. 10.1371/journal.pone.0003828, 2585010, 19043590.
6. Varani AM, de Lima WC, Moreira LM, de Oliveira MC, Souza RC, Civerolo E, de Vasconcelos ATR, Sluys MV. Common genes and genomic breaks: a detailed case study of the Xylella fastidiosa genome backbone and evolutionary insights. Plant Pathogenic Bacteria: Genomics and Molecular Biology 2009, 113-133. Norfolk: Caister Academic Press, Jackson RW.
7. Rott P, Davis M. Leaf scald. A guide to sugarcane diseases 2000, 339. Montpellier: CIRAD-ISSCT, Rott P, Bailey R, Comstock J, Croft B, Saumtally A.
8. Birch RG. Xanthomonas albilineans and the antipathogenesis approach to disease control. Mol Plant Pathol 2001, 2:1-11.
9. Hashimi SM, Wall MK, Smith AB, Maxwell A, Birch RG. The phytotoxin albicidin is a novel inhibitor of DNA gyrase. Antimicrob Agents Chemother 2007, 51:181-187. 10.1128/AAC.00918-06, 1797663, 17074789.
10. Leite RP, Minsavage GV, Bonas U, Stall RE. Detection and identification of phytopathogenic Xanthomonas strains by amplification of DNA sequences related to the hrp genes of Xanthomonas campestris pv. vesicatoria. Appl Environ Microbiol 1994, 60:1068-1077. 201441, 8017904.
11. Champoiseau P, Daugrois J-H, Pieretti I, Cociancich S, Royer M, Rott P. High variation in pathogenicity of genetically closely related strains of Xanthomonas albilineans, the sugarcane leaf scald pathogen, in Guadeloupe. Phytopathol 2006, 96:1081-1091.
12. Ochiai H, Inoue Y, Takeya M, Sasaki A, Kaku H. Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Jpn Agric Res 2005, 39:275-287.
13. da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorell CB, Van Sluys MA, Almeida NF, Alves LM, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host. Nature 2002, 417:459-463. 10.1038/417459a, 12024217.
14. Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Buttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, et al. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 2005, 187:7254-7266. 10.1128/JB.187.21.7254-7266.2005, 1272972, 16237009.
15. Crossman L, Gould V, Dow JM, Vernikos G, Okazaki A, Sebaihia M, Saunders D, Arrowsmith C, Carver T, Peters N, et al. The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol 2008, 9:R74. 10.1186/gb-2008-9-4-r74, 2643945, 18419807.
16. Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, Barac T, Vangronsveld J, Lelie D. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol 2009, 75:748-757. 10.1128/AEM.02239-08, 2632133, 19060168.
17. Van Sluys MA, De Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LEA, Da Silva ACR, Moon DH, Takita MA, Lemos EGM, et al. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 2003, 185:1018-1026. 10.1128/JB.185.3.1018-1026.2003, 142809, 12533478.
18. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
19. Wang Y-D, Zhao S, Hill CW. Rhs elements comprise three subfamilies which diverged prior to acquisition by Escherichia coli. J Bacteriol 1998, 180:4102-4110. 107404, 9696756.
20. Royer M, Costet L, Vivien E, Bes M, Cousin A, Damais A, Pieretti I, Savin A, Megessier S, Viard M, et al. Albicidin pathotoxin produced by Xanthomonas albilineans is encoded by three Large PKS and NRPS genes present in a gene cluster also containing several putative modifying, regulatory, and resistance genes. Mol Plant Microbe Interact 2004, 17:414-427. 10.1094/MPMI.2004.17.4.414, 15077674.
21. Cornelis GR. The type III secretion injectisome. Nat Rev Microbiol 2006, 4:811-825. 10.1038/nrmicro1526, 17041629.
22. Boraston AB, Bolam DN, Gilbert HJ, Davies GJ. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem 2004, 382:769-781.
23. Howard MB, Ekborg N, Taylor L, Hutcheson SW, Weiner RM. Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans. Protein Sci 2004, 13:1422-1425. 10.1110/ps.03511604, 2286767, 15075401.
24. Kay S, Bonas U. How Xanthomonas type III effectors manipulate the host plant. Curr Opinion Microbiol 2009, 12:37-43.
25. Hilaire E, Young SA, Willard LH, McGee JD, Sweat T, Chittoor JM, Guikema JA, Leach JE. Vascular defense responses in rice: Peroxidase accumulation in xylem parenchyma cells and xylem wall thickening. Mol Plant Microbe Interact 2001, 14:1411-1419. 10.1094/MPMI.2001.14.12.1411, 11768536.
26. Chatterjee S, Almeida RPP, Lindow S. Living in two worlds: the plant and insect lifestyles of Xylella fastidiosa. Annu Rev Phytopathol 2008, 46:243-271. 10.1146/annurev.phyto.45.062806.094342, 18422428.
27. Triplett LR, Zhao Y, Sundin GW. Genetic differences between blight-causing Erwinia species with differing host specificities, identified by suppression subtractive hybridization. Appl Environ Microbiol 2006, 72:7359-7364. 10.1128/AEM.01159-06, 1636173, 16963554.
28. Kube M, Migdoll A, Müller I, Kuhl H, Beck A, Reinhardt R, Geider K. The genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia. Environ Microbiol 2008, 10:2211-2222. 10.1111/j.1462-2920.2008.01639.x, 18462403.
29. Moya A, Pereto J, Gil R, Latorre A. Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat Rev Genet 2008, 9:218-229. 10.1038/nrg2319, 18268509.
30. Macnab RM. Flagella and motility. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 1996, 123-145. Washington DC: ASM Press, Neidhardt FC, Curtis R, Ingraham JL, Lin ECC, Magasanik B, Resnikoff WS, Riley M, Schaechter M, Umbarger HE.
31. Salzberg S, Sommer D, Schatz M, Phillippy A, Rabinowicz P, Tsuge S, Furutani A, Ochiai H, Delcher A, Kelley D, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 2008, 9:204. 10.1186/1471-2164-9-204, 2432079, 18452608.
32. Moran NA, Mclaughlin HJ, Sorek R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 2009, 323:379-382. 10.1126/science.1167140, 19150844.
33. Van Ham RCHJ, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernández JM, Jiménez L, Postigo M, Silva FJ, et al. Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci USA 2003, 100:581-586. 10.1073/pnas.0235981100, 141039, 12522265.
34. Klasson L, Andersson SGE. Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways. Mol Biol Evol 2006, 23:1031-1039. 10.1093/molbev/msj107, 16476690.
35. Drlica K, Zhao X. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol Mol Biol Rev 1997, 61:377-392. 232616, 9293187.
36. Mizrahi V, Susan JA. DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?. Mol Microbiol 1998, 29:1331-1339. 10.1046/j.1365-2958.1998.01038.x, 9781872.
37. Boshoff HI, Reed MB, Barry CE, Mizrahi V. DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 2003, 113:183-193. 10.1016/S0092-8674(03)00270-8, 12705867.
38. Phillips I, Culebras E, Moreno F, Baquero F. Induction of the SOS response by new 4-quinolones. J Antimicrob Chemother 1987, 20:631-638. 10.1093/jac/20.5.631, 3323160.
39. Fung-Tomc J, Kolek B, Bonner DP. Ciprofloxacin-induced, low-level resistance to structurally unrelated antibiotics in Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 1993, 37:1289-1296. 187955, 8328778.
40. O'sullivan DM, Hinds J, Butcher PD, Gillespie SH, Mchugh TD. Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin. J Antimicrob Chemother 2008, 62:1199-1202. 10.1093/jac/dkn387, 2583065, 18799471.
41. Bostock JM, Huang G, Hashimi SM, Zhang L, Birch RG. A DHA14 drug efflux gene from Xanthomonas albilineans confers high-level albicidin antibiotic resistance in Escherichia coli. J Appl Microbiol 2006, 101:151-160. 10.1111/j.1365-2672.2006.02899.x, 16834602.
42. Hashimi SM, Huang G, Maxwell A, Birch RG. DNA gyrase from the albicidin producer Xanthomonas albilineans has multiple-antibiotic-resistance and unusual enzymatic properties. Antimicrob Agents Chemother 2008, 52:1382-1390. 10.1128/AAC.01551-07, 2292561, 18268084.
43. Vivien E, Pitorre D, Cociancich S, Pieretti I, Gabriel DW, Rott PC, Royer M. Heterologous Production of albicidin: a promising approach to overproducing and characterizing this potent inhibitor of DNA gyrase. Antimicrob Agents Chemother 2007, 51:1549-1552. 10.1128/AAC.01450-06, 1855474, 17220426.
44. French Collection of Plant Pathogenic Bacteria. , http://www.angers.inra.fr/cfbp/
45. Phred/Phrap/Consed software package. , http://www.phrap.com
46. Thébaut P, Servant F, Schiex T, Kahn D, Gouzy J. JOBIM Conf Proc 2000, 361-365. ENSA, LIRM. Montpellier.
47. Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 2002, 415:497-502. 10.1038/415497a, 11823852.
48. Schiex T, Gouzy J, Moisan A, De Oliveira Y. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucl Acids Res 2003, 31:3738-3741. 10.1093/nar/gkg610, 169016, 12824407.
49. Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJA, Lachaize C, et al. Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem 2003, 27:49-58. 10.1016/S1476-9271(02)00094-4, 12798039.
50. Serres MH, Riley M. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb Comp Genomics 2000, 5:205-222.
51. Complete data regarding annotation of the genome of the X. albilineans strain GPE PC73. , http://iant.toulouse.inra.fr/X.albilineans
52. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
53. PHYML. , http://atgc.lirmm.fr/phyml/