Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes

Palani, Sowmiya; Machida, Yuka; Alvey, Julia R.; Mishra, Vandana; Welter, Allison L.; Cui, Gaofeng; Bragantini , Benoît; Botuyan, Maria Victoria; Cong, Anh T.  Q.; Mer, Georges; Schellenberg, Matthew J.; Machida, Yuichi J.

doi:10.1038/s41467-024-46207-w

Title: Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes

Journal Article · 07 March 2024 · Nature Communications

DOI: https://doi.org/10.1038/s41467-024-46207-w · OSTI ID:2470211

Palani, Sowmiya ^[1]; Machida, Yuka ^[2];

^[1]; Mishra, Vandana ^[3];

^[2];

^[1];

^[2]

Mayo Clinic, Rochester, MN (United States)
Mayo Clinic, Rochester, MN (United States); National Cancer Institute, Bethesda, MD (United States)
National Cancer Institute, Bethesda, MD (United States)

FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme’s biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A’s function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2470211

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (61)

Dwarfism and Cortical Thickening of Tubular Bones Kenny, Frederic M. American Journal of Diseases of Children, Vol. 111, Issue 2 https://doi.org/10.1001/archpedi.1966.02090050133013	journal	February 1966
A recurrent de novo FAM111A mutation causes kenny–caffey syndrome type 2 Isojima, Tsuyoshi; Doi, Koichiro; Mitsui, Jun Journal of Bone and Mineral Research, Vol. 29, Issue 4 https://doi.org/10.1002/jbmr.2091	journal	August 2013
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations Kutzner, Carsten; Páll, Szilárd; Fechner, Martin Journal of Computational Chemistry, Vol. 36, Issue 26 https://doi.org/10.1002/jcc.24030	journal	August 2015
UCSF ChimeraX: Tools for structure building and analysis Meng, Elaine C.; Goddard, Thomas D.; Pettersen, Eric F. Protein Science, Vol. 32, Issue 11 https://doi.org/10.1002/pro.4792	journal	October 2023
Standard protocol for mass photometry experiments Wu, Di; Piszczek, Grzegorz European Biophysics Journal, Vol. 50, Issue 3-4 https://doi.org/10.1007/s00249-021-01513-9	journal	March 2021
SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data Philo, John S. European Biophysics Journal, Vol. 52, Issue 4-5 https://doi.org/10.1007/s00249-023-01629-0	journal	February 2023
Visual detection of peptidase activity using fluorogenic substrates in a microtiter plate assay Irvine, G. Brent; Ennis, Michael; Williams, Carvell H. Analytical Biochemistry, Vol. 185, Issue 2 https://doi.org/10.1016/0003-2697(90)90298-N	journal	March 1990
Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling Schuck, Peter Biophysical Journal, Vol. 78, Issue 3 https://doi.org/10.1016/S0006-3495(00)76713-0	journal	March 2000
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
FAM111A Mutations Result in Hypoparathyroidism and Impaired Skeletal Development Unger, Sheila; Górna, Maria W.; Le Béchec, Antony The American Journal of Human Genetics, Vol. 92, Issue 6 https://doi.org/10.1016/j.ajhg.2013.04.020	journal	June 2013
Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan Li, Faxiang; Raczynska, Joanna E.; Chen, Zhe Cell Reports, Vol. 26, Issue 12 https://doi.org/10.1016/j.celrep.2019.02.082	journal	March 2019
Preventing replication fork collapse to maintain genome integrity Cortez, David DNA Repair, Vol. 32 https://doi.org/10.1016/j.dnarep.2015.04.026	journal	August 2015
Ubiquitin-directed AAA+ ATPase p97/VCP unfolds stable proteins crosslinked to DNA for proteolysis by SPRTN Kröning, Alexander; van den Boom, Johannes; Kracht, Matthias Journal of Biological Chemistry, Vol. 298, Issue 6 https://doi.org/10.1016/j.jbc.2022.101976	journal	June 2022
Activity-based protein profiling reveals active serine proteases that drive malignancy of human ovarian clear cell carcinoma Mehner, Christine; Hockla, Alexandra; Coban, Mathew Journal of Biological Chemistry, Vol. 298, Issue 8 https://doi.org/10.1016/j.jbc.2022.102146	journal	August 2022
Quantifying the Monomer–Dimer Equilibrium of Tubulin with Mass Photometry Fineberg, Adam; Surrey, Thomas; Kukura, Philipp Journal of Molecular Biology, Vol. 432, Issue 23 https://doi.org/10.1016/j.jmb.2020.10.013	journal	November 2020
Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN Stingele, Julian; Bellelli, Roberto; Alte, Ferdinand Molecular Cell, Vol. 64, Issue 4 https://doi.org/10.1016/j.molcel.2016.09.031	journal	November 2016
Metalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Repair Vaz, Bruno; Popovic, Marta; Newman, Joseph A. Molecular Cell, Vol. 64, Issue 4 https://doi.org/10.1016/j.molcel.2016.09.032	journal	November 2016
Replication-Coupled DNA-Protein Crosslink Repair by SPRTN and the Proteasome in Xenopus Egg Extracts Larsen, Nicolai B.; Gao, Alan O.; Sparks, Justin L. Molecular Cell, Vol. 73, Issue 3 https://doi.org/10.1016/j.molcel.2018.11.024	journal	February 2019
DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease Reinking, Hannah K.; Kang, Hyun-Seo; Götz, Maximilian J. Molecular Cell, Vol. 80, Issue 1 https://doi.org/10.1016/j.molcel.2020.08.003	journal	October 2020
DNA replication profiling by molecular combing on single DNA fibers Fu, Haiqing; Aladjem, Mirit I. STAR Protocols, Vol. 3, Issue 2 https://doi.org/10.1016/j.xpro.2022.101290	journal	June 2022
Development and Testing of the OPLS-AA/M Force Field for RNA Robertson, Michael J.; Qian, Yue; Robinson, Matthew C. Journal of Chemical Theory and Computation, Vol. 15, Issue 4 https://doi.org/10.1021/acs.jctc.9b00054	journal	February 2019
Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors Brady, Kenneth; Wei, Anzhi; Ringe, Dagmar Biochemistry, Vol. 29, Issue 33 https://doi.org/10.1021/bi00485a009	journal	August 1990
Serine Protease Mechanism and Specificity Hedstrom, Lizbeth Chemical Reviews, Vol. 102, Issue 12 https://doi.org/10.1021/cr000033x	journal	December 2002
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation Hess, Berk Journal of Chemical Theory and Computation, Vol. 4, Issue 1 https://doi.org/10.1021/ct700200b	journal	December 2007
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Causes and consequences of replication stress Zeman, Michelle K.; Cimprich, Karlene A. Nature Cell Biology, Vol. 16, Issue 1 https://doi.org/10.1038/ncb2897	journal	December 2013
Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau Nature Cell Biology, Vol. 16, Issue 3 https://doi.org/10.1038/ncb2918	journal	February 2014
Fiji: an open-source platform for biological-image analysis Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2019	journal	June 2012
The essential kinase ATR: ensuring faithful duplication of a challenging genome Saldivar, Joshua C.; Cortez, David; Cimprich, Karlene A. Nature Reviews Molecular Cell Biology, Vol. 18, Issue 10 https://doi.org/10.1038/nrm.2017.67	journal	August 2017
DNA–protein crosslink repair Stingele, Julian; Jentsch, Stefan Nature Reviews Molecular Cell Biology, Vol. 16, Issue 8 https://doi.org/10.1038/nrm4015	journal	July 2015
FAM111A protects replication forks from protein obstacles via its trypsin-like domain Kojima, Yusuke; Machida, Yuka; Palani, Sowmiya Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15170-7	journal	March 2020
Human topoisomerases and their roles in genome stability and organization Pommier, Yves; Nussenzweig, André; Takeda, Shunichi Nature Reviews Molecular Cell Biology, Vol. 23, Issue 6 https://doi.org/10.1038/s41580-022-00452-3	journal	February 2022
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
A general purpose model for the condensed phases of water: TIP4P/2005 Abascal, J. L. F.; Vega, C. The Journal of Chemical Physics, Vol. 123, Issue 23 https://doi.org/10.1063/1.2121687	journal	December 2005
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
Replica exchange with solute tempering: A method for sampling biological systems in explicit water Liu, P.; Kim, B.; Friesner, R. A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 39 https://doi.org/10.1073/pnas.0506346102	journal	September 2005
Triad of human cellular proteins, IRF2, FAM111A, and RFC3, restrict replication of orthopoxvirus SPI-1 host-range mutants Panda, Debasis; Fernandez, Daniel J.; Lal, Madhu Proceedings of the National Academy of Sciences, Vol. 114, Issue 14 https://doi.org/10.1073/pnas.1700678114	journal	March 2017
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
MEROPS: the peptidase database Rawlings, N. D.; Morton, F. R.; Kok, C. Y. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm954	journal	December 2007
A new bioinformatics analysis tools framework at EMBL-EBI Goujon, M.; McWilliam, H.; Li, W. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq313	journal	May 2010
Immunodetection of human topoisomerase I-DNA covalent complexes Patel, Anand G.; Flatten, Karen S.; Peterson, Kevin L. Nucleic Acids Research, Vol. 44, Issue 6 https://doi.org/10.1093/nar/gkw109	journal	February 2016
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database Rawlings, Neil D.; Barrett, Alan J.; Thomas, Paul D. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1134	journal	November 2017
Interaction of α-Chymotrypsin with Dimyristoyl Phosphatidylcholine Vesicles Oshima, Genichiro The Journal of Biochemistry, Vol. 95, Issue 4 https://doi.org/10.1093/oxfordjournals.jbchem.a134701	journal	April 1984
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Quantitative mass imaging of single biological macromolecules Young, Gavin; Hundt, Nikolas; Cole, Daniel Science, Vol. 360, Issue 6387 https://doi.org/10.1126/science.aar5839	journal	April 2018
Contribution of DNA Replication to the FAM111A-Mediated Simian Virus 40 Host Range Phenotype Tarnita, Roxana M.; Wilkie, Adrian R.; DeCaprio, James A. Journal of Virology, Vol. 93, Issue 1 https://doi.org/10.1128/JVI.01330-18	journal	January 2019
Trapping of PARP1 and PARP2 by Clinical PARP Inhibitors Murai, J.; Huang, S. -y. N.; Das, B. B. Cancer Research, Vol. 72, Issue 21 https://doi.org/10.1158/0008-5472.CAN-12-2753	journal	October 2012
Stereospecific PARP Trapping by BMN 673 and Comparison with Olaparib and Rucaparib Murai, Junko; Huang, Shar-Yin N.; Renaud, Amèlie Molecular Cancer Therapeutics, Vol. 13, Issue 2 https://doi.org/10.1158/1535-7163.MCT-13-0803	journal	December 2013
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite Fleishman, Sarel J.; Leaver-Fay, Andrew; Corn, Jacob E. PLoS ONE, Vol. 6, Issue 6 https://doi.org/10.1371/journal.pone.0020161	journal	June 2011
Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor Fine, Debrah A.; Rozenblatt-Rosen, Orit; Padi, Megha PLoS Pathogens, Vol. 8, Issue 10 https://doi.org/10.1371/journal.ppat.1002949	journal	October 2012
Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease Zühlsdorf, Martin; Werten, Sebastiaan; Klupp, Barbara G. PLOS Pathogens, Vol. 11, Issue 7 https://doi.org/10.1371/journal.ppat.1005045	journal	July 2015
FAM111 protease activity undermines cellular fitness and is amplified by gain‐of‐function mutations in human disease Hoffmann, Saskia; Pentakota, Satyakrishna; Mund, Andreas EMBO reports, Vol. 21, Issue 10 https://doi.org/10.15252/embr.202050662	journal	August 2020
FAM111A induces nuclear dysfunction in disease and viral restriction Nie, Minghua; Oravcová, Martina; Jami‐Alahmadi, Yasaman EMBO reports, Vol. 22, Issue 2 https://doi.org/10.15252/embr.202050803	journal	December 2020
Congenital Stenosis of Medullary Spaces in Tubular Bones and Calvaria in two Proportionate Dwarfs—Mother and son; Coupled with Transitory Hypocalcemic Tetany Caffey, John American Journal of Roentgenology, Vol. 100, Issue 1 https://doi.org/10.2214/ajr.100.1.1	journal	May 1967
FAM111A regulates replication origin activation and cell fitness Rios-Szwed, Diana O.; Alvarez, Vanesa; Sanchez-Pulido, Luis Life Science Alliance, Vol. 6, Issue 12 https://doi.org/10.26508/lsa.202302111	journal	October 2023
Functions and evolution of FAM111 serine proteases Welter, Allison L.; Machida, Yuichi J. Frontiers in Molecular Biosciences, Vol. 9 https://doi.org/10.3389/fmolb.2022.1081166	journal	December 2022
Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes Cui, Gaofeng figshare https://doi.org/10.6084/m9.figshare.24915123	dataset	January 2024
SPRTN is a mammalian DNA-binding metalloprotease that resolves DNA-protein crosslinks Lopez-Mosqueda, Jaime; Maddi, Karthik; Prgomet, Stefan eLife, Vol. 5 https://doi.org/10.7554/eLife.21491	journal	November 2016

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Title: Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes

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