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Activity and fidelity of human DNA polymerase ? depend on primer structure.

ABSTRACT: DNA polymerase ? (Pol?) plays an important role in genome replication. In a complex with primase, Pol? synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Pol? needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Pol?'s interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Pol? catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Pol? is in the open conformation. Pol? induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Pol? extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Pol? has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Pol? with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.

SUBMITTER: Baranovskiy AG

PROVIDER: S-EPMC5936803 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Activity and fidelity of human DNA polymerase α depend on primer structure.

Baranovskiy Andrey G AG Duong Vincent N VN Babayeva Nigar D ND Zhang Yinbo Y Pavlov Youri I YI Anderson Karen S KS Tahirov Tahir H TH

The Journal of biological chemistry 20180319 18

DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We repor ...[more]

PMID: 29555682

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Project description:The X-family DNA polymerases ? (Pol?) and ? (Pol?) possess similar 5'-2-deoxyribose-5-phosphate lyase (dRPase) and polymerase domains. Besides these domains, Pol? also possesses a BRCA1 C-terminal (BRCT) domain and a proline-rich domain at its N terminus. However, it is unclear how these non-enzymatic domains contribute to the unique biological functions of Pol?. Here, we used primer extension assays and a newly developed high-throughput short oligonucleotide sequencing assay (HT-SOSA) to compare the efficiency of lesion bypass and fidelity of human Pol?, Pol? and two N-terminal deletion constructs of Pol? during the bypass of either an abasic site or an 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) lesion. We demonstrate that the BRCT domain of Pol? enhances the efficiency of abasic site bypass by approximately 1.6-fold. In contrast, deletion of the N-terminal domains of Pol? did not affect the efficiency of 8-oxodG bypass relative to nucleotide incorporations opposite undamaged dG. HT-SOSA analysis demonstrated that Pol? and Pol? preferentially generated -1 or -2 frameshift mutations when bypassing an abasic site and the single or double base deletion frequency was highly sequence dependent. Interestingly, the BRCT and proline-rich domains of Pol? cooperatively promoted the generation of -2 frameshift mutations when the abasic site was situated within a sequence context that was susceptible to homology-driven primer realignment. Furthermore, both N-terminal domains of Pol? increased the generation of -1 frameshift mutations during 8-oxodG bypass and influenced the frequency of substitution mutations produced by Pol? opposite the 8-oxodG lesion. Overall, our data support a model wherein the BRCT and proline-rich domains of Pol? act cooperatively to promote primer/template realignment between DNA strands of limited sequence homology. This function of the N-terminal domains may facilitate the role of Pol? as a gap-filling polymerase within the non-homologous end joining pathway.

Dataset Information

Activity and fidelity of human DNA polymerase ? depend on primer structure.

Publications

Activity and fidelity of human DNA polymerase α depend on primer structure.

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