Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
23
04
2020
accepted:
29
06
2020
pubmed:
19
8
2020
medline:
18
12
2020
entrez:
19
8
2020
Statut:
ppublish
Résumé
DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its importance in TLS, the structure of Polζ is unknown. We present cryo-EM structures of the Saccharomyces cerevisiae Polζ holoenzyme in the act of DNA synthesis (3.1 Å) and without DNA (4.1 Å). Polζ displays a pentameric ring-like architecture, with catalytic Rev3, accessory Pol31' Pol32 and two Rev7 subunits forming an uninterrupted daisy chain of protein-protein interactions. We also uncover the features that impose high fidelity during the nucleotide-incorporation step and those that accommodate mismatches and lesions during the extension reaction. Collectively, we decrypt the molecular underpinnings of Polζ's role in TLS and provide a framework for new cancer therapeutics.
Identifiants
pubmed: 32807989
doi: 10.1038/s41594-020-0476-7
pii: 10.1038/s41594-020-0476-7
pmc: PMC7554088
mid: NIHMS1608256
doi:
Substances chimiques
Pol32 protein, S cerevisiae
0
REV7 protein, S cerevisiae
0
Saccharomyces cerevisiae Proteins
0
DNA
9007-49-2
DNA polymerase zeta
EC 2.7.7.-
DNA Polymerase III
EC 2.7.7.7
DNA-Directed DNA Polymerase
EC 2.7.7.7
POL31 protein, S cerevisiae
EC 2.7.7.7
REV3 protein, S cerevisiae
EC 2.7.7.7
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
913-924Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM124047
Pays : United States
Organisme : NCRR NIH HHS
ID : S10 RR026473
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103311
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103310
Pays : United States
Organisme : NCRR NIH HHS
ID : S10 RR029300
Pays : United States
Organisme : NCRR NIH HHS
ID : P41 RR001209
Pays : United States
Organisme : NIH HHS
ID : S10 OD019994
Pays : United States
Références
Prakash, S., Johnson, R. E. & Prakash, L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem. 74, 317–353 (2005).
doi: 10.1146/annurev.biochem.74.082803.133250
Jain, R., Aggarwal, A. K. & Rechkoblit, O. Eukaryotic DNA polymerases. Curr. Opin. Struct. Biol. 53, 77–87 (2018).
pubmed: 30005324
pmcid: 30005324
Makarova, A. V. & Burgers, P. M. Eukaryotic DNA polymerase ζ. DNA Repair (Amst.). 29, 47–55 (2015).
pubmed: 4426032
pmcid: 4426032
Martin, S. K. & Wood, R. D. DNA polymerase ζ in DNA replication and repair. Nucleic Acids Res. 47, 8348–8361 (2019).
pubmed: 6895278
pmcid: 6895278
Johnson, R. E., Washington, M. T., Haracska, L., Prakash, S. & Prakash, L. Eukaryotic polymerases ι and ζ act sequentially to bypass DNA lesions. Nature 406, 1015–1019 (2000).
Lange, S. S., Takata, K. & Wood, R. D. DNA polymerases and cancer. Nat. Rev. Cancer 11, 96–110 (2011).
pubmed: 3739438
pmcid: 3739438
Sharma, S., Helchowski, C. M. & Canman, C. E. The roles of DNA polymerase ζ and the Y family DNA polymerases in promoting or preventing genome instability. Mutat. Res. 743–744, 97–110 (2013).
Yamanaka, K., Chatterjee, N., Hemann, M. T. & Walker, G. C. Inhibition of mutagenic translesion synthesis: a possible strategy for improving chemotherapy? PLoS Genet. 13, e1006842 (2017).
pubmed: 5560539
pmcid: 5560539
Sharma, S., Shah, N. A., Joiner, A. M., Roberts, K. H. & Canman, C. E. DNA polymerase ζ is a major determinant of resistance to platinum-based chemotherapeutic agents. Mol. Pharmacol. 81, 778–787 (2012).
pubmed: 3362893
pmcid: 3362893
Nelson, J. R., Lawrence, C. W. & Hinkle, D. C. Thymine–thymine dimer bypass by yeast DNA polymerase ζ. Science 272, 1646–1649 (1996).
Khalaj, M. et al. A missense mutation in Rev7 disrupts formation of Polζ, impairing mouse development and repair of genotoxic agent-induced DNA lesions. J. Biol. Chem. 289, 3811–3824 (2014).
Aravind, L. & Koonin, E. V. The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem. Sci. 23, 284–286 (1998).
Rosenberg, S. C. & Corbett, K. D. The multifaceted roles of the HORMA domain in cellular signaling. J. Cell Biol. 211, 745–755 (2015).
pubmed: 4657174
pmcid: 4657174
Baranovskiy, A. G. et al. DNA polymerase δ and ζ switch by sharing accessory subunits of DNA polymerase δ. J. Biol. Chem. 287, 17281–17287 (2012).
pubmed: 3366816
pmcid: 3366816
Johnson, R. E., Prakash, L. & Prakash, S. Pol31 and Pol32 subunits of yeast DNA polymerase δ are also essential subunits of DNA polymerase ζ. Proc. Natl Acad. Sci. USA 109, 12455–12460 (2012).
Makarova, A. V., Stodola, J. L. & Burgers, P. M. A four-subunit DNA polymerase ζ complex containing Pol δ accessory subunits is essential for PCNA-mediated mutagenesis. Nucleic Acids Res. 40, 11618–11626 (2012).
pubmed: 3526297
pmcid: 3526297
Hara, K. et al. Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase ζ and REV1. J. Biol. Chem. 285, 12299–12307 (2010).
pubmed: 2852969
pmcid: 2852969
Rizzo, A. A. et al. Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex. Proc. Natl Acad. Sci. USA 115, Eb191–Eb200 (2018).
Jain, R. et al. Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme. Nat. Struct. Mol. Biol. 26, 955–962 (2019).
doi: 10.1038/s41594-019-0305-z
Baranovskiy, A. G. et al. X-ray structure of the complex of regulatory subunits of human DNA polymerase δ. Cell Cycle 7, 3026–3036 (2008).
pubmed: 2605013
pmcid: 2605013
Lee, Y. S., Gregory, M. T. & Yang, W. Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass. Proc. Natl Acad. Sci. USA 111, 2954–2959 (2014).
Gómez-Llorente, Y. et al. The architecture of yeast DNA polymerase ζ. Cell Rep. 5, 79–86 (2013).
Swan, M. K., Johnson, R. E., Prakash, L., Prakash, S. & Aggarwal, A. K. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nat. Struct. Mol. Biol. 16, 979–986 (2009).
pubmed: 3055789
pmcid: 3055789
Doublie, S. & Zahn, K. E. Structural insights into eukaryotic DNA replication. Front. Microbiol. 5, 444 (2014).
pubmed: 4142720
pmcid: 4142720
Bartels, P. L., Stodola, J. L., Burgers, P. M. J. & Barton, J. K. A redox role for the [4Fe4S] cluster of yeast DNA polymerase δ. J. Am. Chem. Soc. 139, 18339–18348 (2017).
pubmed: 5881389
pmcid: 5881389
Burgers, P. M. J. & Kunkel, T. A. Eukaryotic DNA replication fork. Annu. Rev. Biochem. 86, 417–438 (2017).
pubmed: 5597965
pmcid: 5597965
Hogg, M., Aller, P., Konigsberg, W., Wallace, S. S. & Doublie, S. Structural and biochemical investigation of the role in proofreading of a β hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family. J. Biol. Chem. 282, 1432–1444 (2007).
Stocki, S. A., Nonay, R. L. & Reha-Krantz, L. J. Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 3’ → 5’ exonuclease activities. J. Mol. Biol. 254, 15–28 (1995).
Steitz, T. A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274, 17395–17398 (1999).
Mapelli, M. & Musacchio, A. MAD contortions: conformational dimerization boosts spindle checkpoint signaling. Curr. Opin. Struct. Biol. 17, 716–725 (2007).
pubmed: 17920260
pmcid: 17920260
Luo, X. & Yu, H. Protein metamorphosis: the two-state behavior of Mad2. Structure 16, 1616–1625 (2008).
pubmed: 19000814
pmcid: 19000814
Yang, M. et al. Insights into Mad2 regulation in the spindle checkpoint revealed by the crystal structure of the symmetric Mad2 dimer. PLoS Biol. 6, e50 (2008).
pubmed: 18318601
pmcid: 18318601
Mapelli, M., Massimiliano, L., Santaguida, S. & Musacchio, A. The Mad2 conformational dimer: structure and implications for the spindle assembly checkpoint. Cell 131, 730–743 (2007).
pubmed: 18022367
pmcid: 18022367
Baranovskiy, A. G. et al. Crystal structure of the human Polε B-subunit in complex with the C-terminal domain of the catalytic subunit. J. Biol. Chem. 292, 15717–15730 (2017).
pubmed: 28747437
pmcid: 28747437
Klinge, S., Nuñez-Ramírez, R., Llorca, O. & Pellegrini, L. 3D architecture of DNA Pol α reveals the functional core of multi-subunit replicative polymerases. EMBO J. 28, 1978–1987 (2009).
pubmed: 19494830
pmcid: 19494830
Suwa, Y. et al. Crystal structure of the human Pol α B subunit in complex with the C-terminal domain of the catalytic subunit. J. Biol. Chem. 290, 14328–14337 (2015).
pubmed: 25847248
pmcid: 25847248
Joyce, C. M. & Benkovic, S. J. DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry 43, 14317–14324 (2004).
pubmed: 15533035
pmcid: 15533035
Doublie, S., Sawaya, M. R. & Ellenberger, T. An open and closed case for all polymerases. Structure 7, R31–R35 (1999).
pubmed: 10368292
pmcid: 10368292
Wang, F. & Yang, W. Structural insight into translesion synthesis by DNA Pol II. Cell 139, 1279–1289 (2009).
pubmed: 20064374
pmcid: 20064374
Tomida, J. et al. REV7 is essential for DNA damage tolerance via two REV3L binding sites in mammalian DNA polymerase ζ. Nucleic Acids Res. 43, 1000–1011 (2015).
pubmed: 4333420
pmcid: 4333420
Janin, J., Miller, S. & Chothia, C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204, 155–164 (1988).
Hara, K. et al. Purification, crystallization and initial X-ray diffraction study of human REV7 in complex with a REV3 fragment. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 65, 1302–1305 (2009).
Hanafusa, T. et al. Overlapping in short motif sequences for binding to human REV7 and MAD2 proteins. Genes Cells 15, 281–296 (2010).
Wojtaszek, J. et al. Structural basis of Rev1-mediated assembly of a quaternary vertebrate translesion polymerase complex consisting of Rev1, heterodimeric polymerase (Pol) ζ, and Pol κ. J. Biol. Chem. 287, 33836–33846 (2012).
pubmed: 3460478
pmcid: 3460478
Pustovalova, Y., Bezsonova, I. & Korzhnev, D. M. The C-terminal domain of human Rev1 contains independent binding sites for DNA polymerase η and Rev7 subunit of polymerase ζ. FEBS Lett. 586, 3051–3056 (2012).
pubmed: 3572780
pmcid: 3572780
Pozhidaeva, A. et al. NMR structure and dynamics of the C-terminal domain from human Rev1 and its complex with Rev1 interacting region of DNA polymerase η. Biochemistry 51, 5506–5520 (2012).
pubmed: 3732116
pmcid: 3732116
Ohashi, E. et al. Identification of a novel REV1-interacting motif necessary for DNA polymerase κ function. Genes Cells 14, 101–111 (2009).
pubmed: 3103050
pmcid: 3103050
Pustovalova, Y. et al. Interaction between the Rev1 C-terminal domain and the PolD3 subunit of Polζ suggests a mechanism of polymerase exchange upon Rev1/Polζ-dependent translesion synthesis. Biochemistry 55, 2043–2053 (2016).
pubmed: 4898654
pmcid: 4898654
Doles, J. et al. Suppression of Rev3, the catalytic subunit of Polζ, sensitizes drug-resistant lung tumors to chemotherapy. Proc. Natl Acad. Sci. USA 107, 20786–20791 (2010).
Xu, X. et al. Enhancing tumor cell response to chemotherapy through nanoparticle-mediated codelivery of siRNA and cisplatin prodrug. Proc. Natl Acad. Sci. USA 110, 18638–18643 (2013).
Niimi, K. et al. Suppression of REV7 enhances cisplatin sensitivity in ovarian clear cell carcinoma cells. Cancer Sci. 105, 545–552 (2014).
pubmed: 4317831
pmcid: 4317831
Zhao, J. et al. Mitotic arrest deficient protein MAD2B is overexpressed in human glioma, with depletion enhancing sensitivity to ionizing radiation. J. Clin. Neurosci. 18, 827–833 (2011).
Wojtaszek, J. L. et al. A small molecule targeting mutagenic translesion synthesis improves chemotherapy. Cell 178, 152–159.e11 (2019).
pubmed: 6644000
pmcid: 6644000
Actis, M. L. et al. Identification of the first small-molecule inhibitor of the REV7 DNA repair protein interaction. Bioorg. Med. Chem. 24, 4339–4346 (2016).
pubmed: 5688848
pmcid: 5688848
Green, A. A. & Hughes, W. L. Protein fractionation on the basis of solubility in aqueous solutions of salts and organic solvents. Methods Enzymol. 1, 67–90 (1955).
Jain, T., Sheehan, P., Crum, J., Carragher, B. & Potter, C. S. Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM. J. Struct. Biol. 179, 68–75 (2012).
pubmed: 3378829
pmcid: 3378829
Wei, H. et al. Optimizing “self-wicking” nanowire grids. J. Struct. Biol. 202, 170–174 (2018).
pubmed: 5864531
pmcid: 5864531
Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166, 95–102 (2009).
pubmed: 2775544
pmcid: 2775544
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
pubmed: 5494038
pmcid: 5494038
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
pubmed: 6760662
pmcid: 6760662
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
pubmed: 5533649
pmcid: 5533649
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
pubmed: 26592709
pmcid: 4711343
Roseman, A. M. FindEM — a fast, efficient program for automatic selection of particles from electron micrographs. J. Struct. Biol. 145, 91–99 (2004).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
pmcid: 28165473
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
pubmed: 3690530
pmcid: 3690530
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).
pubmed: 30412051
pmcid: 30412051
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
pubmed: 6858545
pmcid: 6858545
Scheres, S. H. W. & Chen, S. X. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).
pubmed: 4912033
pmcid: 4912033
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
pubmed: 14568533
pmcid: 14568533
Pettersen, E. F. et al. UCSF chimera — a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Klaholz, B. P. Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis. Acta Crystallogr. D Struct. Biol. 75, 878–881 (2019).
pubmed: 31588919
pmcid: 31588919
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EMEM density maps. Nat. Methods 11, 63–65 (2014).
pubmed: 24213166
Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user friendly software for single-particle image processing. Elife 7, e35383 (2018).
pubmed: 29513216
pmcid: 29513216
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
pubmed: 15572765
pmcid: 15572765
Brown, A. et al. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr. D Biol. Crystallogr. 71, 136–153 (2015).
pubmed: 25615868
pmcid: 25615868
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
Barad, B. A. et al. EMRinger: side chain directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015).
pubmed: 26280328
pmcid: 26280328
DeLano, W. L. & Lam, J. W. PyMOL: a communications tool for computational models. Abstr. Pap. Am. Chem. Soc. 230, U1371–U1372 (2005).
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
pubmed: 3261699
pmcid: 3261699
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
pubmed: 5298202
pmcid: 5298202
Pei, J. & Grishin, N. V. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 23, 802–808 (2007).