ライフサイエンスコーパス: Pol beta

1 Pol beta activity is enhanced by flap endonuclease (FEN1

2 Pol beta also misinserts a purine nucleotide opposite th

3 Pol beta also was able to perform intersegmental transfe

4 Pol beta Asn279 and Arg283 are the critical active site

5 Pol beta is also widely used as a model polymerase for s

6 Pol beta is mutated in a large number of colorectal tumo

7 Pol beta is overexpressed in some cancers and is synthet

8 Pol beta localizes to synapsed axes during zygonema and

9 Pol beta promoted incorporation of dCMP and dAMP, along

10 Pol beta-deficient spermatocytes yielded reduced steady-

11 Pol-beta-deficient cells were significantly more suscept

12 a molecule with the active site of the 1 : 1 Pol beta-DNA complex, while the latter demonstrates how

13 -dimensional structural models for the 2 : 1 Pol beta-DNA and 1 : 1 Pol X-DNA complexes were generate

14 plexes, we propose that the asymmetric 2 : 1 Pol beta-DNA complex enhances the function of Pol beta.

15 The results indicated formation of a 2 : 1 Pol beta-DNA complex, whereas only 1 : 1 Pol X-DNA compl

16 We previously reported the presence of a Pol beta transcript containing exon alpha (105-nucleotid

17 at, when repair synthesis proceeds through a Pol beta-dependent single nucleotide replacement mechani

18 lly those with dRP lyase activity, we used a Pol beta null cell extract and BER intermediate as bait

19 2 that results from formation of an abortive Pol beta-gapped DNA-dATP complex is consistent with an o

20 Kinetic studies of exon alpha Pol beta revealed that it is deficient in DNA binding to

21 dicating expression of the 42 kDa exon alpha Pol beta variant in mouse embryonic fibroblasts.

22 These results indicate the exon alpha Pol beta variant is base excision repair deficient, but

23 the 5'-dRP lyase activity of the exon alpha Pol beta variant is similar to that of wild-type Pol bet

24 The exon alpha Pol beta variant was then overexpressed in E. coli, puri

25 e exon alpha-containing Pol beta (exon alpha Pol beta) variant.

26 A second group of polymerases (Pol alpha, Pol beta, and T7(-)) fails to extend all non-H-bonding b

27 utations are further correlated with altered Pol beta enzymatic activity.

28 DNA binding specificity inherent in APE and Pol beta, although coordination also may be facilitated

29 and Pol iota (family Y), and Pol lambda and Pol beta (family X).

30 te in cell extracts prepared from normal and Pol beta-null mouse cells and show that the reduced repa

31 ncised abasic site product (APE1 product and Pol beta substrate) were subsequently bound by Pol beta,

32 ion of Fapy*dG mutagenicity in wild type and Pol beta knockdown HEK 293T cells indicates that Pol bet

33 S. cerevisiae whereas expression of another Pol beta dominant negative mutant, Pol beta-TR, does not

34 ent in Pol lambda exclusively and not in any Pol beta homolog.

35 coordination also may be facilitated by APE.Pol beta.DNA ternary complex formation with appropriate

36 zyme concentrations a ternary complex of APE.Pol beta.DNA that formed specifically at BER intermediat

37 alysis suggests that these motions allow apo Pol beta to sample a conformation similar to the gapped

38 In apo Pol beta, molecular motions, primarily isolated to the D

39 ciency in mitochondrial extracts from APTX-/-Pol beta-/- cells.

40 at they follow the same kinetic mechanism as Pol beta, while differing in relative rates of single-nu

41 DNA polymerases theta (Pol theta) and beta (Pol beta) as mediators of alternative nonhomologous end-

42 me-DNA complexes of rat DNA polymerase beta (Pol beta) and African swine fever virus DNA polymerase X

43 of DNA polymerases: rat DNA polymerase beta (Pol beta) and African swine fever virus DNA polymerase X

44 t TRF2 physically bound DNA polymerase beta (Pol beta) and flap endonuclease 1 (FEN-1).

45 and also interacts with DNA polymerase beta (Pol beta) and other base excision repair (BER) proteins.

46 cised abasic site, both DNA polymerase beta (Pol beta) and the DNA ligase IIIalpha-XRCC1 heterodimer

47 DNA polymerase beta (Pol beta) carries out strand displacement synthesis, fol

48 in RNA-mediated loss of DNA polymerase beta (Pol beta) expression in human breast cancer cells increa

49 topped-flow analyses of DNA polymerase beta (Pol beta) had provided important mechanistic insight, th

50 eotide incorporation by DNA polymerase beta (Pol beta) has been well-studied, a true understanding of

51 excision repair enzyme DNA polymerase beta (Pol beta) in complex with a 1-nt gapped DNA substrate co

52 ate states of mammalian DNA polymerase beta (Pol beta) in its wild-type and an error-prone variant, I

53 negative mutants of rat DNA polymerase beta (Pol beta) interfere with repair of alkylation damage in

54 DNA polymerase beta (Pol beta) is a 39-kDa enzyme that performs the vital cel

55 During DNA repair, DNA polymerase beta (Pol beta) is a highly dynamic enzyme that is able to sel

56 DNA polymerase beta (Pol beta) is a key enzyme in DNA base excision repair, a

57 sphate (dRP) removal by DNA polymerase beta (Pol beta) is a pivotal step in base excision repair (BER

58 rminal domain (NTD) and DNA polymerase beta (Pol beta) is central to base excision repair of damaged

59 DNA polymerase beta (Pol beta) is one of the key enzymes in the base excision

60 DNA polymerase beta (Pol beta) is responsible for the repair synthesis in thi

61 DNA polymerase beta (Pol beta) is the primary enzyme responsible for processi

62 formational step in the DNA polymerase beta (Pol beta) kinetic pathway.

63 have shown earlier that DNA polymerase beta (Pol beta) localizes to the synaptonemal complex (SC) dur

64 DNA polymerase beta (Pol beta) participates in this process by removing the r

65 DNA polymerase beta (Pol beta) plays a key role in base excision repair (BER)

66 Eukaryotic DNA polymerase beta (Pol beta) plays an important role in cellular DNA repair

67 In contrast, DNA polymerase beta (Pol beta) synthesis is inhibited in a major fraction ( a

68 ons and associates with DNA polymerase beta (Pol beta) to function in DNA repair.

69 DNA polymerase beta (Pol beta) was implicated recently as the major polymeras

70 DNA polymerase beta (Pol beta), a key enzyme in the DNA base excision repair

71 DNA polymerase beta (Pol beta), a member of the DNA polymerase X family that

72 his we investigated how DNA polymerase beta (Pol beta), a model mammalian polymerase, bypasses a temp

73 ibly inhibits repair by DNA polymerase beta (Pol beta), an integral enzyme in base-excision repair.

74 erminal 8 kDa domain of DNA polymerase beta (Pol beta), and for the homologous domain of DNA polymera

75 The DNA repair enzyme, DNA polymerase beta (Pol beta), is among the most discriminating, being inact

76 e that can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase.

77 man cancers overexpress DNA polymerase beta (Pol beta), the major DNA polymerase involved in base exc

78 the catalytic cycle of DNA polymerase beta (Pol beta), using a synthetic DNA primer/template contain

79 ce assays for mammalian DNA polymerase beta (Pol beta), we have previously identified a fast fluoresc

80 endonuclease (APE), and DNA polymerase beta (Pol beta), which catalyze the first three steps in BER,

81 ndonuclease 1 (APE) and DNA polymerase beta (Pol beta).

82 he AP lyase activity of DNA polymerase beta (Pol beta).

83 donuclease 1 (APE1) and DNA polymerase beta (Pol beta).

84 s the template base for DNA polymerase beta (Pol beta).

85 avily reliant upon host DNA polymerase beta (Pol beta).

86 that APC interacts with DNA polymerase beta (Pol-beta) and flap endonuclease 1 (Fen-1) and blocks Pol

87 directly interact with DNA polymerase-beta (Pol-beta), a central player in the DNA base excision rep

88 itution also affects the interaction between Pol beta and proliferating cell nuclear antigen (PCNA).

89 more similar to those observed in the binary Pol beta-dATP complex.

90 ) and flap endonuclease 1 (Fen-1) and blocks Pol-beta-directed strand-displacement synthesis.

91 The primary binding sites for both Pol beta and FEN-1 mapped to the TRF2 NH2-terminal and C

92 our findings indicate that APC blocked both Pol-beta-directed SN- and LP-BER pathways and increased

93 we show that removal of the 5'-dRP block by Pol beta is unaffected by NCP constraints at all sites t

94 l beta substrate) were subsequently bound by Pol beta, the Pol beta enzyme dissociated shortly after

95 s to play a minimal role in the catalysis by Pol beta.

96 gap filling and dRP removal are catalyzed by Pol beta, which belongs to the X family of DNA polymeras

97 t these regions can be scanned for damage by Pol beta.

98 mechanisms of damage search and location by Pol beta are largely unknown, but are critical for under

99 p-filling DNA synthesis in the nucleosome by Pol beta.

100 To date, the mechanism used by Pol beta to process a 1-nt gap in the context of chromat

101 BER and c-NHEJ repair pathway is mediated by Pol-beta and Ku70.

102 E1 dissociation during substrate channeling, Pol beta remained bound for a longer period of time to a

103 s leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also report

104 Here, we constructed Pol beta R137Q knock-in mice, and found that homozygous

105 ical properties of the exon alpha-containing Pol beta (exon alpha Pol beta) variant.

106 r stability of newly synthesized cytoplasmic Pol beta that is used as a source for nuclear Pol beta i

107 excision repair (BER) proteins XRCC1 and DNA Pol beta, adding a new level of regulation for BER.

108 t following incision by AP endonuclease, DNA Pol beta recognizes and binds to the incised abasic site

109 man tumors characterized to date express DNA Pol beta variants, many of which result from a single nu

110 ence for a stable preexisting complex of DNA Pol beta with the DNA ligase IIIalpha-XRCC1 heterodimer.

111 W1 and ISW2 from yeast significantly enhance Pol beta accessibility to the refractory nicked sites in

112 approach we find that in human cell extracts Pol beta is the major DNA polymerase incorporating the f

113 orporation into damaged DNA is essential for Pol beta repair function, and several studies have impli

114 localization patterns reflect a function for Pol beta in recombination and/or synapsis, we used condi

115 on-covalent step not previously reported for Pol beta.

116 lexes, this work further validates that, for Pol beta, fidelity is dictated by the differences in fre

117 quantification of fingers movement in human Pol beta reported here provide new insights into the del

118 g and prechemistry fingers movement of human Pol beta.

119 of either wild-type human Pol beta or human Pol beta with an inactivating mutation specific to the p

120 by complementation of either wild-type human Pol beta or human Pol beta with an inactivating mutation

121 ed a processive search assay to determine if Pol beta has evolved a mechanism for efficient DNA damag

122 A (RPA), RAD51 and DMC1 are less abundant in Pol beta-deficient spermatocyte nuclei.

123 of a rate-limiting conformational change in Pol beta's reaction pathway.

124 es have implicated conformational changes in Pol beta as a determinant of this repair fidelity.

125 e to the intimate role of protein motions in Pol beta fidelity.

126 rk, the rate constants for domain motions in Pol beta have been determined by solution NMR relaxation

127 Mutations in Pol beta have been linked to various cancers, and these

128 RPase activity, does not stimulate repair in Pol beta-null cells.

129 se cells and show that the reduced repair in Pol beta-null extracts can be complemented by addition o

130 , we have mapped the APC interaction site in Pol-beta and have found that Thr79, Lys81, and Arg83 of

131 c analyses reveal that the molecules inhibit Pol beta noncompetitively.

132 l-beta blocked SN-BER activity by inhibiting Pol-beta-directed deoxyribose phosphate lyase activity.

133 ay lead to cancer and genetic instabilities, Pol beta has been extensively studied, especially its me

134 iplatin sensitivity and DNA repair involving Pol beta.

135 oxaliplatin treatment compared with isogenic Pol beta-expressing cells.

136 ) or etoposide promote the formation of Ku70-Pol-beta complexes at the repair foci.

137 Second, using acceptor-labeled Pol beta and donor-labeled DNA, we visualized dynamic fi

138 MR studies on [methyl-13C]methionine-labeled Pol beta complexed with double-hairpin DNA, used to mode

139 Mutant Pol beta deficient in DNA synthesis, but with normal dRP

140 ition of purified wild type but not a mutant Pol beta protein that does not interact with the DNA lig

141 to WT Pol beta, suggesting that this mutant Pol beta can be used to incorporate Rp-dNTPalphaS into D

142 f another Pol beta dominant negative mutant, Pol beta-TR, does not.

143 e of the Pol beta dominant negative mutants, Pol beta-14, increases the spontaneous mutation rate of

144 mentation assay, we demonstrate that mutated Pol beta without dRPase activity is able to stimulate lo

145 static relationship of the dominant negative Pol beta mutants to genes known to be involved in repair

146 nd provide a starting point for creating new Pol beta inhibitors that function in cells.

147 milar in fold to those of other noncanonical Pol beta RNA polymerases, and the two zinc knuckle motif

148 We report noncovalent Pol beta inhibitors that are nonnative nucleotides.

149 ol beta that is used as a source for nuclear Pol beta involved in DNA repair.

150 with the intersegmental searching ability of Pol beta being at least 6- and approximately 2-fold high

151 ths, the intramolecular searching ability of Pol beta is at least 4-fold higher than that of Pol mu a

152 A knockdown of Mule leads to accumulation of Pol beta and increased DNA repair.

153 t the dRPase and DNA synthesis activities of Pol beta are coupled and that both of these Pol beta fun

154 he 5'-deoxyribosephosphate lyase activity of Pol beta is essential for repair of both lesions.

155 esions, and that the 5'dRP lyase activity of Pol beta is required to restore resistance to temozolomi

156 synapsis defects and Prophase I apoptosis of Pol beta-deficient spermatocytes are likely a direct con

157 se defects impair the DNA repair capacity of Pol beta in reconstitution assays, as well as in cellula

158 The amino-terminal 8 kDa domain of Pol beta has an activity for excising a 5'-deoxyribose p

159 ing a novel function for the lyase domain of Pol beta.

160 o to the significantly reduced expression of Pol beta.

161 our standing hypothesis that the fidelity of Pol beta originates from destabilization of the mismatch

162 se data suggest that the repair footprint of Pol beta mainly resides within accessible regions of the

163 the apo and substrate-bound, binary forms of Pol beta.

164 ol beta-DNA complex enhances the function of Pol beta.

165 es like EXO1 and FAN1, and the importance of Pol beta, they suggest a plausible model for late steps

166 Irreversible inhibition of Pol beta by DOB suggests that this lesion provides a che

167 the design of a new family of inhibitors of Pol beta.

168 OR cells, small interfering RNA knockdown of Pol beta delayed the repair of oxaliplatin-induced DNA d

169 te its biological significance, knowledge of Pol beta activities on NCPs is still limited.

170 st an alteration in the dynamic landscape of Pol beta due to substrate binding.

171 We further show that the cellular levels of Pol beta and its ubiquitylated derivative are modulated

172 found to have higher constitutive levels of Pol beta protein, faster in vitro repair of a DNA substr

173 ubiquitylated Pol beta, decreased levels of Pol beta, and a subsequent deficiency in BER, leading to

174 Localization of Pol beta to meiotic chromosomes requires the formation o

175 r data suggest that the kinetic mechanism of Pol beta is not an exception among polymerases, and furt

176 ovide useful information to the mechanism of Pol beta.

177 w fluorescence change occurs after mixing of Pol beta.DNA.Rh(III)dNTP with Mg(II).

178 neither dRPase nor DNA synthesis mutants of Pol beta alone, or the two together, were able to comple

179 e-limiting in the overall kinetic pathway of Pol beta, yet is kinetically significant in subdomain re

180 for mutagenesis to occur in the presence of Pol beta-14 but that it is not merely the presence of a

181 ymerases to answer whether the properties of Pol beta are exceptional or general.

182 d to be associated with the stabilization of Pol beta protein on chromatin.

183 ed on the basis of the tertiary structure of Pol beta and the corresponding regions of Pol X were inf

184 tent with recent crystallographic studies of Pol beta complexed with 5-phosphorylated abasic sugar an

185 three probes in the stopped-flow studies of Pol beta to obtain new, direct evidence for our previous

186 , enhanced both its own activity and that of Pol beta on nucleosome substrates.

187 on in this cell type because the Km value of Pol beta is much higher than the dNTP concentrations fou

188 not only promotes the polymerase activity of Pol-beta and BER efficiency but also enhances the classi

189 d have found that Thr79, Lys81, and Arg83 of Pol-beta were critical for its interaction with APC.

190 es proteins involved in BER, including OGG1, Pol beta, APE1, and LIGI, on both telomeric and non-telo

191 One Pol beta mutation that has been identified in tumors, R1

192 tuated within the middle of the BER pathway, Pol beta must efficiently locate its substrates before d

193 biquitylation of the key BER DNA polymerase (Pol beta) and demonstrate that USP47 is required for sta

194 f the stereoselectivity of a DNA polymerase, Pol beta from rat brain, toward Rp and Sp isomers of dAT

195 Three human DNA polymerases (Pol beta, Pol delta and Pol epsilon) have been proposed

196 The molecules are among the most potent Pol beta inhibitors (K(i) <= 70 nM) of the enzyme's poly

197 Nuclear GAPDH promotes Pol beta polymerase activity and increases base excision

198 amino acid site that is essential for proper Pol beta functioning in maintaining genomic stability an

199 can be complemented by addition of purified Pol beta.

200 We demonstrate that the rat Pol beta mutants interfere with the base excision repair

201 the 8 kDa 5'-dRP lyase domain of the second Pol beta molecule with the active site of the 1 : 1 Pol

202 Similarly, Pol-beta knockdown impairs total-NHEJ capacity but only

203 visualized dynamic fingers closing in single Pol beta-DNA complexes upon addition of complementary nu

204 well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of

205 ished to determine whether the S229L somatic Pol beta variant identified in a stage 3 colorectal tumo

206 TRF2 also stimulated Pol beta strand displacement DNA synthesis in reconstitu

207 TRF2 stimulated Pol beta primer extension DNA synthesis on telomeric and

208 omplex was associated with slightly stronger Pol beta gap-filling and much stronger 5'-deoxyribose ph

209 Consistent with previous studies, Pol beta-deficient mouse fibroblasts were not hypersensi

210 In a different model system, Pol beta-deficient fibroblasts were less able to repair

211 When Fapy*dG is present in the template, Pol beta incorporates TMP less efficiently than either d

212 ncentrations in whole cell extracts and that Pol beta has a 7-fold higher affinity to the incised aba

213 We further demonstrate that Pol beta and the DNA ligase IIIalpha-XRCC1 heterodimer a

214 They demonstrate that Pol beta modulates the sensitivity of cells to oxaliplat

215 This work establishes that Pol beta uses a global DNA sculpting mechanism for proce

216 We find that Pol beta-deficient spermatocytes are defective in meioti

217 These results imply that Pol beta-dependent 5'dRP lyase activity is the rate-limi

218 ether, these findings strongly indicate that Pol beta is required at a very early step in the process

219 These results indicate that Pol beta-dependent base excision repair of uracil opposi

220 beta knockdown HEK 293T cells indicates that Pol beta contributes to G -> T transversions but also su

221 rsists on meiotic chromatin, indicating that Pol beta is critical for the repair of SPO11-induced dou

222 into nucleosome core particles revealed that Pol beta is not processive in the context of a nucleosom

223 These assays revealed that Pol beta scans DNA using a processive hopping mechanism

224 a doubly labeled DNA construct, we show that Pol beta bends the gapped DNA substrate less than indica

225 the polymerase-DNA complex, suggesting that Pol beta, when bound to a lesion, has a strong commitmen

226 These results suggest that Pol-beta and Ku70 coordinate 2-way crosstalk between the

227 ed guanine was dramatically decreased at the Pol beta insertion step, but not blocked.

228 te) were subsequently bound by Pol beta, the Pol beta enzyme dissociated shortly after binding in mos

229 tion repair pathway that is disrupted by the Pol beta dominant negative mutants, we studied the epist

230 eterodimer was decreased about 2-fold in the Pol beta-deficient cell extract but was rescued by addit

231 In addition, expression of one of the Pol beta dominant negative mutants, Pol beta-14, increas

232 RET)-based system to monitor movement of the Pol beta fingers domain during catalysis in the presence

233 Expression of the Pol beta-14 mutant in cells lacking APN1 activity does n

234 PCNA could promote the Pol beta-dependent long-patch pathway by stimulation of

235 of predicted structural similarity with the Pol beta superfamily as critical for Trf4p/Pol sigma's e

236 lyase activities than was observed with the Pol beta.DNA binary complex.

237 The Pol-beta protein (T79A/K81A/R83A) blocked strand-displac

238 Pol beta are coupled and that both of these Pol beta functions are essential during short patch BER

239 standing the biological implications of this Pol beta variant warrants further investigation.

240 cks in linker DNA are far more accessible to Pol beta in highly folded oligonucleosomes.

241 ransfer of the BER intermediate from APE1 to Pol beta during BER is dependent on the dissociation kin

242 Expression of wild-type Pol beta in pol beta(-/-) mouse embryonic fibroblast (ME

243 beta variant is similar to that of wild-type Pol beta.

244 7 causes an increased level of ubiquitylated Pol beta, decreased levels of Pol beta, and a subsequent

245 elation to the crystal structures of various Pol beta complexes, as well as previous steady-state kin

246 In the events where Pol beta binding was followed by APE1 dissociation durin

247 cesses, including base excision repair where Pol beta catalyzes two key enzymatic steps: 5'-dRP lyase

248 We examined whether Pol beta, expressed at levels found in tumor cells, is i

249 wo crystal forms of XRCC1-NTD complexed with Pol beta have been solved, revealing that the XRCC1-NTD

250 IIIalpha complex that does not interact with Pol beta and tested their activities in BER reconstitute

251 g XRCC1 protein, that does not interact with Pol beta has reduced ability to rescue the hydrogen pero

252 n which disrupts functional interaction with Pol beta, affected the ligation efficiency of the mutant

253 XRCC1-NTD forms additional interactions with Pol beta, enhancing affinity by an order of magnitude.

254 merase active site, and superimposition with Pol beta in a ternary complex suggests a shift in the po

255 R indicated that the interaction of APC with Pol-beta blocked SN-BER activity by inhibiting Pol-beta-

256 activity toward Rp-dATPalphaS relative to WT Pol beta, suggesting that this mutant Pol beta can be us

257 anism of misincorporation for wild-type (WT) Pol beta and an error-prone I260Q variant using stopped-

258 data suggest an important role for the XRCC1-Pol beta interaction for coordinating the efficiency of