H-NS forms a superhelical protein scaffold for DNA condensation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 36, 2010, Pages 15728-15732

  Arold, Stefan T ^a   Leonard, Paul G ^b,d   Parkinson, Gary N ^c   Ladbury, John E ^a,b  

^a UNIVERSITY OF TEXAS   (United States)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF LONDON   (United Kingdom)

^d UNIVERSITY OF MEDICINE AND DENTISTRY OF NEW JERSEY   (United States)

Author keywords

Chromatin; DNA binding; Nucleoid; Supercoil; Transcriptional regulation

Indexed keywords

DNA; HISTONE LIKE NUCLEOID STRUCTURING PROTEIN; MOLECULAR SCAFFOLD; SUPERHELICAL PROTEIN SCAFFOLD; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; BIOPOLYMER; DNA BINDING PROTEIN; H NS PROTEIN, BACTERIA; H-NS PROTEIN, BACTERIA;

AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL REACTION; CHROMATIN; CRYSTALLOGRAPHY; DNA BINDING; DNA CONDENSATION; OLIGOMERIZATION; PLECTONEMA; PRIORITY JOURNAL; PROTEIN STRUCTURE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; TEMPERATURE;

ENTEROBACTERIACEAE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOPOLYMERS; DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; TEMPERATURE;

EID: 77957683898     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1006966107     Document Type: Article

References (44)

1. Hommais F, et al. (2001) Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol Microbiol 40:20-36.
2. Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G (2006) Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep 7:710-715. (Pubitemid 43986268)
3. Hulton CS, et al. (1990) Histone-like protein H1 (H-NS), DNA supercoiling, and gene expression in bacteria. Cell 63:631-642.
4. Schnetz K, Wang JC (1996) Silencing of the Escherichia coli bgl promoter: effects of template supercoiling and cell extracts on promoter activity in vitro. Nucleic Acids Res 24:2422-2428.
5. Mukerji M, Mahadevan S (1997) Characterization of the negative elements involved in silencing the bgl operon of Escherichia coli: possible roles for DNA gyrase, H-NS, and CRP-cAMP in regulation. Mol Microbiol 24:617-627.
6. Bouffartigues E, Buckle M, Badaut C, Travers A, 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. Dorman CJ (2004) H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2:391-400.
8. Badaut C, et al. (2002) The degree of oligomerization of the H-NS nucleoid structuring protein is related to specific binding to DNA. J Biol Chem 277:41657-41666.
9. Esposito D, et al. (2002) H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. J Mol Biol 324:841-850.
10. Renzoni D, et al. (2001) Structural characterization of the N-terminal oligomerization domain of the bacterial chromatin-structuring protein, H-NS. J Mol Biol 306:1127-1137.
11. Bloch V, et al. (2003) The H-NS dimerization domain defines a new fold contributing to DNA recognition. Nat Struct Biol 10:212-218.
12. Cerdan R, et al. (2003) Crystal structure of the N-terminal dimerization domain of VicH, the H-NS-like protein of Vibrio cholerae. J Mol Biol 334:179-185.
13. Shindo H, et al. (1995) Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS Lett 360:125-131.
14. Leonard PG, Ono S, Gor J, Perkins SJ, Ladbury JE (2009) Investigation of the self-association and hetero-association interactions of H-NS and StpA from Enterobacteria. Mol Microbiol 73:165-179.
15. Leonard PG, Parkinson GN, Gor J, Perkins SJ, Ladbury JE (2010) The absence of inorganic salt is required for the crystallization of the complete oligomerization domain of Salmonella typhimurium histone-like nucleoid-structuring protein. Acta Crystallogr F 66:421-425.
16. Smyth CP, et al. (2000) Oligomerization of the chromatin-structuring protein H-NS. Mol Microbiol 36:962-972.
17. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774-797. (Pubitemid 47321791)
18. Cusick ME, Belfort M (1998) Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA. Mol Microbiol 28:847-857.
19. Shindo H, et al. (1999) Identification of the DNA binding surface of H-NS protein from Escherichia coli by heteronuclear NMR spectroscopy. FEBS Lett 455:63-69.
20. Schroder O, Tippner D, Wagner R (2001) Toward the three-dimensional structure of the Escherichia coli DNA-binding protein H-NS: a CD and fluorescence study. Biochem Biophys Res Commun 282:219-227.
21. Hong SH, Wang X, Wood TK (2010) Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli. Microbial Biotechnology 3:344-356.
22. Ueguchi C, Mizuno T (1996) Purification of H-NS protein and its regulatory effect on transcription in vitro. Methods Enzymol 274:271-276.
23. Schneider R, et al. (2001) An architectural role of the Escherichia colichromatin protein FIS in organizing DNA. Nucleic Acids Res 29:5107-5114.
24. Dame RT, et al. (2005) DNA bridging: a property shared among H-NS-like proteins. J Bacteriol 187:1845-1848.
25. Dorman CJ, Hinton JC, Free A (1999) Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol 7:124-128.
26. Donato GM, Kawula TH (1999) Phenotypic analysis of random hns mutations differentiate DNA-binding activity from properties of fimA promoter inversion modulation and bacterial motility. J Bacteriol 181:941-948.
27. Mojica FJ, Higgins CF (1997) In vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant. J Bacteriol 179:3528-3533.
28. 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.
29. Rimsky S, Zuber F, Buckle M, Buc H (2001) A molecular mechanism for the repression of transcription by the H-NS protein. Mol Microbiol 42:1311-1323.
30. Prosseda G, et al. (1998) A role for H-NS in the regulation of the virF gene of Shigella and enteroinvasive Escherichia coli. Res Microbiol 149:15-25.
31. Amit R, Oppenheim AB, Stavans J (2003) Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor. Biophys J 84:2467-2473.
32. Dame RT, Wyman C, Wurm R, Wagner R, 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. (Pubitemid 34968800)
33. Wiggins PA, Dame RT, Noom MC, Wuite GJ (2009) Protein-mediated molecular bridging: a key mechanism in biopolymer organization. Biophys J 97:1997-2003.
34. Ono S, et al. (2005) H-NS is a part of a thermally controlled mechanism for bacterial gene regulation. Biochem J 391:203-213.
35. Tippner D, Afflerbach H, Bradaczek C, Wagner R (1994) Evidence for a regulatory function of the histone-like Escherichia coliprotein H-NS in ribosomal RNA synthesis. Mol Microbiol 11:589-604.
36. Falconi M, Colonna B, Prosseda G, Micheli G, Gualerzi CO (1998) Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature-dependent structural transition of DNA modulates accessibility of virF promoter to transcriptional repressor H-NS. EMBO J 17:7033-7043.
37. Duong N, et al. (2007) Thermosensing coordinates a cis-regulatory module for transcriptional activation of the intracellular virulence system in Salmonella enterica serovar Typhimurium. J Biol Chem 282:34077-34084.
38. Long F, Vagin AA, Young P, Murshudov GN (2008) BALBES: a molecular-replacement pipeline. Acta Crystallogr D 64:125-132.
39. Emsley P, Cowtan K (2004) COOT: model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
40. Winn MD, Murshudov GN, Papiz MZ (2003) Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol 374:300-321.
41. Davis IW, et al. (2007) Mol Probity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
42. Konarev PV, Petoukhov MV, Volkov VV, Svergun DI (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Applied Crystallogr 39:277-286.
43. Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: A web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38:Suppl:W540-544.
44. Suhre K, Sanejouand YH (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32:W610-W614.