Investigation of quorum sensing-dependent gene expression in burkholderia gladioli bsr3 through rna-seq analyses

Journal of Microbiology and Biotechnology

Volumn 24, Issue 12, 2014, Pages 1609-1621

  Kim, Sunyoung ^a   Park, Jungwook ^a   Choi, Okhee ^b   Kim, Jinwoo ^b   Seo, Young Su ^a  

^a Pusan National University   (South Korea)

^b Gyeongsang National University   (South Korea)

Author keywords

Burkholderia glaidioli; Gene expression; Quorum sensing; RNA seq

Indexed keywords

FLAVOPROTEIN; GLYOXYLIC ACID; INOSITOL; OXALIC ACID; POLYKETIDE; TOXOFLAVIN; UNCLASSIFIED DRUG; GAMMA BUTYROLACTONE DERIVATIVE;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM MUTANT; BGR1 GENE; BIOINFORMATICS; BSR3 GENE; BURKHOLDERIA GLADIOLI; CATABOLISM; CELL MOTILITY; CONTROLLED STUDY; ENRICHMENT CULTURE; GENE; GENE CONSTRUCT; GENE CONTROL; GENE EXPRESSION ASSAY; GENE EXPRESSION SYSTEM; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENE ONTOLOGY; GENETIC DATABASE; GENOTYPE PHENOTYPE CORRELATION; INCUBATION TIME; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; QUORUM SENSING; RNA ANALYSIS; RNA SEQUENCE; TOXIN SYNTHESIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; PLANT DISEASE; RICE; SEQUENCE ANALYSIS;

ALLIUM CEPA; BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA GLADIOLI; BURKHOLDERIA GLUMAE;

ACYL-BUTYROLACTONES; BURKHOLDERIA GLADIOLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; ORYZA SATIVA; PLANT DISEASES; QUORUM SENSING; SEQUENCE ANALYSIS, RNA;

EID: 84917676223     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.1408.08064     Document Type: Article

References (69)

1. Biggins JB, Ternei MA, Brady SF. 2012. Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. J. Am. Chem. Soc. 134: 13192-13195.
2. Cangelosi GA, Ankenbauer RG, Nester EW. 1990. Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc. Natl. Acad. Sci. USA 87: 6708-6712.
3. Choudhary KS, Hudaiberdiev S, Gelencsér Z, Gonçalves Coutinho B, Venturi V, Pongor S. 2013. The organization of the quorum sensing luxI/R family genes in Burkholderia. Int. J. Mol. Sci. 14: 13727-13747.
4. Chun H, Choi O, Goo E, Kim N, Kim H, Kang Y, et al. 2009. The quorum sensing-dependent gene katG of Burkholderia glumae is important for protection from visible light. J. Bacteriol. 191: 4152-4157.
5. Compant S, Nowak J, Coenye T, Clément C, Ait Barka E. 2008. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol. Rev. 32: 607-626.
6. Correa NE, Peng F, Klose KE. 2005. Roles of the regulatory proteins FlhF and FlhG in the Vibrio cholerae flagellar transcription hierarchy. J. Bacteriol. 187: 6324-6332.
7. Devescovi G, Bigirimana J, Degrassi G, Cabrio L, LiPuma JJ, Kim J, et al. 2007. Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of Burkholderia glumae in severe disease symptoms in rice. Appl. Environ. Microbiol. 73: 4950-4958.
8. Djonovi S, Urbach JM, Drenkard E, Bush J, Feinbaum R, Ausubel JL, et al. 2013. Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants. PLoS Pathog. 9: e1003217.
9. Eberl L. 2006. Quorum sensing in the genus Burkholderia. Int. J. Med. Microbiol. 296: 103-110.
10. Engebrecht J, Silverman M. 1984. Identification of genes and gene products necessary for bacterial bioluminescence. Proc. Natl. Acad. Sci. USA 81: 4154-4158.
11. Ensign SA. 2006. Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Mol. Microbiol. 61: 274-276.
12. Fenwick MK, Philmus B, Begley TP, Ealick SE. 2011. Toxoflavin lyase requires a novel 1-His-2-carboxylate facial triad. Biochemistry 50: 1091-1100.
13. Fory PA, Triplett L, Ballen C, Abello JF, Duitama J, Aricapa MG, et al. 2014. Comparative analysis of two emerging rice seed bacterial pathogens. Phytopathology 104: 436-444.
14. Franke J, Ishida K, Hertweck C. 2012. Genomics-driven discovery of burkholderic acid, a noncanonical, cryptic polyketide from human pathogenic Burkholderia species. Angew. Chem. Int. Ed. Engl. 51: 11611-11615.
15. Garg N, Manchanda G, Kumar A. 2014. Bacterial quorum sensing: circuits and applications. Antonie Van Leeuwenhoek 105: 289-305.
16. Geserick C, Tenhaken R. 2013. UDP-sugar pyrophosphorylase is essential for arabinose and xylose recycling, and is required during vegetative and reproductive growth in Arabidopsis. Plant J. 74: 239-247.
17. Goo E, Majerczyk CD, An JH, Chandler JR, Seo Y-S, Ham H, et al. 2012. Bacterial quorum sensing, cooperativity, and anticipation of stationary-phase stress. Proc. Natl. Acad. Sci. USA 109: 19775-19780.
18. Ishida K, Lincke T, Behnken S, Hertweck C. 2010. Induced biosynthesis of cryptic polyketide metabolites in a Burkholderia thailandensis quorum sensing mutant. J. Am. Chem. Soc. 132: 13966-13968.
19. Jang MS, Goo E, An JH, Kim J, Hwang I. 2014. Quorum sensing controls flagellar morphogenesis in Burkholderia glumae. PLoS One 9: e84831.
20. Kalogeraki VS, Winans SC. 1997. Suicide plasmids containing promoterless reporter genes can simultaneously disrupt and create fusions to target genes of diverse bacteria. Gene 188: 69-75.
21. Kato T, Tanaka T, Fujita Y. 1992. Studies on bacterial seedling blight of rice [Oryza sativa], 1: classification of bacteria, obtained from diseased seedling of rice in Yamagata prefecture. Bull. Yamagata Agric. Exp. Stn. 26: 103-109.
22. Keen NT, Tamaki S, Kobayashi D, Trollinger D. 1988. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene 70: 191-197.
23. Kim J, Kang Y, Choi O, Jeong Y, Jeong J-E, Lim JY, et al. 2007. Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae. Mol. Microbiol. 64: 165-179.
24. Kim J, Kim J-G, Kang Y, Jang JY, Jog GJ, Lim JY, et al. 2004. Quorum sensing and the LysR-type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in Burkholderia glumae. Mol. Microbiol. 54: 921-934.
25. Kim S, Park J, Kim JH, Lee J, Bang B, Hwang I, Seo Y-S. 2013. RNAseq-based transcriptome analysis of Burkholderia glumae quorum sensing. Plant Pathol. J. 29: 249-259.
26. Kim S, Park J, Lee J, Shin D, Park DS, Lim JS, et al. 2014. Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses. Gene 547: 77-85.
27. Kim SM, Lee DH, Choi SH. 2012. Evidence that the Vibrio vulnificus flagellar regulator FlhF is regulated by a quorum sensing master regulator SmcR. Microbiology 158: 2017-2025.
28. Kohler PRA, Zheng JY, Schoffers E, Rossbach S. 2010. Inositol catabolism, a key pathway in Sinorhizobium meliloti for competitive host nodulation. Appl. Environ. Microbiol. 76: 7972-7980.
29. Kolter R, Inuzuka M, Helinski DR. 1978. Trans-complementationdependent replication of a low molecular weight origin fragment from plasmid R6K. Cell 15: 1199-1208.
30. Krings E, Krumbach K, Bathe B, Kelle R, Wendisch VF, Sahm H, Eggeling L. 2006. Characterization of myo-inositol utilization by Corynebacterium glutamicum: the stimulon, identification of transporters, and influence on L-lysine formation. J. Bacteriol. 188: 8054-8061.
31. LaRock CN, Yu J, Horswill AR, Parsek MR, Minion FC. 2013. Transcriptome analysis of acetyl-homoserine lactonebased quorum sensing regulation in Yersinia pestis. PLoS One 8: e62337.
32. Lim J, Lee T-H, Nahm BH, Choi YD, Kim M, Hwang I. 2009. Complete genome sequence of Burkholderia glumae BGR1. J. Bacteriol. 191: 3758-3759.
33. Loewus FA, Murthy PPN. 2000. myo-Inositol metabolism in plants. Plant Sci. 150: 1-19.
34. Lorenz MC, Fink GR. 2002. Life and death in a macrophage: role of the glyoxylate cycle in virulence. Eukaryot. Cell 1: 657-662.
35. Mahenthiralingam E, Song L, Sass A, White J, Wilmot C, Marchbank A, et al. 2011. Enacyloxins are products of an unusual hybrid modular polyketide synthase encoded by a cryptic Burkholderia ambifaria genomic island. Chem. Biol. 18: 665-677.
36. Marketon MM, Glenn SA, Eberhard A, González JE. 2003. Quorum sensing controls exopolysaccharide production in Sinorhizobium meliloti. J. Bacteriol. 185: 325-331.
37. McClean KH, Winson MK, Fish L, Taylor A, Chhabra SR, Camara M, et al. 1997. Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. Microbiology 143: 3703-3711.
38. Miller MB, Bassler BL. 2001. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165-199.
39. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628.
40. Murray TS, Kazmierczak BI. 2006. FlhF is required for swimming and swarming in Pseudomonas aeruginosa. J. Bacteriol. 188: 6995-7004.
41. Nakata PA, He C. 2010. Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae. FEMS Microbiol. Lett. 304: 177-182.
42. Nandakumar R, Rush MC, Correa F. 2007. Association of Burkholderia glumae and B. gladioli with panicle blight symptoms on rice in Panama. Plant Dis. 91: 767.
43. Nandakumar R, Shahjahan AKM, Yuan XL, Dickstein ER, Groth DE, Clark CA, et al. 2009. Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the Southern United States. Plant Dis. 93: 896-905.
44. Niehus E, Gressmann H, Ye F, Schlapbach R, Dehio M, Dehio C, et al. 2004. Genome-wide analysis of transcriptional hierarchy and feedback regulation in the flagellar system of Helicobacter pylori. Mol. Microbiol. 52: 947-961.
45. O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. 2014. Computational identification and analysis of orphan assemblyline polyketide synthases. J. Antibiot. 67: 89-97.
46. Ohtani K, Hayashi H, Shimizu T. 2002. The luxS gene is involved in cell-cell signalling for toxin production in Clostridium perfringens. Mol. Microbiol. 44: 171-179.
47. Partida-Martinez LP, Hertweck C. 2007. A gene cluster encoding rhizoxin biosynthesis in “Burkholderia rhizoxina”, the bacterial endosymbiont of the fungus Rhizopus microsporus. Chembiochem 8: 41-45.
48. Quiñones B, Dulla G, Lindow SE. 2005. Quorum sensing regulates exopolysaccharide production, motility, and virulence in Pseudomonas syringae. Mol. Plant Microbe Interact. 18: 682-693.
49. Ridley CP, Lee HY, Khosla C. 2008. Evolution of polyketide synthases in bacteria. Proc. Natl. Acad. Sci. USA 105: 4595-4600.
50. Salvetti S, Ghelardi E, Celandroni F, Ceragioli M, Giannessi F, Senesi S. 2007. FlhF, a signal recognition particle-like GTPase, is involved in the regulation of flagellar arrangement, motility behaviour and protein secretion in Bacillus cereus. Microbiology 153: 2541-2552.
51. Sambrook J, Russell DW. 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
52. Schmidt S, Blom JF, Pernthaler J, Berg G, Baldwin A, Mahenthiralingam E, Eberl L. 2009. Production of the antifungal compound pyrrolnitrin is quorum sensing-regulated in members of the Burkholderia cepacia complex. Environ. Microbiol. 11: 1422-1437.
53. Seo Y-S, Lim J, Choi B-S, Kim H, Goo E, Lee B, et al. 2011. Complete genome sequence of Burkholderia gladioli BSR3. J. Bacteriol. 193: 3149.
54. Severini G. 1913. Una bacteriosi dell' Ixia maculata e del Gladiolus colvilli. Annali di Botanica (Roma) 11: 413-424.
55. Simon R, Priefer U, Pühler A. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Bio/Technology 1: 784-791.
56. Stoyanova M, Pavlina I, Moncheva P, Bogatzevska N. 2014. Biodiversity and incidence of Burkholderia species. Biotechnol. Biotechnol. Equip. 21: 306-310.
57. Straight PD, Fischbach MA, Walsh CT, Rudner DZ, Kolter R. 2007. A singular enzymatic megacomplex from Bacillus subtilis. Proc. Natl. Acad. Sci. USA 104: 305-310.
58. Suntharalingam P, Cvitkovitch DG. 2005. Quorum sensing in streptococcal biofilm formation. Trends Microbiol. 13: 3-6.
59. Suzuki F, Sawada H, Azegami K, Tsuchiya K. 2004. Molecular characterization of the tox operon involved in toxoflavin biosynthesis of Burkholderia glumae. J. Gen. Plant Pathol. 70: 97-107.
60. Ura H, Furuya N, Iiyama K, Hidaka M, Tsuchiya K, Matsuyama N. 2006. Burkholderia gladioli associated with symptoms of bacterial grain rot and leaf-sheath browning of rice plants. J. Gen. Plant Pathol. 72: 98-103.
61. Valvano MA, Keith KE, Cardona ST. 2005. Survival and persistence of opportunistic Burkholderia species in host cells. Curr. Opin. Microbiol. 8: 99-105.
62. Wang L, Feng Z, Wang X, Wang X, Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136-138.
63. Waters CM, Bassler BL. 2005. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21: 319-346.
64. Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, Brinkman FSL. 2008. The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. Bioinformatics 24: 2803-2804.
65. Wolfe AJ. 2005. The acetate switch. Microbiol. Mol. Biol. Rev. 69: 12-50.
66. Wrobel AL, Watkins JE, Steinegger DH. 1992. Pathogenicity of Pseudomonas gladioli pv. gladioli on rhizomatous iris and its possible role in iris scorch. HortScience (USA) 27: 373-373.
67. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, et al. 1992. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol. Immunol. 36: 1251-1275.
68. Yoshida KI, Aoyama D, Ishio I, Shibayama T, Fujita Y. 1997. Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis. J. Bacteriol. 179: 4591-4598.
69. Young JM, Dye DW, Bradbury JF, Panagopoulos CG, Robbs CF. 1978. A proposed nomenclature and classification for plant pathogenic bacteria. NZ. J. Agric. Res. 21: 153-177.