LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA


Autoři: Michaela J. Eickhoff aff001;  Chenyi Fei aff001;  Xiuliang Huang aff001;  Bonnie L. Bassler aff001
Působiště autorů: Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America aff001;  Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America aff002;  Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America aff003
Vyšlo v časopise: LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA. PLoS Genet 17(4): e1009336. doi:10.1371/journal.pgen.1009336
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009336

Souhrn

Quorum sensing (QS) is a process of chemical communication bacteria use to transition between individual and collective behaviors. QS depends on the production, release, and synchronous response to signaling molecules called autoinducers (AIs). The marine bacterium Vibrio harveyi monitors AIs using a signal transduction pathway that relies on five small regulatory RNAs (called Qrr1-5) that post-transcriptionally control target genes. Curiously, the small RNAs largely function redundantly making it difficult to understand the necessity for five of them. Here, we identify LuxT as a transcriptional repressor of qrr1. LuxT does not regulate qrr2-5, demonstrating that qrr genes can be independently controlled to drive unique downstream QS gene expression patterns. LuxT reinforces its control over the same genes it regulates indirectly via repression of qrr1, through a second transcriptional control mechanism. Genes dually regulated by LuxT specify public goods including an aerolysin-type pore-forming toxin. Phylogenetic analyses reveal that LuxT is conserved among Vibrionaceae and sequence comparisons predict that LuxT represses qrr1 in additional species. The present findings reveal that the QS regulatory RNAs can carry out both shared and unique functions to endow bacteria with plasticity in their output behaviors.

Klíčová slova:

Bioluminescence – DNA transcription – Gene expression – Messenger RNA – Regulator genes – Vibrio – Vibrio cholerae – Post-transcriptional gene regulation


Zdroje

1. Papenfort K, Bassler BL. Quorum sensing signal-response systems in Gram-negative bacteria. Nat Rev Microbiol. 2016 Aug 11;14(9):576–88. doi: 10.1038/nrmicro.2016.89 27510864

2. Waters CM, Bassler BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol. 2005 Nov;21(1):319–46.

3. Bassler BL, Wright M, Showalter RE, Silverman MR. Intercellular signalling in Vibrio harveyi: sequence and function of genes regulating expression of luminescence. Mol Microbiol. 1993 Aug;9(4):773–86. doi: 10.1111/j.1365-2958.1993.tb01737.x 8231809

4. Bassler BL, Wright M, Silverman MR. Multiple signalling systems controlling expression of luminescence in Vibrio harveyi: sequence and function of genes encoding a second sensory pathway. Mol Microbiol. 1994 Jul;13(2):273–86. doi: 10.1111/j.1365-2958.1994.tb00422.x 7984107

5. Henke JM, Bassler BL. Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. J Bacteriol. 2004 Jun;186(12):3794–805. doi: 10.1128/JB.186.12.3794-3805.2004 15175293

6. Lilley BN, Bassler BL. Regulation of quorum sensing in Vibrio harveyi by LuxO and Sigma-54. Mol Microbiol. 2000 May;36(4):940–54. doi: 10.1046/j.1365-2958.2000.01913.x 10844680

7. Mok KC, Wingreen NS, Bassler BL. Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression. EMBO J. 2003 Feb 17;22(4):870–81. doi: 10.1093/emboj/cdg085 12574123

8. van Kessel JC, Rutherford ST, Shao Y, Utria AF, Bassler BL. Individual and combined roles of the master regulators AphA and LuxR in control of the Vibrio harveyi quorum-sensing regulon. J Bacteriol. 2013 Feb;195(3):436–43. doi: 10.1128/JB.01998-12 23204455

9. Cao JG, Meighen EA. Purification and structural identification of an autoinducer for the luminescence system of Vibrio harveyi. J Biol Chem. 1989 Dec 25;264(36):21670–6. 2600086

10. Surette MG, Miller MB, Bassler BL. Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: a new family of genes responsible for autoinducer production. Proc Natl Acad Sci USA. 1999 Feb 16;96(4):1639–44. doi: 10.1073/pnas.96.4.1639 9990077

11. Schauder S, Shokat K, Surette MG, Bassler BL. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol Microbiol. 2001 Jul;41(2):463–76. doi: 10.1046/j.1365-2958.2001.02532.x 11489131

12. Chen X, Schauder S, Potier N, Van Dorsselaer A, Pelczer I, Bassler BL, et al. Structural identification of a bacterial quorum-sensing signal containing boron. Nature. 2002 Jan 31;415(6871):545–9. doi: 10.1038/415545a 11823863

13. Miller MB, Skorupski K, Lenz DH, Taylor RK, Bassler BL. Parallel quorum sensing systems converge to regulate virulence in Vibrio cholerae. Cell. 2002 Aug 9;110(3):303–14. doi: 10.1016/s0092-8674(02)00829-2 12176318

14. Henke JM, Bassler BL. Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J Bacteriol. 2004 Oct;186(20):6902–14. doi: 10.1128/JB.186.20.6902-6914.2004 15466044

15. Higgins DA, Pomianek ME, Kraml CM, Taylor RK, Semmelhack MF, Bassler BL. The major Vibrio cholerae autoinducer and its role in virulence factor production. Nature. 2007 Dec 6;450(7171):883–6. doi: 10.1038/nature06284 18004304

16. Ng WL, Perez LJ, Wei Y, Kraml C, Semmelhack MF, Bassler BL. Signal production and detection specificity in Vibrio CqsA/CqsS quorum-sensing systems. Mol Microbiol. 2011 Mar;79(6):1407–17. doi: 10.1111/j.1365-2958.2011.07548.x 21219472

17. Freeman JA, Bassler BL. Sequence and function of LuxU: a two-component phosphorelay protein that regulates quorum sensing in Vibrio harveyi. J Bacteriol. 1999 Feb;181(3):899–906. doi: 10.1128/JB.181.3.899-906.1999 9922254

18. Freeman JA, Bassler BL. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. Mol Microbiol. 1999 Jan;31(2):665–77. doi: 10.1046/j.1365-2958.1999.01208.x 10027982

19. Tu KC, Bassler BL. Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev. 2007 Jan 15;21(2):221–33. doi: 10.1101/gad.1502407 17234887

20. Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004 Jul 9;118(1):69–82. doi: 10.1016/j.cell.2004.06.009 15242645

21. Showalter RE, Martin MO, Silverman MR. Cloning and nucleotide sequence of luxR, a regulatory gene controlling bioluminescence in Vibrio harveyi. J Bacteriol. 1990 Jun;172(6):2946–54. doi: 10.1128/jb.172.6.2946-2954.1990 2160932

22. Swartzman E, Silverman M, Meighen EA. The luxR gene product of Vibrio harveyi is a transcriptional activator of the lux promoter. J Bacteriol. 1992 Nov;174(22):7490–3. doi: 10.1128/jb.174.22.7490-7493.1992 1385389

23. Rutherford ST, van Kessel JC, Shao Y, Bassler BL. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev. 2011 Feb 15;25(4):397–408. doi: 10.1101/gad.2015011 21325136

24. Martin M, Showalter R, Silverman M. Identification of a locus controlling expression of luminescence genes in Vibrio harveyi. J Bacteriol. 1989 May;171(5):2406–14. doi: 10.1128/jb.171.5.2406-2414.1989 2540149

25. Feng L, Rutherford ST, Papenfort K, Bagert JD, van Kessel JC, Tirrell DA, et al. A Qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics. Cell. 2015 Jan 15;160(1–2):228–40. doi: 10.1016/j.cell.2014.11.051 25579683

26. Shao Y, Bassler BL. Quorum-sensing non-coding small RNAs use unique pairing regions to differentially control mRNA targets. Mol Microbiol. 2012 Feb;83(3):599–611. doi: 10.1111/j.1365-2958.2011.07959.x 22229925

27. Freeman JA, Lilley BN, Bassler BL. A genetic analysis of the functions of LuxN: a two-component hybrid sensor kinase that regulates quorum sensing in Vibrio harveyi. Mol Microbiol. 2000 Jan;35(1):139–49. doi: 10.1046/j.1365-2958.2000.01684.x 10632884

28. Tu KC, Long T, Svenningsen SL, Wingreen NS, Bassler BL. Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. Mol Cell. 2010 Feb 26;37(4):567–79. doi: 10.1016/j.molcel.2010.01.022 20188674

29. Teng S-W, Schaffer JN, Tu KC, Mehta P, Lu W, Ong NP, et al. Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol Syst Biol. 2011 May 24;7:491. doi: 10.1038/msb.2011.30 21613980

30. Shao Y, Feng L, Rutherford ST, Papenfort K, Bassler BL. Functional determinants of the quorum-sensing non-coding RNAs and their roles in target regulation. EMBO J. 2013 Jul 31;32(15):2158–71. doi: 10.1038/emboj.2013.155 23838640

31. Lin YH, Miyamoto C, Meighen EA. Purification and characterization of a luxO promoter binding protein LuxT from Vibrio harveyi. Protein Expr Purif. 2000 Oct;20(1):87–94. doi: 10.1006/prep.2000.1285 11035955

32. Lin YH, Miyamoto C, Meighen EA. Cloning and functional studies of a luxO regulator LuxT from Vibrio harveyi. Biochim Biophys Acta. 2000 Dec 1;1494(3):226–35. doi: 10.1016/s0167-4781(00)00236-0 11121579

33. Wang Y, Tu KC, Ong NP, Bassler BL, Wingreen NS. Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit. Biophys J. 2011 Jun 22;100(12):3045–53. doi: 10.1016/j.bpj.2011.05.006 21689539

34. Chaparian RR, Olney SG, Hustmyer CM, Rowe-Magnus DA, van Kessel JC. Integration host factor and LuxR synergistically bind DNA to coactivate quorum-sensing genes in Vibrio harveyi. Mol Microbiol. 2016 Sep;101(5):823–40. doi: 10.1111/mmi.13425 27191515

35. Swartzman E, Meighen EA. Purification and characterization of a poly(dA-dT) lux-specific DNA-binding protein from Vibrio harveyi and identification as LuxR. J Biol Chem. 1993 Aug 5;268(22):16706–16. 8344950

36. Miyamoto CM, Smith EE, Swartzman E, Cao JG, Graham AF, Meighen EA. Proximal and distal sites bind LuxR independently and activate expression of the Vibrio harveyi lux operon. Mol Microbiol. 1994 Oct;14(2):255–62. doi: 10.1111/j.1365-2958.1994.tb01286.x 7830570

37. van Kessel JC, Ulrich LE, Zhulin IB, Bassler BL. Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. mBio. 2013 Jul 9;4(4):e00378–13. doi: 10.1128/mBio.00378-13 23839217

38. Jaques S, McCarter LL. Three new regulators of swarming in Vibrio parahaemolyticus. J Bacteriol. 2006 Apr;188(7):2625–35. doi: 10.1128/JB.188.7.2625-2635.2006 16547050

39. Howard SP, Buckley JT. Membrane glycoprotein receptor and hole-forming properties of a cytolytic protein toxin. Biochemistry. 1982 Mar 30;21(7):1662–7. doi: 10.1021/bi00536a029 7082638

40. Boyaci H, Shah T, Hurley A, Kokona B, Li Z, Ventocilla C, et al. Structure, regulation, and inhibition of the quorum-sensing signal integrator LuxO. PLoS Biol. 2016 May 24;14(5):e1002464. doi: 10.1371/journal.pbio.1002464 27219477

41. Roh J-B, Lee M-A, Lee H-J, Kim S-M, Cho Y, Kim Y-J, et al. Transcriptional regulatory cascade for elastase production in Vibrio vulnificus: LuxO activates luxT expression and LuxT represses smcR expression. J Biol Chem. 2006 Nov 17;281(46):34775–84. doi: 10.1074/jbc.M607844200 16971386

42. Liu H, Gu D, Cao X, Liu Q, Wang Q, Zhang Y. Characterization of a new quorum sensing regulator LuxT and its roles in the extracellular protease production, motility, and virulence in fish pathogen Vibrio alginolyticus. Arch Microbiol. 2012 Jun;194(6):439–52. doi: 10.1007/s00203-011-0774-x 22130678

43. Eickhoff MJ, Bassler BL. Vibrio fischeri siderophore production drives competitive exclusion during dual-species growth. Mol Microbiol. 2020 Aug;114(2):244–61. doi: 10.1111/mmi.14509 32259318

44. Miyashiro T, Wollenberg MS, Cao X, Oehlert D, Ruby EG. A single qrr gene is necessary and sufficient for LuxO-mediated regulation in Vibrio fischeri. Mol Microbiol. 2010 Sep;77(6):1556–67. doi: 10.1111/j.1365-2958.2010.07309.x 20662783

45. Fidopiastis PM, Miyamoto CM, Jobling MG, Meighen EA, Ruby EG. LitR, a new transcriptional activator in Vibrio fischeri, regulates luminescence and symbiotic light organ colonization. Mol Microbiol. 2002 Jul;45(1):131–43. doi: 10.1046/j.1365-2958.2002.02996.x 12100554

46. Stocker R, Seymour JR. Ecology and physics of bacterial chemotaxis in the ocean. Microbiol Mol Biol Rev. 2012 Dec;76(4):792–812. doi: 10.1128/MMBR.00029-12 23204367

47. Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359 25999513

48. Gottesman S. Trouble is coming: Signaling pathways that regulate general stress responses in bacteria. J Biol Chem. 2019 Aug 2;294(31):11685–700. doi: 10.1074/jbc.REV119.005593 31197038

49. Bruger EL, Waters CM. Bacterial quorum sensing stabilizes cooperation by optimizing growth strategies. Appl Environ Microbiol. 2016 Oct 27;82(22):6498–506. doi: 10.1128/AEM.01945-16 27565619

50. Svenningsen SL. Small RNA-based regulation of bacterial quorum sensing and biofilm formation. Microbiol Spectr. 2018 Jul;6(4). doi: 10.1128/microbiolspec.RWR-0017-2018 30003870

51. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 2011 Sep 16;43(6):880–91. doi: 10.1016/j.molcel.2011.08.022 21925377

52. Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol. 2011 Dec 1;3(12):a003798. doi: 10.1101/cshperspect.a003798 20980440

53. Beisel CL, Storz G. The base-pairing RNA Spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell. 2011 Feb 4;41(3):286–97. doi: 10.1016/j.molcel.2010.12.027 21292161

54. Shao Y, Bassler BL. Quorum regulatory small RNAs repress type VI secretion in Vibrio cholerae. Mol Microbiol. 2014 Jun;92(5):921–30. doi: 10.1111/mmi.12599 24698180

55. Ng WL, Perez L, Cong J, Semmelhack MF, Bassler BL. Broad spectrum pro-quorum-sensing molecules as inhibitors of virulence in vibrios. PLoS Pathog. 2012;8(6):e1002767. doi: 10.1371/journal.ppat.1002767 22761573

56. Milton DL. Quorum sensing in vibrios: complexity for diversification. Int J Med Microbiol. 2006 Apr;296(2–3):61–71. doi: 10.1016/j.ijmm.2006.01.044 16487746

57. Ng WL, Bassler BL. Bacterial quorum-sensing network architectures. Annu Rev Genet. 2009;43:197–222. doi: 10.1146/annurev-genet-102108-134304 19686078

58. Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, et al. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev. 2005 Jun;69(2):326–56. doi: 10.1128/MMBR.69.2.326-356.2005 15944459

59. Allen RD, Baumann P. Structure and arrangement of flagella in species of the genus Beneckea and Photobacterium fischeri. J Bacteriol. 1971 Jul;107(1):295–302. doi: 10.1128/JB.107.1.295-302.1971 4105030

60. Shinoda S, Okamoto K. Formation and function of Vibrio parahaemolyticus lateral flagella. J Bacteriol. 1977 Mar;129(3):1266–71. doi: 10.1128/JB.129.3.1266-1271.1977 845115

61. McCarter L, Hilmen M, Silverman M. Flagellar dynamometer controls swarmer cell differentiation of V. parahaemolyticus. Cell. 1988 Jul 29;54(3):345–51. doi: 10.1016/0092-8674(88)90197-3 3396074

62. Bassler BL, Greenberg EP, Stevens AM. Cross-species induction of luminescence in the quorum-sensing bacterium Vibrio harveyi. J Bacteriol. 1997 Jun;179(12):4043–5. doi: 10.1128/jb.179.12.4043-4045.1997 9190823

63. Boettcher KJ, Ruby EG. Depressed light emission by symbiotic Vibrio fischeri of the sepiolid squid Euprymna scolopes. J Bacteriol. 1990 Jul;172(7):3701–6. doi: 10.1128/jb.172.7.3701-3706.1990 2163384

64. Thelin KH, Taylor RK. Toxin-coregulated pilus, but not mannose-sensitive hemagglutinin, is required for colonization by Vibrio cholerae O1 El Tor biotype and O139 strains. Infect Immun. 1996 Jul;64(7):2853–6. doi: 10.1128/IAI.64.7.2853-2856.1996 8698524

65. McCarter LL. OpaR, a homolog of Vibrio harveyi LuxR, controls opacity of Vibrio parahaemolyticus. J Bacteriol. 1998 Jun;180(12):3166–73. doi: 10.1128/JB.180.12.3166-3173.1998 9620967

66. Greenberg EP, Hastings JW, Ulitzur S. Induction of luciferase synthesis in Beneckea harveyi by other marine bacteria. Arch Microbiol. 1979 Feb;120(2):87–91.

67. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009 May;6(5):343–5. doi: 10.1038/nmeth.1318 19363495

68. Bina XR, Wong EA, Bina TF, Bina JE. Construction of a tetracycline inducible expression vector and characterization of its use in Vibrio cholerae. Plasmid. 2014 Nov;76:87–94. doi: 10.1016/j.plasmid.2014.10.004 25451701

69. Edwards RA, Keller LH, Schifferli DM. Improved allelic exchange vectors and their use to analyze 987P fimbria gene expression. Gene. 1998 Jan 30;207(2):149–57. doi: 10.1016/s0378-1119(97)00619-7 9511756

70. Papenfort K, Silpe JE, Schramma KR, Cong J-P, Seyedsayamdost MR, Bassler BL. A Vibrio cholerae autoinducer-receptor pair that controls biofilm formation. Nat Chem Biol. 2017 May;13(5):551–7. doi: 10.1038/nchembio.2336 28319101

71. Bernheimer AW. Assay of hemolytic toxins. Methods Enzymol. 1988;165:213–7. doi: 10.1016/s0076-6879(88)65033-6 2906728

72. Bezar IF, Mashruwala AA, Boyd JM, Stock AM. Drug-like fragments inhibit agr-mediated virulence expression in Staphylococcus aureus. Sci Rep. 2019 May 1;9(1):6786. doi: 10.1038/s41598-019-42853-z 31043623

73. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic Acids Res. 2000 Jan 1;28(1):15–8. doi: 10.1093/nar/28.1.15 10592170

74. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–7. doi: 10.1016/0022-2836(81)90087-5 7265238

75. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205–17. doi: 10.1006/jmbi.2000.4042 10964570

76. Jukes TH, Cantor CR. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press; 1969. pp. 21–132.

77. Sokal RR, Michener C. A statistical method for evaluating systematic relationships. Univ Kansas, Sci Bull. 1958;38:1409–38.

78. Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097–100. doi: 10.1093/nar/18.20.6097 2172928

79. Crooks GE, Hon G, Chandonia J-M, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun;14(6):1188–90. doi: 10.1101/gr.849004 15173120


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