1
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Brankiewicz-Kopcinska W, Kallingal A, Krzemieniecki R, Baginski M. Targeting shelterin proteins for cancer therapy. Drug Discov Today 2024; 29:104056. [PMID: 38844065 DOI: 10.1016/j.drudis.2024.104056] [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: 03/19/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 06/12/2024]
Abstract
As a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia-telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR), establishes its significance in cancer cells. Disrupting these defence mechanisms of shelterins, especially in cancer cells, renders telomeres vulnerable, potentially leading to genomic instability and hindering cancer cell survival. In this review, we outline recent approaches exploring shelterins as potential anticancer targets, highlighting the prospect of developing selective molecules to exploit telomere vulnerabilities toward new innovative cancer treatments.
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Affiliation(s)
- Wioletta Brankiewicz-Kopcinska
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, G. Narutowicza St 11/12, 80-233 Gdansk, Poland; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway.
| | - Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, G. Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Radoslaw Krzemieniecki
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, G. Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, G. Narutowicza St 11/12, 80-233 Gdansk, Poland.
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2
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Wu Z, Gu X, Zha L, Yang Q, Zhou Y, Zeng Z. Structural and functional insights into yeast Tbf1 as an atypical telomeric repeat-binding factor. Structure 2024; 32:889-898.e3. [PMID: 38677290 DOI: 10.1016/j.str.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Telomeric repeat-binding factor 1 (Tbf1) has a similar architecture as the TRF family of telomeric proteins and plays important roles in both telomere homeostasis and ribosome regulation. However, the molecular basis of why Tbf1 has such different functions compared to other TRFs remains unclear. Here, we present the crystal structures of the TRF homology (TRFH) and Myb-L domains from Schizosaccharomyces pombe Tbf1 (spTbf1). TRFH-mediated homodimerization is essential for spTbf1 stability. Importantly, spTbf1TRFH lacks the conserved docking motif for interactions with telomeric proteins, explaining why spTbf1 does not participate in the assembly of the shelterin complex. Finally, structural and biochemical analyses demonstrate that TRFH and Myb-L domains as well as the loop region of spTbf1 coordinate to recognize S. pombe telomeric double-stranded DNA. Overall, our findings provide structural and functional insights into how fungi Tbf1 acts as an atypical telomeric repeat-binding factor, which helps to understand the evolution of TRFH-containing telomeric proteins.
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Affiliation(s)
- Zhenfang Wu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Xin Gu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Zha
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Qingqiu Yang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yuanze Zhou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Zhixiong Zeng
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha 410219, China.
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3
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Erban T, Markovic M, Sopko B. Sublethal acetamiprid exposure induces immunity, suppresses pathways linked to juvenile hormone synthesis in queens and affects cycle-related signaling in emerging bees. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123901. [PMID: 38556147 DOI: 10.1016/j.envpol.2024.123901] [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: 01/27/2024] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Acetamiprid is the only neonicotinoid registered in the European Union because the risks of neonicotinoids to honey bees and other pollinators are strictly regulated. Herein, we orally exposed honey bee colonies to sublethal concentrations of acetamiprid (20 μg/L) under isolated conditions. After one month of continuous exposure, the emerging bees and queens were collected and analyzed via high-throughput label-free quantitative proteomics using a data-independent acquisition strategy. Six and 34 significantly differentially expressed proteins (DEPs) were identified in the emerging bees and queens, respectively. Mrjp3 was the only DEP found in both sample types/castes, and its opposite regulation illustrated a differential response. The DEPs in the emerging bees (H/ACA RNP, Rap1GAP, Mrjp3, and JHE) suggested that sublethal exposure to acetamiprid affected cell cycle-related signaling, which may affect the life history of workers in the colony. The DEPs with increased levels in queens, such as Mrjps 1-4 and 6-7, hymenoptaecin, and apidaecin 22, indicated an activated immune response. Additionally, the level of farnesyl pyrophosphate synthase (FPPS), which is essential for the mevalonate pathway and juvenile hormone biosynthesis, was significantly decreased in queens. The impaired utilization of juvenile hormone in queens supported the identification of additional DEPs. Furthermore, the proteome changes suggested the existence of increased neonicotinoid detoxification by UDP-glucuronosyltransferase and increased amino acid metabolism. The results suggest that the continuous exposure of bee colonies to acetamiprid at low doses (nanograms per gram in feed) may pose a threat to the colonies. The different exposure routes and durations for the emerging bees and queens in our experiment must be considered, i.e., the emerging bees were exposed as larvae via feeding royal jelly and beebread provided by workers (nurse bees), whereas the queens were fed royal jelly throughout the experiment. The biological consequences of the proteomic changes resulting from sublethal/chronic exposure require future determination.
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Affiliation(s)
- Tomas Erban
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia.
| | - Martin Markovic
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
| | - Bruno Sopko
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
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4
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Alanazi AFR, Parkinson GN, Haider S. Structural Motifs at the Telomeres and Their Role in Regulatory Pathways. Biochemistry 2024; 63:827-842. [PMID: 38481135 PMCID: PMC10993422 DOI: 10.1021/acs.biochem.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand. While many essential proteins at telomeres have been identified, the intricacies of their interactions and structural details are still not fully understood. This Perspective highlights recent advancements in comprehending the structures associated with human telomeres. It emphasizes the significance of telomeres, explores various telomeric structural motifs, and delves into the structural biology surrounding telomeres and telomerase. Furthermore, telomeric loops, their topologies, and the associated proteins that contribute to the safeguarding of telomeres are discussed.
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Affiliation(s)
- Abeer F R Alanazi
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, United Kingdom
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5
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Rai R, Sodeinde T, Boston A, Chang S. Telomeres cooperate with the nuclear envelope to maintain genome stability. Bioessays 2024; 46:e2300184. [PMID: 38047499 DOI: 10.1002/bies.202300184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double-stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere-binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology-directed recombination by mediating t-loop protection. Our recent findings also suggest that mammalian telomere-binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in nuclear envelope rupture, promoting telomere-telomere recombination to form structures termed ultrabright telomeres. In this review, we discuss the importance of the interactions between shelterin components and the nuclear envelope to maintain telomere homeostasis and genome stability.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ava Boston
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
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6
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Li B. Unwrap RAP1's Mystery at Kinetoplastid Telomeres. Biomolecules 2024; 14:67. [PMID: 38254667 PMCID: PMC10813129 DOI: 10.3390/biom14010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1's functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.
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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, 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
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7
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Yoshimoto H, Bogaki T. Mechanisms of production and control of acetate esters in yeasts. J Biosci Bioeng 2023; 136:261-269. [PMID: 37607842 DOI: 10.1016/j.jbiosc.2023.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 08/24/2023]
Abstract
Acetate esters, such as isoamyl acetate and ethyl acetate, are major aroma components of alcoholic beverages. They are produced through synthesis from acetyl CoA and the corresponding alcohol by alcohol acetyltransferase (AATase) with specific control of reaction factors, including unsaturated fatty acids and precursors, the percentage of nitrogen, and oxygen. However, the mechanisms by which these specific reaction factors affect acetate ester production remain largely unknown. The cellular mechanisms underlying the effects of these factors on acetate ester production were examined by purifying AATase from yeast, characterizing it, and cloning the ATF gene encoding AATase from sake yeast and bottom-fermenting yeast. Genetic and biochemical studies suggested that the decrease in acetate production with the addition of oxygen and unsaturated fatty acids was due to a decrease in enzyme synthesis resulting from transcriptional repression of the ATF1 gene, which is responsible for most of the AATase activity. Furthermore, these results suggest that expression of the ATF1 gene is intricately regulated by a number of transcriptional regulatory genes such as ROX1 and RAP1. Based on these results, the mechanism of ester regulation by oxygen, unsaturated fatty acids and precursors, and ratio of nitrogen source are becoming clearer from a molecular biological point of view. The physiological significance of ester production by yeast is then discussed. In this review, we summarize the studies on AATase, ATF gene, regulation of ester production, and physiological significance of acetate ester.
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Affiliation(s)
- Hiroyuki Yoshimoto
- Institute for Future Beverages, Research & Development Division, Kirin Holdings Company Limited, Technovilleage Center 3F, 1-17-1 Namamugi, Tsurumi-ku, Yokohama, Kanagawa 236-8628, Japan.
| | - Takayuki Bogaki
- General Research Laboratory, Ozeki Corporation, 4-9 Imazu Dezaike-cho, Nishinomiya, Hyogo 663-8227, Japan
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8
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Rai R, Biju K, Sun W, Sodeinde T, Al-Hiyasat A, Morgan J, Ye X, Li X, Chen Y, Chang S. Homology directed telomere clustering, ultrabright telomere formation and nuclear envelope rupture in cells lacking TRF2 B and RAP1. Nat Commun 2023; 14:2144. [PMID: 37059728 PMCID: PMC10104862 DOI: 10.1038/s41467-023-37761-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Double-strand breaks (DSBs) due to genotoxic stress represent potential threats to genome stability. Dysfunctional telomeres are recognized as DSBs and are repaired by distinct DNA repair mechanisms. RAP1 and TRF2 are telomere binding proteins essential to protect telomeres from engaging in homology directed repair (HDR), but how this occurs remains unclear. In this study, we examined how the basic domain of TRF2 (TRF2B) and RAP1 cooperate to repress HDR at telomeres. Telomeres lacking TRF2B and RAP1 cluster into structures termed ultrabright telomeres (UTs). HDR factors localize to UTs, and UT formation is abolished by RNaseH1, DDX21 and ADAR1p110, suggesting that they contain DNA-RNA hybrids. Interaction between the BRCT domain of RAP1 and KU70/KU80 is also required to repress UT formation. Expressing TRF2∆B in Rap1-/- cells resulted in aberrant lamin A localization in the nuclear envelope and dramatically increased UT formation. Expressing lamin A phosphomimetic mutants induced nuclear envelope rupturing and aberrant HDR-mediated UT formation. Our results highlight the importance of shelterin and proteins in the nuclear envelope in repressing aberrant telomere-telomere recombination to maintain telomere homeostasis.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
| | - Kevin Biju
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wenqi Sun
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Amer Al-Hiyasat
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Jaida Morgan
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Xianwen Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Xueqing Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
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9
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Pennarun G, Picotto J, Bertrand P. Close Ties between the Nuclear Envelope and Mammalian Telomeres: Give Me Shelter. Genes (Basel) 2023; 14:genes14040775. [PMID: 37107534 PMCID: PMC10137478 DOI: 10.3390/genes14040775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
The nuclear envelope (NE) in eukaryotic cells is essential to provide a protective compartment for the genome. Beside its role in connecting the nucleus with the cytoplasm, the NE has numerous important functions including chromatin organization, DNA replication and repair. NE alterations have been linked to different human diseases, such as laminopathies, and are a hallmark of cancer cells. Telomeres, the ends of eukaryotic chromosomes, are crucial for preserving genome stability. Their maintenance involves specific telomeric proteins, repair proteins and several additional factors, including NE proteins. Links between telomere maintenance and the NE have been well established in yeast, in which telomere tethering to the NE is critical for their preservation and beyond. For a long time, in mammalian cells, except during meiosis, telomeres were thought to be randomly localized throughout the nucleus, but recent advances have uncovered close ties between mammalian telomeres and the NE that play important roles for maintaining genome integrity. In this review, we will summarize these connections, with a special focus on telomere dynamics and the nuclear lamina, one of the main NE components, and discuss the evolutionary conservation of these mechanisms.
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Affiliation(s)
- Gaëlle Pennarun
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Julien Picotto
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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10
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Stock AJ, McDevitt RA, Puligilla C, Wang Y, Zhang Y, Wang K, Sun C, Becker KG, Lehrmann E, Wood WH, Gong Y, Aqdas M, Sung MH, Hoffmann V, Liu C, Gorospe M, Harrington L, Ferrucci L, Liu Y. Aberrant expression and localization of the RAP1 shelterin protein contribute to age-related phenotypes. PLoS Genet 2022; 18:e1010506. [PMID: 36441670 PMCID: PMC9704629 DOI: 10.1371/journal.pgen.1010506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/02/2022] [Indexed: 11/29/2022] Open
Abstract
Short telomeres induce a DNA damage response (DDR) that evokes apoptosis and senescence in human cells. An extant question is the contribution of telomere dysfunction-induced DDR to the phenotypes observed in aging and telomere biology disorders. One candidate is RAP1, a telomere-associated protein that also controls transcription at extratelomeric regions. To distinguish these roles, we generated a knockin mouse carrying a mutated Rap1, which was incapable of binding telomeres and did not result in eroded telomeres or a DDR. Primary Rap1 knockin embryonic fibroblasts showed decreased RAP1 expression and re-localization away from telomeres, with an increased cytosolic distribution akin to that observed in human fibroblasts undergoing telomere erosion. Rap1 knockin mice were viable, but exhibited transcriptomic alterations, proinflammatory cytokine/chemokine signaling, reduced lifespan, and decreased healthspan with increased body weight/fasting blood glucose levels, spontaneous tumor incidence, and behavioral deficits. Taken together, our data present mechanisms distinct from telomere-induced DDR that underlie age-related phenotypes.
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Affiliation(s)
- Amanda J. Stock
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ross A. McDevitt
- Comparative Medicine Section, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Chandrakala Puligilla
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yajun Wang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kun Wang
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Chongkui Sun
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - William H. Wood
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Victoria Hoffmann
- Division of Veterinary Resources, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute/National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Lea Harrington
- Institute for Research in Immunology & Cancer, Marcelle-Coutu Pavilion, Université de Montréal, Montreal, Quebec, Canada
| | - Luigi Ferrucci
- Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
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11
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Pan L, Tormey D, Bobon N, Baumann P. Rap1 prevents fusions between long telomeres in fission yeast. EMBO J 2022; 41:e110458. [PMID: 36059259 PMCID: PMC9574727 DOI: 10.15252/embj.2021110458] [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: 12/15/2021] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/15/2022] Open
Abstract
The conserved Rap1 protein is part of the shelterin complex that plays critical roles in chromosome end protection and telomere length regulation. Previous studies have addressed how fission yeast Rap1 contributes to telomere length maintenance, but the mechanism by which the protein inhibits end fusions has remained elusive. Here, we use a mutagenesis screen in combination with high‐throughput sequencing to identify several amino acid positions in Rap1 that have key roles in end protection. Interestingly, mutations at these sites render cells susceptible to genome instability in a conditional manner, whereby longer telomeres are prone to undergoing end fusions, while telomeres within the normal length range are sufficiently protected. The protection of long telomeres is in part dependent on their nuclear envelope attachment mediated by the Rap1–Bqt4 interaction. Our data demonstrate that long telomeres represent a challenge for the maintenance of genome integrity, thereby providing an explanation for species‐specific upper limits on telomere length.
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Affiliation(s)
- Lili Pan
- Department of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Duncan Tormey
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nadine Bobon
- Department of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Peter Baumann
- Department of Biology, Johannes Gutenberg University, Mainz, Germany.,Institute of Molecular Biology, Mainz, Germany
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12
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Abstract
Shelterin is a multiprotein complex that plays central roles in telomere biology. Mutations in shelterin result in premature aging diseases and familial cancer predisposition. Mechanistic understanding of these so-called telomereopathies is hampered by our lack of knowledge regarding the structure and stoichiometry of shelterin. Here, we use multiple methods to probe the stoichiometry and conformational states of shelterin and reveal that it forms a fully dimeric complex with extensive conformational heterogeneity. Our results highlight the dynamic nature of this essential complex and explain why its high-resolution structure determination has yet to be achieved. Human shelterin is a six-subunit complex—composed of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1—that binds telomeres, protects them from the DNA-damage response, and regulates the maintenance of telomeric DNA. Although high-resolution structures have been generated of the individual structured domains within shelterin, the architecture and stoichiometry of the full complex are currently unknown. Here, we report the purification of shelterin subcomplexes and reconstitution of the entire complex using full-length, recombinant subunits. By combining negative-stain electron microscopy (EM), cross-linking mass spectrometry (XLMS), AlphaFold modeling, mass photometry, and native mass spectrometry (MS), we obtain stoichiometries as well as domain-scale architectures of shelterin subcomplexes and determine that they feature extensive conformational heterogeneity. For POT1/TPP1 and POT1/TPP1/TIN2, we observe high variability in the positioning of the POT1 DNA-binding domain, the TPP1 oligonucleotide/oligosaccharide–binding (OB) fold, and the TIN2 TRFH domain with respect to the C-terminal domains of POT1. Truncation of unstructured linker regions in TIN2, TPP1, and POT1 did not reduce the conformational variability of the heterotrimer. Shelterin and TRF1-containing subcomplexes form fully dimeric stoichiometries, even in the absence of DNA substrates. Shelterin and its subcomplexes showed extensive conformational variability, regardless of the presence of DNA substrates. We conclude that shelterin adopts a multitude of conformations and argue that its unusual architectural variability is beneficial for its many functions at telomeres.
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13
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Sun H, Wu Z, Zhou Y, Lu Y, Lu H, Chen H, Shi S, Zeng Z, Wu J, Lei M. Structural insights into Pot1-ssDNA, Pot1-Tpz1 and Tpz1-Ccq1 Interactions within fission yeast shelterin complex. PLoS Genet 2022; 18:e1010308. [PMID: 35849625 PMCID: PMC9333443 DOI: 10.1371/journal.pgen.1010308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/28/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
The conserved shelterin complex caps chromosome ends to protect telomeres and regulate telomere replication. In fission yeast Schizosaccharomyces pombe, shelterin consists of telomeric single- and double-stranded DNA-binding modules Pot1-Tpz1 and Taz1-Rap1 connected by Poz1, and a specific component Ccq1. While individual structures of the two DNA-binding OB folds of Pot1 (Pot1OB1-GGTTAC and Pot1OB2-GGTTACGGT) are available, structural insight into recognition of telomeric repeats with spacers by the complete DNA-binding domain (Pot1DBD) remains an open question. Moreover, structural information about the Tpz1-Ccq1 interaction requires to be revealed for understanding how the specific component Ccq1 of S. pombe shelterin is recruited to telomeres to function as an interacting hub. Here, we report the crystal structures of Pot1DBD-single-stranded-DNA, Pot1372-555-Tpz1185-212 and Tpz1425-470-Ccq1123-439 complexes and propose an integrated model depicting the assembly mechanism of the shelterin complex at telomeres. The structure of Pot1DBD-DNA unveils how Pot1 recognizes S. pombe degenerate telomeric sequences. Our analyses of Tpz1-Ccq1 reveal structural basis for the essential role of the Tpz1-Ccq1 interaction in telomere recruitment of Ccq1 that is required for telomere maintenance and telomeric heterochromatin formation. Overall, our findings provide valuable structural information regarding interactions within fission yeast shelterin complex at 3’ ss telomeric overhang. Telomeres, composed of repetitive DNA sequences and specialized proteins, are protective structures at the ends of linear chromosomes. The telomere structure is essential for the maintenance of genome integrity and stability, and telomere dysfunction has been linked to human development, aging, cancer and a variety of degenerative diseases. An evolutionarily conserved multiple-protein complex called shelterin plays versatile roles in telomere homeostasis regulation, end protection and heterochromatin establishment. However, the highly flexible nature of shelterin complex has greatly impeded our structural and functional understanding for this important complex. In fission yeast, structures of the shelterin dsDNA-binding protein subcomplex Taz1-Rap1 and the bridge subcomplex Tpz1-Poz1-Rap1 are available. Although individual OB-fold subdomains structures have been characterized, structural information about the complete Pot1DBD bound to telomeric repeats with spacers remains to be revealed. Here, by determining the crystal structures of the telomeric overhang binding Pot1DBD-ssDNA, Pot1372-555-Tpz1185-212 and Tpz1425-470-Ccq1123-439 subcomplexes, we provide structural basis not only for the recognition of S. pombe degenerate telomeric sequences by Pot1, but also for the essential function of the Tpz1-Ccq1 interaction in Ccq1 recruitment to telomeres for telomere maintenance and telomeric heterochromatin formation. These findings provide an integrated model depicting the assembly mechanism of the shelterin complex at telomeres and its multiple roles in telomere biology.
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Affiliation(s)
- Hong Sun
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhenfang Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
- * E-mail: (ZW); (ZZ); (JW); (ML)
| | - Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yanjia Lu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Huaisheng Lu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Hongwen Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shaohua Shi
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
| | - Zhixiong Zeng
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Shandong, China
- * E-mail: (ZW); (ZZ); (JW); (ML)
| | - Jian Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
- * E-mail: (ZW); (ZZ); (JW); (ML)
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (ZW); (ZZ); (JW); (ML)
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14
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Barry RM, Sacco O, Mameri A, Stojaspal M, Kartsonis W, Shah P, De Ioannes P, Hofr C, Côté J, Sfeir A. Rap1 regulates TIP60 function during fate transition between two-cell-like and pluripotent states. Genes Dev 2022; 36:313-330. [PMID: 35210222 PMCID: PMC8973845 DOI: 10.1101/gad.349039.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 01/05/2023]
Abstract
In mammals, the conserved telomere binding protein Rap1 serves a diverse set of nontelomeric functions, including activation of the NF-kB signaling pathway, maintenance of metabolic function in vivo, and transcriptional regulation. Here, we uncover the mechanism by which Rap1 modulates gene expression. Using a separation-of-function allele, we show that Rap1 transcriptional regulation is largely independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci. Instead, Rap1 interacts with the TIP60/p400 complex and modulates its histone acetyltransferase activity. Notably, we show that deletion of Rap1 in mouse embryonic stem cells increases the fraction of two-cell-like cells. Specifically, Rap1 enhances the repressive activity of Tip60/p400 across a subset of two-cell-stage genes, including Zscan4 and the endogenous retrovirus MERVL. Preferential up-regulation of genes proximal to MERVL elements in Rap1-deficient settings implicates these endogenous retroviral elements in the derepression of proximal genes. Altogether, our study reveals an unprecedented link between Rap1 and the TIP60/p400 complex in the regulation of pluripotency.
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Affiliation(s)
- Raymond Mario Barry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA.,Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Martin Stojaspal
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA.,LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - William Kartsonis
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pooja Shah
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Ctirad Hofr
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, 612 65 Brno, Czech Republic
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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15
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Smith EW, Lattmann S, Liu ZB, Ahsan B, Rhodes D. Insights into POT1 structural dynamics revealed by cryo-EM. PLoS One 2022; 17:e0264073. [PMID: 35176105 PMCID: PMC8853558 DOI: 10.1371/journal.pone.0264073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Telomeres are protein-DNA complexes that protect the ends of linear eukaryotic chromosomes. Mammalian telomeric DNA consists of 5′-(TTAGGG)n-3′ double-stranded repeats, followed by up to several hundred bases of a 3′ single-stranded G-rich overhang. The G-rich overhang is bound by the shelterin component POT1 which interacts with TPP1, the component involved in telomerase recruitment. A previously published crystal structure of the POT1 N-terminal half bound to the high affinity telomeric ligand 5′-TTAGGGTTAG-3′ showed that the first six nucleotides, TTAGGG, are bound by the OB1 fold, while the adjacent OB2 binds the last four, TTAG. Here, we report two cryo-EM structures of full-length POT1 bound by the POT1-binding domain of TPP1. The structures differ in the relative orientation of the POT1 OB1 and OB2, suggesting that these two DNA-binding OB folds take up alternative conformations. Supporting DNA binding studies using telomeric ligands in which the OB1 and OB2 binding sites were spaced apart, show that POT1 binds with similar affinities to spaced or contiguous binding sites, suggesting plasticity in DNA binding and a role for the alternative conformations observed. A likely explanation is that the structural flexibility of POT1 enhances binding to the tandemly arranged telomeric repeats and hence increases telomere protection.
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Affiliation(s)
- Emmanuel W. Smith
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Simon Lattmann
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Zhehui Barry Liu
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Bilal Ahsan
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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16
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Oh J, Yeom S, Park J, Lee JS. The regional sequestration of heterochromatin structural proteins is critical to form and maintain silent chromatin. Epigenetics Chromatin 2022; 15:5. [PMID: 35101096 PMCID: PMC8805269 DOI: 10.1186/s13072-022-00435-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 12/20/2022] Open
Abstract
Budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe are good models for heterochromatin study. In S. pombe, H3K9 methylation and Swi6, an ortholog of mammalian HP1, lead to heterochromatin formation. However, S. cerevisiae does not have known epigenetic silencing markers and instead has Sir proteins to regulate silent chromatin formation. Although S. cerevisiae and S. pombe form and maintain heterochromatin via mechanisms that appear to be fundamentally different, they share important common features in the heterochromatin structural proteins. Heterochromatin loci are localized at the nuclear periphery by binding to perinuclear membrane proteins, thereby producing distinct heterochromatin foci, which sequester heterochromatin structural proteins. In this review, we discuss the nuclear peripheral anchoring of heterochromatin foci and its functional relevance to heterochromatin formation and maintenance.
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Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jiyeon Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea.
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17
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Kaur P, Barnes R, Pan H, Detwiler AC, Liu M, Mahn C, Hall J, Messenger Z, You C, Piehler J, Smart R, Riehn R, Opresko PL, Wang H. TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA. Nucleic Acids Res 2021; 49:13000-13018. [PMID: 34883513 PMCID: PMC8682769 DOI: 10.1093/nar/gkab1142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
The telomere specific shelterin complex, which includes TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, prevents spurious recognition of telomeres as double-strand DNA breaks and regulates telomerase and DNA repair activities at telomeres. TIN2 is a key component of the shelterin complex that directly interacts with TRF1, TRF2 and TPP1. In vivo, the large majority of TRF1 and TRF2 are in complex with TIN2 but without TPP1 and POT1. Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, previous cell-based assays only provide information on downstream effects after the loss of TRF1/TRF2 and TIN2. Here, we investigated DNA structures promoted by TRF2-TIN2 using single-molecule imaging platforms, including tracking of compaction of long mouse telomeric DNA using fluorescence imaging, atomic force microscopy (AFM) imaging of protein-DNA structures, and monitoring of DNA-DNA and DNA-RNA bridging using the DNA tightrope assay. These techniques enabled us to uncover previously unknown unique activities of TIN2. TIN2S and TIN2L isoforms facilitate TRF2-mediated telomeric DNA compaction (cis-interactions), dsDNA-dsDNA, dsDNA-ssDNA and dsDNA-ssRNA bridging (trans-interactions). Furthermore, TIN2 facilitates TRF2-mediated T-loop formation. We propose a molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Ming Liu
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Chelsea Mahn
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Jonathan Hall
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Zach Messenger
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Changjiang You
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück 49076, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry, Universität Osnabrück, Osnabrück 49076, Germany
| | - Robert C Smart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, UPMC Hillman Cancer Center, PA 15213, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC27695, USA
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18
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Higa M, Matsuda Y, Fujii J, Sugimoto N, Yoshida K, Fujita M. TRF2-mediated ORC recruitment underlies telomere stability upon DNA replication stress. Nucleic Acids Res 2021; 49:12234-12251. [PMID: 34761263 PMCID: PMC8643664 DOI: 10.1093/nar/gkab1004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Telomeres are intrinsically difficult-to-replicate region of eukaryotic chromosomes. Telomeric repeat binding factor 2 (TRF2) binds to origin recognition complex (ORC) to facilitate the loading of ORC and the replicative helicase MCM complex onto DNA at telomeres. However, the biological significance of the TRF2–ORC interaction for telomere maintenance remains largely elusive. Here, we employed a TRF2 mutant with mutations in two acidic acid residues (E111A and E112A) that inhibited the TRF2–ORC interaction in human cells. The TRF2 mutant was impaired in ORC recruitment to telomeres and showed increased replication stress-associated telomeric DNA damage and telomere instability. Furthermore, overexpression of an ORC1 fragment (amino acids 244–511), which competitively inhibited the TRF2–ORC interaction, increased telomeric DNA damage under replication stress conditions. Taken together, these findings suggest that TRF2-mediated ORC recruitment contributes to the suppression of telomere instability.
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Affiliation(s)
- Mitsunori Higa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yukihiro Matsuda
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jumpei Fujii
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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19
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Myler LR, Kinzig CG, Sasi NK, Zakusilo G, Cai SW, de Lange T. The evolution of metazoan shelterin. Genes Dev 2021; 35:1625-1641. [PMID: 34764137 PMCID: PMC8653790 DOI: 10.1101/gad.348835.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
In this study, Myler et al. investigated the evolutionary origins of shelterin complex, which is comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1; blocks the DNA damage response at chromosome ends; and interacts with telomerase and the CST complex to regulate telomere length. They describe the evolution of metazoan shelterin, showing that TRF1 emerged in vertebrates upon duplication of a TRF2-like ancestor, and providing insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins. The mammalian telomeric shelterin complex—comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1—blocks the DNA damage response at chromosome ends and interacts with telomerase and the CST complex to regulate telomere length. The evolutionary origins of shelterin are unclear, partly because unicellular organisms have distinct telomeric proteins. Here, we describe the evolution of metazoan shelterin, showing that TRF1 emerged in vertebrates upon duplication of a TRF2-like ancestor. TRF1 and TRF2 diverged rapidly during vertebrate evolution through the acquisition of new domains and interacting factors. Vertebrate shelterin is also distinguished by the presence of an HJRL domain in the split C-terminal OB fold of POT1, whereas invertebrate POT1s carry inserts of variable nature. Importantly, the data reveal that, apart from the primate and rodent POT1 orthologs, all metazoan POT1s are predicted to have a fourth OB fold at their N termini. Therefore, we propose that POT1 arose from a four-OB-fold ancestor, most likely an RPA70-like protein. This analysis provides insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins.
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Affiliation(s)
- Logan R Myler
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Charles G Kinzig
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - George Zakusilo
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Sarah W Cai
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10021, USA
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20
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Pennarun G, Picotto J, Etourneaud L, Redavid AR, Certain A, Gauthier LR, Fontanilla-Ramirez P, Busso D, Chabance-Okumura C, Thézé B, Boussin FD, Bertrand P. Increase in lamin B1 promotes telomere instability by disrupting the shelterin complex in human cells. Nucleic Acids Res 2021; 49:9886-9905. [PMID: 34469544 PMCID: PMC8464066 DOI: 10.1093/nar/gkab761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Telomere maintenance is essential to preserve genomic stability and involves telomere-specific proteins, DNA replication and repair proteins. Lamins are key components of the nuclear envelope and play numerous roles, including maintenance of the nuclear integrity, regulation of transcription, and DNA replication. Elevated levels of lamin B1, one of the major lamins, have been observed in some human pathologies and several cancers. Yet, the effect of lamin B1 dysregulation on telomere maintenance remains unknown. Here, we unveil that lamin B1 overexpression drives telomere instability through the disruption of the shelterin complex. Indeed, lamin B1 dysregulation leads to an increase in telomere dysfunction-induced foci, telomeric fusions and telomere losses in human cells. Telomere aberrations were preceded by mislocalizations of TRF2 and its binding partner RAP1. Interestingly, we identified new interactions between lamin B1 and these shelterin proteins, which are strongly enhanced at the nuclear periphery upon lamin B1 overexpression. Importantly, chromosomal fusions induced by lamin B1 in excess were rescued by TRF2 overexpression. These data indicated that lamin B1 overexpression triggers telomere instability through a mislocalization of TRF2. Altogether our results point to lamin B1 as a new interacting partner of TRF2, that is involved in telomere stability.
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Affiliation(s)
- Gaëlle Pennarun
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Julien Picotto
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Laure Etourneaud
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Anna-Rita Redavid
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Anaïs Certain
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Laurent R Gauthier
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “Radiopathology” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Paula Fontanilla-Ramirez
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Didier Busso
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Caroline Chabance-Okumura
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Benoît Thézé
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - François D Boussin
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “Radiopathology” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
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21
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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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22
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Liu J, Hu X, Bao K, Kim JK, Zhang C, Jia S, Qiao F. The cooperative assembly of shelterin bridge provides a kinetic gateway that controls telomere length homeostasis. Nucleic Acids Res 2021; 49:8110-8119. [PMID: 34255844 PMCID: PMC8373121 DOI: 10.1093/nar/gkab550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 11/14/2022] Open
Abstract
Shelterin is a six-protein complex that coats chromosome ends to ensure their proper protection and maintenance. Similar to the human shelterin, fission yeast shelterin is composed of telomeric double- and single-stranded DNA-binding proteins, Taz1 and Pot1, respectively, bridged by Rap1, Poz1 and Tpz1. The assembly of the proteinaceous Tpz1-Poz1-Rap1 complex occurs cooperatively and disruption of this shelterin bridge leads to unregulated telomere elongation. However, how this biophysical property of bridge assembly is integrated into shelterin function is not known. Here, utilizing synthetic bridges with a range of binding properties, we find that synthetic shelterin bridge lacking cooperativity requires a linker pair that matches the native bridge in complex lifespan but has dramatically higher affinity. We find that cooperative assembly confers kinetic properties on the shelterin bridge allowing disassembly to function as a molecular timer, regulating the duration of the telomere open state, and consequently telomere lengthening to achieve a defined species-specific length range.
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Affiliation(s)
- Jinqiang Liu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Xichan Hu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Kehan Bao
- Department of Biological Sciences, Columbia University, New York City, NY 92697-4560, USA
| | - Jin-Kwang Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Catherine Zhang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York City, NY 92697-4560, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
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23
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Multifunctionality of the Telomere-Capping Shelterin Complex Explained by Variations in Its Protein Composition. Cells 2021; 10:cells10071753. [PMID: 34359923 PMCID: PMC8305809 DOI: 10.3390/cells10071753] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Protecting telomere from the DNA damage response is essential to avoid the entry into cellular senescence and organismal aging. The progressive telomere DNA shortening in dividing somatic cells, programmed during development, leads to critically short telomeres that trigger replicative senescence and thereby contribute to aging. In several organisms, including mammals, telomeres are protected by a protein complex named Shelterin that counteract at various levels the DNA damage response at chromosome ends through the specific function of each of its subunits. The changes in Shelterin structure and function during development and aging is thus an intense area of research. Here, we review our knowledge on the existence of several Shelterin subcomplexes and the functional independence between them. This leads us to discuss the possibility that the multifunctionality of the Shelterin complex is determined by the formation of different subcomplexes whose composition may change during aging.
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24
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Li B. Keeping Balance Between Genetic Stability and Plasticity at the Telomere and Subtelomere of Trypanosoma brucei. Front Cell Dev Biol 2021; 9:699639. [PMID: 34291053 PMCID: PMC8287324 DOI: 10.3389/fcell.2021.699639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Telomeres, the nucleoprotein complexes at chromosome ends, are well-known for their essential roles in genome integrity and chromosome stability. Yet, telomeres and subtelomeres are frequently less stable than chromosome internal regions. Many subtelomeric genes are important for responding to environmental cues, and subtelomeric instability can facilitate organismal adaptation to extracellular changes, which is a common theme in a number of microbial pathogens. In this review, I will focus on the delicate and important balance between stability and plasticity at telomeres and subtelomeres of a kinetoplastid parasite, Trypanosoma brucei, which causes human African trypanosomiasis and undergoes antigenic variation to evade the host immune response. I will summarize the current understanding about T. brucei telomere protein complex, the telomeric transcript, and telomeric R-loops, focusing on their roles in maintaining telomere and subtelomere stability and integrity. The similarities and differences in functions and underlying mechanisms of T. brucei telomere factors will be compared with those in human and yeast cells.
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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, 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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25
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Abstract
The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N-terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end-resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles' heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well.
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26
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Ben Nasr R, Baudelaire ED, Dicko A, El Ferchichi Ouarda H. Phytochemicals, Antioxidant Attributes and Larvicidal Activity of Mercurialis annua L. ( Euphorbiaceae) Leaf Extracts against Tribolium confusum (Du Val) Larvae ( Coleoptera; Tenebrionidae). BIOLOGY 2021; 10:biology10040344. [PMID: 33923875 PMCID: PMC8073125 DOI: 10.3390/biology10040344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary Mercurialis annua L. is a Euphorbiacea widespread in the Euro-Mediterranean region. This species is known for its toxicity and is used in traditional pharmacopoeia. However, the chemical composition of the aerial parts of this taxon and their larvicidal impact remain to be explored. However, the literature reports only a few studies on the relationship between the polyphenolic profile of the different extracts of Mercurialis annua L. and the larvicidal activity; therefore, we tested different extracts of M. annua against the larvae of Tribolium confusum (Du Val) for better protection of stored foodstuffs attacked by this pest. On the other hand, green chemistry as a distinct discipline has developed in recent years, which allowed us to identify different active compounds by LC-MS, and study the relationship between larvicidal activity and the chemical composition of extracts from male and female leaves of Mercurialis annua L. Abstract This study reports the link between larvicidal activity and the phytochemical composition of male and female leaf extracts of Mercurialis annua L. (M. annua) from four Tunisian regions: Bizerte, Jandouba, Nabeul and Beja. Their antioxidant activity was evaluated using DPPH (2, 2-diphenyl-1-picrylhydrazyl) assays. Phenolic compounds were identified and quantified using liquid chromatography coupled with a UV detector and mass spectrometry (LC-UV-ESI/MS). Higher antioxidant activity (AOA) was found in the leaves of male plant extracts than of female ones. The leaves of male and female plant extracts from Bizerte exhibited the highest AOA: 22.04 and 22.78 mg Trolox equivalent/g dry matter (mg TE/g DM), respectively. For both sexes, plant extracts from Beja had the lowest AOA with 19.71 and 19.67 mg TE/g DM for male and female plants, respectively. Some phenolic compounds such as narcissin, gallocatechin, rutin, epigallocatechin and epicatechin were identified and quantified using LC-MS, which highlighted the abundance of narcissin and rutin in the male leaves of M. annua. We noted that the interaction between the sex of plants and the provenance had a significant effect on TFC (F = 6.63; p = 0.004) and AOA (F = 6.53; p = 0.004) assays, but there was no interaction between sex and origins for TPC (F = 1.76; p = 0.19). The larvicidal activity of aqueous leaf extracts of M. annua against Tribolium confusum (Du Val) (T. confusum), an insect pest of flour and cereal seeds, showed that the mortality could reach 100% after 48 h of exposure in the Bizerte region. The LC50 values for the leaf extract were low in Bizerte, with 0.003 and 0.009 g/mL for male and female plants, respectively, succeeded by Jandouba, which displayed 0.006 and 0.024 g/mL for male and female plants, respectively. Nabeul showed 0.025 g/mL for male plants and 0.046 g/mL for female plants and Beja showed 0.037 and 0.072 g/mL for male and female plants, respectively. This is the first time that a study has revealed a negative correlation between the antioxidant activity and the larvicidal activity of the leaf extracts of M. annua with the following correlation coefficients of Perason: r = −0.975 and r = −0.760 for male and female plants, respectively.
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Affiliation(s)
- Rania Ben Nasr
- Laboratoire de Chimie et de Physique—Approches Multi-échelles des Milieux Complexes (LCP-A2MC)1, Boulevard Arago, CEDEX 03, 57078 Metz, France;
- Laboratory of Plant Toxicology & Environmental Microbiology, Faculty of Science of Bizerte, University of Carthage, Zarzouna 7021, Tunisia;
- Correspondence:
| | | | - Amadou Dicko
- Laboratoire de Chimie et de Physique—Approches Multi-échelles des Milieux Complexes (LCP-A2MC)1, Boulevard Arago, CEDEX 03, 57078 Metz, France;
| | - Hela El Ferchichi Ouarda
- Laboratory of Plant Toxicology & Environmental Microbiology, Faculty of Science of Bizerte, University of Carthage, Zarzouna 7021, Tunisia;
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27
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Oizumi Y, Kaji T, Tashiro S, Takeshita Y, Date Y, Kanoh J. Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation. Nat Commun 2021; 12:611. [PMID: 33504776 PMCID: PMC7840980 DOI: 10.1038/s41467-020-20595-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.
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Affiliation(s)
- Yusuke Oizumi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuto Kaji
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sanki Tashiro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute of Molecular Biology, University of Oregon, 1370 Franklin Blvd, Eugene, OR, USA
| | - Yumiko Takeshita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuko Date
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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28
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Cicconi A, Rai R, Xiong X, Broton C, Al-Hiyasat A, Hu C, Dong S, Sun W, Garbarino J, Bindra RS, Schildkraut C, Chen Y, Chang S. Microcephalin 1/BRIT1-TRF2 interaction promotes telomere replication and repair, linking telomere dysfunction to primary microcephaly. Nat Commun 2020; 11:5861. [PMID: 33203878 PMCID: PMC7672075 DOI: 10.1038/s41467-020-19674-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/22/2020] [Indexed: 01/07/2023] Open
Abstract
Telomeres protect chromosome ends from inappropriately activating the DNA damage and repair responses. Primary microcephaly is a key clinical feature of several human telomere disorder syndromes, but how microcephaly is linked to dysfunctional telomeres is not known. Here, we show that the microcephalin 1/BRCT-repeats inhibitor of hTERT (MCPH1/BRIT1) protein, mutated in primary microcephaly, specifically interacts with the TRFH domain of the telomere binding protein TRF2. The crystal structure of the MCPH1-TRF2 complex reveals that this interaction is mediated by the MCPH1 330YRLSP334 motif. TRF2-dependent recruitment of MCPH1 promotes localization of DNA damage factors and homology directed repair of dysfunctional telomeres lacking POT1-TPP1. Additionally, MCPH1 is involved in the replication stress response, promoting telomere replication fork progression and restart of stalled telomere replication forks. Our work uncovers a previously unrecognized role for MCPH1 in promoting telomere replication, providing evidence that telomere replication defects may contribute to the onset of microcephaly.
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Affiliation(s)
- Alessandro Cicconi
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Rekha Rai
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Xuexue Xiong
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Cayla Broton
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.5386.8000000041936877XTri- Institutional MD/PhD Program, Weill Cornell Medical College, New York, NY 10065 USA
| | - Amer Al-Hiyasat
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Chunyi Hu
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Siying Dong
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Wenqi Sun
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jennifer Garbarino
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Therapeutic Radiology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Ranjit S. Bindra
- grid.47100.320000000419368710Department of Therapeutic Radiology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Experimental Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Carl Schildkraut
- grid.251993.50000000121791997Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Yong Chen
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Sandy Chang
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
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29
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Khattar E, Tergaonkar V. Role of Rap1 in DNA damage response: implications in stem cell homeostasis and cancer. Exp Hematol 2020; 90:12-17. [PMID: 32858091 DOI: 10.1016/j.exphem.2020.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023]
Abstract
Mammalian Rap1 is a part of the telomere binding complex named shelterin and is one of the most conserved telomeric proteins. With its essential requirement in lower species to its becoming necessary in higher species, it appears to have gained and lost several functions simultaneously evolving with telomeres. Mammalian Rap1 has been reported to play a role in inflammation, metabolism, and oxidative stress. Mammalian Rap1 has also been found to regulate DNA damage response from telomeres in senescent cells. Recently our group uncovered its novel role in stem cell maintenance, and modulation of the chemotherapeutic response. Mechanistically it was found to function as an adaptor via protein-protein interactions and to modulate the response to DNA damage. In the current review we highlight newly identified functions of Rap1 in regulating telomeric and general DNA damage response with its impact at the cellular and organismal levels.
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Affiliation(s)
- Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India.
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A-STAR), Singapore
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30
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Mir SM, Samavarchi Tehrani S, Goodarzi G, Jamalpoor Z, Asadi J, Khelghati N, Qujeq D, Maniati M. Shelterin Complex at Telomeres: Implications in Ageing. Clin Interv Aging 2020; 15:827-839. [PMID: 32581523 PMCID: PMC7276337 DOI: 10.2147/cia.s256425] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Different factors influence the development and control of ageing. It is well known that progressive telomere shorting is one of the molecular mechanisms underlying ageing. The shelterin complex consists of six telomere-specific proteins which are involved in the protection of chromosome ends. More particularly, this vital complex protects the telomeres from degradation, prevents from activation of unwanted repair systems, regulates the activity of telomerase, and has a crucial role in cellular senescent and ageing-related pathologies. This review explores the organization and function of telomeric DNA along with the mechanism of telomeres during ageing, followed by a discussion of the critical role of shelterin components and their changes during ageing.
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Affiliation(s)
- Seyed Mostafa Mir
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Jamalpoor
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Durdi Qujeq
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mahmood Maniati
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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31
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Cherdyntseva V, Gagos S. Chromosome extremities under the microscopy lens: molecular cytogenetics in telomere research. Curr Opin Genet Dev 2020; 60:69-76. [PMID: 32193147 DOI: 10.1016/j.gde.2020.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 02/07/2023]
Abstract
At the crossroads of DNA damage repair and genomic instability, telomere research significantly expands our knowledge on fundamental mechanisms involved in cancer initiation and progression, pledging novel tools for targeted and universal onco-therapies. Molecular cytogenetics through the application of a battery of fluorescent hybridization technologies plays an important role toward understanding telomere homeostasis. Herein, we review distinct molecular cytogenetic phenotypes associated with telomere repair, functionality, and elongation. We discuss the underlying mechanisms responsible for their formation or repair, focusing on Break-induced-Replication (BIR)-mediated conservative telomeric neo-synthesis, recently shown to drive the enigmatic Alternative Lengthening of Telomeres in neoplasia.
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Affiliation(s)
- Veronica Cherdyntseva
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Sarantis Gagos
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece.
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Cicconi A, Chang S. Shelterin and the replisome: at the intersection of telomere repair and replication. Curr Opin Genet Dev 2020; 60:77-84. [PMID: 32171974 DOI: 10.1016/j.gde.2020.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/30/2022]
Abstract
Telomeres are G-rich repetitive sequences that are difficult to replicate, resulting in increased replication stress that can threaten genome stability. Shelterin protects telomeres from engaging in aberrant DNA repair and dictates the choice of DNA repair pathway at dysfunctional telomeres. Recently, shelterin has been shown to participate in telomere replication. Here we review the most recent discoveries documenting the mechanisms by which shelterin represses DNA repair pathways at telomeres while assisting its replication. The interplay between shelterin and the replisome complex highlights a novel connection between telomere maintenance and repair.
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Affiliation(s)
- Alessandro Cicconi
- Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
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Trypanosoma brucei RAP1 Has Essential Functional Domains That Are Required for Different Protein Interactions. mSphere 2020; 5:5/1/e00027-20. [PMID: 32102938 PMCID: PMC7045384 DOI: 10.1128/msphere.00027-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing. RAP1 is a telomere protein that is well conserved from protozoa to mammals. It plays important roles in chromosome end protection, telomere length control, and gene expression/silencing at both telomeric and nontelomeric loci. Interaction with different partners is an important mechanism by which RAP1 executes its different functions in yeast. The RAP1 ortholog in Trypanosoma brucei is essential for variant surface glycoprotein (VSG) monoallelic expression, an important aspect of antigenic variation, where T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. Like other RAP1 orthologs, T. brucei RAP1 (TbRAP1) has conserved functional domains, including BRCA1 C terminus (BRCT), Myb, MybLike, and RAP1 C terminus (RCT). To study functions of various TbRAP1 domains, we established a strain in which one endogenous allele of TbRAP1 is flanked by loxP repeats, enabling its conditional deletion by Cre-mediated recombination. We replaced the other TbRAP1 allele with various mutant alleles lacking individual functional domains and examined their nuclear localization and protein interaction abilities. The N terminus, BRCT, and RCT of TbRAP1 are required for normal protein levels, while the Myb and MybLike domains are essential for normal cell growth. Additionally, the Myb domain of TbRAP1 is required for its interaction with T. brucei TTAGGG repeat-binding factor (TbTRF), while the BRCT domain is required for its self-interaction. Furthermore, the TbRAP1 MybLike domain contains a bipartite nuclear localization signal that is required for its interaction with importin α and its nuclear localization. Interestingly, RAP1’s self-interaction and the interaction between RAP1 and TRF are conserved from kinetoplastids to mammals. However, details of the interaction interfaces have changed throughout evolution. IMPORTANCETrypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing.
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Inoue H, Horiguchi M, Ono K, Kanoh J. Casein kinase 2 regulates telomere protein complex formation through Rap1 phosphorylation. Nucleic Acids Res 2020; 47:6871-6884. [PMID: 31131414 PMCID: PMC6648331 DOI: 10.1093/nar/gkz458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 12/23/2022] Open
Abstract
Telomeres located at the ends of linear chromosomes play important roles in the maintenance of life. Rap1, a component of the shelterin telomere protein complex, interacts with multiple proteins to perform various functions; further, formation of shelterin requires Rap1 binding to other components such as Taz1 and Poz1, and telomere tethering to the nuclear envelope (NE) involves interactions between Rap1 and Bqt4, a nuclear membrane protein. Although Rap1 is a hub for telomere protein complexes, the regulatory mechanisms of its interactions with partner proteins are not fully understood. Here, we show that Rap1 is phosphorylated by casein kinase 2 (CK2) at multiple sites, which promotes interactions with Bqt4 and Poz1. Among the multiple CK2-mediated phosphorylation sites of Rap1, phosphorylation at Ser496 was found to be crucial for both Rap1–Bqt4 and Rap1–Poz1 interactions. These mechanisms mediate proper telomere tethering to the NE and the formation of the silenced chromatin structure at chromosome ends.
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Affiliation(s)
- Haruna Inoue
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mayuri Horiguchi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kota Ono
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Junko Kanoh
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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Smith EM, Pendlebury DF, Nandakumar J. Structural biology of telomeres and telomerase. Cell Mol Life Sci 2020; 77:61-79. [PMID: 31728577 PMCID: PMC6986361 DOI: 10.1007/s00018-019-03369-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 01/16/2023]
Abstract
Telomeres are protein-DNA complexes that protect chromosome ends from illicit ligation and resection. Telomerase is a ribonucleoprotein enzyme that synthesizes telomeric DNA to counter telomere shortening. Human telomeres are composed of complexes between telomeric DNA and a six-protein complex known as shelterin. The shelterin proteins TRF1 and TRF2 provide the binding affinity and specificity for double-stranded telomeric DNA, while the POT1-TPP1 shelterin subcomplex coats the single-stranded telomeric G-rich overhang that is characteristic of all our chromosome ends. By capping chromosome ends, shelterin protects telomeric DNA from unwanted degradation and end-to-end fusion events. Structures of the human shelterin proteins reveal a network of constitutive and context-specific interactions. The shelterin protein-DNA structures reveal the basis for both the high affinity and DNA sequence specificity of these interactions, and explain how shelterin efficiently protects chromosome ends from genome instability. Several protein-protein interactions, many provided by the shelterin component TIN2, are critical for upholding the end-protection function of shelterin. A survey of these protein-protein interfaces within shelterin reveals a series of "domain-peptide" interactions that allow for efficient binding and adaptability towards new functions. While the modular nature of shelterin has facilitated its part-by-part structural characterization, the interdependence of subunits within telomerase has made its structural solution more challenging. However, the exploitation of several homologs in combination with recent advancements in cryo-EM capabilities has led to an exponential increase in our knowledge of the structural biology underlying telomerase function. Telomerase homologs from a wide range of eukaryotes show a typical retroviral reverse transcriptase-like protein core reinforced with elements that deliver telomerase-specific functions including recruitment to telomeres and high telomere-repeat addition processivity. In addition to providing the template for reverse transcription, the RNA component of telomerase provides a scaffold for the catalytic and accessory protein subunits, defines the limits of the telomeric repeat sequence, and plays a critical role in RNP assembly, stability, and trafficking. While a high-resolution definition of the human telomerase structure is only beginning to emerge, the quick pace of technical progress forecasts imminent breakthroughs in this area. Here, we review the structural biology surrounding telomeres and telomerase to provide a molecular description of mammalian chromosome end protection and end replication.
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Affiliation(s)
- Eric M Smith
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Devon F Pendlebury
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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Khattar E, Maung KZY, Chew CL, Ghosh A, Mok MMH, Lee P, Zhang J, Chor WHJ, Cildir G, Wang CQ, Mohd-Ismail NK, Chin DWL, Lee SC, Yang H, Shin YJ, Nam DH, Chen L, Kumar AP, Deng LW, Ikawa M, Gunaratne J, Osato M, Tergaonkar V. Rap1 regulates hematopoietic stem cell survival and affects oncogenesis and response to chemotherapy. Nat Commun 2019; 10:5349. [PMID: 31836706 PMCID: PMC6911077 DOI: 10.1038/s41467-019-13082-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/14/2019] [Indexed: 11/09/2022] Open
Abstract
Increased levels and non-telomeric roles have been reported for shelterin proteins, including RAP1 in cancers. Herein using Rap1 null mice, we provide the genetic evidence that mammalian Rap1 plays a major role in hematopoietic stem cell survival, oncogenesis and response to chemotherapy. Strikingly, this function of RAP1 is independent of its association with the telomere or with its known partner TRF2. We show that RAP1 interacts with many members of the DNA damage response (DDR) pathway. RAP1 depleted cells show reduced interaction between XRCC4/DNA Ligase IV and DNA-PK, and are impaired in DNA Ligase IV recruitment to damaged chromatin for efficient repair. Consistent with its role in DNA damage repair, RAP1 loss decreases double-strand break repair via NHEJ in vivo, and consequently reduces B cell class switch recombination. Finally, we discover that RAP1 levels are predictive of the success of chemotherapy in breast and colon cancer.
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Affiliation(s)
- Ekta Khattar
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Kyaw Ze Ya Maung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Chen Li Chew
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Arkasubhra Ghosh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Michelle Meng Huang Mok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pei Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jun Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 210023, Nanjing, P.R. China
| | - Wei Hong Jeff Chor
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Gökhan Cildir
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chelsia Qiuxia Wang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Nur Khairiah Mohd-Ismail
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Desmond Wai Loon Chin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo Chin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yong-Jae Shin
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Liming Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, 210023, Nanjing, P.R. China
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lih Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Rai R, Gu P, Broton C, Kumar-Sinha C, Chen Y, Chang S. The Replisome Mediates A-NHEJ Repair of Telomeres Lacking POT1-TPP1 Independently of MRN Function. Cell Rep 2019; 29:3708-3725.e5. [PMID: 31825846 PMCID: PMC7001145 DOI: 10.1016/j.celrep.2019.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 09/22/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Telomeres use shelterin to protect chromosome ends from activating the DNA damage sensor MRE11-RAD50-NBS1 (MRN), repressing ataxia-telangiectasia, mutated (ATM) and ATM and Rad3-related (ATR) dependent DNA damage checkpoint responses. The MRE11 nuclease is thought to be essential for the resection of the 5' C-strand to generate the microhomologies necessary for alternative non-homologous end joining (A-NHEJ) repair. In the present study, we uncover DNA damage signaling and repair pathways engaged by components of the replisome complex to repair dysfunctional telomeres. In cells lacking MRN, single-stranded telomeric overhangs devoid of POT1-TPP1 do not recruit replication protein A (RPA), ATR-interacting protein (ATRIP), and RAD 51. Rather, components of the replisome complex, including Claspin, Proliferating cell nuclear antigen (PCNA), and Downstream neighbor of SON (DONSON), initiate DNA-PKcs-mediated p-CHK1 activation and A-NHEJ repair. In addition, Claspin directly interacts with TRF2 and recruits EXO1 to newly replicated telomeres to promote 5' end resection. Our data indicate that MRN is dispensable for the repair of dysfunctional telomeres lacking POT1-TPP1 and highlight the contributions of the replisome in telomere repair.
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Affiliation(s)
- Rekha Rai
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
| | - Peili Gu
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Cayla Broton
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Tri-Institutional MD/PhD Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Yong Chen
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Sandy Chang
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
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38
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Chen Y. The structural biology of the shelterin complex. Biol Chem 2019; 400:457-466. [PMID: 30352022 DOI: 10.1515/hsz-2018-0368] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
Abstract
The shelterin complex protects telomeric DNA and plays critical roles in maintaining chromosome stability. The structures and functions of the shelterin complex have been extensively explored in the past decades. This review summarizes the current progress on structural studies of shelterin complexes from different species. It focuses on the structural features and assembly of common structural domains, highlighting the evolutionary plasticity and conserved roles of shelterin proteins in telomere homeostasis and protection.
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Affiliation(s)
- Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China
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Kotla S, Le NT, Vu HT, Ko KA, Gi YJ, Thomas TN, Giancursio C, Lusis AJ, Cooke JP, Fujiwara K, Abe JI. Endothelial senescence-associated secretory phenotype (SASP) is regulated by Makorin-1 ubiquitin E3 ligase. Metabolism 2019; 100:153962. [PMID: 31476350 PMCID: PMC7059097 DOI: 10.1016/j.metabol.2019.153962] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/02/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Disturbed flow (d-flow)-induced senescence and activation of endothelial cells (ECs) have been suggested to have critical roles in promoting atherosclerosis. Telomeric repeat-binding factor 2 (TERF2)-interacting protein (TERF2IP), a member of the shelterin complex at the telomere, regulates the senescence-associated secretory phenotype (SASP), in which EC activation and senescence are engendered simultaneously by p90RSK-induced phosphorylation of TERF2IP S205 and subsequent nuclear export of the TERF2IP-TERF2 complex. In this study, we investigated TERF2IP-dependent gene expression and its role in regulating d-flow-induced SASP. METHODS A principal component analysis and hierarchical clustering were used to identify genes whose expression is regulated by TERF2IP in ECs under d-flow conditions. Senescence was determined by reduced telomere length, increased p53 and p21 expression, and increased apoptosis; EC activation was detected by NF-κB activation and the expression of adhesion molecules. The involvement of TERF2IP S205 phosphorylation in d-flow-induced SASP was assessed by depletion of TERF2IP and mutation of the phosphorylation site. RESULTS Our unbiased transcriptome analysis showed that TERF2IP caused alteration in the expression of a distinct set of genes, including rapamycin-insensitive companion of mTOR (RICTOR) and makorin-1 (MKRN1) ubiquitin E3 ligase, under d-flow conditions. In particular, both depletion of TERF2IP and overexpression of the TERF2IP S205A phosphorylation site mutant in ECs increased the d-flow and p90RSK-induced MKRN1 expression and subsequently inhibited apoptosis, telomere shortening, and NF-κB activation in ECs via suppression of p53, p21, and telomerase (TERT) induction. CONCLUSIONS MKRN1 and RICTOR belong to a distinct reciprocal gene set that is both negatively and positively regulated by p90RSK. TERF2IP S205 phosphorylation, a downstream event of p90RSK activation, uniquely inhibits MKRN1 expression and contributes to EC activation and senescence, which are key events for atherogenesis.
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Affiliation(s)
- Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Hang Thi Vu
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tamlyn N Thomas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carolyn Giancursio
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aldos J Lusis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun-Ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Irie H, Yamamoto I, Tarumoto Y, Tashiro S, Runge KW, Ishikawa F. Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast. PLoS Genet 2019; 15:e1008335. [PMID: 31454352 PMCID: PMC6733473 DOI: 10.1371/journal.pgen.1008335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 09/09/2019] [Accepted: 07/28/2019] [Indexed: 11/19/2022] Open
Abstract
Genomic rearrangements (gross chromosomal rearrangements, GCRs) threatens genome integrity and cause cell death or tumor formation. At the terminus of linear chromosomes, a telomere-binding protein complex, called shelterin, ensures chromosome stability by preventing chromosome end-to-end fusions and regulating telomere length homeostasis. As such, shelterin-mediated telomere functions play a pivotal role in suppressing GCR formation. However, it remains unclear whether the shelterin proteins play any direct role in inhibiting GCR at non-telomeric regions. Here, we have established a GCR assay for the first time in fission yeast and measured GCR rates in various mutants. We found that fission yeast cells lacking shelterin components Taz1 or Rap1 (mammalian TRF1/2 or RAP1 homologues, respectively) showed higher GCR rates compared to wild-type, accumulating large chromosome deletions. Genetic dissection of Rap1 revealed that Rap1 contributes to inhibiting GCRs via two independent pathways. The N-terminal BRCT-domain promotes faithful DSB repair, as determined by I-SceI-mediated DSB-induction experiments; moreover, association with Poz1 mediated by the central Poz1-binding domain regulates telomerase accessibility to DSBs, leading to suppression of de novo telomere additions. Our data highlight unappreciated functions of the shelterin components Taz1 and Rap1 in maintaining genome stability, specifically by preventing non-telomeric GCRs.
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Affiliation(s)
- Hiroyuki Irie
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Io Yamamoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yusuke Tarumoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sanki Tashiro
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kurt W. Runge
- Department of Molecular Genetics, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, United States of America
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail:
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The role of telomere-binding modulators in pluripotent stem cells. Protein Cell 2019; 11:60-70. [PMID: 31350723 PMCID: PMC6949317 DOI: 10.1007/s13238-019-0651-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/07/2019] [Indexed: 01/24/2023] Open
Abstract
Pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs), ESCs derived by somatic cell nuclear transfer (ntESCs), and induced pluripotent stem cells (iPSCs) have unlimited capacity for self-renewal and pluripotency and can give rise to all types of somatic cells. In order to maintain their self-renewal and pluripotency, PSCs need to preserve their telomere length and homeostasis. In recent years, increasing studies have shown that telomere reprogramming is essential for stem cell pluripotency maintenance and its induced pluripotency process. Telomere-associated proteins are not only required for telomere maintenance in both stem cells, their extra-telomeric functions have also been found to be critical as well. Here, we will discuss how telomeres and telomere-associated factors participate and regulate the maintenance of stem cell pluripotency.
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Min J, Wright WE, Shay JW. Clustered telomeres in phase-separated nuclear condensates engage mitotic DNA synthesis through BLM and RAD52. Genes Dev 2019; 33:814-827. [PMID: 31171703 PMCID: PMC6601508 DOI: 10.1101/gad.324905.119] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/24/2019] [Indexed: 11/25/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. One of the hallmarks of ALT cancer is the excessively clustered telomeres in promyelocytic leukemia (PML) bodies, represented as large bright telomere foci. Here, we present a model system that generates telomere clustering in nuclear polySUMO (small ubiquitin-like modification)/polySIM (SUMO-interacting motif) condensates, analogous to PML bodies, and thus artificially engineered ALT-associated PML body (APB)-like condensates in vivo. We observed that the ALT-like phenotypes (i.e., a small fraction of heterogeneous telomere lengths and formation of C circles) are rapidly induced by introducing the APB-like condensates together with BLM through its helicase domain, accompanied by ssDNA generation and RPA accumulation at telomeres. Moreover, these events lead to mitotic DNA synthesis (MiDAS) at telomeres mediated by RAD52 through its highly conserved N-terminal domain. We propose that the clustering of large amounts of telomeres in human cancers promotes ALT that is mediated by MiDAS, analogous to Saccharomyces cerevisiae type II ALT survivors.
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Affiliation(s)
- Jaewon Min
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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43
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Weng G, Wang E, Chen F, Sun H, Wang Z, Hou T. Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes. Phys Chem Chem Phys 2019; 21:10135-10145. [PMID: 31062799 DOI: 10.1039/c9cp01674k] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A significant number of protein-protein interactions (PPIs) are mediated through the interactions between proteins and peptide segments, and therefore determination of protein-peptide interactions (PpIs) is critical to gain an in-depth understanding of the PPI network and even design peptides or small molecules capable of modulating PPIs. Computational approaches, especially molecular docking, provide an efficient way to model PpIs, and a reliable scoring function that can recognize the correct binding conformations for protein-peptide complexes is one of the most important components in protein-peptide docking. The end-point binding free energy calculation methods, such as MM/GBSA and MM/PBSA, are theoretically more rigorous than most empirical and semi-empirical scoring functions designed for protein-peptide docking, but their performance in predicting binding affinities and binding poses for protein-peptide systems has not been systematically assessed. In this study, we first evaluated the capability of MM/GBSA and MM/PBSA with different solvation models, interior dielectric constants (εin) and force fields to predict the binding affinities for 53 protein-peptide complexes. For the 19 short peptides with 5-12 residues, MM/PBSA based on the minimized structures in explicit solvent with the ff99 force field and εin = 2 yields the best correlation between the predicted binding affinities and the experimental data (rp = 0.748), while for the 34 medium-size peptides with 20-25 residues, MM/GBSA based on 1 ns of molecular dynamics (MD) simulations in implicit solvent with the ff03 force field, the GBOBC1 model and a low interior dielectric constant (εin = 1) yields the best accuracy (rp = 0.735). Then, we assessed the rescoring capability of MM/PBSA and MM/GBSA to distinguish the correct binding conformations from the decoys for 112 protein-peptide systems. The results illustrate that MM/PBSA based on the minimized structures with the ff99 or ff14SB force field and MM/GBSA based on the minimized structures with the ff03 force field show excellent capability to recognize the near-native binding poses for the short and medium-size peptides, respectively, and they outperform the predictions given by two popular protein-peptide docking algorithms (pepATTRACT and HPEPDOCK). Therefore, MM/PBSA and MM/GBSA are powerful tools to predict the binding affinities and identify the correct binding poses for protein-peptide systems.
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Affiliation(s)
- Gaoqi Weng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Elbeltagy AR, Bertolini F, Fleming DS, Van Goor A, Ashwell CM, Schmidt CJ, Kugonza DR, Lamont SJ, Rothschild MF. Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes. Front Genet 2019; 10:376. [PMID: 31139205 PMCID: PMC6518202 DOI: 10.3389/fgene.2019.00376] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 04/09/2019] [Indexed: 01/09/2023] Open
Abstract
Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations' ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda-Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda-Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.
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Affiliation(s)
- Ahmed R Elbeltagy
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Damarius S Fleming
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Angelica Van Goor
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Institute of Food Production and Sustainability, National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United States
| | - Chris M Ashwell
- Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Donald R Kugonza
- Department of Agricultural Production, Makerere University, Kampala, Uganda
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Kotla S, Vu HT, Ko KA, Wang Y, Imanishi M, Heo KS, Fujii Y, Thomas TN, Gi YJ, Mazhar H, Paez-Mayorga J, Shin JH, Tao Y, Giancursio CJ, Medina JL, Taunton J, Lusis AJ, Cooke JP, Fujiwara K, Le NT, Abe JI. Endothelial senescence is induced by phosphorylation and nuclear export of telomeric repeat binding factor 2-interacting protein. JCI Insight 2019; 4:124867. [PMID: 31045573 PMCID: PMC6538340 DOI: 10.1172/jci.insight.124867] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
The interplay among signaling events for endothelial cell (EC) senescence, apoptosis, and activation and how these pathological conditions promote atherosclerosis in the area exposed to disturbed flow (d-flow) in concert remain unclear. The aim of this study was to determine whether telomeric repeat-binding factor 2-interacting protein (TERF2IP), a member of the shelterin complex at the telomere, can regulate EC senescence, apoptosis, and activation simultaneously, and if so, by what molecular mechanisms. We found that d-flow induced p90RSK and TERF2IP interaction in a p90RSK kinase activity-dependent manner. An in vitro kinase assay revealed that p90RSK directly phosphorylated TERF2IP at the serine 205 (S205) residue, and d-flow increased TERF2IP S205 phosphorylation as well as EC senescence, apoptosis, and activation by activating p90RSK. TERF2IP phosphorylation was crucial for nuclear export of the TERF2IP-TRF2 complex, which led to EC activation by cytosolic TERF2IP-mediated NF-κB activation and also to senescence and apoptosis of ECs by depleting TRF2 from the nucleus. Lastly, using EC-specific TERF2IP-knockout (TERF2IP-KO) mice, we found that the depletion of TERF2IP inhibited d-flow-induced EC senescence, apoptosis, and activation, as well as atherosclerotic plaque formation. These findings demonstrate that TERF2IP is an important molecular switch that simultaneously accelerates EC senescence, apoptosis, and activation by S205 phosphorylation.
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Affiliation(s)
- Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hang Thi Vu
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yin Wang
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Masaki Imanishi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kyung-Sun Heo
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuka Fujii
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tamlyn N. Thomas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hira Mazhar
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jesus Paez-Mayorga
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, Mexico
| | - Ji-Hyun Shin
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yunting Tao
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Carolyn J. Giancursio
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jan L.M. Medina
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
| | - Aldos J. Lusis
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - John P. Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nhat-Tu Le
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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46
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Holt S, Miks MH, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM. The molecular biology of fruity and floral aromas in beer and other alcoholic beverages. FEMS Microbiol Rev 2019; 43:193-222. [PMID: 30445501 PMCID: PMC6524682 DOI: 10.1093/femsre/fuy041] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.
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Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marta H Miks
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10–726 Olsztyn, Poland
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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Abstract
For more than a decade, it has been known that mammalian cells use shelterin to protect chromosome ends. Much progress has been made on the mechanism by which shelterin prevents telomeres from inadvertently activating DNA damage signaling and double-strand break (DSB) repair pathways. Shelterin averts activation of three DNA damage response enzymes [the ataxia-telangiectasia-mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases and poly(ADP-ribose) polymerase 1 (PARP1)], blocks three DSB repair pathways [classical nonhomologous end joining (c-NHEJ), alternative (alt)-NHEJ, and homology-directed repair (HDR)], and prevents hyper-resection at telomeres. For several of these functions, mechanistic insights have emerged. In addition, much has been learned about how shelterin maintains the telomeric 3' overhang, forms and protects the t-loop structure, and promotes replication through telomeres. These studies revealed that shelterin is compartmentalized, with individual subunits dedicated to distinct aspects of the end-protection problem. This review focuses on the current knowledge of shelterin-mediated telomere protection, highlights differences between human and mouse shelterin, and discusses some of the questions that remain.
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Affiliation(s)
- Titia de Lange
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA;
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48
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Fontana GA, Reinert JK, Thomä NH, Rass U. Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks. MICROBIAL CELL 2018; 5:327-343. [PMID: 29992129 PMCID: PMC6035837 DOI: 10.15698/mic2018.07.639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells have evolved conserved mechanisms to protect DNA ends, such as those at the termini of linear chromosomes, or those at DNA double-strand breaks (DSBs). In eukaryotes, DNA ends at chromosomal termini are packaged into proteinaceous structures called telomeres. Telomeres protect chromosome ends from erosion, inadvertent activation of the cellular DNA damage response (DDR), and telomere fusion. In contrast, cells must respond to damage-induced DNA ends at DSBs by harnessing the DDR to restore chromosome integrity, avoiding genome instability and disease. Intriguingly, Rif1 (Rap1-interacting factor 1) has been implicated in telomere homeostasis as well as DSB repair. The protein was first identified in Saccharomyces cerevisiae as being part of the proteinaceous telosome. In mammals, RIF1 is not associated with intact telomeres, but was found at chromosome breaks, where RIF1 has emerged as a key mediator of pathway choice between the two evolutionary conserved DSB repair pathways of non-homologous end-joining (NHEJ) and homologous recombination (HR). While this functional dichotomy has long been a puzzle, recent findings link yeast Rif1 not only to telomeres, but also to DSB repair, and mechanistic parallels likely exist. In this review, we will provide an overview of the actions of Rif1 at DNA ends and explore how exclusion of end-processing factors might be the underlying principle allowing Rif1 to fulfill diverse biological roles at telomeres and chromosome breaks.
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Affiliation(s)
- Gabriele A Fontana
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Julia K Reinert
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.,University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Ulrich Rass
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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49
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Development and characterization of polyclonal antibodies against the linker region of the telomere-binding protein TRF2. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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50
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Structural and functional analyses of the mammalian TIN2-TPP1-TRF2 telomeric complex. Cell Res 2017; 27:1485-1502. [PMID: 29160297 PMCID: PMC5717407 DOI: 10.1038/cr.2017.144] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/25/2017] [Accepted: 10/17/2017] [Indexed: 01/09/2023] Open
Abstract
Telomeres are nucleoprotein complexes that play essential roles in protecting chromosome ends. Mammalian telomeres consist of repetitive DNA sequences bound by the shelterin complex. In this complex, the POT1-TPP1 heterodimer binds to single-stranded telomeric DNAs, while TRF1 and TRF2-RAP1 interact with double-stranded telomeric DNAs. TIN2, the linchpin of this complex, simultaneously interacts with TRF1, TRF2, and TPP1 to mediate the stable assembly of the shelterin complex. However, the molecular mechanism by which TIN2 interacts with these proteins to orchestrate telomere protection remains poorly understood. Here, we report the crystal structure of the N-terminal domain of TIN2 in complex with TIN2-binding motifs from TPP1 and TRF2, revealing how TIN2 interacts cooperatively with TPP1 and TRF2. Unexpectedly, TIN2 contains a telomeric repeat factor homology (TRFH)-like domain that functions as a protein-protein interaction platform. Structure-based mutagenesis analyses suggest that TIN2 plays an important role in maintaining the stable shelterin complex required for proper telomere end protection.
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