1
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Moreno NC, Korchak EJ, Latancia MT, D'Orlando DA, Adegbenro T, Bezsonova I, Woodgate R, Ashton NW. DNA polymerase η is regulated by mutually exclusive mono-ubiquitination and mono-NEDDylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.12.618026. [PMID: 39416117 PMCID: PMC11482926 DOI: 10.1101/2024.10.12.618026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
DNA polymerase eta (Pol η) is a Y-family translesion polymerase responsible for synthesizing new DNA across UV-damaged templates. It is recruited to replication forks following mono-ubiquitination of the PCNA DNA clamp. This interaction is mediated by PCNA-interacting protein (PIP) motifs within Pol η, as well as by its C-terminal ubiquitin-binding zinc finger (UBZ) domain. Previous work has suggested that Pol η itself is mono-ubiquitinated at four C-terminal lysine residues, which is dependent on prior ubiquitin-binding by its UBZ domain. Here, we show that Pol η can be modified at the same lysine residues by the ubiquitin-like protein, NEDD8. Like ubiquitination, this modification is driven by non-covalent interactions between NEDD8 and the UBZ domain. While only a small proportion of Pol η is mono-NEDDylated under normal conditions, these levels rapidly increase by inhibiting the COP9 signalosome, suggesting that mono-NEDDylation is maintained under strong negative regulation. Finally, we provide data to support that mono-ubiquitination is important for Pol η foci formation and suggest that NEDDylation disrupts this process. These results reveal a new mechanism of Pol η regulation by ubiquitin-like proteins.
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2
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Sellés-Baiget S, Ambjørn SM, Carli A, Hendriks IA, Gallina I, Davey NE, Benedict B, Zarantonello A, Gadi SA, Meeusen B, Hertz EPT, Slappendel L, Semlow D, Sturla S, Nielsen ML, Nilsson J, Miller TCR, Duxin JP. Catalytic and noncatalytic functions of DNA polymerase κ in translesion DNA synthesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01395-3. [PMID: 39300172 DOI: 10.1038/s41594-024-01395-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 08/28/2024] [Indexed: 09/22/2024]
Abstract
Translesion DNA synthesis (TLS) is a cellular process that enables the bypass of DNA lesions encountered during DNA replication and is emerging as a primary target of chemotherapy. Among vertebrate DNA polymerases, polymerase κ (Polκ) has the distinctive ability to bypass minor groove DNA adducts in vitro. However, Polκ is also required for cells to overcome major groove DNA adducts but the basis of this requirement is unclear. Here, we combine CRISPR base-editor screening technology in human cells with TLS analysis of defined DNA lesions in Xenopus egg extracts to unravel the functions and regulations of Polκ during lesion bypass. Strikingly, we show that Polκ has two main functions during TLS, which are differentially regulated by Rev1 binding. On the one hand, Polκ is essential to replicate across a minor groove DNA lesion in a process that depends on PCNA ubiquitylation but is independent of Rev1. On the other hand, through its cooperative interaction with Rev1 and ubiquitylated PCNA, Polκ appears to stabilize the Rev1-Polζ extension complex on DNA to allow extension past major groove DNA lesions and abasic sites, in a process that is independent of Polκ's catalytic activity. Together, our work identifies catalytic and noncatalytic functions of Polκ in TLS and reveals important regulatory mechanisms underlying the unique domain architecture present at the C-terminal end of Y-family TLS polymerases.
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Affiliation(s)
- Selene Sellés-Baiget
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Sara M Ambjørn
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carli
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Irene Gallina
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alessandra Zarantonello
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sampath A Gadi
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bob Meeusen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Laura Slappendel
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Daniel Semlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shana Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C R Miller
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Orndorff KS, Veltri EJ, Hoitsma NM, Williams IL, Hall I, Jaworski GE, Majeres GE, Kallepalli S, Vito AF, Struble LR, Borgstahl GEO, Dieckman LM. Structural Basis for the Interaction Between Yeast Chromatin Assembly Factor 1 and Proliferating Cell Nuclear Antigen. J Mol Biol 2024; 436:168695. [PMID: 38969056 PMCID: PMC11305522 DOI: 10.1016/j.jmb.2024.168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/13/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Proliferating cell nuclear antigen (PCNA), the homotrimeric eukaryotic sliding clamp protein, recruits and coordinates the activities of a multitude of proteins that function on DNA at the replication fork. Chromatin assembly factor 1 (CAF-1), one such protein, is a histone chaperone that deposits histone proteins onto DNA immediately following replication. The interaction between CAF-1 and PCNA is essential for proper nucleosome assembly at silenced genomic regions. Most proteins that bind PCNA contain a PCNA-interacting peptide (PIP) motif, a conserved motif containing only eight amino acids. Precisely how PCNA is able to discriminate between binding partners at the replication fork using only these small motifs remains unclear. Yeast CAF-1 contains a PIP motif on its largest subunit, Cac1. We solved the crystal structure of the PIP motif of CAF-1 bound to PCNA using a new strategy to produce stoichiometric quantities of one PIP motif bound to each monomer of PCNA. The PIP motif of CAF-1 binds to the hydrophobic pocket on the front face of PCNA in a similar manner to most known PIP-PCNA interactions. However, several amino acids immediately flanking either side of the PIP motif bind the IDCL or C-terminus of PCNA, as observed for only a couple other known PIP-PCNA interactions. Furthermore, mutational analysis suggests positively charged amino acids in these flanking regions are responsible for the low micromolar affinity of CAF-1 for PCNA, whereas the presence of a negative charge upstream of the PIP prevents a more robust interaction with PCNA. These results provide additional evidence that positive charges within PIP-flanking regions of PCNA-interacting proteins are crucial for specificity and affinity of their recruitment to PCNA at the replication fork.
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Affiliation(s)
- Keely S Orndorff
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Evan J Veltri
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry, University of Colorado at Boulder, Boulder, Colorado; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Ivy L Williams
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Ian Hall
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Grace E Jaworski
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Grace E Majeres
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Samaya Kallepalli
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Abigayle F Vito
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA
| | - Lucas R Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lynne M Dieckman
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, USA.
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4
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Roske JJ, Yeeles JTP. Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε. Nat Struct Mol Biol 2024:10.1038/s41594-024-01370-y. [PMID: 39112807 DOI: 10.1038/s41594-024-01370-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/11/2024] [Indexed: 10/18/2024]
Abstract
During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear antigen (PCNA) to form a processive holoenzyme. For high-fidelity DNA synthesis, Pol ε relies on nucleotide selectivity and its proofreading ability to detect and excise a misincorporated nucleotide. Here, we present cryo-electron microscopy (cryo-EM) structures of human Pol ε in complex with PCNA, DNA and an incoming nucleotide, revealing how Pol ε associates with PCNA through its PCNA-interacting peptide box and additional unique features of its catalytic domain. Furthermore, by solving a series of cryo-EM structures of Pol ε at a mismatch-containing DNA, we elucidate how Pol ε senses and edits a misincorporated nucleotide. Our structures delineate steps along an intramolecular switching mechanism between polymerase and exonuclease activities, providing the basis for a proofreading mechanism in B-family replicative polymerases.
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5
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Arianna GA, Korzhnev DM. Protein Assemblies in Translesion Synthesis. Genes (Basel) 2024; 15:832. [PMID: 39062611 PMCID: PMC11276120 DOI: 10.3390/genes15070832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Translesion synthesis (TLS) is a mechanism of DNA damage tolerance utilized by eukaryotic cells to replicate DNA across lesions that impede the high-fidelity replication machinery. In TLS, a series of specialized DNA polymerases are employed, which recognize specific DNA lesions, insert nucleotides across the damage, and extend the distorted primer-template. This allows cells to preserve genetic integrity at the cost of mutations. In humans, TLS enzymes include the Y-family, inserter polymerases, Polη, Polι, Polκ, Rev1, and the B-family extender polymerase Polζ, while in S. cerevisiae only Polη, Rev1, and Polζ are present. To bypass DNA lesions, TLS polymerases cooperate, assembling into a complex on the eukaryotic sliding clamp, PCNA, termed the TLS mutasome. The mutasome assembly is contingent on protein-protein interactions (PPIs) between the modular domains and subunits of TLS enzymes, and their interactions with PCNA and DNA. While the structural mechanisms of DNA lesion bypass by the TLS polymerases and PPIs of their individual modules are well understood, the mechanisms by which they cooperate in the context of TLS complexes have remained elusive. This review focuses on structural studies of TLS polymerases and describes the case of TLS holoenzyme assemblies in action emerging from recent high-resolution Cryo-EM studies.
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Affiliation(s)
| | - Dmitry M. Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA;
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6
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Hardebeck S, Jácobo Goebbels N, Michalski C, Schreiber S, Jose J. Identification of a potent PCNA-p15-interaction inhibitor by autodisplay-based peptide library screening. Microb Biotechnol 2024; 17:e14471. [PMID: 38646975 PMCID: PMC11033925 DOI: 10.1111/1751-7915.14471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor for DNA metabolism. The influence of PCNA on DNA replication and repair, combined with the high expression rate of PCNA in various tumours renders PCNA a promising target for cancer therapy. In this context, an autodisplay-based screening method was developed to identify peptidic PCNA interaction inhibitors. A 12-mer randomized peptide library consisting of 2.54 × 106 colony-forming units was constructed and displayed at the surface of Escherichia coli BL21 (DE3) cells by autodisplay. Cells exhibiting an enhanced binding to fluorescent mScarlet-I-PCNA were enriched in four sorting rounds by flow cytometry. This led to the discovery of five peptide variants with affinity to mScarlet-I-PCNA. Among these, P3 (TCPLRWITHDHP) exhibited the highest binding signal. Subsequent flow cytometric analysis revealed a dissociation constant of 0.62 μM for PCNA-P3 interaction. Furthermore, the inhibition of PCNA interactions was investigated using p15, a PIP-box containing protein involved in DNA replication and repair. P3 inhibited the PCNA-p1551-70 interaction with a half maximal inhibitory activity of 16.2 μM, characterizing P3 as a potent inhibitor of the PCNA-p15 interaction.
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Affiliation(s)
- Sarah Hardebeck
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | | | - Caroline Michalski
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Sebastian Schreiber
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
| | - Joachim Jose
- University of MünsterInstitute of Pharmaceutical and Medicinal ChemistryMünsterGermany
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7
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Bacurio JHT, Yawson P, Thomforde J, Zhang Q, Kumar HV, Den Hartog H, Tretyakova NY, Basu AK. 5-Formylcytosine mediated DNA-peptide cross-link induces predominantly semi-targeted mutations in both Escherichia coli and human cells. J Biol Chem 2024; 300:105786. [PMID: 38401843 PMCID: PMC10966706 DOI: 10.1016/j.jbc.2024.105786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Histone proteins can become trapped on DNA in the presence of 5-formylcytosine (5fC) to form toxic DNA-protein conjugates. Their repair may involve proteolytic digestion resulting in DNA-peptide cross-links (DpCs). Here, we have investigated replication of a model DpC comprised of an 11-mer peptide (NH2-GGGKGLGK∗GGA) containing an oxy-lysine residue (K∗) conjugated to 5fC in DNA. Both CXG and CXT (where X = 5fC-DpC) sequence contexts were examined. Replication of both constructs gave low viability (<10%) in Escherichia coli, whereas TLS efficiency was high (72%) in HEK 293T cells. In E. coli, the DpC was bypassed largely error-free, inducing only 2 to 3% mutations, which increased to 4 to 5% with SOS. For both sequences, semi-targeted mutations were dominant, and for CXG, the predominant mutations were G→T and G→C at the 3'-base to the 5fC-DpC. In HEK 293T cells, 7 to 9% mutations occurred, and the dominant mutations were the semi-targeted G → T for CXG and T → G for CXT. These mutations were reduced drastically in cells deficient in hPol η, hPol ι or hPol ζ, suggesting a role of these TLS polymerases in mutagenic TLS. Steady-state kinetics studies using hPol η confirmed that this polymerase induces G → T and T → G transversions at the base immediately 3' to the DpC. This study reveals a unique replication pattern of 5fC-conjugated DpCs, which are bypassed largely error-free in both E. coli and human cells and induce mostly semi-targeted mutations at the 3' position to the lesion.
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Affiliation(s)
| | - Priscilla Yawson
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Jenna Thomforde
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Honnaiah Vijay Kumar
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Holly Den Hartog
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA.
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8
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Cheng X, An J, Lou J, Gu Q, Ding W, Droby GN, Wang Y, Wang C, Gao Y, Anand JR, Shelton A, Satterlee AB, Mann B, Hsiao YC, Liu CW, Lu K, Hingtgen S, Wang J, Liu Z, Miller CR, Wu D, Vaziri C, Yang Y. Trans-lesion synthesis and mismatch repair pathway crosstalk defines chemoresistance and hypermutation mechanisms in glioblastoma. Nat Commun 2024; 15:1957. [PMID: 38438348 PMCID: PMC10912752 DOI: 10.1038/s41467-024-45979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides an aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
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Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Qisheng Gu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Nabil Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jay Ramanlal Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Breanna Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - C Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
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9
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Olsen JG, Prestel A, Kassem N, Broendum SS, Shamim HM, Simonsen S, Grysbæk M, Mortensen J, Rytkjær LL, Haxholm GW, Marabini R, Holmberg C, Carr AM, Crehuet R, Nielsen O, Kragelund BB. Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs. Nucleic Acids Res 2024; 52:2030-2044. [PMID: 38261971 PMCID: PMC10939359 DOI: 10.1093/nar/gkae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Noah Kassem
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sebastian S Broendum
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hossain Mohammad Shamim
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Signe Simonsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Grysbæk
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Josefine Mortensen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Louise Lund Rytkjær
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Gitte W Haxholm
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Holmberg
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, John Maynard Smith Building, Falmer, BN1 9RQ, Brighton
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, c/ Jordi Girona 18-26, 08034 Barcelona
| | - Olaf Nielsen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
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10
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Cheng X, An J, Lou J, Gu Q, Ding W, Droby G, Wang Y, Wang C, Gao Y, Shelton A, Satterlee AB, Mann BE, Hsiao YC, Liu CW, Liu K, Hingtgen S, Wang J, Liu Z, Miller R, Wu D, Vaziri C, Yang Y. Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562506. [PMID: 37905107 PMCID: PMC10614844 DOI: 10.1101/2023.10.16.562506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
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Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Unit of Immunity and Pediatric Infectious Diseases, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Breanna Elizabeth Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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11
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Cheng X, An J, Lou J, Gu Q, Ding W, Droby G, Wang Y, Wang C, Gao Y, Shelton A, Satterlee AB, Mann BE, Hsiao YC, Liu CW, Liu K, Hingtgen S, Wang J, Liu Z, Miller R, Wu D, Vaziri C, Yang Y. Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma. RESEARCH SQUARE 2023:rs.3.rs-2367368. [PMID: 37886584 PMCID: PMC10602147 DOI: 10.21203/rs.3.rs-2367368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
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Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Unit of Immunity and Pediatric Infectious Diseases, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Breanna Elizabeth Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC 27599
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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12
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Horsfall AJ, Chav T, Pederick JL, Kikhtyak Z, Vandborg BC, Kowalczyk W, Scanlon DB, Tilley WD, Hickey TE, Abell AD, Bruning JB. Designing Fluorescent Nuclear Permeable Peptidomimetics to Target Proliferating Cell Nuclear Antigen. J Med Chem 2023; 66:10354-10363. [PMID: 37489955 DOI: 10.1021/acs.jmedchem.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Human proliferating cell nuclear antigen (PCNA) is a critical mediator of DNA replication and repair, acting as a docking platform for replication proteins. Disrupting these interactions with a peptidomimetic agent presents as a promising avenue to limit proliferation of cancerous cells. Here, a p21-derived peptide was employed as a starting scaffold to design a modular peptidomimetic that interacts with PCNA and is cellular and nuclear permeable. Ultimately, a peptidomimetic was produced which met these criteria, consisting of a fluorescein tag and SV40 nuclear localization signal conjugated to the N-terminus of a p21 macrocycle derivative. Attachment of the fluorescein tag was found to directly affect cellular uptake of the peptidomimetic, with fluorescein being requisite for nuclear permeability. This work provides an important step forward in the development of PCNA targeting peptidomimetics for use as anti-cancer agents or as cancer diagnostics.
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Affiliation(s)
- Aimee J Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Theresa Chav
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bethiney C Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Denis B Scanlon
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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13
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Packard JE, Williams MR, Fromuth DP, Dembowski JA. Proliferating cell nuclear antigen inhibitors block distinct stages of herpes simplex virus infection. PLoS Pathog 2023; 19:e1011539. [PMID: 37486931 PMCID: PMC10399828 DOI: 10.1371/journal.ppat.1011539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/03/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) forms a homotrimer that encircles replicating DNA and is bound by DNA polymerases to add processivity to cellular DNA synthesis. In addition, PCNA acts as a scaffold to recruit DNA repair and chromatin remodeling proteins to replicating DNA via its interdomain connecting loop (IDCL). Despite encoding a DNA polymerase processivity factor UL42, it was previously found that PCNA associates with herpes simplex virus type 1 (HSV-1) replication forks and is necessary for productive HSV-1 infection. To define the role that PCNA plays during viral DNA replication or a replication-coupled process, we investigated the effects that two mechanistically distinct PCNA inhibitors, PCNA-I1 and T2AA, have on the HSV-1 infectious cycle. PCNA-I1 binds at the interface between PCNA monomers, stabilizes the homotrimer, and may interfere with protein-protein interactions. T2AA inhibits select protein-protein interactions within the PCNA IDCL. Here we demonstrate that PCNA-I1 treatment results in reduced HSV-1 DNA replication, late gene expression, and virus production, while T2AA treatment results in reduced late viral gene expression and infectious virus production. To pinpoint the mechanisms by which PCNA inhibitors affect viral processes and protein recruitment to replicated viral DNA, we performed accelerated native isolation of proteins on nascent DNA (aniPOND). Results indicate that T2AA inhibits recruitment of the viral uracil glycosylase UL2 and transcription regulatory factors to viral DNA, likely leading to a defect in viral base excision repair and the observed defect in late viral gene expression and infectious virus production. In addition, PCNA-I1 treatment results in decreased association of the viral DNA polymerase UL30 and known PCNA-interacting proteins with viral DNA, consistent with the observed block in viral DNA replication and subsequent processes. Together, we conclude that inhibitors of cellular PCNA block recruitment of key viral and cellular factors to viral DNA to inhibit viral DNA synthesis and coupled processes.
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Affiliation(s)
- Jessica E. Packard
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Maya R. Williams
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel P. Fromuth
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Jill A. Dembowski
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
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14
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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15
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Gopinathan Nair A, Rabas N, Lejon S, Homiski C, Osborne MJ, Cyr N, Sverzhinsky A, Melendy T, Pascal JM, Laue ED, Borden KLB, Omichinski JG, Verreault A. Unorthodox PCNA Binding by Chromatin Assembly Factor 1. Int J Mol Sci 2022; 23:ijms231911099. [PMID: 36232396 PMCID: PMC9570017 DOI: 10.3390/ijms231911099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
The eukaryotic DNA replication fork is a hub of enzymes that continuously act to synthesize DNA, propagate DNA methylation and other epigenetic marks, perform quality control, repair nascent DNA, and package this DNA into chromatin. Many of the enzymes involved in these spatiotemporally correlated processes perform their functions by binding to proliferating cell nuclear antigen (PCNA). A long-standing question has been how the plethora of PCNA-binding enzymes exert their activities without interfering with each other. As a first step towards deciphering this complex regulation, we studied how Chromatin Assembly Factor 1 (CAF-1) binds to PCNA. We demonstrate that CAF-1 binds to PCNA in a heretofore uncharacterized manner that depends upon a cation-pi (π) interaction. An arginine residue, conserved among CAF-1 homologs but absent from other PCNA-binding proteins, inserts into the hydrophobic pocket normally occupied by proteins that contain canonical PCNA interaction peptides (PIPs). Mutation of this arginine disrupts the ability of CAF-1 to bind PCNA and to assemble chromatin. The PIP of the CAF-1 p150 subunit resides at the extreme C-terminus of an apparent long α-helix (119 amino acids) that has been reported to bind DNA. The length of that helix and the presence of a PIP at the C-terminus are evolutionarily conserved among numerous species, ranging from yeast to humans. This arrangement of a very long DNA-binding coiled-coil that terminates in PIPs may serve to coordinate DNA and PCNA binding by CAF-1.
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Affiliation(s)
- Amogh Gopinathan Nair
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Molecular Biology Program, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
| | - Nick Rabas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sara Lejon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Caleb Homiski
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - Michael J. Osborne
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Normand Cyr
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Thomas Melendy
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katherine L. B. Borden
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - James G. Omichinski
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
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16
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Hashimoto H, Hara K, Hishiki A. Structural basis for molecular interactions on the eukaryotic DNA sliding clamps PCNA and RAD9-RAD1-HUS1. J Biochem 2022; 172:189-196. [PMID: 35731009 DOI: 10.1093/jb/mvac053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
DNA sliding clamps are widely conserved in all living organisms and play crucial roles in DNA replication and repair. Each DNA sliding clamp is a doughnut-shaped protein with a quaternary structure that encircles the DNA strand and recruits various factors involved in DNA replication and repair, thereby stimulating their biological functions. Eukaryotes have two types of DNA sliding clamp, proliferating cell nuclear antigen (PCNA) and RAD9-RAD1-HUS1 (9-1-1). The homo-trimer PCNA physically interacts with multiple proteins containing a PIP-box and/or APIM. The two motifs bind to PCNA by a similar mechanism; in addition, the bound PCNA structure is similar, implying a universality of PCNA interactions. In contrast to PCNA, 9-1-1 is a hetero-trimer composed of RAD9, RAD1, and HUS1 subunits. Although 9-1-1 forms a trimeric ring structure similar to PCNA, the C-terminal extension of the RAD9 is intrinsically unstructured. Based on the structural similarity between PCNA and 9-1-1, the mechanism underlying the interaction of 9-1-1 with its partners was thought to be analogous to that of PCNA. Unexpectedly, however, the recent structure of the 9-1-1 ring bound to a partner has revealed a novel interaction distinct from that of PCNA, potentially providing a new principle for molecular interactions on DNA sliding clamps.
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Affiliation(s)
- Hiroshi Hashimoto
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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17
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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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18
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Zuilkoski CM, Skibbens RV. Integrating Sister Chromatid Cohesion Establishment to DNA Replication. Genes (Basel) 2022; 13:genes13040625. [PMID: 35456431 PMCID: PMC9032331 DOI: 10.3390/genes13040625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
The intersection through which two fundamental processes meet provides a unique vantage point from which to view cellular regulation. On the one hand, DNA replication is at the heart of cell division, generating duplicate chromosomes that allow each daughter cell to inherit a complete copy of the parental genome. Among other factors, the PCNA (proliferating cell nuclear antigen) sliding clamp ensures processive DNA replication during S phase and is essential for cell viability. On the other hand, the process of chromosome segregation during M phase—an act that occurs long after DNA replication—is equally fundamental to a successful cell division. Eco1/Ctf7 ensures that chromosomes faithfully segregate during mitosis, but functions during DNA replication to activate cohesins and thereby establish cohesion between sister chromatids. To achieve this, Eco1 binds PCNA and numerous other DNA replication fork factors that include MCM helicase, Chl1 helicase, and the Rtt101-Mms1-Mms22 E3 ubiquitin ligase. Here, we review the multi-faceted coordination between cohesion establishment and DNA replication. SUMMARY STATEMENT: New findings provide important insights into the mechanisms through which DNA replication and the establishment of sister chromatid cohesion are coupled.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47401, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Correspondence: ; Tel.: +610-758-6162
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19
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Lancey C, Tehseen M, Bakshi S, Percival M, Takahashi M, Sobhy MA, Raducanu VS, Blair K, Muskett FW, Ragan TJ, Crehuet R, Hamdan SM, De Biasio A. Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA. Nat Commun 2021; 12:6095. [PMID: 34667155 PMCID: PMC8526622 DOI: 10.1038/s41467-021-26251-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2021] [Indexed: 11/26/2022] Open
Abstract
Y-family DNA polymerase κ (Pol κ) can replicate damaged DNA templates to rescue stalled replication forks. Access of Pol κ to DNA damage sites is facilitated by its interaction with the processivity clamp PCNA and is regulated by PCNA mono-ubiquitylation. Here, we present cryo-EM reconstructions of human Pol κ bound to DNA, an incoming nucleotide, and wild type or mono-ubiquitylated PCNA (Ub-PCNA). In both reconstructions, the internal PIP-box adjacent to the Pol κ Polymerase-Associated Domain (PAD) docks the catalytic core to one PCNA protomer in an angled orientation, bending the DNA exiting the Pol κ active site through PCNA, while Pol κ C-terminal domain containing two Ubiquitin Binding Zinc Fingers (UBZs) is invisible, in agreement with disorder predictions. The ubiquitin moieties are partly flexible and extend radially away from PCNA, with the ubiquitin at the Pol κ-bound protomer appearing more rigid. Activity assays suggest that, when the internal PIP-box interaction is lost, Pol κ is retained on DNA by a secondary interaction between the UBZs and the ubiquitins flexibly conjugated to PCNA. Our data provide a structural basis for the recruitment of a Y-family TLS polymerase to sites of DNA damage. Translesion Synthesis is a process that enables cells to overcome the deleterious effects of replication stalling caused by DNA lesions. Here the authors present a Cryo-EM structure of human Y-family DNA polymerase k (Pol k) bound to PCNA, P/T DNA and an incoming nucleotide; and propose a model for polymerase switching in which “carrier state” Pol k is recruited to PCNA.
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Affiliation(s)
- Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Souvika Bakshi
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Matthew Percival
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Mohamed A Sobhy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Vlad S Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Kerry Blair
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Frederick W Muskett
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Timothy J Ragan
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK
| | - Ramon Crehuet
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC) C/ Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK. .,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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20
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Dash RC, Hadden K. Protein-Protein Interactions in Translesion Synthesis. Molecules 2021; 26:5544. [PMID: 34577015 PMCID: PMC8468184 DOI: 10.3390/molecules26185544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/17/2022] Open
Abstract
Translesion synthesis (TLS) is an error-prone DNA damage tolerance mechanism used by actively replicating cells to copy past DNA lesions and extend the primer strand. TLS ensures that cells continue replication in the presence of damaged DNA bases, albeit at the expense of an increased mutation rate. Recent studies have demonstrated a clear role for TLS in rescuing cancer cells treated with first-line genotoxic agents by allowing them to replicate and survive in the presence of chemotherapy-induced DNA lesions. The importance of TLS in both the initial response to chemotherapy and the long-term development of acquired resistance has allowed it to emerge as an interesting target for small molecule drug discovery. Proper TLS function is a complicated process involving a heteroprotein complex that mediates multiple attachment and switching steps through several protein-protein interactions (PPIs). In this review, we briefly describe the importance of TLS in cancer and provide an in-depth analysis of key TLS PPIs, focusing on key structural features at the PPI interface while also exploring the potential druggability of each key PPI.
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Affiliation(s)
| | - Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Rd, Storrs, CT 06029-3092, USA;
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21
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Shen S, Davidson GA, Yang K, Zhuang Z. Photo-activatable Ub-PCNA probes reveal new structural features of the Saccharomyces cerevisiae Polη/PCNA complex. Nucleic Acids Res 2021; 49:9374-9388. [PMID: 34390346 PMCID: PMC8450101 DOI: 10.1093/nar/gkab646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 07/02/2021] [Accepted: 08/12/2021] [Indexed: 12/05/2022] Open
Abstract
The Y-family DNA polymerase η (Polη) is critical for the synthesis past damaged DNA nucleotides in yeast through translesion DNA synthesis (TLS). TLS is initiated by monoubiquitination of proliferating cell nuclear antigen (PCNA) and the subsequent recruitment of TLS polymerases. Although individual structures of the Polη catalytic core and PCNA have been solved, a high-resolution structure of the complex of Polη/PCNA or Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to the disordered Polη C-terminal region and the flexibility of ubiquitin on PCNA. To circumvent these obstacles and obtain structural insights into this important TLS polymerase complex, we developed photo-activatable PCNA and Ub-PCNA probes containing a p-benzoyl-L-phenylalanine (pBpa) crosslinker at selected positions on PCNA. By photo-crosslinking the probes with full-length Polη, specific crosslinking sites were identified following tryptic digestion and tandem mass spectrometry analysis. We discovered direct interactions of the Polη catalytic core and its C-terminal region with both sides of the PCNA ring. Model building using the crosslinking site information as a restraint revealed multiple conformations of Polη in the polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA probes will also facilitate investigations into other PCNA-containing complexes important for DNA replication, repair and damage tolerance.
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Affiliation(s)
- Siqi Shen
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
| | - Gregory A Davidson
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
| | - Kun Yang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
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22
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'PIPs' in DNA polymerase: PCNA interaction affairs. Biochem Soc Trans 2021; 48:2811-2822. [PMID: 33196097 DOI: 10.1042/bst20200678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 01/15/2023]
Abstract
Interaction of PCNA with DNA polymerase is vital to efficient and processive DNA synthesis. PCNA being a homotrimeric ring possesses three hydrophobic pockets mostly involved in an interaction with its binding partners. PCNA interacting proteins contain a short sequence of eight amino acids, popularly coined as PIP motif, which snuggly fits into the hydrophobic pocket of PCNA to stabilize the interaction. In the last two decades, several PIP motifs have been mapped or predicted in eukaryotic DNA polymerases. In this review, we summarize our understandings of DNA polymerase-PCNA interaction, the function of such interaction during DNA synthesis, and emphasize the lacunae that persist. Because of the presence of multiple ligands in the replisome complex and due to many interaction sites in DNA polymerases, we also propose two modes of DNA polymerase positioning on PCNA required for DNA synthesis to rationalize the tool-belt model of DNA replication.
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23
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Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y. Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer. Nucleic Acids Res 2021; 49:7154-7163. [PMID: 34142156 PMCID: PMC8266592 DOI: 10.1093/nar/gkab492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
Mammalian MutY homologue (MUTYH) is an adenine DNA glycosylase that excises adenine inserted opposite 8-oxoguanine (8-oxoG). The inherited variations in human MUTYH gene are known to cause MUTYH-associated polyposis (MAP), which is associated with colorectal cancer. MUTYH is involved in base excision repair (BER) with proliferating cell nuclear antigen (PCNA) in DNA replication, which is unique and critical for effective mutation-avoidance. It is also reported that MUTYH has a Zn-binding motif in a unique interdomain connector (IDC) region, which interacts with Rad9–Rad1–Hus1 complex (9–1–1) in DNA damage response, and with apurinic/apyrimidinic endonuclease 1 (APE1) in BER. However, the structural basis for the BER pathway by MUTYH and its interacting proteins is unclear. Here, we determined the crystal structures of complexes between mouse MUTYH and DNA, and between the C-terminal domain of mouse MUTYH and human PCNA. The structures elucidated the repair mechanism for the A:8-oxoG mispair including DNA replication-coupled repair process involving MUTYH and PCNA. The Zn-binding motif was revealed to comprise one histidine and three cysteine residues. The IDC, including the Zn-binding motif, is exposed on the MUTYH surface, suggesting its interaction modes with 9–1–1 and APE1, respectively. The structure of MUTYH explains how MAP mutations perturb MUTYH function.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Kohtaro Okabe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shogo Hirayama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Shokei University and Shokei University Junior College, 2-6-78, Kuhonji, Chuo-ku, Kumamoto, 862-8678 Kumamoto, Japan
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24
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Horsfall AJ, Vandborg BA, Kowalczyk W, Chav T, Scanlon DB, Abell AD, Bruning JB. Unlocking the PIP-box: A peptide library reveals interactions that drive high-affinity binding to human PCNA. J Biol Chem 2021; 296:100773. [PMID: 33984330 PMCID: PMC8191301 DOI: 10.1016/j.jbc.2021.100773] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/02/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022] Open
Abstract
The human sliding clamp, Proliferating Cell Nuclear Antigen (hPCNA), interacts with over 200 proteins through a conserved binding motif, the PIP-box, to orchestrate DNA replication and repair. It is not clear how changes to the features of a PIP-box modulate protein binding and thus how they fine-tune downstream processes. Here, we present a systematic study of each position within the PIP-box to reveal how hPCNA-interacting peptides bind with drastically varied affinities. We synthesized a series of 27 peptides derived from the native protein p21 with small PIP-box modifications and another series of 19 peptides containing PIP-box binding motifs from other proteins. The hPCNA-binding affinity of all peptides, characterized as KD values determined by surface plasmon resonance, spanned a 4000-fold range, from 1.83 nM to 7.59 μM. The hPCNA-bound peptide structures determined by X-ray crystallography and modeled computationally revealed intermolecular and intramolecular interaction networks that correlate with high hPCNA affinity. These data informed rational design of three new PIP-box sequences, testing of which revealed the highest affinity hPCNA-binding partner to date, with a KD value of 1.12 nM, from a peptide with PIP-box QTRITEYF. This work showcases the sequence-specific nuances within the PIP-box that are responsible for high-affinity hPCNA binding, which underpins our understanding of how nature tunes hPCNA affinity to regulate DNA replication and repair processes. In addition, these insights will be useful to future design of hPCNA inhibitors.
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Affiliation(s)
- Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Beth A Vandborg
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Theresa Chav
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denis B Scanlon
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics, Institute of Photonics and Advanced Sensing, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - John B Bruning
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
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25
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Szeltner Z, Póti Á, Harami GM, Kovács M, Szüts D. Evaluation and modulation of DNA lesion bypass in an SV40 large T antigen-based in vitro replication system. FEBS Open Bio 2021; 11:1054-1075. [PMID: 33512058 PMCID: PMC8016126 DOI: 10.1002/2211-5463.13099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 11/09/2022] Open
Abstract
DNA damage removal by nucleotide excision repair (NER) and replicative bypass via translesion synthesis (TLS) and template switch (TSw) are important in ensuring genome stability. In this study, we tested the applicability of an SV40 large T antigen‐based replication system for the simultaneous examination of these damage tolerance processes. Using both Sanger and next‐generation sequencing combined with lesion‐specific qPCR and replication efficiency studies, we demonstrate that this system works well for studying NER and TLS, especially its one‐polymerase branch, while it is less suited to investigations of homology‐related repair processes, such as TSw. Cis‐syn cyclobutane pyrimidine dimer photoproducts were replicated with equal efficiency to lesion‐free plasmids in vitro, and the majority of TLS on this lesion could be inhibited by a peptide (PIR) specific for the polη‐PCNA interaction interface. TLS on 6–4 pyrimidine–pyrimidone photoproduct proved to be inefficient and was slightly facilitated by PIR as well as by a recombinant ubiquitin‐binding zinc finger domain of polη in HeLa extract, possibly by promoting polymerase exchange. Supplementation of the extract with recombinant PCNA variants indicated the dependence of TLS on PCNA ubiquitylation. In contrast to active TLS and NER, we found no evidence of successful TSw in cellular extracts. The established methods can promote in vitro investigations of replicative DNA damage bypass.
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Affiliation(s)
- Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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26
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Patel SM, Dash RC, Hadden MK. Translesion synthesis inhibitors as a new class of cancer chemotherapeutics. Expert Opin Investig Drugs 2021; 30:13-24. [PMID: 33179552 PMCID: PMC7832080 DOI: 10.1080/13543784.2021.1850692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Introduction: Translesion synthesis (TLS) is a DNA damage tolerance mechanism that replaces the replicative DNA polymerase with a specialized, low-fidelity TLS DNA polymerase that can copy past DNA lesions during active replication. Recent studies have demonstrated a primary role for TLS in replicating past DNA lesions induced by first-line genotoxic agents, resulting in decreased efficacy and acquired chemoresistance. With this in mind, targeting TLS as a combination strategy with first-line genotoxic agents has emerged as a promising approach to develop a new class of anti-cancer adjuvant agents. Areas covered: In this review, we provide a brief background on TLS and its role in cancer. We also discuss the identification and development of inhibitors that target various TLS DNA polymerases or key protein-protein interactions (PPIs) in the TLS machinery. Expert opinion: TLS inhibitors have demonstrated initial promise; however, their continued study is essential to more fully understand the clinical potential of this emerging class of anti-cancer chemotherapeutics. It will be important to determine whether a specific protein involved in TLS is an optimal target. In addition, an expanded understanding of what current genotoxic chemotherapies synergize with TLS inhibitors will guide the clinical strategies for devising combination therapies.
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Affiliation(s)
- Seema M Patel
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut , Storrs, CT, United States
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27
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Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis 2021; 10:95-122. [PMID: 33579867 PMCID: PMC7990447 DOI: 10.3233/jhd-200448] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FAN1 encodes a DNA repair nuclease. Genetic deficiencies, copy number variants, and single nucleotide variants of FAN1 have been linked to karyomegalic interstitial nephritis, 15q13.3 microdeletion/microduplication syndrome (autism, schizophrenia, and epilepsy), cancer, and most recently repeat expansion diseases. For seven CAG repeat expansion diseases (Huntington's disease (HD) and certain spinocerebellar ataxias), modification of age of onset is linked to variants of specific DNA repair proteins. FAN1 variants are the strongest modifiers. Non-coding disease-delaying FAN1 variants and coding disease-hastening variants (p.R507H and p.R377W) are known, where the former may lead to increased FAN1 levels and the latter have unknown effects upon FAN1 functions. Current thoughts are that ongoing repeat expansions in disease-vulnerable tissues, as individuals age, promote disease onset. Fan1 is required to suppress against high levels of ongoing somatic CAG and CGG repeat expansions in tissues of HD and FMR1 transgenic mice respectively, in addition to participating in DNA interstrand crosslink repair. FAN1 is also a modifier of autism, schizophrenia, and epilepsy. Coupled with the association of these diseases with repeat expansions, this suggests a common mechanism, by which FAN1 modifies repeat diseases. Yet how any of the FAN1 variants modify disease is unknown. Here, we review FAN1 variants, associated clinical effects, protein structure, and the enzyme's attributed functional roles. We highlight how variants may alter its activities in DNA damage response and/or repeat instability. A thorough awareness of the FAN1 gene and FAN1 protein functions will reveal if and how it may be targeted for clinical benefit.
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Affiliation(s)
- Amit L. Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Gagan B. Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Marie-Christine Caron
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | | | - Christopher E. Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- University of Toronto, Program of Molecular Genetics, Toronto, Ontario, Canada
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28
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Wilkinson NA, Mnuskin KS, Ashton NW, Woodgate R. Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass. Cancers (Basel) 2020; 12:cancers12102848. [PMID: 33023096 PMCID: PMC7600381 DOI: 10.3390/cancers12102848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs). However, due to the lower fidelity of the specialized polymerases involved in TLS, the activation and suppression of these pathways must be tightly regulated by post-translational modifications such as ubiquitination in order to limit the risk of mutagenesis. Many cancer cells rely on the deregulation of DNA damage bypass to promote carcinogenesis and tumor formation, often giving them heightened resistance to DNA damage from chemotherapeutic agents. In this review, we discuss the key functions of ubiquitin and ubiquitin-like proteins in regulating DNA damage bypass in human cells, and highlight ways in which these processes are both deregulated in cancer progression and might be targeted in cancer therapy.
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Affiliation(s)
| | | | - Nicholas W. Ashton
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
| | - Roger Woodgate
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
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29
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Ripley BM, Reusch DT, Washington MT. Yeast DNA polymerase η possesses two PIP-like motifs that bind PCNA and Rad6-Rad18 with different specificities. DNA Repair (Amst) 2020; 95:102968. [PMID: 32932109 DOI: 10.1016/j.dnarep.2020.102968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 11/29/2022]
Abstract
In translesion synthesis (TLS), specialized DNA polymerases, such as polymerase (pol) η and Rev1, are recruited to stalled replication forks. These polymerases form a multi-protein complex with PCNA, Rad6-Rad18, and other specialized polymerases. Pol η interacts with PCNA and Rev1 via a PCNA-interacting protein (PIP) motif in its C-terminal unstructured region. Here we report the discovery of a second PIP-like motif in the C-terminal region of pol η, which we have designated as PIP2. We have designated the original PIP motif as PIP1. We show that the pol η PIP1 and PIP2 motifs bind PCNA with different affinities and kinetics. PIP1 binds with higher affinity than does PIP2, and PIP1 dissociates more slowly than does PIP2. In addition, we show that the interaction between pol η and Rad6-Rad18 is also mediated by the pol η PIP1 and PIP2 motifs. Again, we show that the affinity and kinetics by which these motifs bind Rad6-Rad18 is different. These findings are significant, because the multiple PIP-like motifs on pol η likely play quite different roles within the multi-protein complex formed at stalled replication forks. PIP1 likely plays a critical role in the recruiting pol η to this multi-protein complex. PIP2, by contrast, likely plays a critical role in maintaining the architecture and the dynamics of this multi-protein complex needed to maximize the efficiency and accuracy of TLS.
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Affiliation(s)
- Brittany M Ripley
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - Devin T Reusch
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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30
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Kumar M, Gouw M, Michael S, Sámano-Sánchez H, Pancsa R, Glavina J, Diakogianni A, Valverde JA, Bukirova D, Čalyševa J, Palopoli N, Davey NE, Chemes LB, Gibson TJ. ELM-the eukaryotic linear motif resource in 2020. Nucleic Acids Res 2020; 48:D296-D306. [PMID: 31680160 PMCID: PMC7145657 DOI: 10.1093/nar/gkz1030] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins. In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs and motif mimicry by pathogenic bacterial effector proteins. The current release of the ELM database contains 289 motif classes and 3523 individual protein motif instances manually curated from 3467 scientific publications. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Athina Diakogianni
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Dayana Bukirova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Nazarbayev University, Nur-Sultan 010000, Kazakhstan
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Nicolas Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes - CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Norman E Davey
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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31
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González-Magaña A, Blanco FJ. Human PCNA Structure, Function and Interactions. Biomolecules 2020; 10:biom10040570. [PMID: 32276417 PMCID: PMC7225939 DOI: 10.3390/biom10040570] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication and repair. It forms a homotrimeric ring that embraces the DNA and slides along it, anchoring DNA polymerases and other DNA editing enzymes. It also interacts with regulatory proteins through a sequence motif known as PCNA Interacting Protein box (PIP-box). We here review the latest contributions to knowledge regarding the structure-function relationships in human PCNA, particularly the mechanism of sliding, and of the molecular recognition of canonical and non-canonical PIP motifs. The unique binding mode of the oncogene p15 is described in detail, and the implications of the recently discovered structure of PCNA bound to polymerase δ are discussed. The study of the post-translational modifications of PCNA and its partners may yield therapeutic opportunities in cancer treatment, in addition to illuminating the way PCNA coordinates the dynamic exchange of its many partners in DNA replication and repair.
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Affiliation(s)
- Amaia González-Magaña
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
| | - Francisco J. Blanco
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 6 solairua, 48013 Bilbao, Bizkaia, Spain
- Correspondence:
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32
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Tan W, Murphy VJ, Charron A, van Twest S, Sharp M, Constantinou A, Parker MW, Crismani W, Bythell-Douglas R, Deans AJ. Preparation and purification of mono-ubiquitinated proteins using Avi-tagged ubiquitin. PLoS One 2020; 15:e0229000. [PMID: 32092106 PMCID: PMC7039436 DOI: 10.1371/journal.pone.0229000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
Site-specific conjugation of ubiquitin onto a range of DNA repair proteins regulates their critical functions in the DNA damage response. Biochemical and structural characterization of these functions are limited by an absence of tools for the purification of DNA repair proteins in purely the ubiquitinated form. To overcome this barrier, we designed a ubiquitin fusion protein that is N-terminally biotinylated and can be conjugated by E3 RING ligases onto various substrates. Biotin affinity purification of modified proteins, followed by cleavage of the affinity tag leads to release of natively-mono-ubiquitinated substrates. As proof-of-principle, we applied this method to several substrates of mono-ubiquitination in the Fanconi anemia (FA)-BRCA pathway of DNA interstrand crosslink repair. These include the FANCI:FANCD2 complex, the PCNA trimer and BRCA1 modified nucleosomes. This method provides a simple approach to study the role of mono-ubiquitination in DNA repair or any other mono-ubiquitination signaling pathways.
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Affiliation(s)
- Winnie Tan
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Vincent J. Murphy
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Aude Charron
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- National Graduate School of Chemistry of Montpellier (ENSCM), Montpellier, France
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Michael Sharp
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Angelos Constantinou
- Institute of Human Genetics (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Michael W. Parker
- Structural Biology Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Andrew J. Deans
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
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33
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Li M, Larsen L, Hedglin M. Rad6/Rad18 Competes with DNA Polymerases η and δ for PCNA Encircling DNA. Biochemistry 2020; 59:407-416. [PMID: 31887036 DOI: 10.1021/acs.biochem.9b00938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Translesion DNA synthesis (TLS) bypasses DNA lesions encountered during S-phase and is critical for cell survival after exposure to DNA-damaging agents. In humans, Rad6/Rad18 attaches single ubiquitin moieties (i.e., monoubiquitination) to proliferating cell nuclear antigen (PCNA) sliding clamps encircling primer/template (P/T) junctions that are stalled at DNA lesions. TLS occurs via PCNA monoubiquitination-independent and -dependent pathways, and both contribute to cell survival. The interaction of Rad6/Rad18 with PCNA is paramount to PCNA monoubiquitination and remains poorly defined. In particular, the location of the Rad6/Rad18 binding site on PCNA is unknown. Many PCNA-binding proteins, particularly DNA polymerases (pols), converge on PCNA encircling stalled P/T junctions in human cells, and all interact in a similar manner with the universal binding sites on PCNA. We reasoned the following: if Rad6/Rad18 utilizes the universal binding sites (or nearby sites), then PCNA monoubiquitination may be suppressed by pols involved in TLS. Results from quantitative studies reveal that (1) a Y-family pol (pol η) and a B-family pol (pol δ) critical to TLS each inhibit the transfer of ubiquitin from Rad6/Rad18 to PCNA and that (2) the observed inhibitions are dependent on the interaction of these pols with PCNA encircling DNA. These studies suggest that Rad6/Rad18 utilizes the universal PCNA-binding sites or nearby sites and, hence, competes for PCNA encircling DNA with pols η and δ and possibly other PCNA-binding proteins involved in TLS. These findings provide valuable insight into the nature of the interaction between Rad6/Rad18 and PCNA and have important implications for the division of human TLS pathways.
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Affiliation(s)
- Mingjie Li
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Leah Larsen
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Mark Hedglin
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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34
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Lowran K, Campbell L, Popp P, Wu CG. Assembly of a G-Quadruplex Repair Complex by the FANCJ DNA Helicase and the REV1 Polymerase. Genes (Basel) 2019; 11:E5. [PMID: 31861576 PMCID: PMC7017153 DOI: 10.3390/genes11010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The FANCJ helicase unfolds G-quadruplexes (G4s) in human cells to support DNA replication. This action is coupled to the recruitment of REV1 polymerase to synthesize DNA across from a guanine template. The precise mechanisms of these reactions remain unclear. While FANCJ binds to G4s with an AKKQ motif, it is not known whether this site recognizes damaged G4 structures. FANCJ also has a PIP-like (PCNA Interacting Protein) region that may recruit REV1 to G4s either directly or through interactions mediated by PCNA protein. In this work, we measured the affinities of a FANCJ AKKQ peptide for G4s formed by (TTAGGG)4 and (GGGT)4 using fluorescence spectroscopy and biolayer interferometry (BLI). The effects of 8-oxoguanine (8oxoG) on these interactions were tested at different positions. BLI assays were then performed with a FANCJ PIP to examine its recruitment of REV1 and PCNA. FANCJ AKKQ bound tightly to a TTA loop and was sequestered away from the 8oxoG. Reducing the loop length between guanine tetrads increased the affinity of the peptide for 8oxoG4s. FANCJ PIP targeted both REV1 and PCNA but favored interactions with the REV1 polymerase. The impact of these results on the remodeling of damaged G4 DNA is discussed herein.
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Affiliation(s)
- Kaitlin Lowran
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Laura Campbell
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Phillip Popp
- Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Colin G. Wu
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
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35
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Prestel A, Wichmann N, Martins JM, Marabini R, Kassem N, Broendum SS, Otterlei M, Nielsen O, Willemoës M, Ploug M, Boomsma W, Kragelund BB. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cell Mol Life Sci 2019; 76:4923-4943. [PMID: 31134302 PMCID: PMC6881253 DOI: 10.1007/s00018-019-03150-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/16/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a potential drug target. Its binding partners carry a short linear motif (SLiM) known as the PCNA-interacting protein-box (PIP-box), but sequence-divergent motifs have been reported to bind to the same binding pocket. To investigate how PCNA accommodates motif diversity, we assembled a set of 77 experimentally confirmed PCNA-binding proteins and analyzed features underlying their binding affinity. Combining NMR spectroscopy, affinity measurements and computational analyses, we corroborate that most PCNA-binding motifs reside in intrinsically disordered regions, that structure preformation is unrelated to affinity, and that the sequence-patterns that encode binding affinity extend substantially beyond the boundaries of the PIP-box. Our systematic multidisciplinary approach expands current views on PCNA interactions and reveals that the PIP-box affinity can be modulated over four orders of magnitude by positive charges in the flanking regions. Including the flanking regions as part of the motif is expected to have broad implications, particularly for interpretation of disease-causing mutations and drug-design, targeting DNA-replication and -repair.
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Affiliation(s)
- Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Nanna Wichmann
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Joao M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Riccardo Marabini
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Noah Kassem
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian S Broendum
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, 3800, Australia
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Olaf Nielsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Finsen Laboratory, Biotechnology Research Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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36
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Horsfall AJ, Abell AD, Bruning JB. Targeting PCNA with Peptide Mimetics for Therapeutic Purposes. Chembiochem 2019; 21:442-450. [DOI: 10.1002/cbic.201900275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Aimee J. Horsfall
- ARC Centre of Excellence for Nanoscale BioPhotonicsInstitute for Photonics and Advanced Sensing (IPAS)Department of ChemistryUniversity of Adelaide Nth Tce Adelaide 5005 Australia
| | - Andrew D. Abell
- ARC Centre of Excellence for Nanoscale BioPhotonicsInstitute for Photonics and Advanced Sensing (IPAS)Department of ChemistryUniversity of Adelaide Nth Tce Adelaide 5005 Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS)School of Biological SciencesUniversity of Adelaide Nth Tce Adelaide 5005 Australia
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37
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Bartolowits MD, Gast JM, Hasler AJ, Cirrincione AM, O’Connor RJ, Mahmoud AH, Lill MA, Davisson VJ. Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen. ACS OMEGA 2019; 4:15181-15196. [PMID: 31552364 PMCID: PMC6751697 DOI: 10.1021/acsomega.9b02079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a central factor in DNA replication and repair pathways that plays an essential role in genome stability. The functional roles of PCNA are mediated through an extensive list of protein-protein interactions, each of which transmits specific information in protein assemblies. The flexibility at the PCNA-protein interaction interfaces offers opportunities for the discovery of functionally selective inhibitors of DNA repair pathways. Current fragment-based drug design methodologies can be limited by the flexibility of protein interfaces. These factors motivated an approach to defining compounds that could leverage previously identified subpockets on PCNA that are suitable for fragment-binding sites. Methodologies for screening multiple connected fragment-binding events in distinct subpockets are deployed to improve the selection of fragment combinations. A flexible backbone based on N-alkyl-glycine amides offers a scaffold to combinatorically link multiple fragments for in silico screening libraries that explore the diversity of subpockets at protein interfaces. This approach was applied to discover new potential inhibitors of DNA replication and repair that target PCNA in a multiprotein recognition site. The screens of the libraries were designed to computationally filter ligands based upon the fragments and positions to <1%, which were synthesized and tested for direct binding to PCNA. Molecular dynamics simulations also revealed distinct features of these novel molecules that block key PCNA-protein interactions. Furthermore, a Bayesian classifier predicted 15 of the 16 new inhibitors to be modulators of protein-protein interactions, demonstrating the method's utility as an effective screening filter. The cellular activities of example ligands with similar affinity for PCNA demonstrate unique properties for novel selective synergy with therapeutic DNA-damaging agents in drug-resistant contexts.
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Affiliation(s)
- Matthew D. Bartolowits
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonathon M. Gast
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ashlee J. Hasler
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Anthony M. Cirrincione
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rachel J. O’Connor
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amr H. Mahmoud
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Markus A. Lill
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Vincent Jo Davisson
- Department of Medicinal
Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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38
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Tehseen M, Raducanu VS, Rashid F, Shirbini A, Takahashi M, Hamdan SM. Proliferating cell nuclear antigen-agarose column: A tag-free and tag-dependent tool for protein purification affinity chromatography. J Chromatogr A 2019; 1602:341-349. [DOI: 10.1016/j.chroma.2019.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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39
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Abstract
DNA contains information that must be safeguarded, but also accessed for transcription and replication. To perform replication, eukaryotic cells use the B-family DNA polymerase enzymes Polδ and Polɛ, which are optimized for accuracy, speed, and processivity. The molecular basis of these high-performance characteristics causes these replicative polymerases to fail at sites of DNA damage (lesions), which would lead to genomic instability and cell death. To avoid this, cells possess additional DNA polymerases such as the Y-family of polymerases and the B-family member Polζ that can replicate over sites of DNA damage in a process called translesion synthesis (TLS). While able to replicate over DNA lesions, the TLS polymerases exhibit low-fidelity on undamaged DNA and, consequently, must be prevented from replicating DNA under normal circumstances and recruited only when necessary. The replicative bypass of most types of DNA lesions requires the consecutive action of these specialized TLS polymerases assembled into a dynamic multiprotein complex called the Rev1/Polζ mutasome. To this end, posttranslational modifications and a network of protein-protein interactions mediated by accessory domains/subunits of the TLS polymerases control the assembly and rearrangements of the Rev1/Polζ mutasome and recruitment of TLS proteins to sites of DNA damage. This chapter focuses on the structures and interactions that control these processes underlying the function of the Rev1/Polζ mutasome, as well as the development of small molecule inhibitors of the Rev1/Polζ-dependent TLS holding promise as a potential anticancer therapy.
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Affiliation(s)
- Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, United States.
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40
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Jimenji T, Matsumura R, Kori S, Arita K. Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction. Biochem Biophys Res Commun 2019; 516:578-583. [DOI: 10.1016/j.bbrc.2019.06.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
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41
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De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magaña A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A. p15PAF binding to PCNA modulates the DNA sliding surface. Nucleic Acids Res 2019; 46:9816-9828. [PMID: 30102405 PMCID: PMC6182140 DOI: 10.1093/nar/gky723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF–PCNA–DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η–PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Susana Barrera-Vilarmau
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | | | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alfredo De Biasio
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy.,Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
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42
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Garza-Aguilar SM, Axosco-Marín J, Lara-Núñez A, Guerrero-Molina ED, Lemus-Enciso AT, García-Ramírez E, Vázquez-Ramos JM. Proliferating cell nuclear antigen associates to protein complexes containing cyclins/cyclin dependent kinases susceptible of inhibition by KRPs during maize germination. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:297-304. [PMID: 30824007 DOI: 10.1016/j.plantsci.2018.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/28/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
The Proliferating Cell Nuclear Antigen, PCNA, has roles in both G1 and S phases of the cell cycle. Here we show that maize PCNA can be found in cells in structures of a trimer or a dimer of trimer, in complexes of high molecular mass that change in size as germination proceeds, co-eluting with cell cycle proteins as CycD3;1 and CDKs (A/B1;1). Using different methodological strategies, we show that PCNA actually interacts with CycD3;1, CDKA, CDKB1;1, KRP1;1 and KRP4;1, all of which contain PIP or PIP-like motifs. Anti-PCNA immunoprecipitates show kinase activity that is inhibited by KRP1;1 and KRP4;2, indicating the formation of quaternary complexes PCNA-CycD/CDKs-KRPs in which PCNA would act as a platform. This inhibitory effect seems to be differential during the germination process, more pronounced as germination advances, suggesting a complex regulatory mechanism in which PCNA could bind different sets of cyclins/CDKs, some more susceptible to inhibition by KRPs than others.
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Affiliation(s)
- Sara Margarita Garza-Aguilar
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Javier Axosco-Marín
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Aurora Lara-Núñez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Aldo Tonatiuh Lemus-Enciso
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jorge M Vázquez-Ramos
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
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43
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Gonzalez-Magaña A, Ibáñez de Opakua A, Romano-Moreno M, Murciano-Calles J, Merino N, Luque I, Rojas AL, Onesti S, Blanco FJ, De Biasio A. The p12 subunit of human polymerase δ uses an atypical PIP box for molecular recognition of proliferating cell nuclear antigen (PCNA). J Biol Chem 2019; 294:3947-3956. [PMID: 30655288 DOI: 10.1074/jbc.ra118.006391] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/11/2019] [Indexed: 12/28/2022] Open
Abstract
Human DNA polymerase δ is essential for DNA replication and acts in conjunction with the processivity factor proliferating cell nuclear antigen (PCNA). In addition to its catalytic subunit (p125), pol δ comprises three regulatory subunits (p50, p68, and p12). PCNA interacts with all of these subunits, but only the interaction with p68 has been structurally characterized. Here, we report solution NMR-, isothermal calorimetry-, and X-ray crystallography-based analyses of the p12-PCNA interaction, which takes part in the modulation of the rate and fidelity of DNA synthesis by pol δ. We show that p12 binds with micromolar affinity to the classical PIP-binding pocket of PCNA via a highly atypical PIP box located at the p12 N terminus. Unlike the canonical PIP box of p68, the PIP box of p12 lacks the conserved glutamine; binds through a 2-fork plug made of an isoleucine and a tyrosine residue at +3 and +8 positions, respectively; and is stabilized by an aspartate at +6 position, which creates a network of intramolecular hydrogen bonds. These findings add to growing evidence that PCNA can bind a diverse range of protein sequences that may be broadly grouped as PIP-like motifs as has been previously suggested.
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Affiliation(s)
- Amaia Gonzalez-Magaña
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | - Miguel Romano-Moreno
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Javier Murciano-Calles
- the Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Nekane Merino
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Irene Luque
- the Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Adriana L Rojas
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Silvia Onesti
- the Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- From the CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain, .,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain, and
| | - Alfredo De Biasio
- the Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy, .,the Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7HB, United Kingdom
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44
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Powers KT, Washington MT. Eukaryotic translesion synthesis: Choosing the right tool for the job. DNA Repair (Amst) 2018; 71:127-134. [PMID: 30174299 DOI: 10.1016/j.dnarep.2018.08.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Normal DNA replication is blocked by DNA damage in the template strand. Translesion synthesis is a major pathway for overcoming these replication blocks. In this process, multiple non-classical DNA polymerases are thought to form a complex at the stalled replication fork that we refer to as the mutasome. This hypothetical multi-protein complex is structurally organized by the replication accessory factor PCNA and the non-classical polymerase Rev1. One of the non-classical polymerases within this complex then catalyzes replication through the damage. Each non-classical polymerase has one or more cognate lesions, which the enzyme bypasses with high accuracy and efficiency. Thus, the accuracy and efficiency of translesion synthesis depends on which non-classical polymerase is chosen to bypass the damage. In this review article, we discuss how the most appropriate polymerase is chosen. In so doing, we examine the structural motifs that mediate the protein interactions in the mutasome; the multiple architectures that the mutasome can adopt, such as PCNA tool belts and Rev1 bridges; the intrinsically disordered regions that tether the polymerases to PCNA and to one another; and the kinetic selection model in which the most appropriate polymerase is chosen via a competition among the multiple polymerases within the mutasome.
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Affiliation(s)
- Kyle T Powers
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States.
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45
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Maneuvers on PCNA Rings during DNA Replication and Repair. Genes (Basel) 2018; 9:genes9080416. [PMID: 30126151 PMCID: PMC6116012 DOI: 10.3390/genes9080416] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.
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46
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Hara K, Uchida M, Tagata R, Yokoyama H, Ishikawa Y, Hishiki A, Hashimoto H. Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:214-221. [PMID: 29633969 DOI: 10.1107/s2053230x18003242] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 02/25/2018] [Indexed: 12/14/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) provides a molecular platform for numerous protein-protein interactions in DNA metabolism. A large number of proteins associated with PCNA have a well characterized sequence termed the PCNA-interacting protein box motif (PIPM). Another PCNA-interacting sequence termed the AlkB homologue 2 PCNA-interacting motif (APIM), comprising the five consensus residues (K/R)-(F/Y/W)-(L/I/V/A)-(L/I/V/A)-(K/R), has also been identified in various proteins. In contrast to that with PIPM, the PCNA-APIM interaction is less well understood. Here, the crystal structure of PCNA bound to a peptide carrying an APIM consensus sequence, RFLVK, was determined and structure-based interaction analysis was performed. The APIM peptide binds to the PIPM-binding pocket on PCNA in a similar way to PIPM. The phenylalanine and leucine residues within the APIM consensus sequence and a hydrophobic residue that precedes the APIM consensus sequence are crucially involved in interactions with the hydrophobic pocket of PCNA. This interaction is essential for overall binding. These results provide a structural basis for regulation of the PCNA interaction and might aid in the development of specific inhibitors of this interaction.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Masayuki Uchida
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Risa Tagata
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Hideshi Yokoyama
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Yoshinobu Ishikawa
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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47
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The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ. PLoS Genet 2017; 13:e1007119. [PMID: 29281621 PMCID: PMC5760103 DOI: 10.1371/journal.pgen.1007119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/09/2018] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by specialized translesion DNA synthesis (TLS) polymerases to allow DNA replication completion in the presence of DNA damage. In eukaryotes, Rad6- and Rad18-mediated PCNA ubiquitination at lysine 164 promotes recruitment of TLS polymerases, allowing cells to efficiently cope with DNA damage. However, several studies showed that TLS polymerases can be recruited also in the absence of PCNA ubiquitination. We hypothesized that the stability of the interactions between DNA polymerase δ (Pol δ) subunits and/or between Pol δ and PCNA at the primer/template junction is a crucial factor to determine the requirement of PCNA ubiquitination. To test this hypothesis, we used a structural mutant of Pol δ in which the interaction between Pol3 and Pol31 is inhibited. We found that in yeast, rad18Δ-associated UV hypersensitivity is suppressed by pol3-ct, a mutant allele of the POL3 gene that encodes the catalytic subunit of replicative Pol δ. pol3-ct suppressor effect was specifically dependent on the Rev1 and Pol ζ TLS polymerases. This result strongly suggests that TLS polymerases could rely much less on PCNA ubiquitination when Pol δ interaction with PCNA is partially compromised by mutations. In agreement with this model, we found that the pol3-FI allele suppressed rad18Δ-associated UV sensitivity as observed for pol3-ct. This POL3 allele carries mutations within a putative PCNA Interacting Peptide (PIP) motif. We then provided molecular and genetic evidence that this motif could contribute to Pol δ-PCNA interaction indirectly, although it is not a bona fide PIP. Overall, our results suggest that the primary role of PCNA ubiquitination is to allow TLS polymerases to outcompete Pol δ for PCNA access upon DNA damage. Replicative DNA polymerases have the essential role of replicating genomic DNA during the S phase of each cell cycle. DNA replication occurs smoothly and accurately if the DNA to be replicated is undamaged. Conversely, replicative DNA polymerases stall abruptly when they encounter a damaged base on their template. In this case, alternative specialized DNA polymerases are recruited to insert nucleotides at sites of base lesions. However, these translesion polymerases are not processive and they are poorly accurate. Therefore, they need to be tightly regulated. This is achieved by the covalent binding of the small ubiquitin peptide to the polymerase cofactor PCNA that subsequently triggers the recruitment of translesion polymerases at sites of DNA damage. Yet, recruitment of translesion polymerases independently of PCNA ubiquitination also has been documented, although the underlying mechanism is not known. Moreover, this observation makes more difficult to understand the exact role of PCNA ubiquitination. Here, we present strong genetic evidence in Saccharomyces cerevisiae implying that the replicative DNA polymerase δ (Pol δ) prevents the recruitment of the translesion polymerases Pol ζ and Rev1 following UV irradiation unless PCNA is ubiquitinated. Thus, the primary role of PCNA ubiquitination would be to allow translesion polymerases to outcompete Pol δ upon DNA damage. In addition, our results led us to propose that translesion polymerases could be recruited independently of PCNA ubiquitination when Pol δ association with PCNA is challenged, for instance at difficult-to-replicate loci.
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48
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Hashimoto H, Hishiki A, Hara K, Kikuchi S. Structural basis for the molecular interactions in DNA damage tolerances. Biophys Physicobiol 2017; 14:199-205. [PMID: 29362705 PMCID: PMC5773155 DOI: 10.2142/biophysico.14.0_199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/18/2017] [Indexed: 01/01/2023] Open
Abstract
DNA damage tolerance (DDT) is a cell function to avoid replication arrest by DNA damage during DNA replication. DDT includes two pathways, translesion DNA synthesis (TLS) and template-switched DNA synthesis (TS). DDT is regulated by ubiquitination of proliferating cell nuclear antigen that binds to double-stranded DNA and functions as scaffold protein for DNA metabolism. TLS is transient DNA synthesis using damaged DNA as a template by error-prone DNA polymerases termed TLS polymerases specialized for DNA damage. TS, in which one newly synthesized strand is utilized as an undamaged template for replication by replicative polymerases, is error-free process. Thus, DDT is not inherently a repair pathway. DDT is a mechanism to tolerate DNA damage, giving priority to DNA synthesis and enabling finish of DNA replication for cell survival and genome stability. DDT is associated with cancer development and thus is of great interest in drug discovery for cancer therapy. This review article describes recent progress in structural studies on protein-protein and protein-DNA complexes involved in TLS and TS, providing the molecular mechanisms of interactions in DDT.
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Affiliation(s)
- Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8002, Japan
| | - Sotaro Kikuchi
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8002, Japan.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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49
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Li H, Sandhu M, Malkas LH, Hickey RJ, Vaidehi N. How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins? J Chem Inf Model 2017; 57:3011-3021. [DOI: 10.1021/acs.jcim.7b00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hubert Li
- Department
of Molecular Immunology and ‡Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Manbir Sandhu
- Department
of Molecular Immunology and ‡Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Linda H. Malkas
- Department
of Molecular Immunology and ‡Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Robert J. Hickey
- Department
of Molecular Immunology and ‡Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Nagarajan Vaidehi
- Department
of Molecular Immunology and ‡Department of Molecular Medicine, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
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50
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Cordeiro TN, Chen PC, De Biasio A, Sibille N, Blanco FJ, Hub JS, Crehuet R, Bernadó P. Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly. Nucleic Acids Res 2017; 45:1501-1515. [PMID: 28180305 PMCID: PMC5388412 DOI: 10.1093/nar/gkw1183] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
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Affiliation(s)
- Tiago N Cordeiro
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | | | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Francisco J Blanco
- CIC-bioGUNE, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia, CSIC, Barcelona 08034, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
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