Regulation of DNA replication and repair proteins through interaction with the front side of proliferating cell nuclear antigen
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Updated: Oct 30, 2026

Detection of Post-Replicative Gaps Accumulation and Repair in Human Cells Using the DNA Fiber Assay
Published on: February 3, 2022
Z O Jónsson1, R Hindges, U Hübscher
1Department of Veterinary Biochemistry, University Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
Abstract:
The DNA polymerase accessory factor proliferating cell nuclear antigen (PCNA) has been caught in interaction with an ever increasing number of proteins. To characterize the sites and functions of some of these interactions, we constructed four mutants of human PCNA and analysed them in a variety of assays. By targeting loops on the surface of the PCNA trimer and changing three or four residues at a time to alanine, we found that a region including part of the domain-connecting loop of PCNA and loops on one face of the trimer, close to the C-termini, is involved in binding to all of the following proteins: DNA polymerase delta, replication factor C, the flap endonuclease Fen1, the cyclin dependent kinase inhibitor p21 and DNA ligase I. An inhibition of DNA ligation caused by the interaction of PCNA with DNA ligase I was found, and we show that DNA ligase I and Fen1 can inhibit DNA synthesis by DNA polymerase delta/PCNA. We demonstrate that PCNA must be located below a 5' flap on a forked template to stimulate Fen1 activity, and considering the interacting region on PCNA for Fen1, this suggests an orientation for PCNA during DNA replication with the C-termini facing forwards, in the direction of DNA synthesis.
Insights
Proliferating cell nuclear antigen (PCNA) interacts with many proteins crucial for DNA replication. Mutating PCNA surface loops identified a key interaction site involved in binding multiple replication factors and suggested PCNA
Area of Science:
- Molecular Biology
- Biochemistry
- Genetics
Background:
- Proliferating cell nuclear antigen (PCNA) is a key accessory factor for DNA polymerases.
- PCNA interacts with a growing number of proteins involved in DNA replication and repair.
Purpose of the Study:
- To characterize the interaction sites and functions of PCNA with various proteins.
- To identify specific regions on PCNA responsible for binding to DNA polymerase delta, replication factor C, Fen1, p21, and DNA ligase I.
Main Methods:
- Construction and analysis of four human PCNA mutants.
- Targeting surface loops of the PCNA trimer by changing residues to alanine.
- Assaying protein-protein interactions and functional consequences.
Main Results:
- A specific region on the PCNA trimer surface, including the domain-connecting loop and loops near the C-termini, is critical for binding multiple replication proteins.
- PCNA interaction with DNA ligase I inhibits DNA ligation.
- DNA ligase I and Fen1 can inhibit DNA polymerase delta/PCNA-mediated DNA synthesis.
- PCNA orientation at a 5' flap is necessary to stimulate Fen1 activity, suggesting C-termini face the direction of DNA synthesis.
Conclusions:
- The identified PCNA surface region is a multifunctional interaction hub for DNA replication and repair proteins.
- PCNA's orientation during replication is crucial for coordinating the activities of different enzymes.
- These findings provide insights into the mechanism of DNA replication and the role of PCNA in coordinating enzymatic activities.
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