ライフサイエンスコーパス: ori

1 melting of the bovine papillomavirus type 1 ori is a sequence-dependent process which relies on spec

2 in the modeling and regulation of the HPV-11 ori is discussed.

3 The HPV type 11 ori spans 103 bp and contains three palindromic E2 bindi

4 intact genome also greatly augmented HPV-16 ori function.

5 tative E1 protein binding site in the HPV-18 ori.

6 hat rep expression is sufficient to activate ori V.

7 at ori-beta no longer selectively activated ori-beta.

8 mplification, indicating that ACE3 activates ori-beta in cis.

9 that rho- petite mtDNA consisting of active ori repeats is uniquely unstable in the hsp60-ts mutant.

10 First, RTA activates an ori-Lyt promoter and initiates transcription across GC-r

11 an initiate bi-directional unwinding from an ori site.

12 hromosome arms adjacent to each other, in an ori-ter configuration.

13 former supported transient replication of an ori plasmid, whereas the latter was a self-contained rep

14 hermore, E2 can promote the transition to an ori melting complex by recruiting additional E1 molecule

15 An insulator placed between ACE3 and ori-beta inhibited amplification, indicating that ACE3 a

16 , the data suggest a model in which ACE3 and ori-beta nucleate the formation of a ORC2-containing chr

17 ave now deleted ori-beta', both ori-beta and ori-beta', an 11-kb region just downstream from the DHFR

18 in, with two subregions (termed ori-beta and ori-gamma) being somewhat preferred.

19 ion, with two broad subregions (ori-beta and ori-gamma) preferred.

20 n the spacer (two of them being ori-beta and ori-gamma), with ori-beta accounting for a maximum of ap

21 ity in the downstream ori-beta/ori-beta' and ori-gamma regions is completely suppressed.

22 ons within this zone (ori-beta/ori-beta' and ori-gamma) are preferred.

23 al subregions (e.g. ori-beta, ori-beta', and ori-gamma) being preferred.

24 es being preferred (ori-beta, ori-beta', and ori-gamma).

25 ndromes are required for both K8 binding and ori-Lyt-dependent DNA replication.

26 well-characterized T4 origins, ori(uvsY) and ori(34), are believed to initiate replication through an

27 ag binds to sites I to III within and around ori with different affinities and induces structural cha

28 lasmid replicon of Escherichia coli, such as ori gamma of R6K, contains tandem iterons (iterated init

29 that the replicative intermediates formed at ori(uvsY) persist longer in a uvsW mutant infection than

30 lls that were >50% reduced in methylation at ori-beta no longer selectively activated ori-beta.

31 Remethylation at ori-beta did not begin until approximately 500 base pair

32 he initiation of replication specifically at ori gamma of R6K, elongation of the forks, and their ter

33 iled to identify a template strand switch at ori-beta; rather, we observed a gradual, undulating chan

34 ation sites in the spacer (two of them being ori-beta and ori-gamma), with ori-beta accounting for a

35 ase (DHFR) locus containing the origin beta (ori-beta) initiation region was stably transfected into

36 omethylation were determined at origin beta (ori-beta), downstream of the hamster DHFR gene.

37 cer, with several subregions (e.g. ori-beta, ori-beta', and ori-gamma) being preferred.

38 least three sites being preferred (ori-beta, ori-beta', and ori-gamma).

39 g origin activity in the downstream ori-beta/ori-beta' and ori-gamma regions is completely suppressed

40 Two subregions within this zone (ori-beta/ori-beta' and ori-gamma) are preferred.

41 itors (camptothecin and ellipticine) blocked ori-Lyt-dependent DNA replication.

42 t study, we have now deleted ori-beta', both ori-beta and ori-beta', an 11-kb region just downstream

43 ately 1.2 kb S18 chorion gene and the 840 bp ori-beta.

44 In the first, called "ori-ter" and exemplified by Caulobacter crescentus, the

45 re of hp-B6.1, the original hybridoma clone (ori-B6.1) stored frozen since 1995, a subclone of hp-B6.

46 tuberculosis oriC plasmids containing ColE1 ori relative to chromosomal oriC is one and the 5' flank

47 hypersuppressive petites contain a conserved ori sequence that includes a promoter, but it is unclear

48 other gammaherpesviruses, which all contain ori sequences within the unique long sequence outside of

49 Using a template that contained ori gamma flanked by two asymmetrically placed Ter sites

50 located within an 11-kb sequence containing ori-beta.

51 amide and niacinamide) resulted in decreased ori-Lyt-dependent DNA replication, whereas hydroxyurea,

52 In the present study, we have now deleted ori-beta', both ori-beta and ori-beta', an 11-kb region

53 320-bp ACE3 and an 884-bp element designated ori-beta were found to be necessary and sufficient for a

54 s suggest that a 5.8-kb fragment of the DHFR ori-beta region is sufficient to direct initiation and t

55 as used to visualize complexes of HPV-11 DNA ori bound by purified E2 protein.

56 and simultaneously knocks out the downstream ori-beta locus.

57 rly-firing origin activity in the downstream ori-beta/ori-beta' and ori-gamma regions is completely s

58 e functions in the initial melting of duplex ori DNA but not in the processive DNA unwinding of parti

59 al ori, we proposed that TBPc antagonizes E1-ori association indirectly through inhibition of E2-DNA

60 mers bound to ori on one face of the DNA, E1-ori.

61 of E2 nor ATP hydrolysis are required for E1-ori formation, consistent with a need for ATP hydrolysis

62 tion and can be converted to a multimeric E1-ori initiator complex by displacement of E2 in the prese

63 g site positioned distal to the precursor E1-ori complex.

64 quired for stabilization of the resulting E1-ori complex.

65 ATP hydrolysis in E2 displacement from E1E2-ori.

66 bound to DNA, the bovine papillomavirus E1E2-ori complex.

67 ural information for the papillomavirus E1E2-ori preinitiation complex that would otherwise have been

68 plicator generating a sequence-specific E1E2-ori complex.

69 chanism for E1 loading but suggest that E1E2-ori, which forms preferentially on ori, may perform an a

70 BS-2, E2BS-3, and E2BS-4) for the dimeric E2 ori binding protein.

71 and data indicating that TBPc antagonized E2-ori association, we propose that transcription factors r

72 essfully replicated a plasmid containing EBV ori-Lyt in the presence of the Epstein-Barr virus-encode

73 Initiation at ectopic ori-beta in uncloned pools of transfected cells was meas

74 ically required for full activity of ectopic ori-beta in hamster cells.

75 Initiation activity of three ectopic ori-beta deletion mutants was reduced, while the activit

76 rfaQGP suppressors also reduce the elevated ori/ter ratio of the DeltaseqA mutants but, unexpectedly

77 ce assay of the 12-kb subregion encompassing ori-beta has suggested the presence of a relatively smal

78 ay and shown to mimic that at the endogenous ori-beta region in Chinese hamster ovary K1 cells.

79 in vitro was specifically initiated at the F ori (oriV) and required both the bacterial initiator pro

80 hat fail to melt correctly are defective for ori unwinding and DNA replication in vivo.

81 ome cis-acting and trans-acting elements for ori-Lyt-dependent DNA replication have been found.

82 proteins (ICP8, UL42, and UL8) essential for ori-dependent DNA replication.

83 18-bp AT palindrome, which is essential for ori-Lyt function.

84 F50/Rta protein to the RRE was essential for ori-Lyt-dependent DNA replication.

85 pomethylated hamster cells were examined for ori-beta activity.

86 the ori-Lyt, and all were indispensable for ori-Lyt function.

87 in detail, such information was lacking for ori alpha.

88 meric and the monomeric pi are necessary for ori alpha-driven plasmid maintenance.

89 d a transcription event may be necessary for ori-Lyt-dependent DNA replication.

90 s and the trans-acting proteins required for ori gamma function have been analyzed in detail, such in

91 y reducing the E1 concentration required for ori melting.

92 S1 origin sequences could not substitute for ori-beta, thereby confirming the sequence specificity of

93 ificantly less newly replicated DNA at FRA3B ori 1-3, as compared with three control origins located

94 rigins and, to a lesser extent, at the FRA3B ori 1-3.

95 subclone fixed complement like antibody from ori-B6.1.

96 th only the hp-B6.1; the V(H) sequences from ori-B6.1 and the subclone were, however, identical.

97 Two functional ori-Lyts have been identified in the KSHV genome.

98 55-kb spacer, with several subregions (e.g. ori-beta, ori-beta', and ori-gamma) being preferred.

99 gamma ori replication can be uniformly modulated over 100-fold

100 plasmid, we describe the utility of a gamma ori expression vector that allows especially tight regul

101 opening reaction was investigated in a gamma ori system by using hyperactive variants of plasmid R6K-

102 is strain could be compatible with any gamma ori plasmid, we describe the utility of a gamma ori expr

103 potential toxins, and maintaining any gamma ori vector at precise copy levels in a cell.

104 ach protein known to specifically bind gamma ori.

105 site in the (A.T)-rich segment of its gamma ori and activate the gamma ori in vivo and in vitro.

106 Regulation of gamma ori plasmid copy number is achieved through arabinose-in

107 pi, allow four to tenfold increases of gamma ori plasmid DNA in vivo.

108 tein, pi, with seven tandem iterons of gamma ori.

109 ment of its gamma ori and activate the gamma ori in vivo and in vitro.

110 y proposed model of handcuffing in the gamma ori system.

111 o KMnO4 (indicative of opening) within gamma ori DNA occurred in both strands of a superhelical templ

112 NA sequence in the A+T-rich segment of gamma-ori.

113 n process focusing specifically on the gamma-ori of the antibiotic-resistance plasmid R6K.

114 motif displayed defects in E2-dependent HPV ori replication in vivo.

115 ese results suggest that YY1 can inhibit HPV ori replication by interfering with E2 protein functions

116 An EBV/human ori vector is used to carry the system, overcoming the s

117 erase chain reaction and Western blotting in ori-3 cells.

118 tier or collar of the E1 helicase domain in ori processing is described.

119 SNAI1 expression in ori-3 cells repressed CDH1 transcription.

120 Site-directed mutations made in ori and Asn10 of Rep protein suggested that Asn10 recogn

121 ng of K8 and RTA proteins to these motifs in ori-Lyt DNA was demonstrated to be absolutely essential

122 Replication initiates normally in ori-beta knockout cell lines, and the DHFR domain is sti

123 ase, collaborates with the HPV E2 protein in ori-dependent replication.

124 he present study, functional roles of RTA in ori-Lyt-dependent DNA replication have been investigated

125 ization creates the 2-fold symmetric, ter-in/ori-out conformation which, for E. coli, comprises siste

126 rying point mutations that should inactivate ori(34) but not affect the gene 34 reading frame (within

127 s in initiation of DNA replication including ori binding, melting, and unwinding, culminating in the

128 ng the high-frequency initiation region (IR) ori-beta from the hamster dihydrofolate reductase locus

129 A 1.3 kb ori V-rep fragment from IncP-9 plasmid pM3 was sufficien

130 n mutations across the core domain of a KSHV ori-Lyt and tested them for DNA replication function in

131 r with the ability of K8 to bind to the KSHV ori-Lyt, suggests that K8 may function as an OBP in KSHV

132 several cellular proteins that bind to KSHV ori-Lyt.

133 re region is 100% conserved between two KSHV ori-Lyt's.

134 To map cis-acting elements within KSHV ori-Lyt that are required for DNA replication function a

135 into opposite cell halves, generating a left-ori-right pattern.

136 rved in slow-growing Escherichia coli ("left-ori-right"), the two chromosome arms reside in separate

137 n zone in which ori-beta and a second locus (ori-gamma) are somewhat preferred.

138 iator binding sites that is observed in many ori's.

139 e the DNA and function independently to melt ori.

140 ative Poisson's ratio was reported for Miura-ori pattern, which are consistent with the interesting s

141 surfaces of interest with generalized Miura-ori units.

142 ble via switching the folding state of Miura-ori split-ring resonators.

143 from Origami building blocks based on Miura-ori fold.

144 A periodic Miura-ori pattern and a non-periodic Ron Resch pattern were st

145 two folded metamaterials based on the Miura-ori fold pattern.

146 g the possible physical origin for the Miura-ori leaf-folding patterns that arise naturally in insect

147 Working with the Miura-ori tessellation, we find that each unit cell of this cr

148 The deformation of the Miura-ori unit along the third dimension induces net electric

149 ially to the template strand of active mtDNA ori sequences in vitro; and wild-type (rho+) mtDNA is un

150 d by the interaction between Hsp60 and mtDNA ori sequences.

151 As revealed in a novel ori-dependent HPV-16 plasmid amplification assay, the al

152 ns in immortalized human thyroid cells (Nthy-ori 3-1) and NIH 3T3 cells.

153 Overexpression of PPARgamma in Nthy-ori cells did not recapitulate PPFP's growth effects.

154 Treatment of Nthy-ori cells with an irreversible PPARgamma inhibitor mimic

155 Stable Nthy-ori PPFP transfectants grew in soft agar, and PPFP-trans

156 ased the growth of transient and stable Nthy-ori transfectants ( approximately threefold by 72 h).

157 When present in the context of ori, mutation of this sequence was seen to have signific

158 lication in vitro and on the denaturation of ori, indicating that origin activity can be modulated by

159 he three 21-bp repeats located downstream of ori in a construct with reduced replication efficiency.

160 peats, DNA distortion occurred downstream of ori.

161 upstream of ori to a position downstream of ori.

162 romoters are absent or located downstream of ori.

163 This instability of ori rho- mtDNA requires transcription from the canonical

164 Deletion mapping of ori-beta identified two required components: a 140 bp 5'

165 New insights into the mechanism of ori melting are elaborated, suggesting the coordinated i

166 rimarily required for initial recognition of ori.

167 Replication of ori V-rep in E. coli was restored when additional rep wa

168 ereby confirming the sequence specificity of ori-beta.

169 nt on their location, and (iii) unwinding of ori is influenced by the location of the promoters and t

170 Bending occurred both upstream of ori and in the three 21-bp repeats located downstream of

171 ed from their wild-type position upstream of ori to a position downstream of ori.

172 esent in replication initiation complexes on ori-Lyt.

173 that E1E2-ori, which forms preferentially on ori, may perform an additional role in BPV replication.

174 E1-binding site also loads an E1 dimer onto ori.

175 For centuries, practitioners of origami ('ori', fold; 'kami', paper) and kirigami ('kiru', cut) ha

176 The phage replication origin ori(34) is located in a region that has a hotspot in bot

177 uired for helicase activity and also origin (ori) DNA melting.

178 We have analyzed the amplification origin (ori) II/9A of the fly, Sciara coprophila.

179 ic DNA replication initiates from an origin (ori-Lyt) and requires trans-acting elements.

180 ture found within the SV40 T antigen-origin (ori) complex.

181 ulation of gene expression and gamma origin (ori) plasmid copy number.

182 In lytic DNA replication, the lytic origin (ori-Lyt) is bound by a virus-specified origin binding pr

183 was detected within the replicating origin (ori P)-containing fragment, indicating that replication

184 entification of the SaPI replication origin (ori) and replication initiation protein (Rep), which has

185 g sites (iterons) of the replication origin (ori) of a plasmid and the iterons located in a cis-actin

186 rons compose the minimal replication origin (ori) of pBtoxis and that ORF157 and ORF156 are involved

187 papillomavirus (HPV) DNA replication origin (ori) shares a common theme with many DNA control element

188 absence of a lytic cycle replication origin (ori-Lyt) and any known initiator or origin binding prote

189 The origin (ori)-binding protein of herpes simplex virus type 1 (HSV

190 e binding of UL9 protein to an HSV-1 origin, ori(s), and facilitates formation of the multimer from t

191 eplication from the bacteriophage T4 origin, ori(34).

192 Two lytic DNA replication origins (ori-Lyt) of Kaposi's sarcoma-associated herpesvirus (KSH

193 Two well-characterized T4 origins, ori(uvsY) and ori(34), are believed to initiate replicat

194 d is used to tether E1 to the papillomavirus ori.

195 me segregation, polar PopZ captures the ParB*ori complex and thereby anchors sister chromosomes at op

196 cus in trans in the shuttle vector pBAD18kan-ori, plasmid Deltapga-c, restored the high levels of kil

197 fic contact, productive unwinding of plasmid ori gamma and replication is abrogated.

198 on cause failure to load DnaB to the plasmid ori in vitro and to replicate the plasmid in vivo.

199 , with at least three sites being preferred (ori-beta, ori-beta', and ori-gamma).

200 h the in vitro reconstituted system promotes ori gamma-specific initiation of replication by a mutant

201 imary control involve only initiator protein-ori DNA interaction or did it also involve protein-prote

202 in a single TR, suggesting that the putative ori of KSHV is different from those of other gammaherpes

203 on of polyomavirus origin-containing DNA (Py ori-DNA) in vitro when p53 binding sites are present on

204 aining Py T Ag, Py origin-containing DNA (Py ori-DNA), and murine FM3A cell extracts.

205 inhibits replication of gamma-irradiated Py ori-DNA and such inhibition requires both the central DN

206 tion of replication from gamma-irradiated Py ori-DNA, suggesting the possibility of DNA looping cause

207 is incapable of inhibiting replication of Py ori-DNA in vitro.

208 We found that pRb strongly represses Py ori-DNA replication in vitro.

209 sites are present on the late side of the Py ori.

210 orepressor mSin3B inhibits polyomavirus (Py) ori-dependent DNA replication in vivo.

211 Raji ori, a second origin in EBV, functions in vivo but fails

212 initiating element, DS, within oriP and Raji ori to resolve this paradox.

213 i in cis and that after deletion of DS, Raji ori could now act as an ARS in the long term.

214 DS, but not Raji ori, binds EBNA1; whereas both act as ARSs in short-term

215 ted the establishment of a plasmid with Raji ori in cis and that after deletion of DS, Raji ori could

216 deletion of the most active site or region (ori-beta) has no demonstrable effect on initiation in th

217 th the chromosome replication origin region (ori).

218 Plasmids containing the rep-ori complex plus an additional gene, pri, can replicate

219 trand DNA replication origin of mammals, rep/ori sequences have also been proposed to participate in

220 a step to elucidate the function of the rep/ori promoter, we have attempted to detect transcription-

221 ce block immediately downstream from the rep/ori promoter.

222 -1/1R/Z1, whose repeat unit shelters the rep/ori sequence ori1, in strains carrying either wild-type

223 Here we analyze origin of DNA replication (ori) binding by the E1 initiator and show sequential bin

224 e double-stranded origin of DNA replication (ori) DNA in preparation for DH formation.

225 vely to the viral origin of DNA replication (ori), forming a complex which is essential for initiatio

226 protein E1 to the origin of DNA replication (ori).

227 complexes on the origin of DNA replication (ori).

228 ently, the origins of lytic DNA replication (ori-Lyt) in Kaposi's sarcoma-associated herpesvirus (KSH

229 o 3826) and the viral origin of replication (ori) (p11Rc).

230 ssembles on the viral origin of replication (ori) as a series of complexes.

231 cooperatively at the origin of replication (ori) as an (E1)2-(E2)2-DNA complex.

232 he recognition of the origin of replication (ori) by specific Rep proteins that bind to DNA sequences

233 cis elements for the origin of replication (ori) function are located within a single TR, suggesting

234 Although its origin of replication (ori) is essential for DNA replication, there are transcr

235 interaction with the origin of replication (ori) sequences.

236 -binding sites in the origin of replication (ori), giving H-19B six binding sites as opposed to the f

237 irus type 18 (HPV-18) origin of replication (ori)-containing DNA by using purified HPV-18 E1 and E2 g

238 that contain the SV40 origin of replication (ori).

239 cation from the ch-19 origin of replication (ori).

240 We mapped four origins of replication, ori 1-4, using two independent methods.

241 (G254D/S267L) supports replication of an RK2 ori plasmid in trans at a greatly elevated copy number,

242 ic spacer region, with two broad subregions (ori-beta and ori-gamma) preferred.

243 The vector harbors the SV40 ori and large T antigen gene, allowing portability betwe

244 tectural constraints at oriP and at the SV40 ori.

245 id and a heterologous simian virus 40 (SV40) ori plasmid that contains E2 binding sites in cis.

246 nsional gel analysis of the bacteriophage T4 ori(uvsY) region revealed a novel "comet" on the Y arc.

247 l replication of a plasmid containing the T4 ori(uvsY) origin, with a preformed R loop at the positio

248 al replication of plasmids containing the T4 ori(uvsY) replication origin in vitro, beginning with a

249 in this domain, with two subregions (termed ori-beta and ori-gamma) being somewhat preferred.

250 uble hexamer with helicase activity and that ori mutants that fail to melt correctly are defective fo

251 We conclude that ori-beta does not contain an essential replicator, but t

252 To test the hypothesis that ori-beta contains a genetic replicator, we restored a de

253 Two-dimensional gels revealed that ori-beta was acting as the origin.

254 ent fixation assays surprisingly showed that ori-B6.1 antibody fixes C3 more rapidly than does hp-B6.

255 The ori-beta AT-rich element is critical for initiation acti

256 tate open complex formation and activate the ori.

257 iteron binding, and in so doing activate the ori.

258 omal segment containing dnaN, as well as the ori site.

259 om just above background to a maximum at the ori-beta locus.

260 A sharp peak of nascent DNA occurred at the ori-beta origin of bidirectional replication where initi

261 (DUE) is essential for replication, but the ori(uvsY) DUE can be replaced by other DUE sequences.

262 or that increases the affinity of E1 for the ori site through cooperative binding.

263 lecules progressed counterclockwise from the ori, in the same direction that has been observed in viv

264 tion of SV40 nucleic acid sequences from the ori-enhancer and large-T-antigen regions, which reveals

265 tify mutations in the E1 helicase and in the ori that arrest the local melting process.

266 ation and that specific DNA sequences in the ori-beta region are required for efficient initiation ac

267 howed that an AT-palindromic sequence in the ori-Lyt domain is essential for the DNA replication.

268 eqA defect in Escherichia coli increases the ori/ter ratio and causes chromosomal fragmentation, maki

269 ure to form the double trimer that melts the ori and failure to form the double hexamer that unwinds

270 fic defects for melting of the center of the ori containing the binding sites for E1 and demonstrate

271 and synthesis by blocking replication on the ori(uvsY) R loop plasmid until the helicase is loaded.

272 es assembly of the hexameric helicase on the ori.

273 As expected from past studies, the ori(34) mutations also eliminated the hotspot for marker

274 It has been proposed that the ori DNA is first melted by a head-to-tail double trimer

275 y cooperative binding of two proteins to the ori site: the enhancer E2 and the viral initiator E1, a

276 ecules in which the branch points map to the ori(uvsY) transcript region.

277 trate that these mutants fail to untwist the ori DNA.

278 ger E1 complexes that distort and unwind the ori.

279 to form the double hexamer that unwinds the ori.

280 es a promoter, but it is unclear whether the ori confers a segregation or replication advantage.

281 ption from the canonical promoter within the ori element.

282 s found to bind to a DNA sequence within the ori-Lyt by using a DNA binding site selection assay.

283 identification of four components within the ori-Lyt, and all were indispensable for ori-Lyt function

284 e reductase replication initiation zone, the ori-beta locus is preferred over other start sites.

285 complex containing three E1 dimers bound to ori on one face of the DNA, E1-ori.

286 the par operon promoter, required in cis to ori V-rep.

287 NA-binding activity tethers the initiator to ori while another alters DNA structure, is a characteris

288 lex by recruiting additional E1 molecules to ori, effectively reducing the E1 concentration required

289 he prereplication complexes are recruited to ori-Lyt DNA through RTA, which interacts with the RRE, a

290 prereplication complexes and be recruited to ori-Lyt through RTA and K8.

291 if the position of the promoters relative to ori influences the binding of T-ag to these regions.

292 The two ori-Lyt domains share an almost identical 1,153-bp seque

293 sequence-specific binding of E1 to the viral ori, we proposed that TBPc antagonizes E1-ori associatio

294 tion of a preinitiation complex on the viral ori.

295 atible with a broad initiation zone in which ori-beta and a second locus (ori-gamma) are somewhat pre

296 fect the gene 34 reading frame (within which ori(34) is located).

297 dentify cellular factors that associate with ori-Lyt by using DNA affinity purification and mass spec

298 thereby facilitating their association with ori, and limiting the availability of topoisomerase IV (

299 of them being ori-beta and ori-gamma), with ori-beta accounting for a maximum of approximately 20% o

300 Two subregions within this zone (ori-beta/ori-beta' and ori-gamma) are preferred.