USP1/UAF1 targets polyubiquitinated PCNA with an exo-cleavage mechanism that can temporarily enrich for monoubiquitinated PCNA

Niels Keijzer, Jan Sakoltchik, Kaustav Majumder, Nina van Lil, Farid El Oualid, Alexander Fish and Titia K. Sixma ()
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Niels Keijzer: Netherlands Cancer Institute and Oncode Institute
Jan Sakoltchik: Netherlands Cancer Institute and Oncode Institute
Kaustav Majumder: Netherlands Cancer Institute and Oncode Institute
Nina van Lil: Netherlands Cancer Institute and Oncode Institute
Farid El Oualid: Netherlands Cancer Institute and Oncode Institute
Alexander Fish: Netherlands Cancer Institute and Oncode Institute
Titia K. Sixma: Netherlands Cancer Institute and Oncode Institute

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract DNA damage tolerance (DDT) is an important pathway that allows cells to bypass DNA lesions during replication. DDT is orchestrated by ubiquitination of PCNA, where monoubiquitinated PCNA (PCNA-Ub) initiates recruitment of TLS polymerases but also serves as a substrate for further ubiquitination, forming K63-polyubiquitinated PCNA that leads to HR-mediated bypass mechanisms. Recent work on USP1/UAF1 inhibition revealed that formation of K48-linked chains also occurs on PCNA, resulting in its proteasomal degradation. USP1/UAF1 is established as deubiquitinating enzyme (DUB) for PCNA-Ub, but little is known about removal of ubiquitin chains on PCNA. Here we show that USP1/UAF1 cleaves both K48 and K63-linked ubiquitin chains on PCNA efficiently, using an exo-cleavage mechanism. Kinetic analysis reveals that USP1/UAF1 prefers cleaving the ubiquitin-ubiquitin bond over cleavage of the ubiquitin-PCNA bond and therefore treats poly- and monoubiquitinated PCNA as different substrates. A cryo-EM structure of USP1/UAF1 with a K63-diubiquitin and structure-based mutagenesis suggests that this mechanistic preference is maintained in evolution. This unusual mechanism can cause temporal enrichment of monoubiquitinated PCNA during polyubiquitination. It will be interesting to see how this affects DDT pathway balance.

Date: 2025
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DOI: 10.1038/s41467-025-61768-0

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