1
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Tummala H, Walne AJ, Badat M, Patel M, Walne AM, Alnajar J, Chow CC, Albursan I, Frost JM, Ballard D, Killick S, Szitányi P, Kelly AM, Raghavan M, Powell C, Raymakers R, Todd T, Mantadakis E, Polychronopoulou S, Pontikos N, Liao T, Madapura P, Hossain U, Vulliamy T, Dokal I. The evolving genetic landscape of telomere biology disorder dyskeratosis congenita. EMBO Mol Med 2024:10.1038/s44321-024-00118-x. [PMID: 39198715 DOI: 10.1038/s44321-024-00118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 09/01/2024] Open
Abstract
Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome, caused by genetic mutations that principally affect telomere biology. Approximately 35% of cases remain uncharacterised at the genetic level. To explore the genetic landscape, we conducted genetic studies on a large collection of clinically diagnosed cases of DC as well as cases exhibiting features resembling DC, referred to as 'DC-like' (DCL). This led us to identify several novel pathogenic variants within known genetic loci and in the novel X-linked gene, POLA1. In addition, we have also identified several novel variants in POT1 and ZCCHC8 in multiple cases from different families expanding the allelic series of DC and DCL phenotypes. Functional characterisation of novel POLA1 and POT1 variants, revealed pathogenic effects on protein-protein interactions with primase, CTC1-STN1-TEN1 (CST) and shelterin subunit complexes, that are critical for telomere maintenance. ZCCHC8 variants demonstrated ZCCHC8 deficiency and signs of pervasive transcription, triggering inflammation in patients' blood. In conclusion, our studies expand the current genetic architecture and broaden our understanding of disease mechanisms underlying DC and DCL disorders.
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Affiliation(s)
- Hemanth Tummala
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK.
- Barts Health NHS Trust, London, UK.
| | - Amanda J Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Mohsin Badat
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Abigail M Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jenna Alnajar
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Chi Ching Chow
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Ibtehal Albursan
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jennifer M Frost
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - David Ballard
- Department of Analytical, Environmental & Forensic Sciences, Kings College London, Franklin-Wilkins Building, Stamford Street, London, SE1 9NH, UK
| | - Sally Killick
- Department of Haematology, Royal Bournemouth Hospital NHS Foundation Trust, Bournemouth, BH7 7DW, UK
| | - Peter Szitányi
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Prague, Czech Republic
| | - Anne M Kelly
- Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Manoj Raghavan
- Clinical Haematology, Queen Elizabeth Hospital, Edgbaston, Birmingham, B15 2TH, UK
| | - Corrina Powell
- Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B15 2TG, UK
| | - Reinier Raymakers
- University Medical Center Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Tony Todd
- Department of Haematology, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
| | - Elpis Mantadakis
- Department of Pediatrics' University General Hospital of Alexandroupolis, Democritus University of Thrace Faculty of Medicine, 6th Kilometer Alexandroupolis-Makris, 68 100 Alexandroupolis, Thrace, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Athens, Greece
| | - Nikolas Pontikos
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, Gower St, London, WC1E 6BT, UK
| | - Tianyi Liao
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Pradeep Madapura
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Upal Hossain
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Tom Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Inderjeet Dokal
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
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2
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Johnson K, Seidel JM, Cech TR. Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis. RNA (NEW YORK, N.Y.) 2024; 30:1213-1226. [PMID: 38918043 PMCID: PMC11331414 DOI: 10.1261/rna.080043.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Telomere replication is essential for continued proliferation of human cells, such as stem cells and cancer cells. Telomerase lengthens the telomeric G-strand, while C-strand replication is accomplished by CST-polymerase α-primase (CST-PP). Replication of both strands is inhibited by formation of G-quadruplex (GQ) structures in the G-rich single-stranded DNA. TMPyP4 and pyridostatin (PDS), which stabilize GQ structures in both DNA and RNA, inhibit telomerase in vitro, and in human cells they cause telomere shortening that has been attributed to telomerase inhibition. Here, we show that TMPyP4 and PDS also inhibit C-strand synthesis by stabilizing DNA secondary structures and thereby preventing CST-PP from binding to telomeric DNA. We also show that these small molecules inhibit CST-PP binding to a DNA sequence containing no consecutive guanine residues, which is unlikely to form GQs. Thus, while these "telomerase inhibitors" indeed inhibit telomerase, they are also robust inhibitors of telomeric C-strand synthesis. Furthermore, given their binding to GQ RNA and their limited specificity for GQ structures, they may disrupt many other protein-nucleic acid interactions in human cells.
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Affiliation(s)
- Kaitlin Johnson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Julia M Seidel
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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3
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Wysong BC, Schuck PL, Sridharan M, Carrison S, Murakami Y, Balakrishnan L, Stewart JA. Human CST Stimulates Base Excision Repair to Prevent the Accumulation of Oxidative DNA Damage. J Mol Biol 2024; 436:168672. [PMID: 38908783 DOI: 10.1016/j.jmb.2024.168672] [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: 02/14/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
CTC1-STN1-TEN1 (CST) is a single-stranded DNA binding protein vital for telomere length maintenance with additional genome-wide roles in DNA replication and repair. While CST was previously shown to function in double-strand break repair and promote replication restart, it is currently unclear whether it has specialized roles in other DNA repair pathways. Proper and efficient repair of DNA is critical to protecting genome integrity. Telomeres and other G-rich regions are strongly predisposed to oxidative DNA damage in the form of 8-oxoguanines, which are typically repaired by the base-excision repair (BER) pathway. Moreover, recent studies suggest that CST functions in the repair of oxidative DNA lesions. Therefore, we tested whether CST interacts with and regulates BER protein activity. Here, we show that CST robustly stimulates proteins involved in BER, including OGG1, Pol β, APE1, and LIGI, on both telomeric and non-telomeric DNA substrates. Biochemical reconstitution of the pathway indicates that CST stimulates BER. Finally, knockout of STN1 or CTC1 leads to increased levels of 8-oxoguanine, suggesting defective BER in the absence of CST. Combined, our results define an undiscovered function of CST in BER, where it acts as a stimulatory factor to promote efficient genome-wide oxidative repair.
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Affiliation(s)
- Brandon C Wysong
- Department of Biology, School of Science, Indiana University, Indianapolis, IN, USA
| | - P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, USA
| | - Madhumita Sridharan
- Department of Biology, School of Science, Indiana University, Indianapolis, IN, USA
| | - Sophie Carrison
- Department of Biology, School of Science, Indiana University, Indianapolis, IN, USA
| | - Yuichihiro Murakami
- Department of Biology, School of Science, Indiana University, Indianapolis, IN, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University, Indianapolis, IN, USA.
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, USA; Department of Biology, Western Kentucky University, Bowling Green, KY, USA.
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4
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Wentworth K, Nandakumar J. At the end, it is POT1 again: Phosphorylation allows human telomeric protein POT1 to recruit the C-rich strand end replication machinery. Mol Cell 2024; 84:2598-2600. [PMID: 39059369 DOI: 10.1016/j.molcel.2024.06.030] [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: 06/25/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Recently in Cell, Cai et al.1 reported how phosphorylation of human shelterin protein POT1 allows it to recruit the telomeric C-rich strand replication machinery, providing mechanistic insights into an understudied area of telomere biology with implications for telomere biology disorders.
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Affiliation(s)
- Katherine Wentworth
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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5
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Cai SW, Takai H, Zaug AJ, Dilgen TC, Cech TR, Walz T, de Lange T. POT1 recruits and regulates CST-Polα/primase at human telomeres. Cell 2024; 187:3638-3651.e18. [PMID: 38838667 PMCID: PMC11246235 DOI: 10.1016/j.cell.2024.05.002] [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: 06/12/2023] [Revised: 03/12/2024] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Telomere maintenance requires the extension of the G-rich telomeric repeat strand by telomerase and the fill-in synthesis of the C-rich strand by Polα/primase. At telomeres, Polα/primase is bound to Ctc1/Stn1/Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Polα/primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Our findings suggest that POT1 hinge phosphorylation is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Polα/primase in an inactive, autoinhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Polα/primase into an active state that completes telomere replication through fill-in synthesis.
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Affiliation(s)
- Sarah W Cai
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA; Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Hiroyuki Takai
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Arthur J Zaug
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Teague C Dilgen
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA.
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA.
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6
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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Nat Struct Mol Biol 2024; 31:777-790. [PMID: 38491139 PMCID: PMC11102853 DOI: 10.1038/s41594-024-01227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 01/12/2024] [Indexed: 03/18/2024]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Clarissa L Durie
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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7
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Yin Z, Kilkenny ML, Ker DS, Pellegrini L. CryoEM insights into RNA primer synthesis by the human primosome. FEBS J 2024; 291:1813-1829. [PMID: 38335062 DOI: 10.1111/febs.17082] [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: 09/21/2023] [Revised: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Eukaryotic DNA replication depends on the primosome - a complex of DNA polymerase alpha (Pol α) and primase - to initiate DNA synthesis by polymerisation of an RNA-DNA primer. Primer synthesis requires the tight coordination of primase and polymerase activities. Recent cryo-electron microscopy (cryoEM) analyses have elucidated the extensive conformational transitions required for RNA primer handover between primase and Pol α and primer elongation by Pol α. Because of the intrinsic flexibility of the primosome, however, structural information about the initiation of RNA primer synthesis is still lacking. Here, we capture cryoEM snapshots of the priming reaction to reveal the conformational trajectory of the human primosome that brings DNA primase subunits 1 and 2 (PRIM1 and PRIM2, respectively) together, poised for RNA synthesis. Furthermore, we provide experimental evidence for the continuous association of primase subunit PRIM2 with the RNA primer during primer synthesis, and for how both initiation and termination of RNA primer polymerisation are licenced by specific rearrangements of DNA polymerase alpha catalytic subunit (POLA1), the polymerase subunit of Pol α. Our findings fill a critical gap in our understanding of the conformational changes that underpin the synthesis of the RNA primer by the primosome. Together with existing evidence, they provide a complete description of the structural dynamics of the human primosome during DNA replication initiation.
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Affiliation(s)
- Zhan Yin
- Department of Biochemistry, University of Cambridge, UK
| | | | - De-Sheng Ker
- Department of Biochemistry, University of Cambridge, UK
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8
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Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
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9
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Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Human primosome requires replication protein A when copying DNA with inverted repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584335. [PMID: 38559116 PMCID: PMC10979909 DOI: 10.1101/2024.03.11.584335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polε). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA forming a G-quadruplex, RPA provides no assistance for primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Polα but not of Polε. The important factors for an efficient hairpin bypass by primosome are the high affinity of RPA to DNA based on four DNA-binding domains and the interaction of the winged-helix-turn-helix domain of RPA with Polα. Binding studies indicate that this interaction stabilizes the RPA/Polα complex on the primed template. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats.
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10
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Takai H, Aria V, Borges P, Yeeles JTP, de Lange T. CST-polymerase α-primase solves a second telomere end-replication problem. Nature 2024; 627:664-670. [PMID: 38418884 PMCID: PMC11160940 DOI: 10.1038/s41586-024-07137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Telomerase adds G-rich telomeric repeats to the 3' ends of telomeres1, counteracting telomere shortening caused by loss of telomeric 3' overhangs during leading-strand DNA synthesis ('the end-replication problem'2). Here we report a second end-replication problem that originates from the incomplete duplication of the C-rich telomeric repeat strand (C-strand) by lagging-strand DNA synthesis. This problem is resolved by fill-in synthesis mediated by polymerase α-primase bound to Ctc1-Stn1-Ten1 (CST-Polα-primase). In vitro, priming for lagging-strand DNA replication does not occur on the 3' overhang and lagging-strand synthesis stops in a zone of approximately 150 nucleotides (nt) more than 26 nt from the end of the template. Consistent with the in vitro data, lagging-end telomeres of cells lacking CST-Polα-primase lost 50-60 nt of telomeric CCCTAA repeats per population doubling. The C-strands of leading-end telomeres shortened by around 100 nt per population doubling, reflecting the generation of 3' overhangs through resection. The measured overall C-strand shortening in the absence of CST-Polα-primase fill-in is consistent with the combined effects of incomplete lagging-strand synthesis and 5' resection at the leading ends. We conclude that canonical DNA replication creates two telomere end-replication problems that require telomerase to maintain the G-rich strand and CST-Polα-primase to maintain the C-strand.
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Affiliation(s)
- Hiroyuki Takai
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Valentina Aria
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Pamela Borges
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Joseph T P Yeeles
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
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11
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Olson CL, Wuttke DS. Guardians of the Genome: How the Single-Stranded DNA-Binding Proteins RPA and CST Facilitate Telomere Replication. Biomolecules 2024; 14:263. [PMID: 38540683 PMCID: PMC10968030 DOI: 10.3390/biom14030263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024] Open
Abstract
Telomeres act as the protective caps of eukaryotic linear chromosomes; thus, proper telomere maintenance is crucial for genome stability. Successful telomere replication is a cornerstone of telomere length regulation, but this process can be fraught due to the many intrinsic challenges telomeres pose to the replication machinery. In addition to the famous "end replication" problem due to the discontinuous nature of lagging strand synthesis, telomeres require various telomere-specific steps for maintaining the proper 3' overhang length. Bulk telomere replication also encounters its own difficulties as telomeres are prone to various forms of replication roadblocks. These roadblocks can result in an increase in replication stress that can cause replication forks to slow, stall, or become reversed. Ultimately, this leads to excess single-stranded DNA (ssDNA) that needs to be managed and protected for replication to continue and to prevent DNA damage and genome instability. RPA and CST are single-stranded DNA-binding protein complexes that play key roles in performing this task and help stabilize stalled forks for continued replication. The interplay between RPA and CST, their functions at telomeres during replication, and their specialized features for helping overcome replication stress at telomeres are the focus of this review.
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Affiliation(s)
- Conner L. Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
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12
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Takai H, Aria V, Borges P, Yeeles JTP, de Lange T. CST-Polymeraseα-primase solves a second telomere end-replication problem. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.26.564248. [PMID: 37961611 PMCID: PMC10634868 DOI: 10.1101/2023.10.26.564248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Telomerase adds G-rich telomeric repeats to the 3' ends of telomeres1, counteracting telomere shortening caused by loss of telomeric 3' overhangs during leading-strand DNA synthesis ("the end-replication problem"2). We report a second end-replication problem that originates from the incomplete duplication of the C-rich telomeric repeat strand by lagging-strand synthesis. This problem is solved by CST-Polymeraseα(Polα)-primase fill-in synthesis. In vitro, priming for lagging-strand DNA replication does not occur on the 3' overhang and lagging-strand synthesis stops in an ~150-nt zone more than 26 nt from the end of the template. Consistent with the in vitro data, lagging-end telomeres of cells lacking CST-Polα-primase lost ~50-60 nt of CCCTAA repeats per population doubling (PD). The C-strands of leading-end telomeres shortened by ~100 nt/PD, reflecting the generation of 3' overhangs through resection. The measured overall C-strand shortening in absence of CST-Polα-primase fill-in is consistent with the combined effects of incomplete lagging-strand synthesis and 5' resection at the leading-ends. We conclude that canonical DNA replication creates two telomere end-replication problems that require telomerase to maintain the G-strand and CST-Polα-primase to maintain the C-strand.
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Affiliation(s)
- Hiroyuki Takai
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
| | - Valentina Aria
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2, 0QH
| | - Pamela Borges
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
| | - Joseph T. P. Yeeles
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2, 0QH
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, USA
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13
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Nasheuer HP, Meaney AM, Hulshoff T, Thiele I, Onwubiko NO. Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism. Int J Mol Sci 2024; 25:588. [PMID: 38203759 PMCID: PMC10779431 DOI: 10.3390/ijms25010588] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Replication protein A (RPA) is a heterotrimeric protein complex and the main single-stranded DNA (ssDNA)-binding protein in eukaryotes. RPA has key functions in most of the DNA-associated metabolic pathways and DNA damage signalling. Its high affinity for ssDNA helps to stabilise ssDNA structures and protect the DNA sequence from nuclease attacks. RPA consists of multiple DNA-binding domains which are oligonucleotide/oligosaccharide-binding (OB)-folds that are responsible for DNA binding and interactions with proteins. These RPA-ssDNA and RPA-protein interactions are crucial for DNA replication, DNA repair, DNA damage signalling, and the conservation of the genetic information of cells. Proteins such as ATR use RPA to locate to regions of DNA damage for DNA damage signalling. The recruitment of nucleases and DNA exchange factors to sites of double-strand breaks are also an important RPA function to ensure effective DNA recombination to correct these DNA lesions. Due to its high affinity to ssDNA, RPA's removal from ssDNA is of central importance to allow these metabolic pathways to proceed, and processes to exchange RPA against downstream factors are established in all eukaryotes. These faceted and multi-layered functions of RPA as well as its role in a variety of human diseases will be discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Anna Marie Meaney
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
| | - Timothy Hulshoff
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Ines Thiele
- Molecular Systems Physiology Group, School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Nichodemus O. Onwubiko
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland
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14
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Lim CJ. Telomere C-Strand Fill-In Machinery: New Insights into the Human CST-DNA Polymerase Alpha-Primase Structures and Functions. Subcell Biochem 2024; 104:73-100. [PMID: 38963484 DOI: 10.1007/978-3-031-58843-3_5] [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] [Indexed: 07/05/2024]
Abstract
Telomeres at the end of eukaryotic chromosomes are extended by a specialized set of enzymes and telomere-associated proteins, collectively termed here the telomere "replisome." The telomere replisome acts on a unique replicon at each chromosomal end of the telomeres, the 3' DNA overhang. This telomere replication process is distinct from the replisome mechanism deployed to duplicate the human genome. The G-rich overhang is first extended before the complementary C-strand is filled in. This overhang is extended by telomerase, a specialized ribonucleoprotein and reverse transcriptase. The overhang extension process is terminated when telomerase is displaced by CTC1-STN1-TEN1 (CST), a single-stranded DNA-binding protein complex. CST then recruits DNA polymerase α-primase to complete the telomere replication process by filling in the complementary C-strand. In this chapter, the recent structure-function insights into the human telomere C-strand fill-in machinery (DNA polymerase α-primase and CST) will be discussed.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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15
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase. J Mol Biol 2023; 435:168330. [PMID: 37884206 PMCID: PMC10872500 DOI: 10.1016/j.jmb.2023.168330] [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: 08/01/2023] [Revised: 09/22/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ∼20 nucleotides of DNA. Here, we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the surprisingly low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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16
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Lv Q, Zhou F, Liu X, Zhi L. Artificial intelligence in small molecule drug discovery from 2018 to 2023: Does it really work? Bioorg Chem 2023; 141:106894. [PMID: 37776682 DOI: 10.1016/j.bioorg.2023.106894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Utilizing artificial intelligence (AI) in drug design represents an advanced approach for identifying targets and developing new drugs. Integrating AI techniques significantly reduces the workload involved in drug development and enhances the efficiency of early-stage drug discovery. This review aims to present a comprehensive overview of the utilization of AI methods in the field of small drug design, with a specific focus on four key areas: protein structure prediction, molecular virtual screening, molecular design, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction. Additionally, the role and limitations of AI in drug development are explored, and the impact of AI on decision-making processes is studied. It is important to note that while AI can bring numerous benefits to the early stage of drug development, the direction and quality of decision-making should still be emphasized, as AI should be considered as a tool rather than a decisive factor.
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Affiliation(s)
- Qi Lv
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China
| | - Feilong Zhou
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China
| | - Xinhua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China.
| | - Liping Zhi
- School of Health Management, Anhui Medical University Hefei, 230032, PR China.
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17
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Jaiswal RK, Lei KH, Chastain M, Wang Y, Shiva O, Li S, You Z, Chi P, Chai W. CaMKK2 and CHK1 phosphorylate human STN1 in response to replication stress to protect stalled forks from aberrant resection. Nat Commun 2023; 14:7882. [PMID: 38036565 PMCID: PMC10689503 DOI: 10.1038/s41467-023-43685-2] [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: 04/19/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Keeping replication fork stable is essential for safeguarding genome integrity; hence, its protection is highly regulated. The CTC1-STN1-TEN1 (CST) complex protects stalled forks from aberrant MRE11-mediated nascent strand DNA degradation (NSD). However, the activation mechanism for CST at forks is unknown. Here, we report that STN1 is phosphorylated in its intrinsic disordered region. Loss of STN1 phosphorylation reduces the replication stress-induced STN1 localization to stalled forks, elevates NSD, increases MRE11 access to stalled forks, and decreases RAD51 localization at forks, leading to increased genome instability under perturbed DNA replication condition. STN1 is phosphorylated by both the ATR-CHK1 and the calcium-sensing kinase CaMKK2 in response to hydroxyurea/aphidicolin treatment or elevated cytosolic calcium concentration. Cancer-associated STN1 variants impair STN1 phosphorylation, conferring inability of fork protection. Collectively, our study uncovers that CaMKK2 and ATR-CHK1 target STN1 to enable its fork protective function, and suggests an important role of STN1 phosphorylation in cancer development.
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Affiliation(s)
- Rishi Kumar Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Megan Chastain
- Office of Research, Washington State University, Spokane, WA, USA
| | - Yuan Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Olga Shiva
- Office of Research, Washington State University, Spokane, WA, USA
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA.
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18
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Li B. Telomere maintenance in African trypanosomes. Front Mol Biosci 2023; 10:1302557. [PMID: 38074093 PMCID: PMC10704157 DOI: 10.3389/fmolb.2023.1302557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the "end replication problem" is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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19
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Cai SW, Takai H, Walz T, de Lange T. POT1 recruits and regulates CST-Polα/Primase at human telomeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539880. [PMID: 37215005 PMCID: PMC10197580 DOI: 10.1101/2023.05.08.539880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Telomere maintenance requires extension of the G-rich telomeric repeat strand by telomerase and fill-in synthesis of the C-rich strand by Polα/Primase. Telomeric Polα/Primase is bound to Ctc1-Stn1-Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Polα/Primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Phosphorylation of POT1 is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Polα/Primase in an inactive auto-inhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Polα/Primase into an active state that completes telomere replication through fill-in synthesis.
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Affiliation(s)
- Sarah W. Cai
- Laboratory of Cell Biology and Genetics, The Rockefeller University; New York, NY, USA
- Laboratory of Molecular Electron Microscopy, The Rockefeller University; New York, NY, USA
| | - Hiroyuki Takai
- Laboratory of Cell Biology and Genetics, The Rockefeller University; New York, NY, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University; New York, NY, USA
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, The Rockefeller University; New York, NY, USA
- Lead contact
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20
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He Q, Lim CJ. Models for human telomere C-strand fill-in by CST-Polα-primase. Trends Biochem Sci 2023; 48:860-872. [PMID: 37586999 PMCID: PMC10528720 DOI: 10.1016/j.tibs.2023.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Telomere maintenance is essential for the genome integrity of eukaryotes, and this function is underpinned by the two-step telomeric DNA synthesis process: telomere G-overhang extension by telomerase and complementary strand fill-in by DNA polymerase alpha-primase (polα-primase). Compared to the telomerase step, the telomere C-strand fill-in mechanism is less understood. Recent studies have provided new insights into how telomeric single-stranded DNA-binding protein CTC1-STN1-TEN1 (CST) and polα-primase coordinate to synthesize the telomeric C-strand for telomere overhang fill-in. Cryogenic electron microscopy (cryo-EM) structures of CST-polα-primase complexes have provided additional insights into how they assemble at telomeric templates and de novo synthesize the telomere C-strand. In this review, we discuss how these latest findings coalesce with existing understanding to develop a human telomere C-strand fill-in mechanism model.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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21
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Zabrady K, Li AWH, Doherty AJ. Mechanism of primer synthesis by Primase-Polymerases. Curr Opin Struct Biol 2023; 82:102652. [PMID: 37459807 DOI: 10.1016/j.sbi.2023.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 09/16/2023]
Abstract
Members of the primase-polymerase (Prim-Pol) superfamily are found in all domains of life and play diverse roles in genome stability, including primer synthesis during DNA replication, lesion repair and damage tolerance. This review focuses primarily on Prim-Pol members capable of de novo primer synthesis that have experimentally derived structural models available. We discuss the mechanism of DNA primer synthesis initiation by Prim-Pol catalytic domains, based on recent structural and functional studies. We also describe a general model for primer initiation that also includes the ancillary domains/subunits, which stimulate the initiation of primer synthesis.
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Affiliation(s)
- Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK. https://twitter.com/@KZabrady
| | - Arthur W H Li
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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22
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Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533013. [PMID: 36993335 PMCID: PMC10055150 DOI: 10.1101/2023.03.16.533013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.
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23
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Hara T, Nakaoka H, Miyoshi T, Ishikawa F. The CST complex facilitates cell survival under oxidative genotoxic stress. PLoS One 2023; 18:e0289304. [PMID: 37590191 PMCID: PMC10434909 DOI: 10.1371/journal.pone.0289304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
Genomic DNA is constantly exposed to a variety of genotoxic stresses, and it is crucial for organisms to be equipped with mechanisms for repairing the damaged genome. Previously, it was demonstrated that the mammalian CST (CTC1-STN1-TEN1) complex, which was originally identified as a single-stranded DNA-binding trimeric protein complex essential for telomere maintenance, is required for survival in response to hydroxyurea (HU), which induces DNA replication fork stalling. It is still unclear, however, how the CST complex is involved in the repair of diverse types of DNA damage induced by oxidizing agents such as H2O2. STN1 knockdown (KD) sensitized HeLa cells to high doses of H2O2. While H2O2 induced DNA strand breaks throughout the cell cycle, STN1 KD cells were as resistant as control cells to H2O2 treatment when challenged in the G1 phase of the cell cycle, but they were sensitive when exposed to H2O2 in S/G2/M phase. STN1 KD cells showed a failure of DNA synthesis and RAD51 foci formation upon H2O2 treatment. Chemical inhibition of RAD51 in shSTN1 cells did not exacerbate the sensitivity to H2O2, implying that the CST complex and RAD51 act in the same pathway. Collectively, our results suggest that the CST complex is required for maintaining genomic stability in response to oxidative DNA damage, possibly through RAD51-dependent DNA repair/protection mechanisms.
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Affiliation(s)
- Tomohiko Hara
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hidenori Nakaoka
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomoicihiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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24
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Jones ML, Aria V, Baris Y, Yeeles JTP. How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Mol Cell 2023; 83:2911-2924.e16. [PMID: 37506699 PMCID: PMC10501992 DOI: 10.1016/j.molcel.2023.06.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023]
Abstract
During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis.
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Affiliation(s)
- Morgan L Jones
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Valentina Aria
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Yasemin Baris
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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25
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Barbour AT, Wuttke DS. RPA-like single-stranded DNA-binding protein complexes including CST serve as specialized processivity factors for polymerases. Curr Opin Struct Biol 2023; 81:102611. [PMID: 37245465 PMCID: PMC10524659 DOI: 10.1016/j.sbi.2023.102611] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/30/2023]
Abstract
Telomeres and other single-stranded regions of the genome require specialized management to maintain stability and for proper progression of DNA metabolism pathways. Human Replication Protein A and CTC1-STN1-TEN1 are structurally similar heterotrimeric protein complexes that have essential ssDNA-binding roles in DNA replication, repair, and telomeres. Yeast and ciliates have related ssDNA-binding proteins with strikingly conserved structural features to these human heterotrimeric protein complexes. Recent breakthrough structures have extended our understanding of these commonalities by illuminating a common mechanism used by these proteins to act as processivity factors for their partner polymerases through their ability to manage ssDNA.
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Affiliation(s)
- Alexandra T Barbour
- Department of Biochemistry, University of Colorado Bouder, Boulder, CO 80309, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Bouder, Boulder, CO 80309, USA.
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26
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551538. [PMID: 37577606 PMCID: PMC10418221 DOI: 10.1101/2023.08.01.551538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ~20 nucleotides of DNA. Here we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J. Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Elwood A. Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lauren E. Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brandt F. Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Walter J. Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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27
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Abstract
It has been known for decades that telomerase extends the 3' end of linear eukaryotic chromosomes and dictates the telomeric repeat sequence based on the template in its RNA. However, telomerase does not mitigate sequence loss at the 5' ends of chromosomes, which results from lagging strand DNA synthesis and nucleolytic processing. Therefore, a second enzyme is needed to keep telomeres intact: DNA polymerase α/Primase bound to Ctc1-Stn1-Ten1 (CST). CST-Polα/Primase maintains telomeres through a fill-in reaction that replenishes the lost sequences at the 5' ends. CST not only serves to maintain telomeres but also determines their length by keeping telomerase from overelongating telomeres. Here we discuss recent data on the evolution, structure, function, and recruitment of mammalian CST-Polα/Primase, highlighting the role of this complex and telomere length control in human disease.
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Affiliation(s)
- Sarah W Cai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065, USA
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28
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Lue NF, Autexier C. Orchestrating nucleic acid-protein interactions at chromosome ends: telomerase mechanisms come into focus. Nat Struct Mol Biol 2023; 30:878-890. [PMID: 37400652 PMCID: PMC10539978 DOI: 10.1038/s41594-023-01022-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/16/2023] [Indexed: 07/05/2023]
Abstract
Telomerase is a special reverse transcriptase ribonucleoprotein dedicated to the synthesis of telomere repeats that protect chromosome ends. Among reverse transcriptases, telomerase is unique in using a stably associated RNA with an embedded template to synthesize a specified sequence. Moreover, it is capable of iteratively copying the same template region (repeat addition processivity) through multiple rounds of RNA-DNA unpairing and reannealing, that is, the translocation reaction. Biochemical analyses of telomerase over the past 3 decades in protozoa, fungi and mammals have identified structural elements that underpin telomerase mechanisms and have led to models that account for the special attributes of telomerase. Notably, these findings and models can now be interpreted and adjudicated through recent cryo-EM structures of Tetrahymena and human telomerase holoenzyme complexes in association with substrates and regulatory proteins. Collectively, these structures reveal the intricate protein-nucleic acid interactions that potentiate telomerase's unique translocation reaction and clarify how this enzyme reconfigures the basic reverse transcriptase scaffold to craft a polymerase dedicated to the synthesis of telomere DNA. Among the many new insights is the resolution of the telomerase 'anchor site' proposed more than 3 decades ago. The structures also highlight the nearly universal conservation of a protein-protein interface between an oligonucleotide/oligosaccharide-binding (OB)-fold regulatory protein and the telomerase catalytic subunit, which enables spatial and temporal regulation of telomerase function in vivo. In this Review, we discuss key features of the structures in combination with relevant functional analyses. We also examine conserved and divergent aspects of telomerase mechanisms as gleaned from studies in different model organisms.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
| | - Chantal Autexier
- Lady Davis Institute for Medical Research, Jewish General Hospital and Department of Anatomy and Cell Biology and Department of Medicine, McGill University, Montreal, Quebec, Canada.
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29
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Yuan Z, Georgescu R, Li H, O'Donnell ME. Molecular choreography of primer synthesis by the eukaryotic Pol α-primase. Nat Commun 2023; 14:3697. [PMID: 37344454 PMCID: PMC10284912 DOI: 10.1038/s41467-023-39441-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
The eukaryotic polymerase α (Pol α) synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides. Pol α is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2. Pol1 and Pri1 contain the DNA polymerase and RNA primase activities, respectively. It has been unclear how Pol α hands over an RNA primer from Pri1 to Pol1 for DNA primer extension, and how the primer length is defined. Here we report the cryo-EM analysis of yeast Pol α in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states, revealing a series of very large movements. We reveal a critical point at which Pol1-core moves to take over the 3'-end of the RNA from Pri1. DNA extension is limited by a spiral motion of Pol1-core. Since both Pri1 and Pol1-core are flexibly attached to a stable platform, primer growth produces stress that limits the primer length.
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Affiliation(s)
- Zuanning Yuan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- DNA Replication Laboratory and Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA.
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30
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Wang H, Ma T, Zhang X, Chen W, Lan Y, Kuang G, Hsu SJ, He Z, Chen Y, Stewart J, Bhattacharjee A, Luo Z, Price C, Feng X. CTC1 OB-B interaction with TPP1 terminates telomerase and prevents telomere overextension. Nucleic Acids Res 2023; 51:4914-4928. [PMID: 37021555 PMCID: PMC10250220 DOI: 10.1093/nar/gkad237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/16/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
CST (CTC1-STN1-TEN1) is a telomere associated complex that binds ssDNA and is required for multiple steps in telomere replication, including termination of G-strand extension by telomerase and synthesis of the complementary C-strand. CST contains seven OB-folds which appear to mediate CST function by modulating CST binding to ssDNA and the ability of CST to recruit or engage partner proteins. However, the mechanism whereby CST achieves its various functions remains unclear. To address the mechanism, we generated a series of CTC1 mutants and studied their effect on CST binding to ssDNA and their ability to rescue CST function in CTC1-/- cells. We identified the OB-B domain as a key determinant of telomerase termination but not C-strand synthesis. CTC1-ΔB expression rescued C-strand fill-in, prevented telomeric DNA damage signaling and growth arrest. However, it caused progressive telomere elongation and the accumulation of telomerase at telomeres, indicating an inability to limit telomerase action. The CTC1-ΔB mutation greatly reduced CST-TPP1 interaction but only modestly affected ssDNA binding. OB-B point mutations also weakened TPP1 association, with the deficiency in TPP1 interaction tracking with an inability to limit telomerase action. Overall, our results indicate that CTC1-TPP1 interaction plays a key role in telomerase termination.
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Affiliation(s)
- Huan Wang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tengfei Ma
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaotong Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yina Lan
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guotao Kuang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shih-Jui Hsu
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Zibin He
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jason Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | | | - Zhenhua Luo
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Carolyn Price
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Xuyang Feng
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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31
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Yuan Z, Georgescu R, Li H, O'Donnell ME. Molecular choreography of primer synthesis by the eukaryotic Pol α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539257. [PMID: 37205351 PMCID: PMC10187153 DOI: 10.1101/2023.05.03.539257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The eukaryotic polymerase α (Pol α) is a dual-function DNA polymerase/primase complex that synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides for DNA replication. Pol α is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2, with Pol1 and Pri1 containing the DNA polymerase activity and RNA primase activity, respectively, whereas Pol12 and Pri2 serve a structural role. It has been unclear how Pol α hands over an RNA primer made by Pri1 to Pol1 for DNA primer extension, and how the primer length is defined, perhaps due to the difficulty in studying the highly mobile structure. Here we report a comprehensive cryo-EM analysis of the intact 4-subunit yeast Pol α in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states in a 3.5 Å - 5.6 Å resolution range. We found that Pol α is a three-lobed flexible structure. Pri2 functions as a flexible hinge that holds together the catalytic Pol1-core, and the noncatalytic Pol1 CTD that binds to Pol 12 to form a stable platform upon which the other components are organized. In the apo state, Pol1-core is sequestered on the Pol12-Pol1-CTD platform, and Pri1 is mobile perhaps in search of a template. Upon binding a ssDNA template, a large conformation change is induced that enables Pri1 to perform RNA synthesis, and positions Pol1-core to accept the future RNA primed site 50 Å upstream of where Pri1 binds. We reveal in detail the critical point at which Pol1-core takes over the 3'-end of the RNA from Pri1. DNA primer extension appears limited by the spiral motion of Pol1-core while Pri2-CTD stably holds onto the 5' end of the RNA primer. Since both Pri1 and Pol1-core are attached via two linkers to the platform, primer growth will produce stress within this "two-point" attachment that may limit the length of the RNA-DNA hybrid primer. Hence, this study reveals the large and dynamic series of movements that Pol α undergoes to synthesize a primer for DNA replication.
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32
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Nasheuer HP, Onwubiko NO. Lagging Strand Initiation Processes in DNA Replication of Eukaryotes-Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes. Genes (Basel) 2023; 14:genes14051012. [PMID: 37239371 DOI: 10.3390/genes14051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In their influential reviews, Hanahan and Weinberg coined the term 'Hallmarks of Cancer' and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| | - Nichodemus O Onwubiko
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
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33
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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34
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Mirman Z, Cai S, de Lange T. CST/Polα/primase-mediated fill-in synthesis at DSBs. Cell Cycle 2023; 22:379-389. [PMID: 36205622 PMCID: PMC9879193 DOI: 10.1080/15384101.2022.2123886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 01/29/2023] Open
Abstract
DNA double-strand breaks (DSBs) pose a major threat to the genome, so the efficient repair of such breaks is essential. DSB processing and repair is affected by 53BP1, which has been proposed to determine repair pathway choice and/or promote repair fidelity. 53BP1 and its downstream effectors, RIF1 and shieldin, control 3' overhang length, and the mechanism has been a topic of intensive research. Here, we highlight recent evidence that 3' overhang control by 53BP1 occurs through fill-in synthesis of resected DSBs by CST/Polα/primase. We focus on the crucial role of fill-in synthesis in BRCA1-deficient cells treated with PARPi and discuss the notion of fill-in synthesis in other specialized settings and in the repair of random DSBs. We argue that - in addition to other determinants - repair pathway choice may be influenced by the DNA sequence at the break which can impact CST binding and therefore the deployment of Polα/primase fill-in.
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Affiliation(s)
- Zachary Mirman
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, HHMI, Boston, MA, USA
| | - Sarah Cai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
- Laboratory for Molecular Electron Microscopy, The Rockefeller University, New York, NY
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
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35
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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36
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Coloma J, Gonzalez-Rodriguez N, Balaguer FA, Gmurczyk K, Aicart-Ramos C, Nuero ÓM, Luque-Ortega JR, Calugaru K, Lue NF, Moreno-Herrero F, Llorca O. Molecular architecture and oligomerization of Candida glabrata Cdc13 underpin its telomeric DNA-binding and unfolding activity. Nucleic Acids Res 2023; 51:668-686. [PMID: 36629261 PMCID: PMC9881146 DOI: 10.1093/nar/gkac1261] [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: 05/27/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
The CST complex is a key player in telomere replication and stability, which in yeast comprises Cdc13, Stn1 and Ten1. While Stn1 and Ten1 are very well conserved across species, Cdc13 does not resemble its mammalian counterpart CTC1 either in sequence or domain organization, and Cdc13 but not CTC1 displays functions independently of the rest of CST. Whereas the structures of human CTC1 and CST have been determined, the molecular organization of Cdc13 remains poorly understood. Here, we dissect the molecular architecture of Candida glabrata Cdc13 and show how it regulates binding to telomeric sequences. Cdc13 forms dimers through the interaction between OB-fold 2 (OB2) domains. Dimerization stimulates binding of OB3 to telomeric sequences, resulting in the unfolding of ssDNA secondary structure. Once bound to DNA, Cdc13 prevents the refolding of ssDNA by mechanisms involving all domains. OB1 also oligomerizes, inducing higher-order complexes of Cdc13 in vitro. OB1 truncation disrupts these complexes, affects ssDNA unfolding and reduces telomere length in C. glabrata. Together, our results reveal the molecular organization of C. glabrata Cdc13 and how this regulates the binding and the structure of DNA, and suggest that yeast species evolved distinct architectures of Cdc13 that share some common principles.
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Affiliation(s)
- Javier Coloma
- Correspondence may also be addressed to Javier Coloma. Tel: +34 91 732 8000 (Ext 3033);
| | | | - Francisco A Balaguer
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Karolina Gmurczyk
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Óscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Kimberly Calugaru
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, USA
| | - Neal F Lue
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Oscar Llorca
- To whom correspondence should be addressed. Tel: +34 91 732 8000 (Ext 3000);
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37
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov T. Human DNA polymerase α has a strong mutagenic potential at the initial steps of DNA synthesis. Nucleic Acids Res 2022; 50:12266-12273. [PMID: 36454017 PMCID: PMC9757036 DOI: 10.1093/nar/gkac1101] [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: 08/12/2022] [Revised: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
DNA polymerase α (Polα) is essential for DNA replication initiation and makes a notable contribution to genome mutagenesis. The activity and fidelity of Polα during the early steps of DNA replication have not been well studied. Here we show that at the beginning of DNA synthesis, when extending the RNA primer received from primase, Polα is more mutagenic than during the later DNA elongation steps. Kinetic and binding studies revealed substantially higher activity and affinity to the template:primer when Polα interacts with ribonucleotides of a chimeric RNA-DNA primer. Polα activity greatly varies during first six steps of DNA synthesis, and the bias in the rates of correct and incorrect dNTP incorporation leads to impaired fidelity, especially upon the second step of RNA primer extension. Furthermore, increased activity and stability of Polα/template:primer complexes containing RNA-DNA primers result in higher efficiency of mismatch extension.
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Affiliation(s)
| | | | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tahir H Tahirov
- To whom correspondence should be addressed. Tel: +1 402 559 7608; Fax: +1 402 559 3739;
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38
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Structural and functional insights into CST tethering in Tetrahymena thermophila telomerase. Structure 2022; 30:1565-1572.e4. [DOI: 10.1016/j.str.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/11/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022]
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39
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Soman A, Korolev N, Nordenskiöld L. Telomeric chromatin structure. Curr Opin Struct Biol 2022; 77:102492. [PMID: 36335846 DOI: 10.1016/j.sbi.2022.102492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic DNA is packaged into nucleosomes, which further condenses into chromosomes. The telomeres, which form the protective end-capping of chromosomes, play a pivotal role in ageing and cancer. Recently, significant advances have been made in understanding the nucleosomal and telomeric chromatin structure at the molecular level. In addition, recent studies shed light on the nucleosomal organisation at telomeres revealing its ultrastructural organisation, the atomic structure at the nucleosome level, its dynamic properties, and higher-order packaging of telomeric chromatin. Considerable advances have furthermore been made in understanding the structure, function and organisation of shelterin, telomerase and CST complexes. Here we discuss these recent advances in the organisation of telomeric nucleosomes and chromatin and highlight progress in the structural understanding of shelterin, telomerase and CST complexes.
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Affiliation(s)
- Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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40
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Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S. 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources. Gigascience 2022; 11:giac118. [PMID: 36448847 PMCID: PMC9709962 DOI: 10.1093/gigascience/giac118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.
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Affiliation(s)
- Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | - Sreenath Nair
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, UCL, London WC1E 6BT, UK
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Basel 4056, Switzerland
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Stephen Anyango
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | - Stefan Bienert
- Biozentrum, University of Basel, Basel 4056, Switzerland
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Clemente Borges
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Mandar Deshpande
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
| | | | | | - Andras Hatos
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
- Department of Oncology, Lausanne University Hospital, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Swiss Cancer Center Leman, Lausanne 1005, Switzerland
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | | | - Robbie Joosten
- Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | | | | | - Dmitry Molodenskiy
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Edoardo Salladini
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Steven L Salzberg
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Markus J Sommer
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biology, Seoul National University, Seoul 82-2-880-6971, 6977, South Korea
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary
| | - Dmitri Svergun
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany
| | - Luiggi Tenorio-Ku
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | - Silvio Tosatto
- Department of Biomedical Sciences, University of Padova, Padova 35129, Italy
| | | | - Andrew Mark Waterhouse
- Biozentrum, University of Basel, Basel 4056, Switzerland
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | | | - Torsten Schwede
- Biozentrum, University of Basel, Basel 4056, Switzerland
- Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
| | - Christine Orengo
- Department of Structural and Molecular Biology, UCL, London WC1E 6BT, UK
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK
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41
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Varadi M, Anyango S, Appasamy SD, Armstrong D, Bage M, Berrisford J, Choudhary P, Bertoni D, Deshpande M, Leines GD, Ellaway J, Evans G, Gaborova R, Gupta D, Gutmanas A, Harrus D, Kleywegt GJ, Bueno WM, Nadzirin N, Nair S, Pravda L, Afonso MQL, Sehnal D, Tanweer A, Tolchard J, Abrams C, Dunlop R, Velankar S. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Sci 2022; 31:e4439. [PMID: 36173162 PMCID: PMC9517934 DOI: 10.1002/pro.4439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
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Affiliation(s)
- Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Stephen Anyango
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sri Devan Appasamy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - David Armstrong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Marcus Bage
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - John Berrisford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Preeti Choudhary
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Damian Bertoni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Mandar Deshpande
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Grisell Diaz Leines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Joseph Ellaway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Genevieve Evans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Romana Gaborova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Deepti Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Aleksandras Gutmanas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Deborah Harrus
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | | | - Nurul Nadzirin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sreenath Nair
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Lukas Pravda
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | | | - David Sehnal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ahsan Tanweer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - James Tolchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Charlotte Abrams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Roisin Dunlop
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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42
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Olson CL, Barbour AT, Wuttke DS. Filling in the blanks: how the C-strand catches up to the G-strand at replicating telomeres using CST. Nat Struct Mol Biol 2022; 29:730-733. [PMID: 35948770 DOI: 10.1038/s41594-022-00818-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Conner L Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Alexandra T Barbour
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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43
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He Q, Lin X, Chavez BL, Agrawal S, Lusk BL, Lim CJ. Structures of the human CST-Polα-primase complex bound to telomere templates. Nature 2022; 608:826-832. [PMID: 35830881 DOI: 10.1038/s41586-022-05040-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/29/2022] [Indexed: 01/26/2023]
Abstract
The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways1-4 such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα-primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα-primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα-primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα-primase into two separate domains and effectively arranges them in RNA-DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA-DNA primers by Polα-primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα-primase PIC and activation are also revealed in this study.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xiuhua Lin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Bianca L Chavez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sourav Agrawal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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44
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Zaug AJ, Goodrich KJ, Song JJ, Sullivan AE, Cech TR. Reconstitution of a telomeric replicon organized by CST. Nature 2022; 608:819-825. [PMID: 35831508 PMCID: PMC9402439 DOI: 10.1038/s41586-022-04930-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/06/2022] [Indexed: 11/20/2022]
Abstract
Telomeres, the natural ends of linear chromosomes, comprise repeat-sequence DNA and associated proteins1. Replication of telomeres allows continued proliferation of human stem cells and immortality of cancer cells2. This replication requires telomerase3 extension of the single-stranded DNA (ssDNA) of the telomeric G-strand ((TTAGGG)n); the synthesis of the complementary C-strand ((CCCTAA)n) is much less well characterized. The CST (CTC1–STN1–TEN1) protein complex, a DNA polymerase α-primase accessory factor4,5, is known to be required for telomere replication in vivo6–9, and the molecular analysis presented here reveals key features of its mechanism. We find that human CST uses its ssDNA-binding activity to specify the origins for telomeric C-strand synthesis by bound Polα-primase. CST-organized DNA polymerization can copy a telomeric DNA template that folds into G-quadruplex structures, but the challenges presented by this template probably contribute to telomere replication problems observed in vivo. Combining telomerase, a short telomeric ssDNA primer and CST–Polα–primase gives complete telomeric DNA replication, resulting in the same sort of ssDNA 3′ overhang found naturally on human telomeres. We conclude that the CST complex not only terminates telomerase extension10,11 and recruits Polα–primase to telomeric ssDNA4,12,13 but also orchestrates C-strand synthesis. Because replication of the telomere has features distinct from replication of the rest of the genome, targeting telomere-replication components including CST holds promise for cancer therapeutics. The Polα–primase-associated CST complex organizes telomeric C-strand DNA synthesis, and, in combination with telomerase, it carries out complete replication of the single-stranded DNA overhang found at human telomeres.
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Affiliation(s)
- Arthur J Zaug
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karen J Goodrich
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Jessica J Song
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Ashley E Sullivan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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