Nucleoid-associated proteins: Structural properties

Bacterial Chromatin

Volumn 9789048134731, Issue , 2010, Pages 149-173

  Pul, Ümit ^a   Wagner, Rolf ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Bacterial nucleoid; Crystal structure; DNA topology; Protein DNA interaction; Transcription factor

Indexed keywords

EID: 84919663637     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-90-481-3473-1_8     Document Type: Chapter

References (118)

1. Aeling KA, Opel ML, Steffen NR, Tretyachenko-Ladokhina V, Hatfield GW, Lathrop RH, Senear DF (2006) Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy. J Biol Chem 281:39236-39248
2. Afflerbach H, Schröder O, Wagner R (1999) Conformational changes of the upstream DNA mediated by H-NS and FIS regulate E. coli rrnB P1 promoter activity. J Mol Biol 286:339-353
3. Almirón M, Link AJ, Furlong D, Kolter R (1992) A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev 6:2646-2654
4. Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW (2000) Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J Biol Chem 275:29672-29684
5. Badaut C, Williams R, Arlusion V, Bouffartigues E, Robert B, Buc H, Rimsky S (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
6. Beloin C, Jeusset J, Revet B, Mirambeau G, Le Hegarat F, Le Cam E (2003) Contribution of DNA conformation and topology in right-handed DNA wrapping by the Bacillus subtilis LrpC protein. J Biol Chem 278:5333-5342
7. Bertin P, Benhabiles N, Krin E, Laurent-Winter C, Tendeng C, Turlin E, Thomas A, Danchin A, Brasseur R (1999) The structural and functional organization of H-NS-like proteins is evolutionarily conserved in Gram-negative bacteria. Mol Microbiol 31:319-329
8. Bewley CA, Gronenborn AM, Clore GM (1998) Minor groove-binding architectural proteins: structure, function, and DNA recognition. Annu Rev Biophys Biomol Struct 27:105-131
9. Bloch V, Yang Y, Margeat E, Chavanieu A, Auge MT, Robert B, Arold S, Rimsky S, Kochoyan M (2003) The H-NS dimerization domain defines a new fold contributing to DNA recognition. Nat Struct Biol 10:212-218
10. Bokal AJ, Ross W, Gaal T, Johnson RC, Gourse RL (1997) Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter. EMBO J 16:154-162
11. 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
12. Brandi A, Spurio R, Gualerzi CO, Pon CL (1999) Massive presence of the Escherichia coli 'major cold-shock protein' CspA under non-stress conditions. EMBO J 18:1653-1659
13. Calvo JM, Matthews RG (1994) The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 58:466-490
14. Ceci P, Ilari A, Falvo E, Chiancone E (2003) The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties. J Biol Chem 278:20319-20326
15. Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E (2004) DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res 32:5935-5944
16. Ceschini S, Lupidi G, Coletta M, Pon CL, Fioretti E, Angeletti M (2000) Multimeric self-assembly equilibria involving the histone-like protein H-NS. A thermodynamic study. J Biol Chem 275:729-734
17. Chen S, Calvo JM (2002) Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers. J Mol Biol 318:1031-1042
18. Chen S, Rosner MH, Calvo JM (2001) Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli. J Mol Biol 312:625-635
19. Chen S, Iannolo M, Calvo JM (2005) Cooperative binding of the leucine-responsive regulatory protein (Lrp) to DNA. J Mol Biol 345:251-264
20. Cheng YS, Yang WZ, Johnson RC, Yuan HS (2000) Structural analysis of the transcriptional activation region on Fis: crystal structures of six Fis mutants with different activation properties. J Mol Biol 302:1139-1151
21. Cho BK, Knight EM, Barrett CL, Palsson BO (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18:900-910
22. Chodavarapu S, Gomez R, Vicente M, Kaguni JM (2008) Escherichia coli Dps interacts with DnaA protein to impede initiation: a model of adaptive mutation. Mol Microbiol 67:1331-1346
23. Choi SH, Baumler DJ, Kaspar CW (2000) Contribution of dps to acid stress tolerance and oxidative stress tolerance in Escherichia coli O157:H7. Appl Environ Microbiol 66:3911-3916
24. Claret L, Rouvière-Yaniv J (1997) Variation in HU composition during growth of Escherichia coli: heterodimer is required for long term survival. J Mol Biol 273:93-104
25. Claret L, Rouvière-Yaniv J (1996) Regulation of HUa and HUb by CRP and FIS in Escherichia coli. J Mol Biol 263:126-139
26. Colland F, Barth M, Hengge-Aronis R, Kolb A (2000) Sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and Lrp transcription factors. EMBO J 19:3028-3037
27. Cui Y, Wang Q, Stormo GD, Calvo JM (1995) A consensus sequence for binding of Lrp to DNA. J Bacteriol 177:4872-4880
28. Dame RT, Goosen N (2002) HU: promoting or counteracting DNA compaction? FEBS Lett 529:151
29. Dame RT, Wyman C, Goosen N (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28:3504-3510
30. 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 rrnB P1. J Biol Chem 277:2146-2150
31. Dame RT, Luijsterburg MS, Krin E, Bertin PN, Wagner R, Wuite GJ (2005) DNA Bridging: a property shared among H-NS-like proteins. J Bacteriol 187:1845-1848
32. Dame RT, Noom MC, Wuite GJ (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444:387-390
33. de los Rios S, Perona JJ (2007) Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly. J Mol Biol 366:1589-1602
34. Donato GM, Kawula TH (1998) Enhanced binding of altered H-NS protein to flagellar rotor protein FliG causes increased flagellar rotational speed and hypermotility in Escherichia coli. J Biol Chem 273:24030-24036
35. Dorman CJ (2004) H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2:391-400
36. Dorman CJ (2007) H-NS, the genome sentinel. Nat Rev Microbiol 5:157-161
37. 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
38. Esposito D, Gerard GF (2003) The Escherichia coli Fis protein stimulates bacteriophage lambda integrative recombination in vitro. J Bacteriol 185:3076-3080
39. Esposito D, Petrovic A, Harris R, Ono S, Eccleston JF, Mbabaali A, Haq I, Higgins CF, Hinton JC, Driscoll PC, Ladbury JE (2002) H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. J Mol Biol 324:841-850
40. Ettema TJ, Brinkman AB, Tani TH, Rafferty JB, van der Oost J (2002) A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes. J Biol Chem 277:37464-37468
41. Falconi M, Brandi A, La Teana A, Gualerzi CO, Pon CL (1996) Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression. Mol Microbiol 19:965-975
42. 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
43. Fang FC, Rimsky S (2008) New insights into transcriptional regulation by H-NS. Curr Opin Microbiol 11:113-120
44. Feldman-Cohen LS, Shao Y, Meinhold D, Miller C, Colon W, Osuna R (2006) Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences. J Bacteriol 188:2081-2095
45. Ferrario M, Ernsting BR, Borst DW, Wiese DE, Blumenthal RM, Matthews RG (1995) The leucineresponsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF. J Bacteriol 177:103-113
46. Frenkiel-Krispin D, Ben-Avraham I, Englander J, Shimoni E, Wolf SG, Minsky A (2004) Nucleoid restructuring in stationary-state bacteria. Mol Microbiol 51:395-405
47. Friedberg D, Midkiff M, Calvo JM (2001) Global versus local regulatory roles for Lrp-related proteins: Haemophilus influenzae as a case study. J Bacteriol 183:4004-4011
48. Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36(Database issue):D120-4
49. Grainger DC, Hurd D, Goldberg MD, Busby SJ (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 34:4642-4652
50. Grainger DC, Goldberg MD, Lee DJ, Busby SJ (2008) Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol Microbiol 68:1366-1377
51. Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM (1998) The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5:294-303
52. Hales LM, Gumport RI, Gardner JF (1994) Determining the DNA sequence elements required for binding integration host factor to two different target sites. J Bacteriol 176:2999-3006
53. Haykinson MJ, Johnson RC (1993) DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J 12:2503-2512
54. Hillebrand A, Wurm R, Menzel A, Wagner R (2005) The seven E. coli ribosomal RNA operon upstream regulatory regions differ in structure and transcription factor binding efficiencies. Biol Chem 386:523-534
55. Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SE, Newburn VH, Gourse RL (2001) Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J Bacteriol 183:6305-6314
56. Kajitani M, Ishihama A (1991) Identification and sequence determination of the host factor gene for bacteriophage Q beta. Nucleic Acids Res 19:1063-1066
57. Koh J, Saecker RM, Record MT Jr (2008) DNA binding mode transitions of Escherichia coli HU (alphabeta): evidence for formation of a bent DNA - protein complex on intact, linear duplex DNA. J Mol Biol 383:324-346
58. Kostrewa D, Granzin J, Koch C, Choe HW (1991) Three-dimensional structure of the E. coli DNA-binding protein Fis. Nature 349:178-180
59. Kostrewa D, Granzin J, Stock D, Choe H-W, Labahn J, Saenger W (1992) Crystal structure of the factor for inversion stimulation FIS at 2 Å resolution. J Mol Biol 226:209-226
60. Landgraf JR, Wu J, Calvo JM (1996) Effects of nutrition and growth rate on Lrp levels in Escherichia coli. J Bacteriol 178:6930-6936
61. Lang B, Blot N, Bouffartigues E, Buckle M, Geertz M, Gualerzi CO, Mavathur R, Muskhelishvili G, Pon CL, Rimsky S, Stella S, Babu MM, Travers A (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
62. Leonard PM, Smits SH, Sedelnikova SE, Brinkman AB, de Vos WM, van der Oost J, Rice DW, Rafferty JB (2001) Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J 20:990-997
63. Liu Q, Richardson CC (1993) Gene 5.5 protein of bacteriophage T7 inhibits the nucleoid protein H-NS of Escherichia coli. Proc Natl Acad Sci USA 90:1761-1765
64. Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JC (2006) H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog 2:e81
65. Luijsterburg MS, Noom MC, Wuite GJ, Dame RT (2006) The architectural role of nucleoidassociated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol 156:262-272
66. Luijsterburg MS, White MF, van Driel R, Dame RT (2008) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43:393-418
67. Martinez A, Kolter R (1997) Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J Bacteriol 179:5188-5194
68. McFarland KA, Dorman CJ (2008) Autoregulated expression of the gene coding for the leucineresponsive protein, Lrp, a global regulator in Salmonella enterica serovar Typhimurium. Microbiology 154:2008-2016
69. Müller CM, Aberg A, Straseviciene J, Emody L, Uhlin BE, Balsalobre C (2009) Type 1 fimbriae, a colonization factor of uropathogenic Escherichia coli, are controlled by the metabolic sensor CRP-cAMP. PLoS Pathog 5:e1000303
70. Muskhelishvili G, Buckle M, Heumann H, Kahmann R, Travers AA (1997) FIS activates sequential steps during transcription initiation at a stable RNA promoter. EMBO J 12:3655-3665
71. Nair S, Finkel SE (2004) Dps protects cells against multiple stresses during stationary phase. J Bacteriol 186:4192-4198
72. Navarre WW, McClelland M, Libby SJ, Fang FC (2007) Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 21:1456-1471
73. Nieto JM, Madrid C, Miquelay E, Parra JL, Rodriguez S, Juarez A (2002) Evidence for direct protein-protein interaction between members of the enterobacterial Hha/YmoA and H-NS families of proteins. J Bacteriol 184:629-635
74. Nilsson L, Vanet A, Vijgenboom E, Bosch L (1990) The role of Fis in trans activation of stable RNA operons of E. coli. EMBO J 9:727-734
75. Nilsson L, Verbeek H, Vijgenboom E, van Drunen C, Vanet A, Bosch L (1992) Fis-dependent trans-activation of stable RNA operons of Escherichia coli under various growth conditions. J Bacteriol 174:921-929
76. Nou X, Braaten B, Kaltenbach L, Low DA (1995) Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli. EMBO J 14:5785-5797
77. Pan CQ, Feng JA, Finkel SE, Landgraf R, Sigman D, Johnson RC (1994) Structure of the Escherichia coli Fis-DNA complex probed by protein conjugated with 1, 10-phenanthroline copper (I) complex. Proc Natl Acad Sci USA 91:1721-1725
78. Pan CQ, Finkel SE, Cramton SE, Feng J-A, Sigman DS, Johnson RC (1996) Variable structures of Fis-DNA complexes determined by flanking DNA - protein contacts. J Mol Biol 264:675-695
79. Peterson SN, Dahlquist FW, Reich NO (2007) The role of high affinity non-specific DNA binding by Lrp in transcriptional regulation and DNA organization. J Mol Biol 369:1307-1317
80. Platko J V, Calvo JM (1993) Mutations affecting the ability of Escherichia coli Lrp to bind DNA, activate transcription, or respond to leucine. J Bacteriol 175:1110-1117
81. Pul Ü, Wagner R (2007) DNA-binding proteins: nucleoid associated proteins in microorganisms. BioSpektrum 13:495-497
82. Pul Ü, Wurm R, Lux B, Meltzer M, Menzel A, Wagner R (2005) LRP and H-NS - cooperative partners for transcription regulation at E. coli rRNA promoters. Mol Microbiol 58:864-876
83. Pul Ü, Wurm R, Wagner R (2007) The role of LRP and H-NS in transcription regulation: involvement of synergism, allostery and macromolecular crowding. J Mol Biol 366:900-915
84. Pul Ü, Lux B, Wurm R, Wagner R (2008) Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 - a phasing analysis. Microbiology 154:2546-2558
85. Renzoni D, Esposito D, Pfuhl M, Hinton JC, Higgins CF, Driscoll PC, Ladbury JE (2001) Structural characterization of the N-terminal oligomerization domain of the bacterial chromatin-structuring protein, H-NS. J Mol Biol 306:1127-1137
86. Rice PA (1997) Making DNA do a U-turn: IHF and related proteins. Curr Opin Struct Biol 7:86-93
87. Rice PA, Yang S-W, Mizuuchi K, Nash H (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 27:1295-1306
88. 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
89. Schneider R, Lurz R, Luder G, Tolksdorf C, Travers A, Muskhelishvili G (2001) An architectural role of the Escherichia coli chromatin protein Fis in organising DNA. Nucleic Acids Res 29:5107-5114
90. Schröder O, Wagner R (2000) The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription by trapping RNA polymerase in the initiation complex. J Mol Biol 298:737-748
91. Schröder O, Wagner R (2002) The bacterial regulatory protein H-NS - a versatile modulator of nucleic acid structures. Biol Chem 383:945-960
92. Schröder O, Tippner D, Wagner R (2001) Towards the three-dimensional structure of the E. coli DNA-binding protein H-NS: a CD- and fluorescence study. Biochem Biophys Res Commun 282:219-227
93. Semsey S, Geanacopoulos M, Lewis DE, Adhya S (2002) Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J 21:4349-4356
94. Sette M, Spurio R, Trotta E, Brandizi C, Brandi A, Pon CL, Barbato G, Boelens R, Gualerzi CO (2009) Sequence-specific recognition of DNA by the C-terminal domain of Escherichia coli nucleoid-associated protein H-NS. J Biol Chem 284:30453-30462
95. Shao Y, Feldman-Cohen LS, Osuna R (2008a) Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site. J Mol Biol 380:327-339
96. Shao Y, Feldman-Cohen LS, Osuna R (2008b) Functional characterization of the Escherichia coli Fis-DNA binding sequence. J Mol Biol 376:771-785
97. Shin M, Song M, Rhee JH, Hong Y, Kim YJ, Seok YJ, Ha KS, Jung SH, Choy HE (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
98. Shindo H, Iwaki T, Ieda R, Kurumizaka H, Ueguchi C, Mizuno T, Morikawa S, Nakamura H, Kuboniwa H (1995) Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS Lett 360:125-131
99. Shindo H, Ohnuki A, Ginba H, Katoh E, Ueguchi C, Mizuno T, Yamazaki T (1999) Identification of the DNA binding surface of H-NS protein from Escherichia coli by heteronuclear NMR spectroscopy. FEBS Lett 455:63-69
100. Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod SM, Marko JF, Johnson RC (2006) Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. J Mol Biol 364:777-798
101. Spurio R, Falconi M, Brandi A, Pon CL, Gualerzi CO (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
102. Stauffer LT, Stauffer GV (1994) Characterization of the gcv control region from Escherichia coli. FEMS Microbiol Lett 131:95-98
103. Stella S, Spurio R, Falconi M, Pon CL, Gualerzi CO (2005) Nature and mechanism of the in vivo oligomerization of nucleoid protein H-NS. EMBO J 24:2896-2905
104. Stoebel DM, Free A, Dorman CJ (2008) Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154:2533-2545
105. Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J 22:3749-3760
106. Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG (2002) Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Natl Acad Sci USA 99:13471-13476
107. Thaw P, Sedelnikova SE, Muranova T, Wiese S, Ayora S, Alonso JC, Brinkman AB, Akerboom J, van der Oost J, Rafferty JB (2006) Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res 34:1439-1449
108. Turner EC, Dorman CJ (2007) H-NS antagonism in Shigella flexneri by VirB, a virulence gene transcription regulator that is closely related to plasmid partition factors. J Bacteriol 189:3403-3413
109. Ueguchi C, Suzuki T, Yoshida T, Tanaka K, Mizuno T (1996) Systematic mutational analysis revealing the functional domain organization of Escherichia coli nucleoid protein H-NS. J Mol Biol 263:149-162
110. van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT (2004) Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci USA 101:6969-6974
111. Varshavsky AJ, Nedospasov SA, Bakajeva V V, Georgiev GP (1977) Histone-like proteins in the purified Escherichia coli deoxyribonucleoprotein. Nucleic Acids Res 4:2725-2745
112. Wang Q, Calvo JM (1993) Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvIH. J Mol Biol 229:306-318
113. White SW, Wilson KS, Appelt K, Tanaka I (1999) The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus. Acta Crystallogr D Biol Crystallogr 55:801-809
114. Weisberg RA, Freundlich M, Friedman D, Gardner J, Goosen N, Nash, H Oppenheim A, Rouvière-Yaniv J (1996) Nomenclature of the genes encoding IHF. Mol Microbiol 19:642
115. Williams RM, Rimsky S, Buc H (1996) Probing the structure, function, and interactions of the Escherichia coli H-NS and StpA proteins by using dominant negative derivatives. J Bacteriol 178:4335-4343
116. Yamada H, Muramatsu S, Mizuno T (1990) An Escherichia coli protein that preferentially binds to sharply curved DNA. J Biochem (Tokyo) 108:420-425
117. Yokoyama K, Ishijima SA, Clowney L, Koike H, Aramaki H, Tanaka C, Makino K, Suzuki M (2006) Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors. FEMS Microbiol Rev 30:89-108
118. Zhang A, Rimsky S, Reaban ME, Buc H, Belfort M (1996) Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J 15:1340-1349