FAM111A protects replication forks from protein obstacles via its trypsin-like domain

Yusuke Kojima,Evette S Radisky,Yuichi J Machida,Thomas R Caulfield,Yuka Machida,Scott H Kaufmann,Sowmiya Palani

doi:10.1038/s41467-020-15170-7

Yusuke Kojima, Evette S Radisky + Show 5 more

Open Access

https://doi.org/10.1038/s41467-020-15170-7

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Journal: Nature Communications	Publication Date: Mar 12, 2020
Citations: 72	License type: open-access

Affiliation: Mayo Clinic, Winneshiek Medical Center

Abstract

Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a replication-coupled manner; however, additional proteolytic mechanisms may exist to cope with the diversity of protein obstacles. Here, we show that FAM111A, a PCNA-interacting protein, plays an important role in mitigating the effect of protein obstacles on replication forks. This function of FAM111A requires an intact trypsin-like protease domain, the PCNA interaction, and the DNA-binding domain that is necessary for protease activity in vivo. FAM111A, but not SPRTN, protects replication forks from stalling at poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes trapped by PARP inhibitors, thereby promoting cell survival after drug treatment. Altogether, our findings reveal a role of FAM111A in overcoming protein obstacles to replication forks, shedding light on cellular responses to anti-cancer therapies.

Highlights

Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks
We previously reported that Sprtn hypomorphic mouse embryonic fibroblasts (MEFs) are not hypersensitive to PARPis, implying that SPRTN is unlikely to be involved in removal of poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes[27]
We demonstrate that the putative serine protease FAM111A (Family with sequence similarity 111 member A) protects replication forks from stalling at PARP1-DNA complexes and topoisomerase 1 cleavage complexes (TOP1ccs)

Summary

Introduction

Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPis) induce nucleoprotein complexes by trapping PARP1 protein at DNA single-strand breaks (SSBs) during the SSB repair process[8,9,10]. We previously reported that Sprtn hypomorphic mouse embryonic fibroblasts (MEFs) are not hypersensitive to PARPis, implying that SPRTN is unlikely to be involved in removal of PARP1-DNA complexes[27] It is currently unknown whether a cellular mechanism exists to remove trapped PARPs, but such a system would be expected to undermine the therapeutic effect of PARPis. In this study, we demonstrate that the putative serine protease FAM111A (Family with sequence similarity 111 member A) protects replication forks from stalling at PARP1-DNA complexes and TOP1ccs. Our findings uncover a critical role of FAM111A in promoting DNA replication fork progression at DPCs, and at PARP1-DNA nucleoprotein complexes

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