OpaR controls a network of downstream transcription factors in Vibrio parahaemolyticus BB22OP

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Burke, Alison Kernell ^a   Guthrie, Leah T C ^a   Modise, Thero ^a   Cormier, Guy ^b   Jensen, Roderick V ^a   McCarter, Linda L ^c   Stevens, Ann M ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MESSENGER RNA; OPAR PROTEIN; UNCLASSIFIED DRUG; OPAR PROTEIN, VIBRIO PARAHAEMOLYTICUS; TRANSCRIPTION FACTOR; VIRULENCE FACTOR;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; GENE SEQUENCE; NEXT GENERATION SEQUENCING; NONHUMAN; OPAR GENE; PROTEIN EXPRESSION; PROTEIN FUNCTION; REGULON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SIGNAL TRANSDUCTION; VIBRIO PARAHAEMOLYTICUS; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; PROCEDURES; PROMOTER REGION; QUORUM SENSING; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY SEQUENCE; WESTERN BLOTTING;

VIBRIO PARAHAEMOLYTICUS;

BACTERIAL PROTEINS; BLOTTING, WESTERN; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROMOTER REGIONS, GENETIC; QUORUM SENSING; REAL-TIME POLYMERASE CHAIN REACTION; REGULATORY SEQUENCES, NUCLEIC ACID; REGULON; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TRANSCRIPTION FACTORS; VIBRIO PARAHAEMOLYTICUS; VIRULENCE FACTORS;

EID: 84930654284     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121863     Document Type: Article

References (44)

1. Daniels NA, MacKinnon L, Bishop R, Altekruse S, Ray B, Hammond RM, et al. Vibrio parahaemolyticus infections in the United States, 1973-1998. J Infect Dis. 2000; 181(5):1661-6. Epub 2000/05/15. PMID: 10823766
2. Reen FJ, Almagro-Moreno S, Ussery D, Boyd EF. The genomic code: inferring Vibrionaceae niche specialization. Nat Rev Microbiol. 2006; 4(9):697-704. Epub 2006/08/07. PMID: 16894340
3. Nair GB, Ramamurthy T, Bhattacharya SK, Dutta B, Takeda Y, Sack DA. Global dissemination of Vibrio parahaemolyticus serotype O3:K6 and its serovariants. Clin Microbiol Rev. 2007; 20(1):39-48. PMID: 17223622
4. DePaola A, Jones JL, Woods J, Burkhardt W 3rd, Calci KR, Krantz JA, et al. Bacterial and viral pathogens in live oysters: 2007 United States market survey. Appl Environ Microbiol. 2010; 76(9):2754-68. Epub 2010/02/26. doi: 10.1128/AEM.02590-09 PMID: 20190085
5. McLaughlin JB, DePaola A, Bopp CA, Martinek KA, Napolilli NP, Allison CG, et al. Outbreak of Vibrio parahaemolyticus gastroenteritis associated with Alaskan oysters. N Engl J Med. 2005; 353(14):1463-70. Epub 2005/10/06. PMID: 16207848
6. Belas R, Simon M, Silverman M. Regulation of lateral flagella gene transcription in Vibrio parahaemolyticus. J Bacteriol. 1986; 167(1):210-8. PMID: 3013835
7. McCarter LL. OpaR, a homolog of Vibrio harveyi LuxR, controls opacity of Vibrio parahaemolyticus. J Bacteriol. 1998; 180(12):3166-73. PMID: 9620967
8. Joint I, Allan Downie J, Williams P. Bacterial conversations: talking, listening and eavesdropping. An introduction. Philos Trans R Soc Lond B Biol Sci. 2007; 362(1483):1115-7. PMID: 17360281
9. Fuqua WC, Winans SC, Greenberg EP. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. J Bacteriol. 1994; 176(2):269-75. PMID: 8288518
10. Waters CM, Bassler BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol. 2005; 21:319-46. PMID: 16212498
11. von Bodman SB, Willey JM, Diggle SP. Cell-cell communication in bacteria: united we stand. J Bacteriol. 2008; 190(13):4377-91. Epub 2008/05/02. doi: 10.1128/JB.00486-08 PMID: 18456806
12. Whitehead NA, Barnard AM, Slater H, Simpson NJ, Salmond GP. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol Rev. 2001; 25(4):365-404. PMID: 11524130
13. Gode-Potratz CJ, McCarter LL. Quorum sensing and silencing in Vibrio parahaemolyticus. J Bacteriol. 2011; 193(16):4224-37. Epub 2011/06/24. doi: 10.1128/JB.00432-11 PMID: 21705592
14. Tu KC, Waters CM, Svenningsen SL, Bassler BL. A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi. Mol Microbiol. 2008; 70(4):896-907. Epub 2008/09/18. doi: 10.1111/j.1365-2958.2008.06452.x PMID: 18808382
15. Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, Bassler BL. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol Microbiol. 2008; 70(1):76-88. Epub 2008/08/04. doi: 10.1111/j.1365-2958.2008.06389.x PMID: 18681939
16. Jensen RV, Depasquale SM, Harbolick EA, Hong T, Kernell AL, Kruchko DH, et al. Complete genome sequence of prepandemic Vibrio parahaemolyticus BB22OP. Genome Announc. 2013; 1(1). Epub 2013/02/21.
17. Croucher NJ, Thomson NR. Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol. 2010; 13(5):619-24. Epub 2010/10/29. doi: 10.1016/j.mib.2010.09.009 PMID: 20888288
18. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009; 10(1):57-63. doi: 10.1038/nrg2484 PMID: 19015660
19. Ramachandran R, Burke AK, Cormier G, Jensen RV, Stevens AM. Transcriptome-based analysis of the Pantoea stewartii quorum-sensing regulon and identification of EsaR direct targets. Appl Environ Microbiol. 2014; 80(18):5790-800. Epub 2014/07/11. doi: 10.1128/AEM.01489-14 PMID: 25015891
20. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422-3. Epub 2009/03/20. doi: 10.1093/bioinformatics/btp163 PMID: 19304878
21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. PMID: 2231712
22. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:421. doi: 10.1186/1471-2105-10-421 PMID: 20003500
23. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. Epub 2009/05/18. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
24. Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, et al. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics. 2009; 10:264. doi: 10.1186/1471-2164-10-264 PMID: 19523228
25. Gode-Potratz CJ, Kustusch RJ, Breheny PJ, Weiss DS, McCarter LL. Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence. Mol Microbiol. 2011; 79(1):240-63. Epub 2010/11/16. doi: 10.1111/j.1365-2958.2010.07445.x PMID: 21166906
26. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001; 29(9):e45. PMID: 11328886
27. Zhang Y, Qiu Y, Tan Y, Guo Z, Yang R, Zhou D. Transcriptional regulation of opaR, qrr2-4 and aphA by the master quorum-sensing regulator OpaR in Vibrio parahaemolyticus. PLoS One. 2012; 7(4):e34622. Epub 2012/04/10. doi: 10.1371/journal.pone.0034622 PMID: 22506036
28. Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999; 15(7-8):563-77. PMID: 10366656
29. Livny J. Efficient annotation of bacterial genomes for small, noncoding RNAs using the integrative computational tool sRNAPredict2. Methods Mol Biol. 2007; 395:475-88. PMID: 17993693
30. Li L, Huang D, Cheung MK, Nong W, Huang Q, Kwan HS. BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Res. 2013; 41(Database issue):D233-8. Epub 2012/11/29. doi: 10.1093/nar/gks1264 PMID: 23203879
31. Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, et al. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet. 2003; 361(9359):743-9. PMID: 12620739
32. Ferreira RB, Chodur DM, Antunes LC, Trimble MJ, McCarter LL. Output targets and transcriptional regulation by a cyclic dimeric GMP-responsive circuit in the Vibrio parahaemolyticus Scr network. J Bacteriol. 2012; 194(5):914-24. Epub 2011/12/22. doi: 10.1128/JB.05807-11 PMID: 22194449
33. Guvener ZT, McCarter LL. Multiple regulators control capsular polysaccharide production in Vibrio parahaemolyticus. J Bacteriol. 2003; 185(18):5431-41. PMID: 12949095
34. Salomon D, Gonzalez H, Updegraff BL, Orth K. Vibrio parahaemolyticus type VI secretion system 1 is activated in marine conditions to target bacteria, and is differentially regulated from system 2. PLoS One. 2013; 8(4):e61086. doi: 10.1371/journal.pone.0061086 PMID: 23613791
35. Gode-Potratz CJ, Chodur DM, McCarter LL. Calcium and iron regulate swarming and type III secretion in Vibrio parahaemolyticus. J Bacteriol. 2010; 192(22):6025-38. Epub 2010/09/17. doi: 10.1128/JB.00654-10 PMID: 20851895
36. Brutinel ED, Vakulskas CA, Yahr TL. Functional domains of ExsA, the transcriptional activator of the Pseudomonas aeruginosa type III secretion system. J Bacteriol. 2009; 191(12):3811-21. Epub 2009/04/17. doi: 10.1128/JB.00002-09 PMID: 19376850
37. Park KS, Ono T, Rokuda M, Jang MH, Okada K, Iida T, et al. Functional characterization of two type III secretion systems of Vibrio parahaemolyticus. Infect Immun. 2004; 72(11):6659-65. PMID: 15501799
38. Stewart BJ, McCarter LL. Lateral flagellar gene system of Vibrio parahaemolyticus. J Bacteriol. 2003; 185(15):4508-18. PMID: 12867460
39. Jaques S, McCarter LL. Three new regulators of swarming in Vibrio parahaemolyticus. J Bacteriol. 2006; 188(7):2625-35. PMID: 16547050
40. Boles BR, McCarter LL. Vibrio parahaemolyticus scrABC, a novel operon affecting swarming and capsular polysaccharide regulation. J Bacteriol. 2002; 184(21):5946-54. PMID: 12374828
41. Enos-Berlage JL, Guvener ZT, Keenan CE, McCarter LL. Genetic determinants of biofilm development of opaque and translucent Vibrio parahaemolyticus. Mol Microbiol. 2005; 55(4):1160-82. PMID: 15686562
42. Arnqvist A, Olsen A, Pfeifer J, Russell DG, Normark S. The Crl protein activates cryptic genes for curli formation and fibronectin binding in Escherichia coli HB101. Mol Microbiol. 1992; 6(17):2443-52. PMID: 1357528
43. Busenlehner LS, Pennella MA, Giedroc DP. The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev. 2003; 27(2-3):131-43. PMID: 14638417
44. Krasteva PV, Fong JC, Shikuma NJ, Beyhan S, Navarro MV, Yildiz FH, et al. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science. 2010; 327(5967):866-8. doi: 10.1126/science.1181185 PMID: 20150502