Elucidation of Sigma Factor-Associated Networks in Reveals a Modular Architecture with Limited and Function-Specific Crosstalk

English version České info

Pseudomonas aeruginosa is well known for its high adaptability to a large range of environmental conditions, including those encountered within the human host. Transcription initiation represents a major regulatory target which drives versatility, and enables bacterial adaptation to challenging conditions and expression of virulence and pathogenicity. In bacteria, this process is largely orchestrated by sigma factors. Here, we performed an integrative approach, and by the combined use of three global profiling technologies uncovered the networks of 10 alternative sigma factors in the opportunistic pathogen P. aeruginosa. We demonstrate that these networks largely represent self-contained functional modules which exhibit a limited but highly specific crosstalk to build up higher-level functions. Our results do not only give extensive information on sigma factor binding sites throughout the P. aeruginosa genome, but also advance the understanding of sigma factor network architecture which provides bacteria with a framework to function adequately in their environment.

Vyšlo v časopise: Elucidation of Sigma Factor-Associated Networks in Reveals a Modular Architecture with Limited and Function-Specific Crosstalk. PLoS Pathog 11(3): e32767. doi:10.1371/journal.ppat.1004744
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004744

Souhrn

Zdroje

1. Goldberg JB (2000) Pseudomonas: global bacteria. Trends Microbiol 8: 55–57. 10755833

2. Pukatzki S, Kessin RH, Mekalanos JJ (2002) The human pathogen Pseudomonas aeruginosa utilizes conserved virulence pathways to infect the social amoeba Dictyostelium discoideum. Proc Natl Acad Sci U S A 99: 3159–3164. 11867744

3. Lyczak JB, Cannon CL, Pier GB (2000) Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist. Microbes Infect 2: 1051–1060. 10967285

4. Sadikot RT, Blackwell TS, Christman JW, Prince AS (2005) Pathogen-host interactions in Pseudomonas aeruginosa pneumonia. Am J Respir Crit Care Med 171: 1209–1223. 15695491

5. Estahbanati HK, Kashani PP, Ghanaatpisheh F (2002) Frequency of Pseudomonas aeruginosa serotypes in burn wound infections and their resistance to antibiotics. Burns 28: 340–348. 12052372

6. Oliver A, Canton R, Campo P, Baquero F, Blazquez J (2000) High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288: 1251–1254. 10818002

7. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959–964. 10984043

8. Wolfgang MC, Kulasekara BR, Liang X, Boyd D, Wu K, et al. (2003) Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 100: 8484–8489. 12815109

9. Lee DG, Urbach JM, Wu G, Liberati NT, Feinbaum RL, et al. (2006) Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol 7: R90. 17038190

10. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, et al. (2002) Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell 9: 527–539. 11931761

11. Murakami KS, Masuda S, Darst SA (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296: 1280–1284. 12016306

12. Burgess RR, Travers AA, Dunn JJ, Bautz EK (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43–46. 4882047

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

14. Potvin E, Sanschagrin F, Levesque RC (2008) Sigma factors in Pseudomonas aeruginosa. FEMS Microbiol Rev 32: 38–55. 18070067

15. Llamas MA, van der Sar A, Chu BC, Sparrius M, Vogel HJ, et al. (2009) A Novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa. PLoS Pathog 5: e1000572. doi: 10.1371/journal.ppat.1000572 19730690

16. Staron A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, et al. (2009) The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Mol Microbiol 74: 557–581. doi: 10.1111/j.1365-2958.2009.06870.x 19737356

17. Bashyam MD, Hasnain SE (2004) The extracytoplasmic function sigma factors: role in bacterial pathogenesis. Infect Genet Evol 4: 301–308. 15374527

18. Kazmierczak MJ, Wiedmann M, Boor KJ (2005) Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev 69: 527–543. 16339734

19. Blanka A, Schulz S, Eckweiler D, Franke R, Bielecka A, et al. (2013) Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity. J Bacteriol.

20. Goodman AL, Lory S (2004) Analysis of regulatory networks in Pseudomonas aeruginosa by genomewide transcriptional profiling. Curr Opin Microbiol 7: 39–44. 15036138

21. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290: 2306–2309. 11125145

22. Sala C, Grainger DC, Cole ST (2009) Dissecting regulatory networks in host-pathogen interaction using ChIP-on-chip technology. Cell Host Microbe 5: 430–437. doi: 10.1016/j.chom.2009.04.007 19454347

23. Grainger DC, Lee DJ, Busby SJ (2009) Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria. Curr Opin Microbiol 12: 531–535. doi: 10.1016/j.mib.2009.08.006 19762273

24. Rodrigue S, Brodeur J, Jacques PE, Gervais AL, Brzezinski R, et al. (2007) Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays. J Bacteriol 189: 1505–1513. 17158685

25. Rodriguez-Herva JJ, Duque E, Molina-Henares MA, Navarro-Aviles G, van Dillewijn P, et al. (2010) Physiological and transcriptomic characterization of a fliA mutant of Pseudomonas putida KT2440. Environmental Microbiology Reports 2: 373–380. doi: 10.1111/j.1758-2229.2009.00084.x 23766109

26. Slamti L, Livny J, Waldor MK (2007) Global gene expression and phenotypic analysis of a Vibrio cholerae rpoH deletion mutant. J Bacteriol 189: 351–362. 17085549

27. Zhao K, Liu M, Burgess RR (2010) Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis. Nucleic Acids Res 38: 1273–1283. doi: 10.1093/nar/gkp1123 19969540

28. Dong T, Yu R, Schellhorn H (2011) Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli. Mol Microbiol 79: 375–386. doi: 10.1111/j.1365-2958.2010.07449.x 21219458

29. Schuster M, Hawkins AC, Harwood CS, Greenberg EP (2004) The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing. Mol Microbiol 51: 973–985. 14763974

30. Newman JR, Fuqua C (1999) Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator. Gene 227: 197–203. 10023058

31. Godeke J, Heun M, Bubendorfer S, Paul K, Thormann KM (2011) Roles of two Shewanella oneidensis MR-1 extracellular endonucleases. Appl Environ Microbiol 77: 5342–5351. doi: 10.1128/AEM.00643-11 21705528

32. Choi KH, Kumar A, Schweizer HP (2006) A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J Microbiol Methods 64: 391–397. 15987659

33. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51–59. 2744487

34. Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP (1998) A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212: 77–86. 9661666

35. Overhage J, Bains M, Brazas MD, Hancock RE (2008) Swarming of Pseudomonas aeruginosa is a complex adaptation leading to increased production of virulence factors and antibiotic resistance. J Bacteriol 190: 2671–2679. doi: 10.1128/JB.01659-07 18245294

36. Choi KH, Schweizer HP (2006) mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc 1: 153–161. 17406227

37. Dotsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, et al. (2012) The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS One 7: e31092. doi: 10.1371/journal.pone.0031092 22319605

38. Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21: 936–939. doi: 10.1101/gr.111120.110 20980556

39. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106 20979621

40. Bourgon R, Gentleman R, Huber W (2010) Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A 107: 9546–9551. doi: 10.1073/pnas.0914005107 20460310

41. Shankaranarayanan P, Mendoza-Parra MA, van Gool W, Trindade LM, Gronemeyer H (2012) Single-tube linear DNA amplification for genome-wide studies using a few thousand cells. Nat Protoc 7: 328–338. doi: 10.1038/nprot.2011.447 22281868

42. Aronesty E (2011) ea-utils: "Command-line tools for processing biological sequencing data".

43. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25 19261174

44. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi: 10.1186/gb-2008-9-9-r137 18798982

45. Schmidt J (2011) Regulation of the transition between motile planktonic and sessile biofilm-associated lifestyles in Pseudomonas aeruginosa.

46. Dotsch A, Pommerenke C, Bredenbruch F, Geffers R, Haussler S (2009) Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome. BMC Genomics 10: 29. doi: 10.1186/1471-2164-10-29 19152677

47. Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, et al. (2009) Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 37: D483–488. doi: 10.1093/nar/gkn861 18978025

48. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250–255. doi: 10.1038/nature08756 20164839

49. Mao F, Dam P, Chou J, Olman V, Xu Y (2009) DOOR: a database for prokaryotic operons. Nucleic Acids Res 37: D459–463. doi: 10.1093/nar/gkn757 18988623

50. Dam P, Olman V, Harris K, Su Z, Xu Y (2007) Operon prediction using both genome-specific and general genomic information. Nucleic Acids Research 35: 288–298. 17170009

51. Brouwer RW, Kuipers OP, van Hijum SA (2008) The relative value of operon predictions. Brief Bioinform 9: 367–375. doi: 10.1093/bib/bbn019 18420711

52. Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, et al. (2012) The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature. PLoS Pathog 8: e1002945. doi: 10.1371/journal.ppat.1002945 23028334

53. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208. doi: 10.1093/nar/gkp335 19458158

54. Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017–1018. doi: 10.1093/bioinformatics/btr064 21330290

55. Winsor GL, Lo R, Ho Sui SJ, Ung KS, Huang S, et al. (2005) Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 33: D338–343. 15608211

56. Llamas MA, Mooij MJ, Sparrius M, Vandenbroucke-Grauls CM, Ratledge C, et al. (2008) Characterization of five novel Pseudomonas aeruginosa cell-surface signalling systems. Mol Microbiol 67: 458–472. 18086184

57. Beare PA, For RJ, Martin LW, Lamont IL (2003) Siderophore-mediated cell signalling in Pseudomonas aeruginosa: divergent pathways regulate virulence factor production and siderophore receptor synthesis. Mol Microbiol 47: 195–207. 12492864

58. Llamas MA, Sparrius M, Kloet R, Jimenez CR, Vandenbroucke-Grauls C, et al. (2006) The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J Bacteriol 188: 1882–1891. 16484199

59. Hershberger CD, Ye RW, Parsek MR, Xie ZD, Chakrabarty AM (1995) The algT (algU) gene of Pseudomonas aeruginosa, a key regulator involved in alginate biosynthesis, encodes an alternative sigma factor (sigma E). Proc Natl Acad Sci U S A 92: 7941–7945. 7644517

60. Schurr MJ, Yu H, Boucher JC, Hibler NS, Deretic V (1995) Multiple promoters and induction by heat shock of the gene encoding the alternative sigma factor AlgU (sigma E) which controls mucoidy in cystic fibrosis isolates of Pseudomonas aeruginosa. J Bacteriol 177: 5670–5679. 7559357

61. Yu H, Schurr MJ, Deretic V (1995) Functional equivalence of Escherichia coli sigma E and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. J Bacteriol 177: 3259–3268. 7768826

62. Wood LF, Leech AJ, Ohman DE (2006) Cell wall-inhibitory antibiotics activate the alginate biosynthesis operon in Pseudomonas aeruginosa: Roles of sigma (AlgT) and the AlgW and Prc proteases. Mol Microbiol 62: 412–426. 17020580

63. Crabbe A, Pycke B, Van Houdt R, Monsieurs P, Nickerson C, et al. (2010) Response of Pseudomonas aeruginosa PAO1 to low shear modelled microgravity involves AlgU regulation. Environ Microbiol 12: 1545–1564. doi: 10.1111/j.1462-2920.2010.02184.x 20236169

64. Starnbach MN, Lory S (1992) The fliA (rpoF) gene of Pseudomonas aeruginosa encodes an alternative sigma factor required for flagellin synthesis. Mol Microbiol 6: 459–469. 1560774

65. Arnosti DN, Chamberlin MJ (1989) Secondary sigma factor controls transcription of flagellar and chemotaxis genes in Escherichia coli. Proc Natl Acad Sci U S A 86: 830–834. 2644646

66. Cunliffe HE, Merriman TR, Lamont IL (1995) Cloning and characterization of pvdS, a gene required for pyoverdine synthesis in Pseudomonas aeruginosa: PvdS is probably an alternative sigma factor. J Bacteriol 177: 2744–2750. 7751284

67. Grossman AD, Erickson JW, Gross CA (1984) The htpR gene product of E. coli is a sigma factor for heat-shock promoters. Cell 38: 383–390. 6380765

68. Gussin GN, Ronson CW, Ausubel FM (1986) Regulation of nitrogen fixation genes. Annu Rev Genet 20: 567–591. 3545064

69. Ishimoto KS, Lory S (1989) Formation of Pilin in Pseudomonas-Aeruginosa Requires the Alternative Sigma-Factor (RpoN) of RNA-Polymerase. Proceedings of the National Academy of Sciences of the United States of America 86: 1954–1957. 2564676

70. Totten PA, Lara JC, Lory S (1990) The RpoN Gene-Product of Pseudomonas Aeruginosa Is Required for Expression of Diverse Genes, Including the Flagellin Gene. Journal of Bacteriology 172: 389–396. 2152909

71. Whiteley M, Parsek MR, Greenberg EP (2000) Regulation of quorum sensing by RpoS in Pseudomonas aeruginosa. J Bacteriol 182: 4356–4360. 10894749

72. Lange R, Hengge-Aronis R (1991) Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol 5: 49–59. 1849609

73. Martin DW, Schurr MJ, Yu H, Deretic V (1994) Analysis of promoters controlled by the putative sigma factor AlgU regulating conversion to mucoidy in Pseudomonas aeruginosa: relationship to sigma E and stress response. J Bacteriol 176: 6688–6696. 7961422

74. Xiong YQ, Vasil ML, Johnson Z, Ochsner UA, Bayer AS (2000) The oxygen- and iron-dependent sigma factor pvdS of Pseudomonas aeruginosa is an important virulence factor in experimental infective endocarditis. J Infect Dis 181: 1020–1026. 10720526

75. Deretic V, Schurr MJ, Boucher JC, Martin DW (1994) Conversion of Pseudomonas aeruginosa to mucoidy in cystic fibrosis: environmental stress and regulation of bacterial virulence by alternative sigma factors. J Bacteriol 176: 2773–2780. 8188579

76. Cho BK, Kim D, Knight EM, Zengler K, Palsson BO (2014) Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol 12: 4. doi: 10.1186/1741-7007-12-4 24461193

77. Carson M, Johnson DH, McDonald H, Brouillette C, Delucas LJ (2007) His-tag impact on structure. Acta Crystallogr D Biol Crystallogr 63: 295–301. 17327666

78. Metz B, Kersten GF, Hoogerhout P, Brugghe HF, Timmermans HA, et al. (2004) Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J Biol Chem 279: 6235–6243. 14638685

79. Vani K, Bogen SA, Sompuram SR (2006) A high throughput combinatorial library technique for identifying formalin-sensitive epitopes. J Immunol Methods 317: 80–89. 17056057

80. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103–1106. doi: 10.1126/science.1206848 22383849

81. Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, et al. (2013) Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. Nat Commun 4: 1755. doi: 10.1038/ncomms2743 23612296

82. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature.

83. Dasgupta N, Wolfgang MC, Goodman AL, Arora SK, Jyot J, et al. (2003) A four-tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa. Mol Microbiol 50: 809–824. 14617143

84. Merrick MJ (1993) In a class of its own—the RNA polymerase sigma factor sigma 54 (sigma N). Mol Microbiol 10: 903–909. 7934866

85. Hofmann N, Wurm R, Wagner R (2011) The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression. PLoS One 6: e19235. doi: 10.1371/journal.pone.0019235 21573101

86. Studholme DJ, Buck M (2000) The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiol Lett 186: 1–9. 10779705

87. Kohler T, Harayama S, Ramos JL, Timmis KN (1989) Involvement of Pseudomonas putida RpoN sigma factor in regulation of various metabolic functions. J Bacteriol 171: 4326–4333. 2666396

88. Hendrickson EL, Guevera P, Penaloza-Vazquez A, Shao J, Bender C, et al. (2000) Virulence of the phytopathogen Pseudomonas syringae pv. maculicola is rpoN dependent. Journal of Bacteriology 182: 3498–3507. 10852883

89. Hendrickson EL, Plotnikova J, Mahajan-Miklos S, Rahme LG, Ausubel FM (2001) Differential roles of the Pseudomonas aeruginosa PA14 rpoN gene in pathogenicity in plants, nematodes, insects, and mice. Journal of Bacteriology 183: 7126–7134. 11717271

90. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A 105: 3100–3105. doi: 10.1073/pnas.0711982105 18287045

91. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645. doi: 10.1101/gr.092759.109 19541911