scholarly journals Exploring the role of large conformational changes in the fidelity of DNA polymerase β

2007 ◽  
Vol 70 (1) ◽  
pp. 231-247 ◽  
Author(s):  
Yun Xiang ◽  
Myron F. Goodman ◽  
William A. Beard ◽  
Samuel H. Wilson ◽  
Arieh Warshel
Keyword(s):  
Dna Polymerase ◽  
Conformational Changes ◽  
Dna Polymerase Β

scholarly journals A Role for DNA Polymerase β in Mutagenic UV Lesion Bypass

2002 ◽  
Vol 277 (51) ◽  
pp. 50046-50053 ◽  
Author(s):  
Laurence Servant ◽  
Christophe Cazaux ◽  
Anne Bieth ◽  
Shigenori Iwai ◽  
Fumio Hanaoka ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Genetic Instability ◽  
Mammalian Cells ◽  
Excision Repair ◽  
Pyrimidine Dimer ◽  
Dna Polymerase Β ◽  
Lesion Bypass ◽  
Base Excision

We report here that DNA polymerase β (pol β), the base excision repair polymerase, is highly expressed in human melanoma tissues, known to be associated with UV radiation exposure. To investigate the potential role of pol β in UV-induced genetic instability, we analyzed the cellular and molecular effects of excess pol β. We firstly demonstrated that mammalian cells overexpressing pol β are resistant and hypermutagenic after UV irradiation and that replicative extracts from these cells are able to catalyze complete translesion replication of a thymine-thymine cyclobutane pyrimidine dimer (CPD). By usingin vitroprimer extension reactions with purified pol β, we showed that CPD as well as, to a lesser extent, the thymine-thymine pyrimidine-pyrimidone (6-4) photoproduct, were bypassed. pol β mostly incorporates the correct dATP opposite the 3′-terminus of both CPD and the (6-4) photoproduct but can also misinsert dCTP at a frequency of 32 and 26%, respectively. In the case of CPD, efficient and error-prone extension of the correct dATP was found. These data support a biological role of pol β in UV lesion bypass and suggest that deregulated pol β may enhance UV-induced genetic instability.

scholarly journals Role of DNA Polymerase β in the Excision Step of Long Patch Mammalian Base Excision Repair

1999 ◽  
Vol 274 (20) ◽  
pp. 13741-13743 ◽  
Author(s):  
Grigory L. Dianov ◽  
Rajendra Prasad ◽  
Samuel H. Wilson ◽  
Vilhelm A. Bohr
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Polymerase Β ◽  
Base Excision

scholarly journals DNA Polymerase β:  Multiple Conformational Changes in the Mechanism of Catalysis†

Biochemistry ◽  
1997 ◽  
Vol 36 (39) ◽  
pp. 11891-11900 ◽  
Author(s):  
Xuejun Zhong ◽  
Smita S. Patel ◽  
Brian G. Werneburg ◽  
Ming-Daw Tsai
Keyword(s):  
Dna Polymerase ◽  
Conformational Changes ◽  
Dna Polymerase Β ◽  
Mechanism Of Catalysis

scholarly journals The nature of the DNA substrate influences pre-catalytic conformational changes of DNA polymerase β

2018 ◽  
Vol 293 (39) ◽  
pp. 15084-15094 ◽  
Author(s):  
Ji Huang ◽  
Khadijeh S. Alnajjar ◽  
Mariam M. Mahmoud ◽  
Brian Eckenroth ◽  
Sylvie Doublié ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Conformational Changes ◽  
Dna Polymerase Β ◽  
Dna Substrate

scholarly journals A pre-catalytic non-covalent step governs DNA polymerase β fidelity

2019 ◽  
Author(s):  
Khadijeh S Alnajjar ◽  
Ivan S Krylov ◽  
Amirsoheil Negahbani ◽  
Pouya Haratipour ◽  
Boris A Kashemirov ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Polymerase ◽  
Conformational Changes ◽  
Bond Formation ◽  
Underlying Mechanism ◽  
Apc Gene ◽  
Substrate Selection ◽  
Dna Polymerase Β ◽  
Specific Sequence ◽  
Phosphodiester Bond

Abstract DNA polymerase β (pol β) selects the correct deoxyribonucleoside triphosphate for incorporation into the DNA polymer. Mistakes made by pol β lead to mutations, some of which occur within specific sequence contexts to generate mutation hotspots. The adenomatous polyposis coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the underlying mechanism is not fully understood. In previous work, we demonstrated that a somatic colon cancer variant of pol β, K289M, misincorporates deoxynucleotides at significantly increased frequencies over wild-type pol β within a mutation hotspot that is present several times within the APC gene. Kinetic studies provide evidence that the rate-determining step of pol β catalysis is phosphodiester bond formation and suggest that substrate selection is governed at this step. Remarkably, we show that, unlike WT, a pre-catalytic step in the K289M pol β kinetic pathway becomes slower than phosphodiester bond formation with the APC DNA sequence but not with a different DNA substrate. Based on our studies, we propose that pre-catalytic conformational changes are of critical importance for DNA polymerase fidelity within specific DNA sequence contexts.

scholarly journals Revealing the role of the product metal in DNA polymerase β catalysis

2017 ◽  
pp. gkw1363 ◽  
Author(s):  
Lalith Perera ◽  
Bret D. Freudenthal ◽  
William A. Beard ◽  
Lee G. Pedersen ◽  
Samuel H. Wilson
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerase Β

scholarly journals Impact of ERCC1, XPF and DNA Polymerase β Expression on Platinum Response in Patient-Derived Ovarian Cancer Xenografts

Cancers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2398 ◽  
Author(s):  
Federica Guffanti ◽  
Maria Francesca Alvisi ◽  
Elisa Caiola ◽  
Francesca Ricci ◽  
Marcella De Maglie ◽  
...  
Keyword(s):  
Ovarian Carcinoma ◽  
Dna Polymerase ◽  
Excision Repair ◽  
Proximity Ligation Assay ◽  
Platinum Resistance ◽  
Mrna Levels ◽  
Dna Polymerase Β ◽  
Β Protein ◽  
Base Excision

Platinum resistance is an unmet medical need in ovarian carcinoma. Molecular biomarkers to predict the response to platinum-based therapy could allow patient stratification and alternative therapeutic strategies early in clinical management. Sensitivity and resistance to platinum therapy are partially determined by the tumor’s intrinsic DNA repair activities, including nucleotide excision repair (NER) and base excision repair (BER). We investigated the role of the NER proteins—ERCC1, XPF, ERCC1/XPF complex—and of the BER protein DNA polymerase β, as possible biomarkers of cisplatin (DDP) response in a platform of recently established patient-derived ovarian carcinoma xenografts (OC-PDXs). ERCC1 and DNA polymerase β protein expressions were measured by immunohistochemistry, the ERCC1/XPF foci number was detected by proximity ligation assay (PLA) and their mRNA levels by real-time PCR. We then correlated the proteins, gene expression and ERCC1/XPF complexes with OC-PDXs’ response to platinum. To the best of our knowledge, this is the first investigation of the role of the ERCC1/XPF complex, detected by PLA, in relation to the response to DDP in ovarian carcinoma. None of the proteins in the BER and NER pathways studied predicted platinum activity in this panel of OC-PDXs, nor did the ERCC1/XPF foci number. These results were partially explained by the experimental evidence that the ERCC1/XPF complex increases after DDP treatment and this possibly better associates with the cancer cells’ abilities to activate the NER pathway to repair platinum-induced damage than its basal level. Our findings highlight the need for DNA functional assays to predict the response to platinum-based therapy.

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