Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
20 12 2022
20 12 2022
Historique:
received:
19
02
2022
accepted:
05
12
2022
entrez:
20
12
2022
pubmed:
21
12
2022
medline:
23
12
2022
Statut:
epublish
Résumé
During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIP
Identifiants
pubmed: 36539424
doi: 10.1038/s41467-022-35475-z
pii: 10.1038/s41467-022-35475-z
pmc: PMC9767926
doi:
Substances chimiques
Okazaki fragments
0
Proliferating Cell Nuclear Antigen
0
DNA Polymerase III
EC 2.7.7.7
Ligases
EC 6.-
DNA
9007-49-2
Flap Endonucleases
EC 3.1.-
LIG1 protein, human
0
DNA Ligase ATP
EC 6.5.1.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7833Subventions
Organisme : Medical Research Council
ID : MC_PC_17136
Pays : United Kingdom
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2022. The Author(s).
Références
Stodola, J. L. & Burgers, P. M. Mechanism of lagging-strand DNA replication in eukaryotes. Adv. Exp. Med. Biol. 1042, 117–133 (2017).
Guilliam, T. A. & Yeeles, J. T. P. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit. Rev. Biochem. Mol. Biol. 55, 469–481 (2020).
doi: 10.1080/10409238.2020.1811630
Prelich, G. et al. Functional identity of proliferating cell nuclear antigen and a DNA polymerase-δ auxiliary protein. Nature 326, 517–520 (1987).
doi: 10.1038/326517a0
Choe, K. N. & Moldovan, G. Review forging ahead through darkness: PCNA, still the principal conductor at the replication fork. Mol. Cell 65, 380–392 (2017).
doi: 10.1016/j.molcel.2016.12.020
Stodola, J. L. & Burgers, P. M. Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nat. Struct. Mol. Biol. 23, 402–409 (2016).
doi: 10.1038/nsmb.3207
Sallmyr, A., Rashid, I., Bhandari, S. K., Naila, T. & Tomkinson, A. E. Human DNA ligases in replication and repair. DNA Repair 93, 102908 (2020).
doi: 10.1016/j.dnarep.2020.102908
Howes, T. R. L. & Tomkinson, A. E. DNA ligase I, the replicative DNA ligase. Subcell Biochem. 62, 327–341 (2012).
Johnson, A. & O’Donnell, M. DNA ligase: getting a grip to seal the deal. Curr. Biol. 15, R90–R92 (2005).
doi: 10.1016/j.cub.2005.01.025
Pascal, J. M., O’Brien, P. J., Tomkinson, A. E. & Ellenberger, T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473–478 (2004).
doi: 10.1038/nature03082
Levin, D. S., Bai, W., Yao, N., O’Donnell, M. & Tomkinson, A. E. An interaction between DNA ligase I and proliferating cell nuclear antigen: implications for Okazaki fragment synthesis and joining. Proc. Natl Acad. Sci. USA 94, 12863–12868 (1997).
doi: 10.1073/pnas.94.24.12863
Montecucco, A. et al. DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: identification of a common targeting mechanism for the assembly of replication factories. EMBO J. 17, 3786–3795 (1998).
doi: 10.1093/emboj/17.13.3786
Tom, S., Henricksen, L. A., Park, M. S. & Bambara, R. A. DNA ligase I and proliferating cell nuclear antigen form a functional complex. J. Biol. Chem. 276, 24817–24825 (2001).
doi: 10.1074/jbc.M101673200
Levin, D. S. et al. A conserved interaction between the replicative clamp loader and DNA ligase in eukaryotes: Implications for Okazaki fragment joining. J. Biol. Chem. 279, 55196–55201 (2004).
doi: 10.1074/jbc.M409250200
Levin, D. S., McKenna, A. E., Motycka, T. A., Matsumoto, Y. & Tomkinson, A. E. Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr. Biol. 10, 919–S2 (2000).
doi: 10.1016/S0960-9822(00)00619-9
Vijayakumar, S. et al. The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res. 35, 1624–1637 (2007).
doi: 10.1093/nar/gkm006
Song, W., Pascal, J. M., Ellenberger, T. & Tomkinson, A. E. The DNA binding domain of human DNA ligase I interacts with both nicked DNA and the DNA sliding clamps, PCNA and hRad9-hRad1-hHus1. DNA Repair 8, 912–919 (2009).
doi: 10.1016/j.dnarep.2009.05.002
Pascal, J. M. et al. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol. Cell 24, 279–291 (2006).
doi: 10.1016/j.molcel.2006.08.015
Sverzhinsky, A., Tomkinson, A. E. & Pascal, J. M. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure 30, 1–15 (2021).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2
Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. V. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923–927 (2020).
doi: 10.1038/s41592-020-0914-9
Teraoka, H. et al. Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct. J. Biol. Chem. 268, 24156–24162 (1993).
doi: 10.1016/S0021-9258(20)80505-5
Taylor, M. R., Conrad, J. A., Wahl, D. & O’Brien, P. J. Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency. J. Biol. Chem. 286, 23054–23062 (2011).
doi: 10.1074/jbc.M111.248831
Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021).
doi: 10.1038/s41592-020-01049-4
Nakane, T., Kimanius, D., Lindahl, E. & Scheres, S. H. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. Elife https://doi.org/10.7554/eLife.36861.001 (2018).
doi: 10.7554/eLife.36861.001
Prestel, A. et al. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cell. Mol. Life Sci. 76, 4923–4943 (2019).
doi: 10.1007/s00018-019-03150-0
Boehm, E. M. & Washington, M. T. R.I.P. to the PIP: PCNA-binding motif no longer considered specific: PIP motifs and other related sequences are not distinct entities and can bind multiple proteins involved in genome maintenance. BioEssays 38, 1117–1122 (2016).
doi: 10.1002/bies.201600116
Balakrishnan, L. & Bambara, R. A. Flap Endonuclease 1. Annu. Rev. Biochem. 82, 119–138 (2013).
doi: 10.1146/annurev-biochem-072511-122603
Tsutakawa, S. E. et al. Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 145, 198–211 (2011).
doi: 10.1016/j.cell.2011.03.004
Rashid, F. et al. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife 6, e21884 (2017).
Tsutakawa, S. E. et al. Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability. Nat Commun 8, 15855 (2017).
Rashid, F. et al. Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation. Nat. Commun. 10, 2104 (2019).
Sakurai, S. et al. Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO J. 24, 683–693 (2005).
doi: 10.1038/sj.emboj.7600519
Craggs, T. D., Hutton, R. D., Brenlla, A., White, M. F. & Penedo, J. C. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res. 42, 1857–1872 (2014).
doi: 10.1093/nar/gkt1116
Zaher, M. S. et al. Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Nucleic Acids Res. 46, 2956–2974 (2018).
doi: 10.1093/nar/gky082
Sobhy, M. A. et al. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Comput. Struct. Biotechnol. J. 19, 4456–4471 (2021).
Querol-Audí, J. et al. Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proc. Natl Acad. Sci. USA 109, 8528–8533 (2012).
doi: 10.1073/pnas.1121116109
Kochaniak, A. B. et al. Proliferating cell nuclear antigen uses two distinct modes to move along DNA. J. Biol. Chem. 284, 17700–17710 (2009).
doi: 10.1074/jbc.M109.008706
Nishida, H., Kiyonari, S., Ishino, Y. & Morikawa, K. The closed structure of an archaeal DNA ligase from Pyrococcus furiosus. J. Mol. Biol. 360, 956–967 (2006).
doi: 10.1016/j.jmb.2006.05.062
Mayanagi, K. et al. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc. Natl Acad. Sci. USA 106, 4647–4652 (2009).
doi: 10.1073/pnas.0811196106
Beattie, T. R. & Bell, S. D. Coordination of multiple enzyme activities by a single PCNA in archaeal Okazaki fragment maturation. EMBO J. 31, 1556–1567 (2012).
doi: 10.1038/emboj.2012.12
Dovrat, D., Stodola, J. L., Burgers, P. M. J. & Aharoni, A. Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation. Proc. Natl Acad. Sci. USA 111, 1–6 (2014).
doi: 10.1073/pnas.1321349111
Lancey, C. et al. Structure of the processive human Pol δ holoenzyme. Nat. Commun. 11, 1109 (2020).
Raducanu, V. S. et al. Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Nat. Commun. 13, 6973 (2022).
Lancey, C. et al. Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA. Nat. Commun. 12, 6095 (2021).
Chen, X. et al. Human DNA ligases I, III, and IV-purification and new specific assays for these enzymes. Methods Enzymol. 409, 39–52 (2006).
Kim, D. et al. DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging. Nucleic Acids Res. 47, e107 (2019).
doi: 10.1093/nar/gkz625
Jarmoskaite, I., Alsadhan, I., Vaidyanathan, P. P. & Herschlag, D. How to measure and evaluate binding affinities. Elife 9, 1–34 (2020).
doi: 10.7554/eLife.57264
Raducanu, V. S. et al. TSGIT: an N- and C-terminal tandem tag system for purification of native and intein-mediated ligation-ready proteins. Protein Sci. 30, 497–512 (2021).
doi: 10.1002/pro.3989
Sassa, A., Beard, W. A., Shock, D. D. & Wilson, S. H. Steady-state, pre-steady-state, and single-turnover kinetic measurement for DNA glycosylase activity. J. Vis. Exp. https://doi.org/10.3791/50695 (2013).
doi: 10.3791/50695
Schnell, S. & Mendoza, C. Closed form solution for time-dependent enzyme kinetics. J. Theor. Biol. 187, 207–212 (1997).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).
Zheng, S. Q. et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
doi: 10.1016/j.jsb.2015.08.008
Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Gulbis, J. M. & Kelman, Z. Structure of the C-Terminal region of p21 WAF1/CIP1 complexed with human PCNA. Cell 87, 297–306 (1996).
Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D. Struct. Biol. 74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
doi: 10.1038/s41592-022-01488-1
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. https://doi.org/10.1101/2021.10.04.463034 (2022).
Mirdita, M., Steinegger, M. & Söding, J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35, 2856–2858 (2019).
doi: 10.1093/bioinformatics/bty1057
Hart, K. et al. Optimization of the CHARMM additive force field for DNA: improved treatment of the BI/BII conformational equilibrium. J. Chem. Theory Comput. 8, 348–362 (2012).
doi: 10.1021/ct200723y
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2016).
doi: 10.1038/nmeth.4067
Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91, 43–56 (1995).
van der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005).
Abraham, M. J. et al. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
doi: 10.1016/j.softx.2015.06.001
McGibbon, R. T. et al. MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys. J. 109, 1528–1532 (2015).
doi: 10.1016/j.bpj.2015.08.015
Pedregosa, F. et al. Scikit-learn: Machine Learning in Python Gaël Varoquaux Bertrand Thirion Vincent Dubourg Alexandre Passos PEDREGOSA, VAROQUAUX, GRAMFORT ET AL. Matthieu Perrot. J. Mach. Learn. Res. 12, 2825–2830 (2011).
Ishida, T. & Kinoshita, K. PrDOS: Prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res. 35, W460-4 (2007).