ライフサイエンスコーパス: IHF

1 IHF and HU are small basic proteins of eubacteria that b

2 IHF and HU are two heterodimeric nucleoid-associated pro

3 IHF and LuxR synergistically bind luxCDABE promoter DNA

4 IHF binding bends the DNA sharply, bringing an upstream

5 IHF binding to the promoter region was found to stabiliz

6 IHF binds tightly to only one of two transposon ends wit

7 IHF binds to all duplex DNA with micromolar affinity and

8 IHF binds to multiple sites in the luxCDABE promoter and

9 IHF binds to the leader sequence and induces a sharp DNA

10 IHF can dissociate from the transposon arm on the beta s

11 IHF is a sequence-specific DNA-binding protein that bend

12 IHF is known to exhibit both direct and indirect recogni

13 IHF is known to induce sharp bends in the helical axis o

14 IHF most likely brings about interactions between distal

15 IHF or supercoiling is required early in Tn10 transposit

16 IHF was found to bind specifically to this site and dele

17 IHF was found to directly bind to and bend the tcpA prom

18 IHF, examined singly, enhanced reactivity to KMnO4.

19 contains a second IHF site at position -115 (IHF II) and a third Fis site at position -97 (Fis III),

20 d by IHF binding to a site at position -115 (IHF II).

21 We propose that up to 22 of the 23 IHF cationic side-chains that are located within 6 A of

22 tically significant partial separation of 60 IHF binding sites from random and intragenic sequences a

23 F binding to a site centred at position -88 (IHF I) and Fis binding to sites centred at positions -14

24 F and Fis to sites centered at position -88 (IHF I) and position -142 (Fis I) and activated by IHF bi

25 An IHF site lies between these two kinds of sites in the Ch

26 ng sites for a monomer of transposase and an IHF heterodimer.

27 two kinds of sites in the Chr2 origin and an IHF-induced looping out of the intervening DNA mediates

28 d to and bend the tcpA promoter region at an IHF consensus site centered at position -162 by using ge

29 h phased recombination sites separated by an IHF-induced U-turn); this serves as a direct report on t

30 DnaA box enhanced plasmid replication in an IHF-dependent manner.

31 te the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at lea

32 The a side consists of an IHF protomer initially immobilized by a DNA-loop, but su

33 The additional DNA provides an IHF site and most likely a weak DnaA binding site, becau

34 of transcription factor PrpR, sigma-54, and IHF.

35 Comparison of HU-DNA and IHF-DNA structures suggests that sharper bending is corr

36 ed by the DNA binding activities of FarR and IHF.

37 monstrate that the nucleoid proteins FIS and IHF each bind multiple sites within the acs regulatory r

38 We propose that FIS and IHF each function directly as anti-activators of CRP, ea

39 d in E. coli, opposing activities of Fis and IHF ensure an abrupt transition from a repressed complex

40 repression, and made binding of both Fis and IHF essential.

41 ription assays, we demonstrated that FIS and IHF independently reduce CRP-dependent acs transcription

42 e the pairwise binding of FNR, NarL, Fis and IHF proteins to the nrfA-acs intergenic region.

43 Both Fis and IHF repress in vivo expression from pacsP1, but have sma

44 iator DnaA and DNA bending proteins, Fis and IHF, comprise prereplication complexes (pre-RC) that unw

45 binding of two DNA bending proteins, Fis and IHF, serving as inhibitor and activator respectively.

46 g presumed cooperative assembly of gpNu1 and IHF at the cos sequence of lambda DNA.

47 Here, we characterize cooperative gpNu1 and IHF binding to the cos site in lambda DNA using a quanti

48 We further proposed that gpNu1 and IHF cooperatively bind and bend viral DNA to regulate th

49 oli pre-RC, two histone-like proteins HU and IHF (integration host factor), stimulate initiator DnaA-

50 HU and IHF are members of a family of prokaryotic proteins that

51 HU and IHF are prokaryotic proteins that induce very large bend

52 HU and IHF have become paradigms for understanding DNA bending

53 e we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using

54 ffinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs.

55 The binding of NarL and IHF is mutually exclusive, whereas all other combination

56 ally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence len

57 inding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo.

58 ted with combinations of bound FIS, H-NS and IHF.

59 cR, whereas the suf operon requires OxyR and IHF for the response to oxidative stress and Fur for ind

60 s increased, Fis repression was relieved and IHF rapidly redistributed DnaA to all unfilled binding s

61 TraY and IHF bind conserved oriT sites sbyA and ihfA, respectivel

62 These results are consistent with TraY and IHF recognizing sbyA and ihfA with limited sequence spec

63 Unlike TraY and IHF, TraM is not essential for the formation of the rela

64 components of the relaxosome, TraI, TraY and IHF.

65 nding of transiently dissociated IHF by anti-IHF even when physically separated from the biofilm by a

66 model in which DNA bending proteins, such as IHF and HU, promote the condensation of DNA into rodlike

67 iation of DNA architectural proteins such as IHF and HU.

68 During transpososome assembly, IHF is bound with high affinity.

69 tion that arise from structural variation at IHF-DNA interfaces while the resulting energetic compens

70 The interplay between IHF and H-NS likely serves to couple the rate of transpo

71 iff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences with differ

72 is inhibited oriC unwinding by blocking both IHF and DnaA binding to low affinity sites.

73 e global analyses by demonstrating that both IHF and LuxR are required for transcriptional activation

74 The TraM binding site sbmC, along with both IHF binding sites, is essential for stimulation of the r

75 n the dinucleotide step and not on the bound IHF variant.

76 an displace IHF bound at the IHF I site, but IHF is unable to displace bound NarL.

77 ) and position -142 (Fis I) and activated by IHF binding to a site at position -115 (IHF II).

78 at biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning me

79 NA site is altered much more dramatically by IHF than by HU binding.

80 ion by decreasing the repression mediated by IHF and Fis binding at the other sites.

81 lic AMP receptor protein and is modulated by IHF and Fis binding at multiple sites.

82 ist plays a major role in DNA recognition by IHF, and that this geometric parameter is dependent on t

83 is subject to transcriptional regulation by IHF and post-transcriptional regulation by cleavage in t

84 hat FNR-dependent activation is repressed by IHF binding to a site centred at position -88 (IHF I) an

85 and is enhanced by NarL, but is repressed by IHF or Fis.

86 volves (i) attenuation of H-NS repression by IHF and (ii) RpoS-dependent transcription initiation res

87 NarL counteracts repression by IHF but is unable to alter repression by Fis.

88 resF) which allows Hbsu to be substituted by IHF, binding specifically between site I (the crossover

89 Thus, the V. cholerae IHF mutant appears to have a general defect in conjugati

90 efect in SXT transmission in the V. cholerae IHF mutant is probably not related to IHF's ability to p

91 The V. cholerae IHF mutant was also highly impaired as a donor of RP4, a

92 crystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed t

93 ome specific examples, involving the E. coli IHF and Fis proteins, that illustrate new principles, ar

94 Escherichia coli IHF mutants were not impaired as donors or recipients of

95 rmation is sequential at high concentration: IHF binds rapidly to DNA, followed by slower DNA bending

96 structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence.

97 In contrast, IHF does not enhance the ability of NanR to activate fim

98 In contrast, IHF proved to be required for V. cholerae to act as an S

99 ntify 8 new regulatory interactions for CRP, IHF or Fis responsible for the control of the promoters

100 st before DNA synthesis initiates, we detect IHF binding coincident with a shift of DnaA to weaker ce

101 We now show that NarL can displace IHF bound at the IHF I site, but IHF is unable to displa

102 diated by binding of transiently dissociated IHF by anti-IHF even when physically separated from the

103 to adopt the DNA structure of the bound DNA-IHF complex.

104 stablishing the relaxosome: the host-encoded IHF and the plasmid-encoded TraY.

105 ect to DNA-binding specificity, for example, IHF is sequence specific, while HU is not.

106 nsposon ends and the DNA-bending host-factor IHF (Integration Host Factor).

107 ream binding of the integration host factor (IHF) and Fis (factor for inversion stimulation) proteins

108 ein family includes integration host factor (IHF) and histone-like protein (HU); both are present in

109 logous to bacterial integration host factor (IHF) and the heat-unstable nucleoid protein (HU), bound

110 on is suppressed by integration host factor (IHF) binding at position -54, and this suppression is co

111 Integration host factor (IHF) binds to and represses the leukotoxin promoter, but

112 E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA.

113 on Escherichia coli integration host factor (IHF) for these activities.

114 Integration host factor (IHF) is a bacterial histone-like protein whose primary b

115 Integration host factor (IHF) is a DNA-bending protein that recognizes its cognat

116 Integration host factor (IHF) is a heterodimeric Escherichia coli protein that pl

117 Here, we show that integration host factor (IHF) is a key coactivator of the luxCDABE bioluminescenc

118 Integration host factor (IHF) is a prokaryotic protein required for the integrati

119 e we tested whether integration host factor (IHF) or Fis, two host-encoded nucleoid proteins, are req

120 he global regulator integration host factor (IHF) positively affects virulence gene expression in V.

121 ic Escherichia coli integration host factor (IHF) protein has been used as a test system.

122 ow that the E. coli integration host factor (IHF) protein is required for spacer acquisition in vivo

123 study of binding of integration host factor (IHF) protein to its specific 34-bp H' DNA site.

124 of Escherichia coli integration host factor (IHF) protein.

125 inding site for the integration host factor (IHF) was present at the centre of the Correia element up

126 Integration host factor (IHF), a nucleoid-associated protein in bacterial cells,

127 substrate bound to integration host factor (IHF), an architectural protein from Escherichia coli.

128 th Escherichia coli integration host factor (IHF), an architectural protein that bends specific sites

129 nd the host protein integration host factor (IHF), are united in an asymmetrical complex.

130 of wt pi, DnaA and integration host factor (IHF), each protein known to specifically bind gamma ori.

131 DNA-binding protein integration host factor (IHF), located between the upstream FlbD binding site and

132 one DNABII protein, Integration Host Factor (IHF), results in significant disruption.

133 xpression, and that integration host factor (IHF), which binds midway between O(NC1) and O(NC2), faci

134 on was regulated by Integration Host Factor (IHF), which bound within the PR1 region to repress trans

135 the DNABII protein, integration host factor (IHF), which induce catastrophic structural collapse of b

136 he transcription of integration host factor (IHF), which positively affected the expression of flrA a

137 red the presence of Integration Host Factor (IHF), which was found to bind to sequences located betwe

138 proteins, TraY and integration host factor (IHF).

139 and independent of integration host factor (IHF).

140 -remodeling protein integration host factor (IHF).

141 olypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated protei

142 a binding site for integration host factor (IHF); this site plays a less critical role but is requir

143 egrase complex is promoted by a host factor, IHF (integration host factor), that binds and bends CRIS

144 nantly), and influenced by auxiliary factors IHF, Lrp and H-NS.

145 , we observed a dynamic interplay among Fis, IHF and DnaA on supercoiled oriC templates.

146 contrast, 'histone-like' protein (i.e. Fis, IHF and H-NS) -binding sites did not cluster, and their

147 Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nuc

148 However, the affinity for IHF drops dramatically after cleavage of the first trans

149 C DNA construct and unlabeled duplex DNA for IHF binding allows the determination of K(D) values as a

150 e context of Record and coworker's model for IHF binding.

151 plex are detected for HU:DNA, though not for IHF:DNA.

152 nd motility analysis revealed a key role for IHF as a repressor of cell motility through the control

153 on mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles ( ap

154 A sites for FIS or deletion of DNA sites for IHF increases acs transcription.

155 t the bottleneck in the recognition step for IHF is spontaneous kinking of cognate DNA to adopt a par

156 for a highly condensed synapse in which Hbsu/IHF has a purely architectural function.

157 se sites, which are bent by binding the host IHF protein.

158 However, IHF is locked onto the alpha side of the complex, probab

159 al strains lacking the nucleoid proteins HU, IHF or H-NS.

160 from the kink sites, as well as mutations in IHF designed to destabilize the complex, have negligible

161 of association become faster with increasing IHF concentration showing that complex formation is seco

162 Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement o

163 We investigated IHF binding and found that appropriate structural distor

164 We find that like IHF, Hbb relies exclusively on indirect readout to recog

165 However, placing the NanR, IHF and NagC binding sites closer to the fimB promoter e

166 ral nucleoid-associated proteins (i.e. NAPs) IHF and Fis, the regulatory protein SlyA, and the two-co

167 formed in sequence-specific and -nonspecific IHF-DNA complexes.

168 the leukotoxin promoter, but neither CRP nor IHF is responsible for the anaerobic induction of ltxA R

169 be 1.0(+/-0.2)x10(3)] from the 5340 A(2) of IHF and H' DNA surface buried in complex formation, and

170 In the absence of IHF, spermidine and spermine condense DNA primarily into

171 In the absence of IHF, V. cholerae displayed a modest defect for serving a

172 ated pattern of expression in the absence of IHF.

173 d biochemistry to investigate the actions of IHF and Fis at these sites.

174 The DNA bending activity of IHF stimulates assembly of an intermediate with tightly

175 d involves cyclic changes in the affinity of IHF for its binding site.

176 on initiation is repressed by the binding of IHF and Fis to sites centered at position -88 (IHF I) an

177 easurements, demonstrate that the binding of IHF to its cognate DNA site involves an intermediate sta

178 Parallel studies of solution complexes of IHF and HU with the same DNA nonadecamer (5' --> 3' sequ

179 therapeutic vaccine formulation comprised of IHF plus the powerful adjuvant dmLT and delivered via a

180 Deletion of IHF has little effect.

181 We show that the effects of IHF and Fis are position dependent and that IHF II funct

182 and counteracting the repressive effects of IHF and Fis.

183 nsulate the nrf promoter from the effects of IHF.

184 The ejection of IHF promotes cleavage of the second end, which is follow

185 duced DNA conformations to the energetics of IHF binding.

186 A remarkable feature of IHF is that it employs an indirect readout mechanism to

187 We propose that a common function of IHF and HU in bacterial cells is to facilitate DNA organ

188 on the face of the DNA helix, independent of IHF binding at other locations, and found only when NarL

189 t and that IHF II functions independently of IHF I and Fis I.

190 A IHF consensus site resulted in the loss of IHF binding and additionally disrupted the binding of th

191 llar promoters were decreased by the loss of IHF.

192 e results differentiate structural motifs of IHF:DNA and HU:DNA solution complexes, provide Raman sig

193 indirect recognition, which explains part of IHF sequence-specific binding.

194 used to confirm the direct participation of IHF in gltBDF promoter regulation.

195 condensation in the absence and presence of IHF binding lend support to our model in which DNA bendi

196 oidal structures, whereas in the presence of IHF, polyamines condense DNA primarily into rodlike stru

197 The sequence-specific binding profile of IHF encompasses approximately 30% of all operons, though

198 The rate of IHF dissociation from site-specifically bound DNA increa

199 The role of IHF in activating P1 origin by allowing DnaA binding to

200 NA in both modes of binding, but the role of IHF in controlling DNA condensation within bacterial cel

201 romoters and the positive regulatory role of IHF in regulating lsrACDBFG expression were confirmed wi

202 re the phage lambda H1 consensus sequence of IHF is underlined) show the following.

203 chanism of action to be the sequestration of IHF upon dissociation from the biofilm eDNA, forcing an

204 The three sites of IHF protection on the DNA develop with similar time-depe

205 eriments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we defin

206 In addition, we show that both subunits of IHF, yet only one subunit of HU (HupB), are critical for

207 To explain the unusual thermodynamics of IHF-DNA interactions, we propose that both specific and

208 b are related to, yet distinct from those of IHF.

209 eptide positioned at the DNA-binding tips of IHF were as effective as antibodies directed against the

210 Two Sin dimers and one IHF dimer can bind together to the closely adjoining sit

211 omplex is composed of four protomers and one IHF heterodimer bound at the cos site.

212 Loss of either Fis or IHF perturbs synchronous initiation from oriC copies in

213 nd TraM cannot substitute for either TraY or IHF in this process.

214 substitution of betaGlu44 with Ala prevented IHF from discriminating between A and T at this position

215 ion complex, including the accessory protein IHF (integration host factor).

216 ndicate that the nucleoid-associated protein IHF is one such protein.

217 ogether with the nucleoid-associated protein IHF, which bind to overlapping targets adjacent to the D

218 and functionally related DNA bending protein IHF could not efficiently substitute for HU.

219 The DNA-bending protein IHF was needed for optimal replication and its substitut

220 d a binding site for the DNA-bending protein IHF.

221 richia coli integration host factor protein (IHF) is required for efficient lambda-development in viv

222 ound to the integration host factor protein (IHF) of E. coli.

223 richia coli integration host factor protein (IHF), which binds to a consensus sequence also located w

224 ribution of the nucleoid-associated protein, IHF, is little altered when cells enter stationary phase

225 taining integrase and the accessory proteins IHF (integration host factor) and Xis form rapidly on at

226 ther with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA co

227 ates with its accessory DNA bending proteins IHF, Xis, and Fis to assemble two distinct, very large,

228 The host proteins IHF and H-NS, which also are global regulators of gene e

229 ion) occurs in the absence of host proteins (IHF/HU or DnaA) and it is positioned in the A + T-rich r

230 relative levels of the 3 accessory proteins, IHF, Xis, and Fis.

231 binding of two nucleoid associated proteins, IHF and Fis.

232 lly related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-

233 ere, we have studied the binding of purified IHF, Fis and FNR to the nir promoter in vitro.

234 wn to bind to probes containing the putative IHF recognition sequences.

235 anism, we report that this effect was rapid, IHF-specific and mediated by binding of transiently diss

236 Later in the reaction, IHF inhibits target interactions.

237 are separated by up to 90 bp, Fis represses IHF binding and weak DnaA interactions until accumulatin

238 related to lambda integrase, did not require IHF.

239 s1-Cas2-mediated spacer integration requires IHF-induced target DNA bending and explain the elusive r

240 ype pi-mediated replication in vivo requires IHF.

241 nteractions are demonstrated at a saturating IHF concentration.

242 show that the nir promoter contains a second IHF site at position -115 (IHF II) and a third Fis site

243 rance of the target binding site by a single IHF-folded transposon arm.

244 nt lambda-development in vivo and a specific IHF recognition sequence is found within cos.

245 the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabil

246 Surprisingly, IHF binding at the IHF II site increases FNR-dependent a

247 Deletion or mutation of the tcpA IHF consensus site resulted in the loss of IHF binding a

248 overlapping and neighbouring sites and that IHF binds independently of either FIS or CRP.

249 IHF and Fis are position dependent and that IHF II functions independently of IHF I and Fis I.

250 polymerase (RNAP) activity directly and that IHF represses ltxA RNA synthesis mainly by blocking Mlc

251 Fis site at position -97 (Fis III), and that IHF, Fis and FNR can bind together to form multiprotein

252 Here we demonstrate that IHF influences the morphology of DNA condensed by polyam

253 RNA-seq analysis demonstrated that IHF regulates 300 genes in V. harveyi, and among these a

254 We determined that IHF binding to the farAB promoter region could inhibit t

255 or recipients of SXT or RP4, indicating that IHF is a V. cholerae-specific conjugation factor.

256 Using in vitro assays, we report that IHF and Fis repress transcription initiation by interfer

257 We show that IHF and the terminase protomer cooperatively assemble at

258 We show that IHF binding to one of these sites, located at position -

259 We show that IHF recognizes pre-formed conformational characteristics

260 hfA and DeltaihfB mutant strains showed that IHF differentially regulates the lsr locus and functions

261 crystal structure of the complex shows that IHF binds to the minor groove of DNA and bends the doubl

262 These data suggest that IHF bending of the duplex at the cos site in viral DNA p

263 f a protein-DNA interaction and suggest that IHF binds its specific site through a multiple-step mech

264 These results suggest that IHF may function at the tcpA promoter to alleviate H-NS

265 Based on these results, we suggest that IHF plays a crucial architectural role, bringing the dis

266 These data suggest that IHF plays an integral role in one mechanism of transcrip

267 The IHF-dependent reactive residues, however, are distinct f

268 The IHF-DNA interface extends over three helical turns and i

269 show that NarL can displace IHF bound at the IHF I site, but IHF is unable to displace bound NarL.

270 Surprisingly, IHF binding at the IHF II site increases FNR-dependent activation by decrea

271 hese include transposase contacts beyond the IHF site that chaperone assembly of the complex and are

272 that H-NS protection overlaps with both the IHF and the ToxT binding sites at the tcpA promoter.

273 ators, NarL or NarP, but is repressed by the IHF and Fis proteins.

274 ion of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two

275 ere compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformatio

276 (ii) In the IHF complex, the structural perturbations encompass both

277 of formation of DNA-protein contacts in the IHF-DNA complex with single base-pair spatial, and milli

278 he DNA helix (DNA deformation energy) in the IHF-DNA complex.

279 pecifically to this site and deletion of the IHF binding site enhanced mtrC transcription.

280 ically significant partial separation of the IHF binding sites from random and intragenic sequences.

281 The precise position of the IHF site within the site I-site II spacer determines the

282 centus gene encoding the beta-subunit of the IHF, ihfB (himD), and examined the effect on flagellar g

283 site for H-NS, which promotes opening of the IHF-loop, which is required for productive target intera

284 This recombination requires the IHF protein, is unidirectional, and is regulated by the

285 erminal' DNA contacts, located distal to the IHF site.

286 ercoiling-dependent mechanism similar to the IHF-mediated mechanism described previously for the ilvP

287 elation to pnrfA transcription), whereas the IHF protein binds to a site centred at position -54.

288 Thus, IHF is required for maximal transcription of several lat

289 vage of the first transposon end, leading to IHF ejection and unfolding of the complex.

290 olerae IHF mutant is probably not related to IHF's ability to promote DNA recombination.

291 Differences in the upstream IHF and Fis binding sites at the nir promoter in related

292 While IHF shows significant sequence specificity, HU binds pre

293 kink DNA before forming a tight complex with IHF.

294 ation for an important virulence factor with IHF playing a role in regulating growth phase expression

295 differing flexibility have interactions with IHF that compensate for unfavorable deformation energy.

296 We suggest that NarL interferes with IHF binding at the nir promoter by distorting the minor

297 esting that ORF CT267 encodes a protein with IHF-like activity, and recombinant protein had a positiv

298 ee partially mixed low-energy sequences with IHF binding sites but separated high-energy sequences.

299 es have shown that binding of wild-type (WT)-IHF is disrupted by a T to A mutation at the center posi

300 inding affinities for all combinations of WT-IHF and IHF-betaGlu44Ala bound to the WT and mutant DNAs