Investigation of Quorum Sensing-Dependent Gene Expression in Burkholderia gladioli BSR3 through RNA-seq Analyses |
Kim, Sunyoung
(Department of Microbiology, Pusan National University)
Park, Jungwook (Department of Microbiology, Pusan National University) Choi, Okhee (Division of Applied Life Science and Institute of Agriculture and Life Science, Gyeongsang National University) Kim, Jinwoo (Division of Applied Life Science and Institute of Agriculture and Life Science, Gyeongsang National University) Seo, Young-Su (Department of Microbiology, Pusan National University) |
1 | Ensign SA. 2006. Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation. Mol. Microbiol. 61: 274-276. DOI ScienceOn |
2 | Fenwick MK, Philmus B, Begley TP, Ealick SE. 2011. Toxoflavin lyase requires a novel 1-His-2-carboxylate facial triad. Biochemistry 50: 1091-1100. DOI ScienceOn |
3 | 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. DOI ScienceOn |
4 | Garg N, Manchanda G, Kumar A. 2014. Bacterial quorum sensing: circuits and applications. Antonie Van Leeuwenhoek 105: 289-305. DOI ScienceOn |
5 | 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. DOI ScienceOn |
6 | 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. DOI |
7 | 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. DOI ScienceOn |
8 | Jang MS, Goo E, An JH, Kim J, Hwang I. 2014. Quorum sensing controls flagellar morphogenesis in Burkholderia glumae. PLoS One 9: e84831. DOI |
9 | 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. DOI ScienceOn |
10 | 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. DOI ScienceOn |
11 | 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. DOI |
12 | 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. DOI ScienceOn |
13 | Lorenz MC, Fink GR. 2002. Life and death in a macrophage: role of the glyoxylate cycle in virulence. Eukaryot. Cell 1: 657-662. DOI |
14 | Marketon MM, Glenn SA, Eberhard A, Gonzalez JE. 2003. Quorum sensing controls exopolysaccharide production in Sinorhizobium meliloti. J. Bacteriol. 185: 325-331. DOI |
15 | 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. DOI ScienceOn |
16 | Miller MB, Bassler BL. 2001. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165-199. DOI ScienceOn |
17 | Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. DOI ScienceOn |
18 | Murray TS, Kazmierczak BI. 2006. FlhF is required for swimming and swarming in Pseudomonas aeruginosa. J. Bacteriol. 188: 6995-7004. DOI ScienceOn |
19 | 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. DOI ScienceOn |
20 | 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. DOI |
21 | Valvano MA, Keith KE, Cardona ST. 2005. Survival and persistence of opportunistic Burkholderia species in host cells. Curr. Opin. Microbiol. 8: 99-105. DOI ScienceOn |
22 | 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. DOI ScienceOn |
23 | Waters CM, Bassler BL. 2005. Quorum sensing: cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21: 319-346. DOI ScienceOn |
24 | 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. DOI ScienceOn |
25 | Wolfe AJ. 2005. The acetate switch. Microbiol. Mol. Biol. Rev. 69: 12-50. DOI ScienceOn |
26 | 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. DOI |
27 | 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. DOI ScienceOn |
28 | 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. DOI ScienceOn |
29 | Choudhary KS, Hudaiberdiev S, Gelencser Z, Goncalves 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. DOI ScienceOn |
30 | 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. DOI ScienceOn |
31 | 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. DOI ScienceOn |
32 | 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. DOI |
33 | Eberl L. 2006. Quorum sensing in the genus Burkholderia. Int. J. Med. Microbiol. 296: 103-110. |
34 | Engebrecht J, Silverman M. 1984. Identification of genes and gene products necessary for bacterial bioluminescence. Proc. Natl. Acad. Sci. USA 81: 4154-4158. DOI |
35 | 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. DOI ScienceOn |
36 | 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. DOI ScienceOn |
37 | 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. DOI ScienceOn |
38 | 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. DOI ScienceOn |
39 | 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. DOI ScienceOn |
40 | 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. DOI ScienceOn |
41 | 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. DOI ScienceOn |
42 | Kolter R, Inuzuka M, Helinski DR. 1978. Trans-complementationdependent replication of a low molecular weight origin fragment from plasmid R6K. Cell 15: 1199-1208. DOI ScienceOn |
43 | 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. DOI ScienceOn |
44 | Nakata PA, He C. 2010. Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae. FEMS Microbiol. Lett. 304: 177-182. DOI ScienceOn |
45 | 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. |
46 | 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. DOI ScienceOn |
47 | O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. 2014. Computational identification and analysis of orphan assemblyline polyketide synthases. J. Antibiot. 67: 89-97. DOI |
48 | 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. DOI ScienceOn |
49 | 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. DOI ScienceOn |
50 | Ridley CP, Lee HY, Khosla C. 2008. Evolution of polyketide synthases in bacteria. Proc. Natl. Acad. Sci. USA 105: 4595-4600. DOI ScienceOn |
51 | 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. DOI ScienceOn |
52 | 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. DOI |
53 | 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. DOI |
54 | 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. DOI ScienceOn |
55 | Sambrook J, Russell DW. 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. |
56 | 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. DOI ScienceOn |
57 | Severini G. 1913. Una bacteriosi dell' Ixia maculata e del Gladiolus colvilli. Annali di Botanica (Roma) 11: 413-424. |
58 | 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. DOI |
59 | Stoyanova M, Pavlina I, Moncheva P, Bogatzevska N. 2014. Biodiversity and incidence of Burkholderia species. Biotechnol. Biotechnol. Equip. 21: 306-310. |
60 | 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. DOI ScienceOn |
61 | 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. DOI ScienceOn |
62 | 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. DOI ScienceOn |
63 | Compant S, Nowak J, Coenye T, Clement C, Ait Barka E. 2008. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol. Rev. 32: 607-626. DOI ScienceOn |
64 | 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. DOI ScienceOn |
65 | 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. |
66 | Loewus FA, Murthy PPN. 2000. myo-Inositol metabolism in plants. Plant Sci. 150: 1-19. DOI ScienceOn |
67 | Quinones B, Dulla G, Lindow SE. 2005. Quorum sensing regulates exopolysaccharide production, motility, and virulence in Pseudomonas syringae. Mol. Plant Microbe Interact. 18: 682-693. DOI ScienceOn |
68 | Suntharalingam P, Cvitkovitch DG. 2005. Quorum sensing in streptococcal biofilm formation. Trends Microbiol. 13: 3-6. DOI ScienceOn |
69 | 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. |
![]() |