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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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2
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Simonsen S, Søgaard CK, Olsen JG, Otterlei M, Kragelund BB. The bacterial DNA sliding clamp, β-clamp: structure, interactions, dynamics and drug discovery. Cell Mol Life Sci 2024; 81:245. [PMID: 38814467 PMCID: PMC11139829 DOI: 10.1007/s00018-024-05252-w] [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: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
DNA replication is a tightly coordinated event carried out by a multiprotein replication complex. An essential factor in the bacterial replication complex is the ring-shaped DNA sliding clamp, β-clamp, ensuring processive DNA replication and DNA repair through tethering of polymerases and DNA repair proteins to DNA. β -clamp is a hub protein with multiple interaction partners all binding through a conserved clamp binding sequence motif. Due to its central role as a DNA scaffold protein, β-clamp is an interesting target for antimicrobial drugs, yet little effort has been put into understanding the functional interactions of β-clamp. In this review, we scrutinize the β-clamp structure and dynamics, examine how its interactions with a plethora of binding partners are regulated through short linear binding motifs and discuss how contexts play into selection. We describe the dynamic process of clamp loading onto DNA and cover the recent advances in drug development targeting β-clamp. Despite decades of research in β-clamps and recent landmark structural insight, much remains undisclosed fostering an increased focus on this very central protein.
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Affiliation(s)
- Signe Simonsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Johan G Olsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| | - Birthe B Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
- Department of Biology, REPIN, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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3
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Søgaard CK, Otterlei M. Targeting proliferating cell nuclear antigen (PCNA) for cancer therapy. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2024; 100:209-246. [PMID: 39034053 DOI: 10.1016/bs.apha.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential scaffold protein in many cellular processes. It is best known for its role as a DNA sliding clamp and processivity factor during DNA replication, which has been extensively reviewed by others. However, the importance of PCNA extends beyond its DNA-associated functions in DNA replication, chromatin remodelling, DNA repair and DNA damage tolerance (DDT), as new non-canonical roles of PCNA in the cytosol have recently been identified. These include roles in the regulation of immune evasion, apoptosis, metabolism, and cellular signalling. The diverse roles of PCNA are largely mediated by its myriad protein interactions, and its centrality to cellular processes makes PCNA a valid therapeutic anticancer target. PCNA is expressed in all cells and plays an essential role in normal cellular homeostasis; therefore, the main challenge in targeting PCNA is to selectively kill cancer cells while avoiding unacceptable toxicity to healthy cells. This chapter focuses on the stress-related roles of PCNA, and how targeting these PCNA roles can be exploited in cancer therapy.
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Affiliation(s)
- Caroline K Søgaard
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, Trondheim, Norway; APIM Therapeutics A/S, Trondheim, Norway.
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4
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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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Hara K, Tatsukawa K, Nagata K, Iida N, Hishiki A, Ohashi E, Hashimoto H. Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO. J Biol Chem 2024; 300:105751. [PMID: 38354779 PMCID: PMC10937111 DOI: 10.1016/j.jbc.2024.105751] [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: 12/01/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Eukaryotic DNA clamp is a trimeric protein featuring a toroidal ring structure that binds DNA on the inside of the ring and multiple proteins involved in DNA transactions on the outside. Eukaryotes have two types of DNA clamps: the replication clamp PCNA and the checkpoint clamp RAD9-RAD1-HUS1 (9-1-1). 9-1-1 activates the ATR-CHK1 pathway in DNA damage checkpoint, regulating cell cycle progression. Structure of 9-1-1 consists of two moieties: a hetero-trimeric ring formed by PCNA-like domains of three subunits and an intrinsically disordered C-terminal region of the RAD9 subunit, called RAD9 C-tail. The RAD9 C-tail interacts with the 9-1-1 ring and disrupts the interaction between 9-1-1 and DNA, suggesting a negative regulatory role for this intramolecular interaction. In contrast, RHINO, a 9-1-1 binding protein, interacts with both RAD1 and RAD9 subunits, positively regulating checkpoint activation by 9-1-1. This study presents a biochemical and structural analysis of intra- and inter-molecular interactions on the 9-1-1 ring. Biochemical analysis indicates that RAD9 C-tail binds to the hydrophobic pocket on the PCNA-like domain of RAD9, implying that the pocket is involved in multiple protein-protein interactions. The crystal structure of the 9-1-1 ring in complex with a RHINO peptide reveals that RHINO binds to the hydrophobic pocket of RAD9, shedding light on the RAD9-binding motif. Additionally, the study proposes a structural model of the 9-1-1-RHINO quaternary complex. Together, these findings provide functional insights into the intra- and inter-molecular interactions on the front side of RAD9, elucidating the roles of RAD9 C-tail and RHINO in checkpoint activation.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kensuke Tatsukawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Kiho Nagata
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nao Iida
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Ohashi
- Faculty of Science, Department of Biology, Kyushu University, Fukuoka, Japan; Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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Gu L, Li M, Li CM, Haratipour P, Lingeman R, Jossart J, Gutova M, Flores L, Hyde C, Kenjić N, Li H, Chung V, Li H, Lomenick B, Von Hoff DD, Synold TW, Aboody KS, Liu Y, Horne D, Hickey RJ, Perry JJP, Malkas LH. Small molecule targeting of transcription-replication conflict for selective chemotherapy. Cell Chem Biol 2023; 30:1235-1247.e6. [PMID: 37531956 PMCID: PMC10592352 DOI: 10.1016/j.chembiol.2023.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 02/12/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023]
Abstract
Targeting transcription replication conflicts, a major source of endogenous DNA double-stranded breaks and genomic instability could have important anticancer therapeutic implications. Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes. Through a rational drug design approach, we identified a small molecule PCNA inhibitor, AOH1996, which selectively kills cancer cells. AOH1996 enhances the interaction between PCNA and the largest subunit of RNA polymerase II, RPB1, and dissociates PCNA from actively transcribed chromatin regions, while inducing DNA double-stranded breaks in a transcription-dependent manner. Attenuation of RPB1 interaction with PCNA, by a point mutation in RPB1's PCNA-binding region, confers resistance to AOH1996. Orally administrable and metabolically stable, AOH1996 suppresses tumor growth as a monotherapy or as a combination treatment but causes no discernable side effects. Inhibitors of transcription replication conflict resolution may provide a new and unique therapeutic avenue for exploiting this cancer-selective vulnerability.
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Affiliation(s)
- Long Gu
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caroline M Li
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Pouya Haratipour
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert Lingeman
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer Jossart
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Margarita Gutova
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Flores
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caitlyn Hyde
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Nikola Kenjić
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Haiqing Li
- Department of Genomics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Vincent Chung
- Department of Medical Oncology, City of Hope, Duarte, CA, USA
| | - Hongzhi Li
- Department of Bioinformatics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Daniel D Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, 445N 5th Street, Phoenix, AZ 85004, USA
| | - Timothy W Synold
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Karen S Aboody
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - David Horne
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert J Hickey
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - J Jefferson P Perry
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda H Malkas
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
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7
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Carnie CJ, Armstrong L, Sebesta M, Ariza A, Wang X, Graham E, Zhu K, Ahel D. ERCC6L2 mitigates replication stress and promotes centromere stability. Cell Rep 2023; 42:112329. [PMID: 37014751 DOI: 10.1016/j.celrep.2023.112329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2-/- cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease.
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Affiliation(s)
| | - Lucy Armstrong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Xiaomeng Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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8
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Osman Y, Elsharkawy T, Hashim TM, Alratroot JA, Aljindan F, Almulla L, Alsuwat HS, Al Otaibi WM, Hegazi FM, Ibrahim AM, Borgio JF, AbdulAzeez S. Study of Single Nucleotide Polymorphisms Associated with Breast Cancer Patients among Arab Ancestries. Int J Breast Cancer 2022; 2022:2442109. [PMID: 36268271 PMCID: PMC9578870 DOI: 10.1155/2022/2442109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/27/2022] Open
Abstract
The aim of this study is to investigate the single nucleotide polymorphisms (SNPs) associated with breast cancer in our population of Arab patients. We investigated 26 breast cancer patients and an equal number of healthy age- and sex-matched control volunteers. We examined the exome wide microarray-based biomarkers and screened 243,345 SNPs for their possible significant association with our breast cancer patients. Successfully, we identified the most significant (p value ≤9.14 × 10-09) four associated SNPs [SNRK and SNRK-AS1-rs202018563G; BRCA2-rs2227943C; ZNF484-rs199826847C; and DCPS-rs1695739G] among persons with breast cancer versus the healthy controls even after Bonferroni corrections (p value <2.05 × 10-07). Although our patients' numbers were limited, the identified SNPs might shed some light on certain breast cancer-associated functional multigenic variations in Arab patients. We assert on the importance of more extensive large-scale analysis to confirm the candidate biomarkers and possible target genes of breast cancer among Arab ancestries.
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Affiliation(s)
- Yasser Osman
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Tarek Elsharkawy
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Tariq Mohammad Hashim
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Jumana Abdulwahab Alratroot
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Fatima Aljindan
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Liqa Almulla
- Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Waad Mohammed Al Otaibi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Fatma Mohammed Hegazi
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Abdallah M. Ibrahim
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Department of Fundamentals of Nursing, College of Nursing, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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9
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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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10
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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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11
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Gravina GL, Colapietro A, Mancini A, Rossetti A, Martellucci S, Ventura L, Di Franco M, Marampon F, Mattei V, Biordi LA, Otterlei M, Festuccia C. ATX-101, a Peptide Targeting PCNA, Has Antitumor Efficacy Alone or in Combination with Radiotherapy in Murine Models of Human Glioblastoma. Cancers (Basel) 2022; 14:289. [PMID: 35053455 PMCID: PMC8773508 DOI: 10.3390/cancers14020289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Cell proliferation requires the orchestrated actions of a myriad of proteins regulating DNA replication, DNA repair and damage tolerance, and cell cycle. Proliferating cell nuclear antigen (PCNA) is a master regulator which interacts with multiple proteins functioning in these processes, and this makes PCNA an attractive target in anticancer therapies. Here, we show that a cell-penetrating peptide containing the AlkB homolog 2 PCNA-interacting motif (APIM), ATX-101, has antitumor activity in a panel of human glioblastoma multiforme (GBM) cell lines and patient-derived glioma-initiating cells (GICs). Their sensitivity to ATX-101 was not related to cellular levels of PCNA, or p53, PTEN, or MGMT status. However, ATX-101 reduced Akt/mTOR and DNA-PKcs signaling, and a correlation between high Akt activation and sensitivity for ATX-101 was found. ATX-101 increased the levels of γH2AX, DNA fragmentation, and apoptosis when combined with radiotherapy (RT). In line with the in vitro results, ATX-101 strongly reduced tumor growth in two subcutaneous xenografts and two orthotopic GBM models, both as a single agent and in combination with RT. The ability of ATX-101 to sensitize cells to RT is promising for further development of this compound for use in GBM.
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Affiliation(s)
- Giovanni Luca Gravina
- Department of Biotechnological and Applied Clinical Sciences, Division of Radiation Oncology, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Alessandro Colapietro
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Andrea Mancini
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Alessandra Rossetti
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
| | - Stefano Martellucci
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Cellular Pathology, University of L’Aquila, 67100 L’Aquila, Italy;
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy;
| | - Luca Ventura
- Division of Pathology, San Salvatore Hospital, 67100 L’Aquila, Italy; (L.V.); (M.D.F.)
| | - Martina Di Franco
- Division of Pathology, San Salvatore Hospital, 67100 L’Aquila, Italy; (L.V.); (M.D.F.)
| | - Francesco Marampon
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, 00100 Rome, Italy;
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy;
| | - Leda Assunta Biordi
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Medical Oncology, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Marit Otterlei
- APIM Therapeutics A/S, N-7100 Rissa, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7006 Trondheim, Norway
| | - Claudio Festuccia
- Department of Biotechnological and Applied Clinical Sciences, Laboratory of Radiobiology, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.M.); (A.R.)
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12
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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13
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Ihle M, Biber S, Schroeder IS, Blattner C, Deniz M, Damia G, Gottifredi V, Wiesmüller L. Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices. Nucleic Acids Res 2021; 49:7457-7475. [PMID: 34165573 PMCID: PMC8287946 DOI: 10.1093/nar/gkab526] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Using human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53–POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.
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Affiliation(s)
- Michaela Ihle
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Insa S Schroeder
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt 64291, Germany
| | - Christine Blattner
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe 76021, Germany
| | - Miriam Deniz
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Giovanna Damia
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS Milan, Milan 20156, Italy
| | - Vanesa Gottifredi
- Cell cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, Buenos Aires C1405BWE, Argentina
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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14
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Tye S, Ronson GE, Morris JR. A fork in the road: Where homologous recombination and stalled replication fork protection part ways. Semin Cell Dev Biol 2021; 113:14-26. [PMID: 32653304 PMCID: PMC8082280 DOI: 10.1016/j.semcdb.2020.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
In response to replication hindrances, DNA replication forks frequently stall and are remodelled into a four-way junction. In such a structure the annealed nascent strand is thought to resemble a DNA double-strand break and remodelled forks are vulnerable to nuclease attack by MRE11 and DNA2. Proteins that promote the recruitment, loading and stabilisation of RAD51 onto single-stranded DNA for homology search and strand exchange in homologous recombination (HR) repair and inter-strand cross-link repair also act to set up RAD51-mediated protection of nascent DNA at stalled replication forks. However, despite the similarities of these pathways, several lines of evidence indicate that fork protection is not simply analogous to the RAD51 loading step of HR. Protection of stalled forks not only requires separate functions of a number of recombination proteins, but also utilises nucleases important for the resection steps of HR in alternative ways. Here we discuss how fork protection arises and how its differences with HR give insights into the differing contexts of these two pathways.
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Affiliation(s)
- Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - George E Ronson
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
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15
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Wu CC, Lin JL, Yuan HS. Structures, Mechanisms, and Functions of His-Me Finger Nucleases. Trends Biochem Sci 2020; 45:935-946. [DOI: 10.1016/j.tibs.2020.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
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16
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Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y. Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. BMC Biol 2020; 18:152. [PMID: 33115459 PMCID: PMC7594292 DOI: 10.1186/s12915-020-00889-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3'-5' editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM). RESULTS Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus abyssi onto our EM map showed the 3D atomic structural model of PolD-PCNA-DNA. In addition to the canonical interaction between PCNA and PolD via PIP (PCNA-interacting protein)-box motif, we found a new contact point consisting of a glutamate residue at position 171 in a β-hairpin of PCNA, which mediates interactions with DP1 and DP2. The DNA synthesis activity of a mutant PolD with disruption of the E171-mediated PCNA interaction was not stimulated by PCNA in vitro. CONCLUSIONS Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for conversion of its activity. This hook function of the clamp molecule may be conserved in the three domains of life.
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Affiliation(s)
- Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan.
| | - Keisuke Oki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Present address: Life Science Center for Survival Dynamics Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Present address: Life Science Center for Survival Dynamics Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan.
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan.
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17
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Nedal A, Ræder SB, Dalhus B, Helgesen E, Forstrøm RJ, Lindland K, Sumabe BK, Martinsen JH, Kragelund BB, Skarstad K, Bjørås M, Otterlei M. Peptides containing the PCNA interacting motif APIM bind to the β-clamp and inhibit bacterial growth and mutagenesis. Nucleic Acids Res 2020; 48:5540-5554. [PMID: 32347931 PMCID: PMC7261172 DOI: 10.1093/nar/gkaa278] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
In the fight against antimicrobial resistance, the bacterial DNA sliding clamp, β-clamp, is a promising drug target for inhibition of DNA replication and translesion synthesis. The β-clamp and its eukaryotic homolog, PCNA, share a C-terminal hydrophobic pocket where all the DNA polymerases bind. Here we report that cell penetrating peptides containing the PCNA-interacting motif APIM (APIM-peptides) inhibit bacterial growth at low concentrations in vitro, and in vivo in a bacterial skin infection model in mice. Surface plasmon resonance analysis and computer modeling suggest that APIM bind to the hydrophobic pocket on the β-clamp, and accordingly, we find that APIM-peptides inhibit bacterial DNA replication. Interestingly, at sub-lethal concentrations, APIM-peptides have anti-mutagenic activities, and this activity is increased after SOS induction. Our results show that although the sequence homology between the β-clamp and PCNA are modest, the presence of similar polymerase binding pockets in the DNA clamps allows for binding of the eukaryotic binding motif APIM to the bacterial β-clamp. Importantly, because APIM-peptides display both anti-mutagenic and growth inhibitory properties, they may have clinical potential both in combination with other antibiotics and as single agents.
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Affiliation(s)
- Aina Nedal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Synnøve B Ræder
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Emily Helgesen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Rune J Forstrøm
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Kim Lindland
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Balagra K Sumabe
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
| | - Jacob H Martinsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Kirsten Skarstad
- Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital, and University of Oslo, 0424, Oslo, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, 7489 Trondheim, Norway
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18
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Joseph SA, Taglialatela A, Leuzzi G, Huang JW, Cuella-Martin R, Ciccia A. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease. DNA Repair (Amst) 2020; 95:102943. [PMID: 32971328 DOI: 10.1016/j.dnarep.2020.102943] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to replication stress leads to genomic instability and predisposes to the development of cancer and other genetic disorders. Multiple DNA damage and repair pathways have evolved to allow completion of DNA replication following replication stress, thus preserving genomic integrity. One of the processes commonly induced in response to replication stress is fork reversal, which consists in the remodeling of stalled replication forks into four-way DNA junctions. In normal conditions, fork reversal slows down replication fork progression to ensure accurate repair of DNA lesions and facilitates replication fork restart once the DNA lesions have been removed. However, in certain pathological situations, such as the deficiency of DNA repair factors that protect regressed forks from nuclease-mediated degradation, fork reversal can cause genomic instability. In this review, we describe the complex molecular mechanisms regulating fork reversal, with a focus on the role of the SNF2-family fork remodelers SMARCAL1, ZRANB3 and HLTF, and highlight the implications of fork reversal for tumorigenesis and cancer therapy.
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Affiliation(s)
- Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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19
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Bugge K, Brakti I, Fernandes CB, Dreier JE, Lundsgaard JE, Olsen JG, Skriver K, Kragelund BB. Interactions by Disorder - A Matter of Context. Front Mol Biosci 2020; 7:110. [PMID: 32613009 PMCID: PMC7308724 DOI: 10.3389/fmolb.2020.00110] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Living organisms depend on timely and organized interactions between proteins linked in interactomes of high complexity. The recent increased precision by which protein interactions can be studied, and the enclosure of intrinsic structural disorder, suggest that it is time to zoom out and embrace protein interactions beyond the most central points of physical encounter. The present paper discusses protein-protein interactions in the view of structural disorder with an emphasis on flanking regions and contexts of disorder-based interactions. Context constitutes an overarching concept being of physicochemical, biomolecular, and physiological nature, but it also includes the immediate molecular context of the interaction. For intrinsically disordered proteins, which often function by exploiting short linear motifs, context contributes in highly regulatory and decisive manners and constitute a yet largely unrecognized source of interaction potential in a multitude of biological processes. Through selected examples, this review emphasizes how multivalency, charges and charge clusters, hydrophobic patches, dynamics, energetic frustration, and ensemble redistribution of flanking regions or disordered contexts are emerging as important contributors to allosteric regulation, positive and negative cooperativity, feedback regulation and negative selection in binding. The review emphasizes that understanding context, and in particular the role the molecular disordered context and flanking regions take on in protein interactions, constitute an untapped well of energetic modulation potential, also of relevance to drug discovery and development.
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Affiliation(s)
- Katrine Bugge
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Inna Brakti
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Catarina B. Fernandes
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesper E. Dreier
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe E. Lundsgaard
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan G. Olsen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karen Skriver
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B. Kragelund
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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20
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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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21
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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: 154] [Impact Index Per Article: 38.5] [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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22
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HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding, cos Site Digestion, and In Vivo Activities. J Bacteriol 2020; 202:JB.00644-19. [PMID: 31988081 DOI: 10.1128/jb.00644-19] [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: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 11/20/2022] Open
Abstract
The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle.IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.
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23
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Helicase-Like Transcription Factor HLTF and E3 Ubiquitin Ligase SHPRH Confer DNA Damage Tolerance through Direct Interactions with Proliferating Cell Nuclear Antigen (PCNA). Int J Mol Sci 2020; 21:ijms21030693. [PMID: 31973093 PMCID: PMC7037221 DOI: 10.3390/ijms21030693] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/09/2020] [Accepted: 01/19/2020] [Indexed: 12/15/2022] Open
Abstract
To prevent replication fork collapse and genome instability under replicative stress, DNA damage tolerance (DDT) mechanisms have evolved. The RAD5 homologs, HLTF (helicase-like transcription factor) and SHPRH (SNF2, histone-linker, PHD and RING finger domain-containing helicase), both ubiquitin ligases, are involved in several DDT mechanisms; DNA translesion synthesis (TLS), fork reversal/remodeling and template switch (TS). Here we show that these two human RAD5 homologs contain functional APIM PCNA interacting motifs. Our results show that both the role of HLTF in TLS in HLTF overexpressing cells, and nuclear localization of SHPRH, are dependent on interaction of HLTF and SHPRH with PCNA. Additionally, we detected multiple changes in the mutation spectra when APIM in overexpressed HLTF or SHPRH were mutated compared to overexpressed wild type proteins. In plasmids from cells overexpressing the APIM mutant version of HLTF, we observed a decrease in C to T transitions, the most common mutation caused by UV irradiation, and an increase in mutations on the transcribed strand. These results strongly suggest that direct binding of HLTF and SHPRH to PCNA is vital for their function in DDT.
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24
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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: 63] [Impact Index Per Article: 12.6] [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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25
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Long MJC, Van Hall-Beauvais A, Aye Y. The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase. Curr Opin Chem Biol 2019; 54:10-18. [PMID: 31734537 DOI: 10.1016/j.cbpa.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 02/05/2023]
Abstract
Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of 'omics', we discuss what makes the larger subunit of this enzyme (RNR-α) so interesting, highlighting its emerging cellular interactome based on its unique oligomeric dynamism that dictates its compartment-specific occupations. Linking the history of the field with the multivariable nature of this exceedingly sophisticated enzyme, we further discuss implications of new data pertaining to DNA-damage response, S-phase checkpoints, and ultimately tumor suppression. We hereby hope to provide ideas for those interested in these fields and exemplify conceptual frameworks and tools that are useful to study RNR's broader roles in biology.
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Affiliation(s)
| | - Alexandra Van Hall-Beauvais
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland.
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26
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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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27
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Garbrecht J, Hornegger H, Herbert S, Kaufmann T, Gotzmann J, Elsayad K, Slade D. Simultaneous dual-channel imaging to quantify interdependent protein recruitment to laser-induced DNA damage sites. Nucleus 2019; 9:474-491. [PMID: 30205747 PMCID: PMC6284507 DOI: 10.1080/19491034.2018.1516485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fluorescence microscopy in combination with the induction of localized DNA damage using focused light beams has played a major role in the study of protein recruitment kinetics to DNA damage sites in recent years. Currently published methods are dedicated to the study of single fluorophore/single protein kinetics. However, these methods may be limited when studying the relative recruitment dynamics between two or more proteins due to cell-to-cell variability in gene expression and recruitment kinetics, and are not suitable for comparative analysis of fast-recruiting proteins. To tackle these limitations, we have established a time-lapse fluorescence microscopy method based on simultaneous dual-channel acquisition following UV-A-induced local DNA damage coupled with a standardized image and recruitment analysis workflow. Simultaneous acquisition is achieved by spectrally splitting the emitted light into two light paths, which are simultaneously imaged on two halves of the same camera chip. To validate this method, we studied the recruitment of poly(ADP-ribose) polymerase 1 (PARP1), poly (ADP-ribose) glycohydrolase (PARG), proliferating cell nuclear antigen (PCNA) and the chromatin remodeler ALC1. In accordance with the published data based on single fluorophore imaging, simultaneous dual-channel imaging revealed that PARP1 regulates fast recruitment and dissociation of PARG and that in PARP1-depleted cells PARG and PCNA are recruited with comparable kinetics. This approach is particularly advantageous for analyzing the recruitment sequence of fast-recruiting proteins such as PARP1 and ALC1, and revealed that PARP1 is recruited faster than ALC1. Split-view imaging can be incorporated into any laser microirradiation-adapted microscopy setup together with a recruitment-dedicated image analysis package.
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Affiliation(s)
- Joachim Garbrecht
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Harald Hornegger
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Sebastien Herbert
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Tanja Kaufmann
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Josef Gotzmann
- b Department of Medical Biochemistry, Max F. Perutz Laboratories (MFPL) , Medical University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
| | - Kareem Elsayad
- c VBCF-Advanced Microscopy , Vienna Biocenter (VBC) , Vienna , Austria
| | - Dea Slade
- a Department of Biochemistry, Max F. Perutz Laboratories , University of Vienna, Vienna Biocenter (VBC) , Vienna , Austria
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28
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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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29
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Kisiala M, Copelas A, Czapinska H, Xu SY, Bochtler M. Crystal structure of the modification-dependent SRA-HNH endonuclease TagI. Nucleic Acids Res 2019; 46:10489-10503. [PMID: 30202937 PMCID: PMC6212794 DOI: 10.1093/nar/gky781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers. The nuclease domains have characteristic features of HNH/ββα-Me REases, and catalyze nicks or double strand breaks, with preference for /RY and RYN/RY sites, respectively. The SRA domains have the canonical fold. Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base.
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Affiliation(s)
- Marlena Kisiala
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland.,Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Alyssa Copelas
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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30
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Long MJC, Hnedzko D, Kim BK, Aye Y. Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery. Chembiochem 2019; 20:1091-1104. [PMID: 30589188 PMCID: PMC6499692 DOI: 10.1002/cbic.201800716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPIs) are an effective means to orchestrate intricate biological processes required to sustain life. Approximately 650 000 PPIs underlie the human interactome; thus underscoring its complexity and the manifold signaling outputs altered in response to changes in specific PPIs. This minireview illustrates the growing arsenal of PPI assemblies and offers insights into how these varied PPI regulatory modalities are relevant to customized drug discovery, with a focus on cancer. First, known and emerging PPIs and PPI-targeted drugs of both natural and synthetic origin are categorized. Building on these discussions, the merits of PPI-guided therapeutics over traditional drug design are discussed. Finally, a compare-and-contrast section for different PPI blockers, with gain-of-function PPI interventions, such as PROTACS, is provided.
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Affiliation(s)
- Marcus J. C. Long
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, HU17 8QH, UK
| | - Dziyana Hnedzko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Bo Kyoung Kim
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, HU17 8QH, UK
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31
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Griffin WC, Trakselis MA. The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance. DNA Repair (Amst) 2019; 76:1-10. [PMID: 30743181 DOI: 10.1016/j.dnarep.2019.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly implicated in genetic diseases including cancer, rapid aging, and infertility. MCM8/9 are recent additions to the catalog of helicases involved in recombination, and so far, the evidence is sparse, making assignment of function difficult. Mutations in MCM8/9 correlate principally with primary ovarian failure/insufficiency (POF/POI) and infertility indicating a meiotic defect. However, they also act when replication forks collapse/break shuttling products into mitotic recombination and several mutations are found in various somatic cancers. This review puts MCM8/9 in context with other replication and recombination helicases to narrow down its genomic maintenance role. We discuss the known structure/function relationship, the mutational spectrum, and dissect the available cellular and organismal data to better define its role in recombination.
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Affiliation(s)
- Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA.
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32
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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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33
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APIM-Mediated REV3L⁻PCNA Interaction Important for Error Free TLS Over UV-Induced DNA Lesions in Human Cells. Int J Mol Sci 2018; 20:ijms20010100. [PMID: 30597836 PMCID: PMC6337749 DOI: 10.3390/ijms20010100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/22/2018] [Indexed: 12/23/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is essential for the organization of DNA replication and the bypass of DNA lesions via translesion synthesis (TLS). TLS is mediated by specialized DNA polymerases, which all interact, directly or indirectly, with PCNA. How interactions between the TLS polymerases and PCNA affects TLS specificity and/or coordination is not fully understood. Here we show that the catalytic subunit of the essential mammalian TLS polymerase POLζ, REV3L, contains a functional AlkB homolog 2 PCNA interacting motif, APIM. APIM from REV3L fused to YFP, and full-length REV3L-YFP colocalizes with PCNA in replication foci. Colocalization of REV3L-YFP with PCNA is strongly reduced when an APIM-CFP construct is overexpressed. We also found that overexpression of full-length REV3L with mutated APIM leads to significantly altered mutation frequencies and mutation spectra, when compared to overexpression of full-length REV3L wild-type (WT) protein in multiple cell lines. Altogether, these data suggest that APIM is a functional PCNA-interacting motif in REV3L, and that the APIM-mediated PCNA interaction is important for the function and specificity of POLζ in TLS. Finally, a PCNA-targeting cell-penetrating peptide, containing APIM, reduced the mutation frequencies and changed the mutation spectra in several cell lines, suggesting that efficient TLS requires coordination mediated by interactions with PCNA.
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34
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Altieri AS, Kelman Z. DNA Sliding Clamps as Therapeutic Targets. Front Mol Biosci 2018; 5:87. [PMID: 30406112 PMCID: PMC6204406 DOI: 10.3389/fmolb.2018.00087] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/10/2018] [Indexed: 01/12/2023] Open
Abstract
Chromosomal DNA replication is achieved by an assembly of multi-protein complexes at the replication fork. DNA sliding clamps play an important role in this assembly and are essential for cell viability. Inhibitors of bacterial (β-clamp) and eukaryal DNA clamps, proliferating cell nuclear antigen (PCNA), have been explored for use as antibacterial and anti-cancer drugs, respectively. Inhibitors for bacterial β-clamps include modified peptides, small molecule inhibitors, natural products, and modified non-steroidal anti-inflammatory drugs. Targeting eukaryotic PCNA sliding clamp in its role in replication can be complicated by undesired effects on healthy cells. Some success has been seen in the design of peptide inhibitors, however, other research has focused on targeting PCNA molecules that are modified in diseased states. These inhibitors that are targeted to PCNA involved in DNA repair can sensitize cancer cells to existing anti-cancer therapeutics, and a DNA aptamer has also been shown to inhibit PCNA. In this review, studies in the use of both bacterial and eukaryotic sliding clamps as therapeutic targets are summarized.
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Affiliation(s)
- Amanda S Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, Rockville, MD, United States
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, Rockville, MD, United States.,Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
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35
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [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: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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36
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Søgaard CK, Blindheim A, Røst LM, Petrović V, Nepal A, Bachke S, Liabakk NB, Gederaas OA, Viset T, Arum CJ, Bruheim P, Otterlei M. "Two hits - one stone"; increased efficacy of cisplatin-based therapies by targeting PCNA's role in both DNA repair and cellular signaling. Oncotarget 2018; 9:32448-32465. [PMID: 30197755 PMCID: PMC6126690 DOI: 10.18632/oncotarget.25963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
Low response rate and rapid development of resistance against commonly used chemotherapeutic regimes demand new multi-targeting anti-cancer strategies. In this study, we target the stress-related roles of the scaffold protein PCNA with a cell-penetrating peptide containing the PCNA-interacting motif APIM. The APIM-peptide increased the efficacy of cisplatin-based therapies in a muscle-invasive bladder cancer (MIBC) solid tumor model in rat and in bladder cancer (BC) cell lines. By combining multiple omics-levels, from gene expression to proteome/kinome and metabolome, we revealed a unique downregulation of the EGFR/ERBB2 and PI3K/Akt/mTOR pathways in the APIM-peptide-cisplatin combination treated cells. Additionally, the combination treatment reduced the expression of anti-apoptotic proteins and proteins involved in development of resistance to cisplatin. Concurrently, we observed increased levels of DNA breaks in combination treated cells, suggesting that the APIM-peptide impaired PCNA - DNA repair protein interactions and reduced the efficacy of repair. This was also seen in cisplatin-resistant cells, which notably was re-sensitized to cisplatin by the APIM-peptide. Our data indicate that the increased efficacy of cisplatin treatment is mediated both via downregulation of known oncogenic signaling pathways and inhibition of DNA repair/translesion synthesis (TLS), thus the APIM-peptide hits both nuclear and cytosolic functions of PCNA. The novel multi-targeting strategy of the APIM-peptide could potentially improve the efficacy of chemotherapeutic regiments for treatment of MIBC, and likely other solid tumors.
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Affiliation(s)
- Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Augun Blindheim
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Urology and Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Lisa M Røst
- Department of Biotechnology and Food Science, NTNU, Trondheim, Norway
| | - Voin Petrović
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anala Nepal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Siri Bachke
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nina-Beate Liabakk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Odrun A Gederaas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Trond Viset
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Carl-Jørgen Arum
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Urology and Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,APIM Therapeutics A/S, Trondheim, Norway
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37
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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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38
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Olaisen C, Kvitvang HFN, Lee S, Almaas E, Bruheim P, Drabløs F, Otterlei M. The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. FEBS Open Bio 2018; 8:1135-1145. [PMID: 29988559 PMCID: PMC6026702 DOI: 10.1002/2211-5463.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/19/2018] [Accepted: 05/01/2018] [Indexed: 12/11/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA), a member of the highly conserved DNA sliding clamp family, is an essential protein for cellular processes including DNA replication and repair. A large number of proteins from higher eukaryotes contain one of two PCNA-interacting motifs: PCNA-interacting protein box (PIP box) and AlkB homologue 2 PCNA-interacting motif (APIM). APIM has been shown to be especially important during cellular stress. PIP box is known to be functionally conserved in yeast, and here, we show that this is also the case for APIM. Several of the 84 APIM-containing yeast proteins are associated with cellular signaling as hub proteins, which are able to interact with a large number of other proteins. Cellular signaling is highly conserved throughout evolution, and we recently suggested a novel role for PCNA as a scaffold protein in cellular signaling in human cells. A cell-penetrating peptide containing the APIM sequence increases the sensitivity toward the chemotherapeutic agent cisplatin in both yeast and human cells, and both yeast and human cells become hypersensitive when the Hog1/p38 MAPK pathway is blocked. These results suggest that the interactions between APIM-containing signaling proteins and PCNA during the DNA damage response is evolutionary conserved between yeast and mammals and that PCNA has a role in cellular signaling also in yeast.
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Affiliation(s)
- Camilla Olaisen
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Hans Fredrik N. Kvitvang
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Sungmin Lee
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Eivind Almaas
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Per Bruheim
- Department of Biotechnology and Food ScienceFaculty of Natural SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Finn Drabløs
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Marit Otterlei
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNorwegian University of Science and Technology (NTNU)TrondheimNorway
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39
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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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40
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Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol 2018; 20:162-174. [PMID: 29335528 DOI: 10.1038/s41556-017-0016-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/27/2017] [Indexed: 02/08/2023]
Abstract
Mitochondria are subcellular organelles that are critical for meeting the bioenergetic and biosynthetic needs of the cell. Mitochondrial function relies on genes and RNA species encoded both in the nucleus and mitochondria, and on their coordinated translation, import and respiratory complex assembly. Here, we characterize EXD2 (exonuclease 3'-5' domain-containing 2), a nuclear-encoded gene, and show that it is targeted to the mitochondria and prevents the aberrant association of messenger RNAs with the mitochondrial ribosome. Loss of EXD2 results in defective mitochondrial translation, impaired respiration, reduced ATP production, increased reactive oxygen species and widespread metabolic abnormalities. Depletion of the Drosophila melanogaster EXD2 orthologue (CG6744) causes developmental delays and premature female germline stem cell attrition, reduced fecundity and a dramatic extension of lifespan that is reversed with an antioxidant diet. Our results define a conserved role for EXD2 in mitochondrial translation that influences development and ageing.
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Affiliation(s)
- Joana Silva
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department for Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Laura J Bailey
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Andreu Casali
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Vinaixa
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexis A Jourdain
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pablo Pérez-Ferreros
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,EMBL Australia, University of New South Wales, Lowy Cancer Research Center, Single Molecule Science Node, Sydney and Arc Center of Excellence in Advance Molecular Imaging, Sydney, New South Wales, Australia
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville (IBIS/CSIC/US/JA), Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Albert Antolin-Fontes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Samino-Gené
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Acaimo González-Reyes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Seville, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.,Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
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41
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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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42
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Abstract
A large number of SNF2 family, DNA and ATP-dependent motor proteins are needed during transcription, DNA replication, and DNA repair to manipulate protein-DNA interactions and change DNA structure. SMARCAL1, ZRANB3, and HLTF are three related members of this family with specialized functions that maintain genome stability during DNA replication. These proteins are recruited to replication forks through protein-protein interactions and bind DNA using both their motor and substrate recognition domains (SRDs). The SRD provides specificity to DNA structures like forks and junctions and confers DNA remodeling activity to the motor domains. Remodeling reactions include fork reversal and branch migration to promote fork stabilization, template switching, and repair. Regulation ensures these powerful activities remain controlled and restricted to damaged replication forks. Inherited mutations in SMARCAL1 cause a severe developmental disorder and mutations in ZRANB3 and HLTF are linked to cancer illustrating the importance of these enzymes in ensuring complete and accurate DNA replication. In this review, we examine how these proteins function, concentrating on their common and unique attributes and regulatory mechanisms.
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Affiliation(s)
- Lisa A Poole
- a Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
| | - David Cortez
- a Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
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43
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Structure insights into the molecular mechanism of the interaction between UHRF2 and PCNA. Biochem Biophys Res Commun 2017; 494:575-580. [PMID: 28951215 DOI: 10.1016/j.bbrc.2017.09.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 11/24/2022]
Abstract
UHRF2 (Ubiquitin-like with PHD and ring finger domains 2) is an E3 ubiquitin ligase that plays important roles in DNA methylation, histone modifications and cell cycle regulation by interacting with multiple epigenetic or cell-cycle related proteins. Previous studied have identified PCNA (Proliferating cell nuclear antigen) as an interacting partner of UHRF2 by using the antibody microarray. However, the molecular mechanism and the function of UHRF2-PCNA interaction remains unclear. Here, we report the complex structure of PCNA and the peptide (784NEILQTLLDLFFPGYSK800) derived from UHRF2 that contains a PIP box. Structural analysis combined with mutagenesis experiments provide the molecular basis for the recognition of UHRF2 by PCNA via PIP-box.
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