Ubiquitous Promoter-Localization of Essential Virulence Regulators in

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Most transcription regulators are found only at those promoters they control. Here we show that the most prominent regulators of virulence gene expression in Francisella tularensis are found ubiquitously at promoters including those they do control and those they do not. Furthermore, we present evidence that these regulators—the RNA polymerase-associated SspA family members MglA and SspA, and the putative DNA-binding protein PigR—exert their coordinate regulatory effects only at promoters that contain a small DNA sequence element. Our findings reveal how transcription factors can associate with many promoters but only exert regulatory effects at a few. They also have implications for how SspA family members and other RNAP-associated transcription regulators might exert their effects in other pathogens.

Vyšlo v časopise: Ubiquitous Promoter-Localization of Essential Virulence Regulators in. PLoS Pathog 11(4): e32767. doi:10.1371/journal.ppat.1004793
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004793

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Zdroje

1. Sjöstedt A. Tularemia: history, epidemiology, pathogen physiology, and clinical manifestations. Ann N Y Acad Sci. 2007 Jun;1105:1–29. 17395726

2. Oyston PCF, Sjöstedt A, Titball RW. Tularaemia: bioterrorism defence renews interest in Francisella tularensis. Nat Rev Microbiol. 2004 Dec;2(12):967–78. 15550942

3. Gray CG, Cowley SC, Cheung KKM, Nano FE. The identification of five genetic loci of Francisella novicida associated with intracellular growth. FEMS Microbiology Letters. 2002 Sep 24;215(1):53–6. 12393200

4. Chong A, Celli J. The Francisella intracellular life cycle: toward molecular mechanisms of intracellular survival and proliferation. Front Microbiol. 2010;1:138. doi: 10.3389/fmicb.2010.00138 21687806

5. Barel M, Charbit A. Francisella tularensis intracellular survival: to eat or to die. Microbes and Infection. 2013 Oct 15;15(14–15):989–97. doi: 10.1016/j.micinf.2013.08.005 23999313

6. Nano FE, Zhang N, Cowley SC, Klose KE, Cheung KKM, Roberts MJ, et al. A Francisella tularensis pathogenicity island required for intramacrophage growth. J Bacteriol. 2004 Oct;186(19):6430–6. 15375123

7. Larsson P, Oyston PCF, Chain P, Chu MC, Duffield M, Fuxelius H-H, et al. The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nat Genet. 2005 Feb;37(2):153–9. 15640799

8. Nano FE, Schmerk C. The Francisella pathogenicity island. Ann N Y Acad Sci. 2007 Jun;1105:122–37. 17395722

9. Barker JR, Chong A, Wehrly TD, Yu J-J, Rodriguez SA, Liu J, et al. The Francisella tularensis pathogenicity island encodes a secretion system that is required for phagosome escape and virulence. Mol Microbiol. 2009 Dec;74(6):1459–70. 20054881

10. Russell AB, Wexler AG, Harding BN, Whitney JC, Bohn AJ, Goo YA, et al. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe. 2014 Aug 13;16(2):227–36. doi: 10.1016/j.chom.2014.07.007 25070807

11. Golovliov I, Baranov V, Krocova Z, Kovarova H, Sjöstedt A. An attenuated strain of the facultative intracellular bacterium Francisella tularensis can escape the phagosome of monocytic cells. Infect Immun. 2003 Oct;71(10):5940–50. 14500514

12. Clemens DL, Lee B-Y, Horwitz MA. Virulent and avirulent strains of Francisella tularensis prevent acidification and maturation of their phagosomes and escape into the cytoplasm in human macrophages. Infect Immun. American Society for Microbiology; 2004 Jun;72(6):3204–17. 15155622

13. Lauriano CM, Barker JR, Yoon S-S, Nano FE, Arulanandam BP, Hassett DJ, et al. MglA regulates transcription of virulence factors necessary for Francisella tularensis intraamoebae and intramacrophage survival. Proc Natl Acad Sci USA. 2004 Mar 23;101(12):4246–9. 15010524

14. Brotcke A, Weiss DS, Kim CC, Chain P, Malfatti S, Garcia E, et al. Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infect Immun. 2006 Dec;74(12):6642–55. 17000729

15. Charity JC, Costante-Hamm MM, Balon EL, Boyd DH, Rubin EJ, Dove SL. Twin RNA polymerase-associated proteins control virulence gene expression in Francisella tularensis. PLoS Pathog. 2007 Jun;3(6):e84. 17571921

16. Brotcke A, Monack DM. Identification of fevR, a novel regulator of virulence gene expression in Francisella novicida. Infect Immun. 2008 Aug;76(8):3473–80. doi: 10.1128/IAI.00430-08 18559431

17. Charity JC, Blalock LT, Costante-Hamm MM, Kasper DL, Dove SL. Small molecule control of virulence gene expression in Francisella tularensis. PLoS Pathog. 2009 Oct;5(10):e1000641. doi: 10.1371/journal.ppat.1000641 19876386

18. Rohlfing AE, Dove SL. Coordinate Control of Virulence Gene Expression in Francisella tularensis Involves Direct Interaction between Key Regulators. J Bacteriol. 2014 Oct 1;196(19):3516–26. doi: 10.1128/JB.01700-14 25070738

19. Baron GS, Nano FE. MglA and MglB are required for the intramacrophage growth of Francisella novicida. Mol Microbiol. 1998 Jul;29(1):247–59. 9701818

20. Wehrly TD, Chong A, Virtaneva K, Sturdevant DE, Child R, Edwards JA, et al. Intracellular biology and virulence determinants of Francisella tularensis revealed by transcriptional profiling inside macrophages. Cell Microbiol. 2009 Jul;11(7):1128–50. doi: 10.1111/j.1462-5822.2009.01316.x 19388904

21. Hochschild A, Dove SL. Protein-protein contacts that activate and repress prokaryotic transcription. Cell. 1998 Mar 6;92(5):597–600. 9506513

22. Browning DF, Busby SJ. The regulation of bacterial transcription initiation. Nat Rev Microbiol. 2004 Jan;2(1):57–65. 15035009

23. Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, et al. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell. 2001 Mar 23;104(6):901–12. 11290327

24. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, et al. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol. 2005 Sep;187(17):6166–74. 16109958

25. Grall N, Livny J, Waldor M, Barel M, Charbit A, Meibom KL. Pivotal role of the Francisella tularensis heat-shock sigma factor RpoH. Microbiology. 2009 Aug;155(Pt 8):2560–72. doi: 10.1099/mic.0.029058-0 19443547

26. Black DS, Irwin B, Moyed HS. Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol. 1994 Jul;176(13):4081–91. 8021189

27. Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ. Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Molecular Cell. 2005 Nov 11;20(3):357–66. 16285918

28. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28–36. 7584402

29. Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, et al. Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev. 2012 Jul 1;26(13):1498–507. doi: 10.1101/gad.192732.112 22751503

30. Sharma CM, Vogel J. Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol. 2014 Jun;19:97–105. doi: 10.1016/j.mib.2014.06.010 25024085

31. Fuller JR, Kijek TM, Taft-Benz S, Kawula TH. Environmental and intracellular regulation of Francisella tularensis ripA. BMC Microbiol. 2009;9:216. doi: 10.1186/1471-2180-9-216 19821974

32. Roberts CW, Roberts JW. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 1996 Aug 9;86(3):495–501. 8756731

33. Stallings CL, Stephanou NC, Chu L, Hochschild A, Nickels BE, Glickman MS. CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence. Cell. 2009 Jul 10;138(1):146–59. doi: 10.1016/j.cell.2009.04.041 19596241

34. Srivastava DB, Leon K, Osmundson J, Garner AL, Weiss LA, Westblade LF, et al. Structure and function of CarD, an essential mycobacterial transcription factor. Proc Natl Acad Sci USA. 2013 Jul 15;110(31):12619–24. doi: 10.1073/pnas.1308270110 23858468

35. Martin RG, Gillette WK, Martin NI, Rosner JL. Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli. Mol Microbiol. 2002 Jan;43(2):355–70. 11985714

36. Griffith KL, Shah IM, Myers TE, O'Neill MC, Wolf RE. Evidence for “pre-recruitment” as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell. Biochem Biophys Res Commun. 2002 Mar 8;291(4):979–86. 11866462

37. Griffith KL, Wolf RE. Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS. J Mol Biol. 2004 Nov 12;344(1):1–10. 15504398

38. Gourse RL, Ross W, Gaal T. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol. 2000 Aug;37(4):687–95. 10972792

39. Hansen A-M, Lehnherr H, Wang X, Mobley V, Jin DJ. Escherichia coli SspA is a transcription activator for bacteriophage P1 late genes. Mol Microbiol. 2003 Jun;48(6):1621–31. 12791143

40. Hansen A-M, Gu Y, Li M, Andrykovitch M, Waugh DS, Jin DJ, et al. Structural Basis for the Function of Stringent Starvation Protein A as a Transcription Factor. J Biol Chem. 2005 Apr 29;280(17):17380–91. 15735307

41. Bell BL, Mohapatra NP, Gunn JS. Regulation of virulence gene transcripts by the Francisella novicida orphan response regulator PmrA: role of phosphorylation and evidence of MglA/SspA interaction. Infect Immun. 2010 May;78(5):2189–98. doi: 10.1128/IAI.00021-10 20231408

42. De Reuse H, Taha MK. RegF, an SspA homologue, regulates the expression of the Neisseria gonorrhoeae pilE gene. Res Microbiol. 1997 May;148(4):289–303. 9765808

43. Badger JL, Miller VL. Expression of invasin and motility are coordinately regulated in Yersinia enterocolitica. J Bacteriol. 1998 Feb;180(4):793–800. 9473031

44. Merrell DS, Hava DL, Camilli A. Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae. Mol Microbiol. 2002 Mar;43(6):1471–91. 11952899

45. Hansen A-M, Jin DJ. SspA up-regulates gene expression of the LEE pathogenicity island by decreasing H-NS levels in enterohemorrhagic Escherichia coli. BMC Microbiol. 2012;12:231. doi: 10.1186/1471-2180-12-231 23051860

46. Yin Y, Withers TR, Wang X, Yu HD. Evidence for sigma factor competition in the regulation of alginate production by Pseudomonas aeruginosa. PLoS ONE. 2013;8(8):e72329. doi: 10.1371/journal.pone.0072329 23991093

47. Skurnik D, Roux D, Aschard H, Cattoir V, Yoder-Himes D, Lory S, et al. A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries. PLoS Pathog. 2013 Sep;9(9):e1003582. doi: 10.1371/journal.ppat.1003582 24039572

48. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene. 1989 Apr 15;77(1):51–9. 2744487

49. Maier TM, Havig A, Casey M, Nano FE, Frank DW, Zahrt TC. Construction and characterization of a highly efficient Francisella shuttle plasmid. Appl Environ Microbiol. 2004 Dec;70(12):7511–9. 15574954

50. Castang S, McManus HR, Turner KH, Dove SL. H-NS family members function coordinately in an opportunistic pathogen. Proc Natl Acad Sci USA. 2008 Dec 2;105(48):18947–52. doi: 10.1073/pnas.0808215105 19028873

51. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012 Apr;9(4):357–9.

52. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Meth. 2008 Sep;5(9):829–34.

53. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinformatics. 2013 Mar;14(2):178–92. doi: 10.1093/bib/bbs017 22517427

54. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. Oxford University Press; 2009 Aug 15;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943

55. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841–2. doi: 10.1093/bioinformatics/btq033 20110278

56. Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE. NanoRNAs prime transcription initiation in vivo. Molecular Cell. 2011 Jun 24;42(6):817–25. doi: 10.1016/j.molcel.2011.06.005 21700226

57. Dove SL, Joung JK, Hochschild A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 1997 Apr 10;386(6625):627–30. 9121589

58. Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011 Apr 1;27(7):1017–8. doi: 10.1093/bioinformatics/btr064 21330290