Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Seo, Young Su ^a   Lim, Jae Yun ^b   Park, Jungwook ^a   Kim, Sunyoung ^a   Lee, Hyun Hee ^a   Cheong, Hoon ^c   Kim, Sang Mok ^c   Moon, Jae Sun ^d   Hwang, Ingyu ^b  

^a Pusan National University   (South Korea)

^b Seoul National University   (South Korea)

^c Animal Plant and Fisheries Quarantine and Inspection Agency   (South Korea)

^d Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

B. glumae; B. plantarii; Burkholderia gladioli; Comparative genomics; Pathogen; Rice

Indexed keywords

ANIMALIA; BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA GLADIOLI; BURKHOLDERIA GLUMAE; BURKHOLDERIA PLANTARII;

BACTERIAL SECRETION SYSTEM; BACTERIAL TOXIN;

ADAPTATION; ANIMAL; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL SECRETION SYSTEM; BIOSYNTHESIS; BURKHOLDERIA; COMPARATIVE STUDY; CRISPR CAS SYSTEM; CYTOLOGY; ENVIRONMENT; GENETICS; GENOMICS; HOST RANGE; HUMAN; MICROBIOLOGY; MOLECULAR GENETICS; ORYZA; PHYSIOLOGY; QUORUM SENSING;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BACTERIAL SECRETION SYSTEMS; BACTERIAL TOXINS; BURKHOLDERIA; CRISPR-CAS SYSTEMS; ENVIRONMENT; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; HOST SPECIFICITY; HUMANS; MOLECULAR SEQUENCE DATA; ORYZA; QUORUM SENSING;

EID: 84928791884     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1558-5     Document Type: Article

References (45)

1. Compant S, Nowak J, Coenye T, Clément C, Ait Barka E. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev. 2008;32:607-26.
2. Vial L, Groleau M-C, Dekimpe V, Déziel E. Burkholderia diversity and versatility: an inventory of the extracellular products. J Microbiol Biotechnol. 2007;17:1407-29.
3. Valvano MA, Keith KE, Cardona ST. Survival and persistence of opportunistic Burkholderia species in host cells. Curr Opin Microbiol. 2005;8:99-105.
4. Ait Barka E, Nowak J, Clément C. Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans strain PsJN. Appl Environ Microbiol. 2006;72:7246-52.
5. Compant S, Reiter B, Sessitsch A, Nowak J, Clément C, Ait Barka E. Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl Environ Microbiol. 2005;71:1685-93.
6. Reis VM, Estrada-de los Santos P, Tenorio-Salgado S, Vogel J, Stoffels M, Guyon S, et al. Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. Int J Syst Evol Microbiol. 2004;54(Pt 6):2155-62.
7. Ham JH, Melanson RA, Rush MC. Burkholderia glumae: next major pathogen of rice? Mol Plant Pathol. 2011;12:329-39.
8. Chun H, Choi O, Goo E, Kim N, Kim H, Kang Y, et al. The quorum sensing-dependent gene katG of Burkholderia glumae is important for protection from visible light. J Bacteriol. 2009;191:4152-7.
9. Kim J, Kang Y, Choi O, Jeong Y, Jeong J-E, Lim JY, et al. Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae. Mol Microbiol. 2007;64:165-79.
10. Kim J, Kim J-G, Kang Y, Jang JY, Jog GJ, Lim JY, et al. Quorum sensing and the LysR-type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in Burkholderia glumae. Mol Microbiol. 2004;54:921-34.
11. Nandakumar R, Shahjahan AKM, Yuan XL, Dickstein ER, Groth DE, Clark CA, et al. Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the southern united states. Plant Dis. 2009;93:896-905.
12. Solis R, Bertani I, Degrassi G, Devescovi G, Venturi V. Involvement of quorum sensing and RpoS in rice seedling blight caused by Burkholderia plantarii. FEMS Microbiol Lett. 2006;259:106-12.
13. Lim J, Lee T-H, Nahm BH, Choi YD, Kim M, Hwang I. Complete genome sequence of Burkholderia glumae BGR1. J Bacteriol. 2009;191:3758-9.
14. Seo Y-S, Lim J, Choi B-S, Kim H, Goo E, Lee B, et al. Complete genome sequence of Burkholderia gladioli BSR3. J Bacteriol. 2011;193:3149.
15. Francis F, Kim J, Ramaraj T, Farmer A, Rush MC, Ham JH. Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands. Mol Genet Genomics. 2013;288:195-203.
16. Fory PA, Triplett L, Ballen C, Abello JF, Duitama J, Aricapa MG, et al. Comparative analysis of two emerging rice seed bacterial pathogens. Phytopathology. 2014;104:436-44.
17. Hayes CS, Aoki SK, Low DA. Bacterial contact-dependent delivery systems. Annu Rev Genet. 2010;44:71-90.
18. Thanassi DG, Bliska JB, Christie PJ. Surface organelles assembled by secretion systems of Gram-negative bacteria: diversity in structure and function. FEMS Microbiol Rev. 2012;36:1046-82.
19. Ho BT, Dong TG, Mekalanos JJ. A view to a kill: the bacterial type VI secretion system. Cell Host Microbe. 2014;15:9-21.
20. Kapitein N, Mogk A. Deadly syringes: type VI secretion system activities in pathogenicity and interbacterial competition. Curr Opin Microbiol. 2013;16:52-8.
21. Burtnick MN, Brett PJ, Harding SV, Ngugi SA, Ribot WJ, Chantratita N, et al. The cluster 1 type VI secretion system is a major virulence determinant in Burkholderia pseudomallei. Infect Immun. 2011;79:1512-25.
22. Chen J, Xie J. Role and regulation of bacterial LuxR-like regulators. J Cell Biochem. 2011;112:2694-702.
23. Fuqua WC, Winans SC, Greenberg EP. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol. 1994;176:269-75.
24. Goo E, Majerczyk CD, An JH, Chandler JR, Seo Y-S, Ham H, et al. Bacterial quorum sensing, cooperativity, and anticipation of stationary-phase stress. Proc Natl Acad Sci U S A. 2012;109:19775-80.
25. Azegami K, Nishiyama K, Watanabe Y, Suzuki T, Yoshida M. Tropolone as a root growth-inhibitor produced by a plant pathogenic Pseudomonas sp. causing seedling blight of rice. Ann Phytopathol Soc Japan. 1985;51:315-7.
26. Tsuruo T, Oh-hara T, Iida H, Tsukagoshi S, Sato Z, Matsuda I, et al. Rhizoxin, a macrocyclic lactone antibiotic, as a new antitumor agent against human and murine tumor cells and their vincristine-resistant sublines. Cancer Res. 1986;46:381-5.
27. Degrassi G, Devescovi G, Kim J, Hwang I, Venturi V. Identification, characterization and regulation of two secreted polygalacturonases of the emerging rice pathogen Burkholderia glumae. FEMS Microbiol Ecol. 2008;65:251-62.
28. Devescovi G, Bigirimana J, Degrassi G, Cabrio L, LiPuma JJ, Kim J, et al. Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of Burkholderia glumae in severe disease symptoms in rice. Appl Environ Microbiol. 2007;73:4950-8.
29. Mullen T, Markey K, Murphy P, McClean S, Callaghan M. Role of lipase in Burkholderia cepacia complex (Bcc) invasion of lung epithelial cells. Eur J Clin Microbiol Infect Dis. 2007;26:869-77.
30. Louwen R, Staals RHJ, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev. 2014;78:74-88.
31. Koonin EV, Makarova KS. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol. 2013;10:679-86.
32. Hatoum-Aslan A, Marraffini LA. Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Curr Opin Microbiol. 2014;17:82-90.
33. Gasiunas G, Sinkunas T, Siksnys V. Molecular mechanisms of CRISPR-mediated microbial immunity. Cell Mol Life Sci. 2014;71:449-65.
34. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011;9:467-77.
35. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709-12.
36. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 2010;26:335-40.
37. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19:1117-23.
38. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27:4636-41.
39. Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 1998;26:1107-15.
40. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
41. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2008;36(Database issue):D25-30.
42. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, et al. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16:944-5.
43. Liang W, Zhao Y, Chen C, Cui X, Yu J, Xiao J, et al. Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One. 2012;7, e45346.
44. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. PGAP: pan-genomes analysis pipeline. Bioinformatics. 2012;28:416-8.
45. Van Dongen S. A Cluster Algorithm for Graphs. PhD thesis, National Research Institute for Mathematics and Computer Science in the Netherlands, 2000.