1
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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] [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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2
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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] [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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3
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Joo SY, Sung K, Lee H. Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity. Bioessays 2024; 46:e2300229. [PMID: 38922965 DOI: 10.1002/bies.202300229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.
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Affiliation(s)
- So Young Joo
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
| | - Keewon Sung
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, South Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
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4
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Kipcak A, Sezan S, Karpat O, Kaya E, Baylan S, Sariyar E, Yandim C, Karagonlar ZF. Suppression of CTC1 inhibits hepatocellular carcinoma cell growth and enhances RHPS4 cytotoxicity. Mol Biol Rep 2024; 51:799. [PMID: 39001931 DOI: 10.1007/s11033-024-09756-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Although DNA repair mechanisms function to maintain genomic integrity, in cancer cells these mechanisms may negatively affect treatment efficiency. The strategy of targeting cancer cells via inhibiting DNA damage repair has been successfully used in breast and ovarian cancer using PARP inhibitors. Unfortunately, such strategies have not yet yielded results in liver cancer. Hepatocellular carcinoma (HCC), the most common type of liver cancer, is a treatment-resistant malignancy. Despite the development of guided therapies, treatment regimens for advanced HCC patients still fall short of the current need and significant problems such as cancer relapse with resistance still exist. In this paper, we targeted telomeric replication protein CTC1, which is responsible for telomere maintenance. METHODS CTC expression was analyzed using tumor and matched-tissue RNA-sequencing data from TCGA and GTEx. In HCC cell lines, q-RT-PCR and Western blotting were used to detect CTC1 expression. The knock-down of CTC1 was achieved using lentiviral plasmids. The effects of CTC1 silencing on HCC cells were analyzed by flow cytometry, MTT, spheroid and colony formation assays. RESULTS CTC1 is significantly downregulated in HCC tumor samples. However, CTC1 protein levels were higher in sorafenib-resistant cell lines compared to the parental groups. CTC1 inhibition reduced cell proliferation in sorafenib-resistant HCC cell lines and diminished their spheroid and colony forming capacities. Moreover, these cells were more sensitive to single and combined drug treatment with G4 stabilizer RHPS4 and sorafenib. CONCLUSION Our results suggest that targeting CTC1 might be a viable option for combinational therapies designed for sorafenib resistant HCC patients.
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Affiliation(s)
- Arda Kipcak
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
- Department of Psychology, University of Virginia, Charlottesville, VA, USA
| | - Sila Sezan
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ozum Karpat
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ezgi Kaya
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Sude Baylan
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ece Sariyar
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | - Cihangir Yandim
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Zeynep Firtina Karagonlar
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey.
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey.
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5
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Yang Z, Li D, Chen L, Qiu F, Yan S, Tang M, Wang C, Wang L, Luo Y, Sun F, Han J, Fan C, Li J, Wang H. Near-Field Terahertz Morphological Reconstruction Nanoscopy for Subsurface Imaging of Protein Layers. ACS NANO 2024; 18:10104-10112. [PMID: 38527229 DOI: 10.1021/acsnano.3c12776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Protein layers formed on solid surfaces have important applications in various fields. High-resolution characterization of the morphological structures of protein forms in the process of developing protein layers has significant implications for the control of the layer's quality as well as for the evaluation of the layer's performance. However, it remains challenging to precisely characterize all possible morphological structures of protein in various forms, including individuals, networks, and layers involved in the formation of protein layers with currently available methods. Here, we report a terahertz (THz) morphological reconstruction nanoscopy (THz-MRN), which can reveal the nanoscale three-dimensional structural information on a protein sample from its THz near-field image by exploiting an extended finite dipole model for a thin sample. THz-MRN allows for both surface imaging and subsurface imaging with a vertical resolution of ∼0.5 nm, enabling the characterization of various forms of proteins at the single-molecule level. We demonstrate the imaging and morphological reconstruction of single immunoglobulin G (IgG) molecules, their networks, a monolayer, and a heterogeneous double layer comprising an IgG monolayer and a horseradish peroxidase-conjugated anti-IgG layer. The established THz-MRN presents a useful approach for the label-free and nondestructive study of the formation of protein layers.
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Affiliation(s)
- Zhongbo Yang
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Dandan Li
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Ligang Chen
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Fucheng Qiu
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Shihan Yan
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Mingjie Tang
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Chunlei Wang
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Lihua Wang
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing 400044, China
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaguang Han
- Guangxi Key Laboratory of Optoelectronic Information Processing, School of Optoelectronic Engineering, Guilin University of Electronic Technology, Guilin 541004, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200024, China
| | - Jiang Li
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Huabin Wang
- Center of Super-Resolution Optics and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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6
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Guo L, Bao Y, Zhao Y, Ren Z, Bi L, Zhang X, Liu C, Hou X, Wang MD, Sun B. Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307696. [PMID: 38126671 PMCID: PMC10916570 DOI: 10.1002/advs.202307696] [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: 10/13/2023] [Revised: 11/28/2023] [Indexed: 12/23/2023]
Abstract
G-quadruplex (G4) is a four-stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single-molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging-strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single-stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading-strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome.
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Affiliation(s)
- Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yanling Bao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yilin Zhao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhiyun Ren
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai201210China
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State PhysicsCornell UniversityIthacaNY14853USA
- Howard Hughes Medical InstituteCornell UniversityIthacaNY14853USA
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
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7
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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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8
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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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9
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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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10
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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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11
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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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12
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Takasugi T, Gu P, Liang F, Staco I, Chang S. Pot1b -/- tumors activate G-quadruplex-induced DNA damage to promote telomere hyper-elongation. Nucleic Acids Res 2023; 51:9227-9247. [PMID: 37560909 PMCID: PMC10516629 DOI: 10.1093/nar/gkad648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/11/2023] Open
Abstract
Malignant cancers must activate telomere maintenance mechanisms to achieve replicative immortality. Mutations in the human Protection of Telomeres 1 (POT1) gene are frequently detected in cancers with abnormally long telomeres, suggesting that the loss of POT1 function disrupts the regulation of telomere length homeostasis to promote telomere elongation. However, our understanding of the mechanisms leading to elongated telomeres remains incomplete. The mouse genome encodes two POT1 proteins, POT1a and POT1b possessing separation of hPOT1 functions. We performed serial transplantation of Pot1b-/- sarcomas to better understand the role of POT1b in regulating telomere length maintenance. While early-generation Pot1b-/- sarcomas initially possessed shortened telomeres, late-generation Pot1b-/- cells display markedly hyper-elongated telomeres that were recognized as damaged DNA by the Replication Protein A (RPA) complex. The RPA-ATR-dependent DNA damage response at telomeres promotes telomerase recruitment to facilitate telomere hyper-elongation. POT1b, but not POT1a, was able to unfold G-quadruplex present in hyper-elongated telomeres to repress the DNA damage response. Our findings demonstrate that the repression of the RPA-ATR DDR is conserved between POT1b and human POT1, suggesting that similar mechanisms may underly the phenotypes observed in human cancers harboring human POT1 mutations.
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Affiliation(s)
- Taylor Takasugi
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peili Gu
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Fengshan Liang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Isabelle Staco
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
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13
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Li T, Zhang M, Li Y, Han X, Tang L, Ma T, Zhao X, Zhao R, Wang Y, Bai X, Zhang K, Geng X, Sui L, Feng X, Zhang Q, Zhao Y, Liu Y, Stewart JA, Wang F. Cooperative interaction of CST and RECQ4 resolves G-quadruplexes and maintains telomere stability. EMBO Rep 2023; 24:e55494. [PMID: 37493024 PMCID: PMC10481657 DOI: 10.15252/embr.202255494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
Human CST (CTC1-STN1-TEN1) is a ssDNA-binding complex that interacts with the replisome to aid in stalled fork rescue. We previously found that CST promotes telomere replication to maintain genomic integrity via G-quadruplex (G4) resolution. However, the detailed mechanism by which CST resolves G4s in vivo and whether additional factors are involved remains unclear. Here, we identify RECQ4 as a novel CST-interacting partner and show that RECQ4 can unwind G4 structures in vitro using a FRET assay. Moreover, G4s accumulate at the telomere after RECQ4 depletion, resulting in telomere dysfunction, including the formation of MTSs, SFEs, and TIFs, suggesting that RECQ4 is crucial for telomere integrity. Furthermore, CST is also required for RECQ4 telomere or chromatin localization in response to G4 stabilizers. RECQ4 is involved in preserving genomic stability by CST and RECQ4 disruption impairs restart of replication forks stalled by G4s. Overall, our findings highlight the essential roles of CST and RECQ4 in resolving G-rich regions, where they collaborate to resolve G4-induced replication deficiencies and maintain genomic homeostasis.
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Affiliation(s)
- Tingfang Li
- Department of Genetics, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Geriatrics Institute General Hospital, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Miaomiao Zhang
- Medical Research CenterAffiliated Hospital of Jining Medical UniversityJiningChina
| | - Yanjing Li
- Department of Prosthodontics, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Xinyu Han
- Department of Genetics, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Geriatrics Institute General Hospital, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Lu Tang
- Department of Prosthodontics, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Tengfei Ma
- Institute of Precision MedicineThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Xiaotong Zhao
- Department of Radiobiology, Institute of Radiation MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Rui Zhao
- Department of Genetics, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Geriatrics Institute General Hospital, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Yuwen Wang
- Department of Genetics, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Geriatrics Institute General Hospital, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Xue Bai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsTianjin Medical UniversityTianjinChina
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsTianjin Medical UniversityTianjinChina
| | - Xin Geng
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Lei Sui
- Department of Prosthodontics, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
| | - Xuyang Feng
- Institute of Precision MedicineThe First Affiliated Hospital, Sun Yat‐Sen UniversityGuangzhouChina
| | - Qiang Zhang
- Department of Geriatrics, Tianjin Medical University General HospitalTianjin Geriatrics InstituteTianjinChina
| | - Yang Zhao
- Department of Radiology, Tianjin Institute of UrologyThe Second Hospital of Tianjin Medical UniversityTianjinChina
| | - Yang Liu
- Department of Radiobiology, Institute of Radiation MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jason A Stewart
- Department of BiologyWestern Kentucky UniversityBowling GreenKYUSA
- Department of Biological SciencesUniversity of South CarolinaColumbiaSCUSA
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Geriatrics Institute General Hospital, School and Hospital of StomatologyTianjin Medical UniversityTianjinChina
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14
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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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15
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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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16
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Olson CL, Barbour AT, Wieser TA, Wuttke DS. RPA engages telomeric G-quadruplexes more effectively than CST. Nucleic Acids Res 2023; 51:5073-5086. [PMID: 37140062 PMCID: PMC10250233 DOI: 10.1093/nar/gkad315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
G-quadruplexes (G4s) are a set of stable secondary structures that form within guanine-rich regions of single-stranded nucleic acids that pose challenges for DNA maintenance. The G-rich DNA sequence at telomeres has a propensity to form G4s of various topologies. The human protein complexes Replication Protein A (RPA) and CTC1-STN1-TEN1 (CST) are implicated in managing G4s at telomeres, leading to DNA unfolding and allowing telomere replication to proceed. Here, we use fluorescence anisotropy equilibrium binding measurements to determine the ability of these proteins to bind various telomeric G4s. We find that the ability of CST to specifically bind G-rich ssDNA is substantially inhibited by the presence of G4s. In contrast, RPA tightly binds telomeric G4s, showing negligible changes in affinity for G4 structure compared to linear ssDNAs. Using a mutagenesis strategy, we found that RPA DNA-binding domains work together for G4 binding, and simultaneous disruption of these domains reduces the affinity of RPA for G4 ssDNA. The relative inability of CST to disrupt G4s, combined with the greater cellular abundance of RPA, suggests that RPA could act as a primary protein complex responsible for resolving G4s at telomeres.
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Affiliation(s)
- Conner L Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Alexandra T Barbour
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Thomas A Wieser
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
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17
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Zade NH, Khattar E. POT1 mutations cause differential effects on telomere length leading to opposing disease phenotypes. J Cell Physiol 2023; 238:1237-1255. [PMID: 37183325 DOI: 10.1002/jcp.31034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
The protection of telomere protein (POT1) is a telomere-binding protein and is an essential component of the six-membered shelterin complex, which is associated with the telomeres. POT1 directly binds to the 3' single-stranded telomeric overhang and prevents the activation of DNA damage response at telomeres thus preventing the telomere-telomere fusions and genomic instability. POT1 also plays a pivotal role in maintaining telomere length by regulating telomerase-mediated telomere elongation. Mutations in POT1 proteins result in three different telomere phenotypes, which include long, short, or aberrant telomere length. Long telomeres predispose individuals to cancer, while short or aberrant telomere phenotypes result in pro-aging diseases referred to as telomeropathies. Here, we review the function of POT1 proteins in telomere length hemostasis and how the spectrum of mutations reported in POT1 can be segregated toward developing very distinct disease phenotypes of cancer and telomeropathies.
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Affiliation(s)
- Nikita Harish Zade
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
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18
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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19
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Nguyen DD, Kim E, Le NT, Ding X, Jaiswal RK, Kostlan RJ, Nguyen TNT, Shiva O, Le MT, Chai W. Deficiency in mammalian STN1 promotes colon cancer development via inhibiting DNA repair. SCIENCE ADVANCES 2023; 9:eadd8023. [PMID: 37163605 PMCID: PMC10171824 DOI: 10.1126/sciadv.add8023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Despite the high lethality of colorectal cancers (CRCs), only a limited number of genetic risk factors are identified. The mammalian ssDNA-binding protein complex CTC1-STN1-TEN1 protects genome stability, yet its role in tumorigenesis is unknown. Here, we show that attenuated CTC1/STN1 expression is common in CRCs. We generated an inducible STN1 knockout mouse model and found that STN1 deficiency in young adult mice increased CRC incidence, tumor size, and tumor load. CRC tumors exhibited enhanced proliferation, reduced apoptosis, and elevated DNA damage and replication stress. We found that STN1 deficiency down-regulated multiple DNA glycosylases, resulting in defective base excision repair (BER) and accumulation of oxidative damage. Collectively, this study identifies STN1 deficiency as a risk factor for CRC and implicates the previously unknown STN1-BER axis in protecting colon tissues from oxidative damage, therefore providing insights into the CRC tumor-suppressing mechanism.
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Affiliation(s)
- Dinh Duc Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Eugene Kim
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Nhat Thong Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
| | - Xianzhong Ding
- Department of Pathology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Rishi Kumar Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Raymond Joseph Kostlan
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Thi Ngoc Thanh Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Olga Shiva
- Office of Research, Washington State University-Spokane, Spokane, WA, USA
| | - Minh Thong Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
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20
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G4-interacting proteins endangering genomic stability at G4 DNA-forming sites. Biochem Soc Trans 2023; 51:403-413. [PMID: 36629511 PMCID: PMC10018705 DOI: 10.1042/bst20221018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
In guanine-rich DNA strands, base-base interactions among guanines allow the conformational shift from the B-form DNA to the non-canonical quadruplex or G4 structure. The functional significance of G4 DNA in vivo is largely dependent on the interaction with protein factors, many of which contain the arginine-glycine-glycine or RGG repeat and other consensus G4-binding motifs. These G4-interacting proteins can significantly modulate the effect of G4 DNA structure on genome maintenance, either preventing or aggravating G4-assoicated genome instability. While the role of helicases in resolving G4 DNA structure has been extensively discussed, identification and characterization of protein factors contributing to elevation in G4-associated genome instability has been relatively sparse. In this minireview, we will particularly highlight recent discoveries regarding how interaction between certain G4-binding proteins and G4 DNA could exacerbate genome instability potentiated by G4 DNA-forming sequences.
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21
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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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22
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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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23
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Miglietta G, Marinello J, Russo M, Capranico G. Ligands stimulating antitumour immunity as the next G-quadruplex challenge. Mol Cancer 2022; 21:180. [PMID: 36114513 PMCID: PMC9482198 DOI: 10.1186/s12943-022-01649-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractG-quadruplex (G4) binders have been investigated to discover new anticancer drugs worldwide in past decades. As these ligands are generally not highly cytotoxic, the discovery rational was mainly based on increasing the cell-killing potency. Nevertheless, no G4 binder has been shown yet to be effective in cancer patients. Here, G4 binder activity at low dosages will be discussed as a critical feature to discover ligands with therapeutic effects in cancer patients. Specific effects of G4 binders al low doses have been reported to occur in cancer and normal cells. Among them, genome instability and the stimulation of cytoplasmic processes related to autophagy and innate immune response open to the use of G4 binders as immune-stimulating agents. Thus, we propose a new rational of drug discovery, which is not based on cytotoxic potency but rather on immune gene activation at non-cytotoxic dosage.
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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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25
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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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26
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules 2022; 12:biom12050648. [PMID: 35625576 PMCID: PMC9138358 DOI: 10.3390/biom12050648] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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29
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Pan-cancer analysis reveals that CTC1-STN1-TEN1 (CST) complex may have a key position in oncology. Cancer Genet 2022; 262-263:80-90. [DOI: 10.1016/j.cancergen.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/07/2022] [Accepted: 01/30/2022] [Indexed: 12/14/2022]
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30
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Wang L, Ma T, Liu W, Li H, Luo Z, Feng X. Pan-Cancer Analyses Identify the CTC1-STN1-TEN1 Complex as a Protective Factor and Predictive Biomarker for Immune Checkpoint Blockade in Cancer. Front Genet 2022; 13:859617. [PMID: 35368664 PMCID: PMC8966541 DOI: 10.3389/fgene.2022.859617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
The CTC1-STN1-TEN1 (CST) complex plays a crucial role in telomere replication and genome stability. However, the detailed mechanisms of CST regulation in cancer remain largely unknown. Here, we perform a comprehensive analysis of CST across 33 cancer types using multi-omic data from The Cancer Genome Atlas. In the genomic landscape, we identify CTC1/STN1 deletion and mutation and TEN1 amplification as the dominant alteration events. Expressions of CTC1 and STN1 are decreased in tumors compared to those in adjacent normal tissues. Clustering analysis based on CST expression reveals three cancer clusters displaying differences in survival, telomerase activity, cell proliferation, and genome stability. Interestingly, we find that CTC1 and STN1, but not TEN1, are co-expressed and associated with better survival. CTC1-STN1 is positively correlated with CD8 T cells and B cells and predicts a better response to immune checkpoint blockade in external datasets of cancer immunotherapy. Pathway analysis shows that MYC targets are negatively correlated with CTC1-STN1. We experimentally validated that knockout of CTC1 increased the mRNA level of c-MYC. Furthermore, CTC1 and STN1 are repressed by miRNAs and lncRNAs. Finally, by mining the connective map database, we discover a number of potential drugs that may target CST. In sum, this study illustrates CTC1-STN1 as a protective factor and provides broad molecular signatures for further functional and therapeutic studies of CST in cancer.
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Affiliation(s)
- Lishuai Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tengfei Ma
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weijin Liu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Heping Li
- Department of Medical Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Heping Li, ; Zhenhua Luo, ; Xuyang Feng,
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Heping Li, ; Zhenhua Luo, ; Xuyang Feng,
| | - Xuyang Feng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Heping Li, ; Zhenhua Luo, ; Xuyang Feng,
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31
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Aicart-Ramos C, Hormeno S, Wilkinson OJ, Dillingham MS, Moreno-Herrero F. Long DNA constructs to study helicases and nucleic acid translocases using optical tweezers. Methods Enzymol 2022; 673:311-358. [DOI: 10.1016/bs.mie.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Telomeres and Cancer. Life (Basel) 2021; 11:life11121405. [PMID: 34947936 PMCID: PMC8704776 DOI: 10.3390/life11121405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Telomeres cap the ends of eukaryotic chromosomes and are indispensable chromatin structures for genome protection and replication. Telomere length maintenance has been attributed to several functional modulators, including telomerase, the shelterin complex, and the CST complex, synergizing with DNA replication, repair, and the RNA metabolism pathway components. As dysfunctional telomere maintenance and telomerase activation are associated with several human diseases, including cancer, the molecular mechanisms behind telomere length regulation and protection need particular emphasis. Cancer cells exhibit telomerase activation, enabling replicative immortality. Telomerase reverse transcriptase (TERT) activation is involved in cancer development through diverse activities other than mediating telomere elongation. This review describes the telomere functions, the role of functional modulators, the implications in cancer development, and the future therapeutic opportunities.
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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Lei KH, Yang HL, Chang HY, Yeh HY, Nguyen DD, Lee TY, Lyu X, Chastain M, Chai W, Li HW, Chi P. Crosstalk between CST and RPA regulates RAD51 activity during replication stress. Nat Commun 2021; 12:6412. [PMID: 34741010 PMCID: PMC8571288 DOI: 10.1038/s41467-021-26624-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Replication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.
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Affiliation(s)
- Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Han-Lin Yang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Dinh Duc Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Tzu-Yu Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Megan Chastain
- Office of Research, Washington State University, Spokane, WA, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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36
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Glousker G, Lingner J. Challenging endings: How telomeres prevent fragility. Bioessays 2021; 43:e2100157. [PMID: 34436787 DOI: 10.1002/bies.202100157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022]
Abstract
It has become apparent that difficulties to replicate telomeres concern not only the very ends of eukaryotic chromosomes. The challenges already start when the replication fork enters the telomeric repeats. The obstacles encountered consist mainly of noncanonical nucleic acid structures that interfere with replication if not resolved. Replication stress at telomeres promotes the formation of so-called fragile telomeres displaying an abnormal appearance in metaphase chromosomes though their exact molecular nature remains to be elucidated. A substantial number of factors is required to counteract fragility. In this review we promote the hypothesis that telomere fragility is not caused directly by an initial insult during replication but it results as a secondary consequence of DNA repair of damaged replication forks by the homologous DNA recombination machinery. Incomplete DNA synthesis at repair sites or partial chromatin condensation may become apparent as telomere fragility. Fragility and DNA repair during telomere replication emerges as a common phenomenon which exacerbates in multiple disease conditions.
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Affiliation(s)
- Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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37
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Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, Tijsterman M. Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini. Nat Commun 2021; 12:4843. [PMID: 34376693 PMCID: PMC8355091 DOI: 10.1038/s41467-021-25154-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3′ ssDNA protrusions. By including so-called primase deserts in CRISPR/Cas9-induced DNA break configurations, we reveal that fill-in synthesis preferentially starts at the 3′ tip, and find this activity to be dependent on 53BP1, and the CTC1-STN1-TEN1 (CST) and Shieldin complexes. This axis generates near-blunt ends specifically at DNA breaks with 3′ overhangs, which are subsequently repaired by non-homologous end-joining. Our study provides a mechanistic explanation for a mutational signature abundantly observed in the genomes of species and cancer cells. Error-prone repair of DNA double-strand breaks have been implied to cause cancer-associated genome alterations, but the mechanism of their formation remains unclear. Here the authors find that DNA polymerase α primase plays part in tandem duplication formation at CRISPR/Cas9-induced complementary 3′ ssDNA protrusions.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. .,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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38
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Li B, Zhao Y. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities. Pathogens 2021; 10:pathogens10080967. [PMID: 34451431 PMCID: PMC8402208 DOI: 10.3390/pathogens10080967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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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 Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence: (B.L.); (Y.Z.)
| | - Yanxiang Zhao
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
- Correspondence: (B.L.); (Y.Z.)
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39
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Par S, Vaides S, VanderVere-Carozza PS, Pawelczak KS, Stewart J, Turchi JJ. OB-Folds and Genome Maintenance: Targeting Protein-DNA Interactions for Cancer Therapy. Cancers (Basel) 2021; 13:3346. [PMID: 34283091 PMCID: PMC8269290 DOI: 10.3390/cancers13133346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
Genome stability and maintenance pathways along with their requisite proteins are critical for the accurate duplication of genetic material, mutation avoidance, and suppression of human diseases including cancer. Many of these proteins participate in these pathways by binding directly to DNA, and a subset employ oligonucleotide/oligosaccharide binding folds (OB-fold) to facilitate the protein-DNA interactions. OB-fold motifs allow for sequence independent binding to single-stranded DNA (ssDNA) and can serve to position specific proteins at specific DNA structures and then, via protein-protein interaction motifs, assemble the machinery to catalyze the replication, repair, or recombination of DNA. This review provides an overview of the OB-fold structural organization of some of the most relevant OB-fold containing proteins for oncology and drug discovery. We discuss their individual roles in DNA metabolism, progress toward drugging these motifs and their utility as potential cancer therapeutics. While protein-DNA interactions were initially thought to be undruggable, recent reports of success with molecules targeting OB-fold containing proteins suggest otherwise. The potential for the development of agents targeting OB-folds is in its infancy, but if successful, would expand the opportunities to impinge on genome stability and maintenance pathways for more effective cancer treatment.
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Affiliation(s)
- Sui Par
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.P.); (S.V.)
| | - Sofia Vaides
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.P.); (S.V.)
| | | | | | - Jason Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - John J. Turchi
- Indiana University Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (S.P.); (S.V.)
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- NERx Biosciences, Indianapolis, IN 46202, USA;
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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40
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Lyu X, Sang PB, Chai W. CST in maintaining genome stability: Beyond telomeres. DNA Repair (Amst) 2021; 102:103104. [PMID: 33780718 PMCID: PMC8081025 DOI: 10.1016/j.dnarep.2021.103104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
The human CST (CTC1-STN1-TEN1) complex is an RPA-like single-stranded DNA binding protein complex. While its telomeric functions have been well investigated, numerous studies have revealed that hCST also plays important roles in maintaining genome stability beyond telomeres. Here, we review and discuss recent discoveries on CST in various global genome maintenance pathways, including findings on the CST supercomplex structure, its functions in unperturbed DNA replication, stalled replication, double-strand break repair, and the ATR-CHK1 activation pathway. By summarizing these recent discoveries, we hope to offer new insights into genome maintenance mechanisms and the pathogenesis of CST mutation-associated diseases.
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Affiliation(s)
- Xinxing Lyu
- Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250062, China; Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, 60153, United States.
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41
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Choudhury A, Mohammad T, Samarth N, Hussain A, Rehman MT, Islam A, Alajmi MF, Singh S, Hassan MI. Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1. Sci Rep 2021; 11:10202. [PMID: 33986331 PMCID: PMC8119478 DOI: 10.1038/s41598-021-89450-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Conserved telomere maintenance component 1 (CTC1) is an important component of the CST (CTC1-STN1-TEN1) complex, involved in maintaining the stability of telomeric DNA. Several non-synonymous single-nucleotide polymorphisms (nsSNPs) in CTC1 have been reported to cause Coats plus syndrome and Dyskeratosis congenital diseases. Here, we have performed sequence and structure analyses of nsSNPs of CTC1 using state-of-the-art computational methods. The structure-based study focuses on the C-terminal OB-fold region of CTC1. There are 11 pathogenic mutations identified, and detailed structural analyses were performed. These mutations cause a significant disruption of noncovalent interactions, which may be a possible reason for CTC1 instability and consequent diseases. To see the impact of such mutations on the protein conformation, all-atom molecular dynamics (MD) simulations of CTC1-wild-type (WT) and two of the selected mutations, R806C and R806L for 200 ns, were carried out. A significant conformational change in the structure of the R806C mutant was observed. This study provides a valuable direction to understand the molecular basis of CTC1 dysfunction in disease progression, including Coats plus syndrome.
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Affiliation(s)
- Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Nikhil Samarth
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University, Campus, Pune, 411007, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University, Campus, Pune, 411007, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Pol α-primase dependent nuclear localization of the mammalian CST complex. Commun Biol 2021; 4:349. [PMID: 33731801 PMCID: PMC7969954 DOI: 10.1038/s42003-021-01845-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The human CST complex composed of CTC1, STN1, and TEN1 is critically involved in telomere maintenance and homeostasis. Specifically, CST terminates telomere extension by inhibiting telomerase access to the telomeric overhang and facilitates lagging strand fill in by recruiting DNA Polymerase alpha primase (Pol α-primase) to the telomeric C-strand. Here we reveal that CST has a dynamic intracellular localization that is cell cycle dependent. We report an increase in nuclear CST several hours after the initiation of DNA replication, followed by exit from the nucleus prior to mitosis. We identify amino acids of CTC1 involved in Pol α-primase binding and nuclear localization. We conclude, the CST complex does not contain a nuclear localization signal (NLS) and suggest that its nuclear localization is reliant on Pol α-primase. Hypomorphic mutations affecting CST nuclear import are associated with telomere syndromes and cancer, emphasizing the important role of this process in health.
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Lim CJ, Cech TR. Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization. Nat Rev Mol Cell Biol 2021; 22:283-298. [PMID: 33564154 DOI: 10.1038/s41580-021-00328-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
The regulation of telomere length in mammals is crucial for chromosome end-capping and thus for maintaining genome stability and cellular lifespan. This process requires coordination between telomeric protein complexes and the ribonucleoprotein telomerase, which extends the telomeric DNA. Telomeric proteins modulate telomere architecture, recruit telomerase to accessible telomeres and orchestrate the conversion of the newly synthesized telomeric single-stranded DNA tail into double-stranded DNA. Dysfunctional telomere maintenance leads to telomere shortening, which causes human diseases including bone marrow failure, premature ageing and cancer. Recent studies provide new insights into telomerase-related interactions (the 'telomere replisome') and reveal new challenges for future telomere structural biology endeavours owing to the dynamic nature of telomere architecture and the great number of structures that telomeres form. In this Review, we discuss recently determined structures of the shelterin and CTC1-STN1-TEN1 (CST) complexes, how they may participate in the regulation of telomere replication and chromosome end-capping, and how disease-causing mutations in their encoding genes may affect specific functions. Major outstanding questions in the field include how all of the telomere components assemble relative to each other and how the switching between different telomere structures is achieved.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, 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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Lyu X, Lei K, Biak Sang P, Shiva O, Chastain M, Chi P, Chai W. Human CST complex protects stalled replication forks by directly blocking MRE11 degradation of nascent-strand DNA. EMBO J 2021; 40:e103654. [PMID: 33210317 PMCID: PMC7809791 DOI: 10.15252/embj.2019103654] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/07/2020] [Accepted: 10/20/2020] [Indexed: 01/31/2023] Open
Abstract
Degradation and collapse of stalled replication forks are main sources of genomic instability, yet the molecular mechanisms for protecting forks from degradation/collapse are not well understood. Here, we report that human CST (CTC1-STN1-TEN1) proteins, which form a single-stranded DNA-binding complex, localize at stalled forks and protect stalled forks from degradation by the MRE11 nuclease. CST deficiency increases MRE11 binding to stalled forks, leading to nascent-strand degradation at reversed forks and ssDNA accumulation. In addition, purified CST complex binds to 5' DNA overhangs and directly blocks MRE11 degradation in vitro, and the DNA-binding ability of CST is required for blocking MRE11-mediated nascent-strand degradation. Our results suggest that CST inhibits MRE11 binding to reversed forks, thus antagonizing excessive nascent-strand degradation. Finally, we uncover that CST complex inactivation exacerbates genome instability in BRCA2 deficient cells. Collectively, our findings identify the CST complex as an important fork protector that preserves genome integrity under replication perturbation.
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Affiliation(s)
- Xinxing Lyu
- Department of Cancer BiologyCardinal Bernardin Cancer CenterLoyola University Chicago Stritch School of MedicineMaywoodILUSA
- Department of Biomedical SciencesESF College of MedicineWashington State UniversitySpokaneWAUSA
| | - Kai‐Hang Lei
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Pau Biak Sang
- Department of Cancer BiologyCardinal Bernardin Cancer CenterLoyola University Chicago Stritch School of MedicineMaywoodILUSA
| | - Olga Shiva
- Department of Biomedical SciencesESF College of MedicineWashington State UniversitySpokaneWAUSA
| | - Megan Chastain
- Department of Biomedical SciencesESF College of MedicineWashington State UniversitySpokaneWAUSA
| | - Peter Chi
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
| | - Weihang Chai
- Department of Cancer BiologyCardinal Bernardin Cancer CenterLoyola University Chicago Stritch School of MedicineMaywoodILUSA
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45
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Grill S, Nandakumar J. Molecular mechanisms of telomere biology disorders. J Biol Chem 2021; 296:100064. [PMID: 33482595 PMCID: PMC7948428 DOI: 10.1074/jbc.rev120.014017] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mutations that affect telomerase function or telomere maintenance result in a variety of diseases collectively called telomeropathies. This wide spectrum of disorders, which include dyskeratosis congenita, pulmonary fibrosis, and aplastic anemia, is characterized by severely short telomeres, often resulting in hematopoietic stem cell failure in the most severe cases. Recent work has focused on understanding the molecular basis of these diseases. Mutations in the catalytic TERT and TR subunits of telomerase compromise activity, while others, such as those found in the telomeric protein TPP1, reduce the recruitment of telomerase to the telomere. Mutant telomerase-associated proteins TCAB1 and dyskerin and the telomerase RNA maturation component poly(A)-specific ribonuclease affect the maturation and stability of telomerase. In contrast, disease-associated mutations in either CTC1 or RTEL1 are more broadly associated with telomere replication defects. Yet even with the recent surge in studies decoding the mechanisms underlying these diseases, a significant proportion of dyskeratosis congenita mutations remain uncharacterized or poorly understood. Here we review the current understanding of the molecular basis of telomeropathies and highlight experimental data that illustrate how genetic mutations drive telomere shortening and dysfunction in these patients. This review connects insights from both clinical and molecular studies to create a comprehensive view of the underlying mechanisms that drive these diseases. Through this, we emphasize recent advances in therapeutics and pinpoint disease-associated variants that remain poorly defined in their mechanism of action. Finally, we suggest future avenues of research that will deepen our understanding of telomere biology and telomere-related disease.
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Affiliation(s)
- Sherilyn Grill
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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46
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Ackerson SM, Gable CI, Stewart JA. Human CTC1 promotes TopBP1 stability and CHK1 phosphorylation in response to telomere dysfunction and global replication stress. Cell Cycle 2020; 19:3491-3507. [PMID: 33269665 PMCID: PMC7781613 DOI: 10.1080/15384101.2020.1849979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/30/2020] [Accepted: 11/07/2020] [Indexed: 01/21/2023] Open
Abstract
CST (CTC1-STN1-TEN1) is a heterotrimeric, RPA-like complex that binds to single-stranded DNA (ssDNA) and functions in the replication of telomeric and non-telomeric DNA. Previous studies demonstrated that deletion of CTC1 results in decreased cell proliferation and telomere DNA damage signaling. However, a detailed analysis of the consequences of conditional CTC1 knockout (KO) has not been fully elucidated. Here, we investigated the effects of CTC1 KO on cell cycle progression, genome-wide replication and activation of the DNA damage response. Consistent with previous findings, we demonstrate that CTC1 KO results in decreased cell proliferation, G2 arrest and RPA-bound telomeric ssDNA. However, despite the increased levels of telomeric RPA-ssDNA, global ATR-dependent CHK1 and p53 phosphorylation was not detected in CTC1 KO cells. Nevertheless, we show that RPA-ssDNA does activate ATR, leading to the phosphorylation of RPA and autophosphorylation of ATR. Further analysis determined that inactivation of ATR, but not CHK1 or ATM, suppressed the accumulation of G2 arrested cells and phosphorylated RPA following CTC1 removal. These results suggest that ATR is localized and active at telomeres but is unable to elicit a global checkpoint response through CHK1. Furthermore, CTC1 KO inhibited CHK1 phosphorylation following hydroxyurea-induced replication stress. Additional studies revealed that this suppression of CHK1 phosphorylation, following replication stress, is caused by decreased levels of the ATR activator TopBP1. Overall, our results identify CST as a novel regulator of the ATR-CHK1 pathway.
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Affiliation(s)
| | - Caroline I. Gable
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Jason A. Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
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Singh S, Berroyer A, Kim M, Kim N. Yeast Nucleolin Nsr1 Impedes Replication and Elevates Genome Instability at an Actively Transcribed Guanine-Rich G4 DNA-Forming Sequence. Genetics 2020; 216:1023-1037. [PMID: 33106247 PMCID: PMC7768239 DOI: 10.1534/genetics.120.303736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/21/2020] [Indexed: 12/01/2022] Open
Abstract
A significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNA in vivo has been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin (NCL) is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. The consequence of the in vivo interaction between G4 DNA and nucleolin in respect to the genome instability has not been previously investigated. We show here that the yeast nucleolin Nsr1 is enriched at a G4 DNA-forming sequence in vivo and is a major factor in inducing the genome instability associated with the cotranscriptionally formed G4 DNA in the yeast genome. We also show that Nsr1 results in impeding replication past such a G4 DNA-forming sequence. The G4-associated genome instability and the G4 DNA-binding in vivo require the arginine-glycine-glycine (RGG) repeats located at the C-terminus of the Nsr1 protein. Nsr1 with the deletion of RGG domain supports normal cell growth and is sufficient for its pre-rRNA processing function. However, the truncation of the RGG domain of Nsr1 significantly weakens its interaction with G4 DNA in vivo and restores unhindered replication, overall resulting in a sharp reduction in the genome instability associated with a guanine-rich G4 DNA-forming sequence. Our data suggest that the interaction between Nsr1 with the intact RGG repeats and G4 DNA impairs genome stability by precluding the access of G4-resolving proteins and impeding replication.
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Affiliation(s)
- Shivani Singh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alexandra Berroyer
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Minseon Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
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48
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Nguyen DD, Kim EY, Sang PB, Chai W. Roles of OB-Fold Proteins in Replication Stress. Front Cell Dev Biol 2020; 8:574466. [PMID: 33043007 PMCID: PMC7517361 DOI: 10.3389/fcell.2020.574466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate DNA replication is essential for maintaining genome stability. However, this stability becomes vulnerable when replication fork progression is stalled or slowed - a condition known as replication stress. Prolonged fork stalling can cause DNA damage, leading to genome instabilities. Thus, cells have developed several pathways and a complex set of proteins to overcome the challenge at stalled replication forks. Oligonucleotide/oligosaccharide binding (OB)-fold containing proteins are a group of proteins that play a crucial role in fork protection and fork restart. These proteins bind to single-stranded DNA with high affinity and prevent premature annealing and unwanted nuclease digestion. Among these OB-fold containing proteins, the best studied in eukaryotic cells are replication protein A (RPA) and breast cancer susceptibility protein 2 (BRCA2). Recently, another RPA-like protein complex CTC1-STN1-TEN1 (CST) complex has been found to counter replication perturbation. In this review, we discuss the latest findings on how these OB-fold containing proteins (RPA, BRCA2, CST) cooperate to safeguard DNA replication and maintain genome stability.
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Affiliation(s)
| | | | | | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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50
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Jurikova K, Gajarsky M, Hajikazemi M, Nosek J, Prochazkova K, Paeschke K, Trantirek L, Tomaska L. Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae. J Biol Chem 2020; 295:8958-8971. [PMID: 32385108 PMCID: PMC7335780 DOI: 10.1074/jbc.ra120.012914] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The ends of eukaryotic chromosomes typically contain a 3' ssDNA G-rich protrusion (G-overhang). This overhang must be protected against detrimental activities of nucleases and of the DNA damage response machinery and participates in the regulation of telomerase, a ribonucleoprotein complex that maintains telomere integrity. These functions are mediated by DNA-binding proteins, such as Cdc13 in Saccharomyces cerevisiae, and the propensity of G-rich sequences to form various non-B DNA structures. Using CD and NMR spectroscopies, we show here that G-overhangs of S. cerevisiae form distinct Hoogsteen pairing-based secondary structures, depending on their length. Whereas short telomeric oligonucleotides form a G-hairpin, their longer counterparts form parallel and/or antiparallel G-quadruplexes (G4s). Regardless of their topologies, non-B DNA structures exhibited impaired binding to Cdc13 in vitro as demonstrated by electrophoretic mobility shift assays. Importantly, whereas G4 structures formed relatively quickly, G-hairpins folded extremely slowly, indicating that short G-overhangs, which are typical for most of the cell cycle, are present predominantly as single-stranded oligonucleotides and are suitable substrates for Cdc13. Using ChIP, we show that the occurrence of G4 structures peaks at the late S phase, thus correlating with the accumulation of long G-overhangs. We present a model of how time- and length-dependent formation of non-B DNA structures at chromosomal termini participates in telomere maintenance.
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Affiliation(s)
- Katarina Jurikova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martin Gajarsky
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mona Hajikazemi
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Prochazkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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