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Modulation of strand displacement synthesis of DNA polymerase ε byprocessive 3'- 5' exonuclease activity.
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
Umeå University.
(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

DNA polymerase epilson (Pol ε) is a replicative DNA polymerase with a processive 3'-5' exonuclease activity. Here we ask if Pol ε is capable of performing strand displacement synthesis, which influence many DNA processes in vivo. We found that Polε is unable to carry out extended strand displacement synthesis unless the proofreading is inactivated. However, Pol ε efficiently displaced one nucleotide when encountering double stranded DNA after filling a gap of 8 nucleotides. An abasic moiety at the 5'-end of the downstream primer was as efficiently displaced and still only with one nucleotide. Pol ε also efficiently recognized the 3'-OH innicked DNA and displaced the 5'- nucleotide, regardless if it was a normal phosphorylated deoxyribonucleotide or a ribonucleotide. A flap, mimicking a D-loop or a hairpin structure, on the 5'-end of the blocking primer inhibited Pol ε, and did not allow Pol ε to efficiently synthesize DNA up to the junction with double-stranded DNA. Finally, we show that strand displacement synthesis is limited by the processive 3'–5' exonuclease activity in Pol ε. Our results suggests that Pol ε is unable to extend D-loops during homologous recombination or participate in long-patch base excision repair based on the inhibition by the 5'–flap of the downstream primer. Our results do, however, support that Pol ε may participate in short patch base excision repair and ribonucleotide excision repair.

National Category
Natural Sciences
Research subject
URN: urn:nbn:se:umu:diva-97699OAI: diva2:777577
Available from: 2015-01-08 Created: 2015-01-05 Last updated: 2015-02-12Bibliographically approved
In thesis
1. Structural and biochemical basis for the high fidelity and processivity of DNA polymerase ε
Open this publication in new window or tab >>Structural and biochemical basis for the high fidelity and processivity of DNA polymerase ε
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε.

To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide.

B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites.

In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.

Place, publisher, year, edition, pages
Umeå: Umeå universitet, 2015. 52 p.
Umeå University medical dissertations, ISSN 0346-6612 ; 1693
DNA polymerase ε, Crystal structure, P domain, Pre-steady state kinetics, β-hairpin loop, Primer switching, Strand displacement
National Category
Cell and Molecular Biology Biochemistry and Molecular Biology
Research subject
urn:nbn:se:umu:diva-97689 (URN)978-91-7601-199-7 (ISBN)
Public defence
2015-01-30, N300, Naturvetarhuset, UMEÅ, 10:00 (English)
Knut and Alice Wallenberg FoundationSwedish Cancer SocietySwedish Research Council
Available from: 2015-01-09 Created: 2015-01-05 Last updated: 2015-01-09Bibliographically approved

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Ganai, Rais AhmadJohansson, Erik
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