Gene silencing by H-NS from distal DNA site

Molecular Microbiology

Volumn 86, Issue 3, 2012, Pages 707-719

  Shin, Minsang ^a,c,d   Lagda, Arvin Cesar ^a,d   Lee, Jae Woong ^a   Bhat, Abhay ^a   Rhee, Joon Haeng ^a   Kim, Jeong Sun ^b,c   Takeyasu, Kunio ^c   Choy, Hyon E ^a  

^a Center for Host Defense against Enteropathogenic Bacteria Infection   (South Korea)

^b Chonnam National University Medical School   (South Korea)

^c Chonnam National University   (South Korea)

^d KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE LIKE NUCLEOID STRUCTURING PROTEIN; RNA POLYMERASE;

ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; ENTEROPATHOGENIC ESCHERICHIA COLI; GENE SILENCING; NONHUMAN; OLIGOMERIZATION; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; BINDING SITES; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENE SILENCING; PHOSPHOPROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84868156302     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/mmi.12012     Document Type: Article

References (60)

1. Arold, S.T., Leonard, P.G., Parkinson, G.N., and Ladbury, J.E. (2010) H-NS forms a superhelical protein scaffold for DNA condensation. Proc Natl Acad Sci USA 107: 15728-15732.
2. Azam, T.A., and Ishihama, A. (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 274: 33105-33113.
3. Beatty, C.M., Browning, D.F., Busby, S.J., and Wolfe, A.J. (2003) Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism. J Bacteriol 185: 5148-5157.
4. Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., etal. (2002) Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science 297: 1562-1566.
5. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L., and Ebright, R.H. (1994) Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78: 889-896.
6. Bouffartigues, E., Buckle, M., Badaut, C., Travers, A., and Rimsky, S. (2007) H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat Struct Mol Biol 14: 441-448.
7. Brenowitz, M., Senear, D.F., Shea, M.A., and Ackers, G.K. (1986) Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol 130: 132-181.
8. Browning, D.F., Lee, D.J., Spiro, S., and Busby, S.J. (2010) Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site. J Bacteriol 192: 3824-3828.
9. Busby, S., and Ebright, R.H. (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
10. Chen, H., Tang, H., and Ebright, R.H. (2003) Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription. Mol Cell 11: 1621-1633.
11. Choy, H., and Adhya, S. (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology. p. 1 v. (1287, 1299 p.). Washington, DC: ASM Press.
12. Choy, H.E., and Adhya, S. (1992) Control of gal transcription through DNA looping: inhibition of the initial transcribing complex. Proc Natl Acad Sci USA 89: 11264-11268.
13. Choy, H.E., and Adhya, S. (1993) RNA polymerase idling and clearance in gal promoters: use of supercoiled minicircle DNA template made in vivo. Proc Natl Acad Sci USA 90: 472-476.
14. Choy, H.E., Park, S.W., Parrack, P., and Adhya, S. (1995a) Transcription regulation by inflexibility of promoter DNA in a looped complex. Proc Natl Acad Sci USA 92: 7327-7331.
15. Choy, H.E., Park, S.W., Aki, T., Parrack, P., Fujita, N., Ishihama, A., and Adhya, S. (1995b) Repression and activation of transcription by Gal and Lac repressors: involvement of alpha subunit of RNA polymerase. EMBO J 14: 4523-4529.
16. Clarke, S.C., Haigh, R.D., Freestone, P., and Williams, P.H. (2003) Virulence of enteropathogenic Escherichia coli, a global pathogen. Clin Microbiol Rev 16: 365-378.
17. Dame, R.T., Wyman, C., Wurm, R., Wagner, R., and Goosen, N. (2002) Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J Biol Chem 277: 2146-2150.
18. Dersch, P., Schmidt, K., and Bremer, E. (1993) Synthesis of the Escherichia coli K-12 nucleoid-associated DNA-binding protein H-NS is subjected to growth-phase control and autoregulation. Mol Microbiol 8: 875-889.
19. Dorman, C.J. (2004) H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2: 391-400.
20. Dorman, C.J. (2007) H-NS, the genome sentinel. Nat Rev Microbiol 5: 157-161.
21. Dorman, C.J. (2009) Nucleoid-associated proteins and bacterial physiology. Adv Appl Microbiol 67: 47-64.
22. Ebright, R.H. (1998) RNA polymerase-DNA interaction: structures of intermediate, open, and elongation complexes. Cold Spring Harb Symp Quant Biol 63: 11-20.
23. Fang, F.C., and Rimsky, S. (2008) New insights into transcriptional regulation by H-NS. Curr Opin Microbiol 11: 113-120.
24. Gourse, R.L., Ross, W., and Gaal, T. (2000) UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37: 687-695.
25. Grigorova, I.L., Phleger, N.J., Mutalik, V.K., and Gross, C.A. (2006) Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA. Proc Natl Acad Sci USA 103: 5332-5337.
26. Haack, K.R., Robinson, C.L., Miller, K.J., Fowlkes, J.W., and Mellies, J.L. (2003) Interaction of Ler at the LEE5 (tir) operon of enteropathogenic Escherichia coli. Infect Immun 71: 384-392.
27. Haugen, S.P., Ross, W., and Gourse, R.L. (2008) Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol 6: 507-519.
28. Hochschild, A., and Ptashne, M. (1986) Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix. Cell 44: 681-687.
29. Hsu, L.M. (2002) Promoter clearance and escape in prokaryotes. Biochim Biophys Acta 1577: 191-207.
30. Igarashi, K., and Ishihama, A. (1991) Bipartite functional map of the E. coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP. Cell 65: 1015-1022.
31. Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A., and Kyogoku, Y. (1995) Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science 270: 1495-1497.
32. Lang, B., Blot, N., Bouffartigues, E., Buckle, M., Geertz, M., Gualerzi, C.O., etal. (2007) High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res 35: 6330-6337.
33. Lawson, C.L., Swigon, D., Murakami, K.S., Darst, S.A., Berman, H.M., and Ebright, R.H. (2004) Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 14: 10-20.
34. Lebbink, J.H., Georgijevic, D., Natrajan, G., Fish, A., Winterwerp, H.H., Sixma, T.K., and de Wind, N. (2006) Dual role of MutS glutamate 38 in DNA mismatch discrimination and in the authorization of repair. EMBO J 25: 409-419.
35. Levine, M.M., Bergquist, E.J., Nalin, D.R., Waterman, D.H., Hornick, R.B., Young, C.R., and Sotman, S. (1978) Escherichia coli strains that cause diarrhoea but do not produce heat-labile or heat-stable enterotoxins and are non-invasive. Lancet 1: 1119-1122.
36. Liu, Y., Chen, H., Kenney, L.J., and Yan, J. (2010) A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes. Genes Dev 24: 339-344.
37. Miele, A., and Dekker, J. (2008) Long-range chromosomal interactions and gene regulation. Mol Biosyst 4: 1046-1057.
38. Miller, J.H. (1972) Experiments in Molecular Genetics. p. xvi, 466 p. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
39. Monsalve, M., Mencia, M., Salas, M., and Rojo, F. (1996) Protein p4 represses phage phi 29 A2c promoter by interacting with the alpha subunit of Bacillus subtilis RNA polymerase. Proc Natl Acad Sci USA 93: 8913-8918.
40. Monsalve, M., Calles, B., Mencia, M., Salas, M., and Rojo, F. (1997) Transcription activation or repression by phage psi 29 protein p4 depends on the strength of the RNA polymerase-promoter interactions. Mol Cell 1: 99-107.
41. Nagarajavel, V., Madhusudan, S., Dole, S., Rahmouni, A.R., and Schnetz, K. (2007) Repression by binding of H-NS within the transcription unit. J Biol Chem 282: 23622-23630.
42. Noom, M.C., Navarre, W.W., Oshima, T., Wuite, G.J., and Dame, R.T. (2007) H-NS promotes looped domain formation in the bacterial chromosome. Curr Biol 17: R913-R914.
43. Oshima, T., Ishikawa, S., Kurokawa, K., Aiba, H., and Ogasawara, N. (2006) Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 13: 141-153.
44. Pon, C.L., Stella, S., and Gualerzi, C.O. (2005) Repression of Transcription by Curved DNA and Nucleoid Protein H-NS: A Mode of Bacterial Gene Regulation. pp. 52-65. Austin: Landes Bioscience.
45. Putnam, S.L., and Koch, A.L. (1975) Complications in the simplest cellular enzyme assay: lysis of Escherichia coli for the assay of beta-galactosidase. Anal Biochem 63: 350-360.
46. Record, M.T., Jr (1996) Escherichia coli and Salmonella: Cellular and Molecular Biology. p. 1 v. (792, 820 p.). Washington, DC: ASM Press.
47. Rimsky, S. (2004) Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol 7: 109-114.
48. Ross, W., Schneider, D.A., Paul, B.J., Mertens, A., and Gourse, R.L. (2003) An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev 17: 1293-1307.
49. Rostoks, N., Park, S., and Choy, H.E. (2000) Reiterative transcription initiation from galP2 promoter of Escherichia coli. Biochim Biophys Acta 1491: 185-195.
50. Roy, S., Garges, S., and Adhya, S. (1998) Activation and repression of transcription by differential contact: two sides of a coin. J Biol Chem 273: 14059-14062.
51. Rutherford, S.T., Villers, C.L., Lee, J.H., Ross, W., and Gourse, R.L. (2009) Allosteric control of Escherichia coli rRNA promoter complexes by DksA. Genes Dev 23: 236-248.
52. 4 as a probe for lac promoter DNA melting and mechanism in vivo. J Biol Chem 264: 8074-8081.
53. Schneider, R., Travers, A., Kutateladze, T., and Muskhelishvili, G. (1999) A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli. Mol Microbiol 34: 953-964.
54. Semsey, S., Virnik, K., and Adhya, S. (2005) A gamut of loops: meandering DNA. Trends Biochem Sci 30: 334-341.
55. Shin, M., Kang, S., Hyun, S.J., Fujita, N., Ishihama, A., Valentin-Hansen, P., and Choy, H.E. (2001) Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor. EMBO J 20: 5392-5399.
56. Shin, M., Song, M., Rhee, J.H., Hong, Y., Kim, Y.J., Seok, Y.J., etal. (2005) DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping. Genes Dev 19: 2388-2398.
57. Shindo, H., Iwaki, T., Ieda, R., Kurumizaka, H., Ueguchi, C., Mizuno, T., etal. (1995) Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS Lett 360: 125-131.
58. Simons, R.W., Houman, F., and Kleckner, N. (1987) Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53: 85-96.
59. Spurio, R., Falconi, M., Brandi, A., Pon, C.L., and Gualerzi, C.O. (1997) The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending. EMBO J 16: 1795-1805.
60. Tang, H., Severinov, K., Goldfarb, A., Fenyo, D., Chait, B., and Ebright, R.H. (1994) Location, structure, and function of the target of a transcriptional activator protein. Genes Dev 8: 3058-3067.