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Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 2024; 626:194-206. [PMID: 38096902 PMCID: PMC10830420 DOI: 10.1038/s41586-023-06947-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6-8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1.
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Affiliation(s)
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Bryant D Miller
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Matthew Hancock
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Esin Işik
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Carlos Mendez-Dorantes
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thomas Walpole
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Charles Nichols
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Paul Wan
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Kirsi Riento
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Rowan Halls-Kass
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Alfred Lammens
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Paula Upla
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Kera Xibinaku
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | | | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna M Schneider
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Weichenrieder
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Kathleen H Burns
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands.
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Kines KJ, Sokolowski M, DeFreece C, Shareef A, deHaro DL, Belancio VP. Large Deletions, Cleavage of the Telomeric Repeat Sequence, and Reverse Transcriptase-Mediated DNA Damage Response Associated with Long Interspersed Element-1 ORF2p Enzymatic Activities. Genes (Basel) 2024; 15:143. [PMID: 38397133 PMCID: PMC10887698 DOI: 10.3390/genes15020143] [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: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
L1 elements can cause DNA damage and genomic variation via retrotransposition and the generation of endonuclease-dependent DNA breaks. These processes require L1 ORF2p protein that contains an endonuclease domain, which cuts genomic DNA, and a reverse transcriptase domain, which synthesizes cDNA. The complete impact of L1 enzymatic activities on genome stability and cellular function remains understudied, and the spectrum of L1-induced mutations, other than L1 insertions, is mostly unknown. Using an inducible system, we demonstrate that an ORF2p containing functional reverse transcriptase is sufficient to elicit DNA damage response even in the absence of the functional endonuclease. Using a TK/Neo reporter system that captures misrepaired DNA breaks, we demonstrate that L1 expression results in large genomic deletions that lack any signatures of L1 involvement. Using an in vitro cleavage assay, we demonstrate that L1 endonuclease efficiently cuts telomeric repeat sequences. These findings support that L1 could be an unrecognized source of disease-promoting genomic deletions, telomere dysfunction, and an underappreciated source of chronic RT-mediated DNA damage response in mammalian cells. Our findings expand the spectrum of biological processes that can be triggered by functional and nonfunctional L1s, which have impactful evolutionary- and health-relevant consequences.
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Affiliation(s)
- Kristine J. Kines
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Cecily DeFreece
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Afzaal Shareef
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Dawn L. deHaro
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
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4
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Du Q, Stow EC, LaCoste D, Freeman B, Baddoo M, Shareef A, Miller KM, Belancio VP. A novel role of TRIM28 B box domain in L1 retrotransposition and ORF2p-mediated cDNA synthesis. Nucleic Acids Res 2023; 51:4429-4450. [PMID: 37070200 PMCID: PMC10201437 DOI: 10.1093/nar/gkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 04/19/2023] Open
Abstract
The long interspersed element 1 (LINE-1 or L1) integration is affected by many cellular factors through various mechanisms. Some of these factors are required for L1 amplification, while others either suppress or enhance specific steps during L1 propagation. Previously, TRIM28 has been identified to suppress transposable elements, including L1 expression via its canonical role in chromatin remodeling. Here, we report that TRIM28 through its B box domain increases L1 retrotransposition and facilitates shorter cDNA and L1 insert generation in cultured cells. Consistent with the latter, we observe that tumor specific L1 inserts are shorter in endometrial, ovarian, and prostate tumors with higher TRIM28 mRNA expression than in those with lower TRIM28 expression. We determine that three amino acids in the B box domain that are involved in TRIM28 multimerization are critical for its effect on both L1 retrotransposition and cDNA synthesis. We provide evidence that B boxes from the other two members in the Class VI TRIM proteins, TRIM24 and TRIM33, also increase L1 retrotransposition. Our findings could lead to a better understanding of the host/L1 evolutionary arms race in the germline and their interplay during tumorigenesis.
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Affiliation(s)
- Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Dawn LaCoste
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Benjamin Freeman
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Afzaal M Shareef
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 100 E 24th Street, Austin, TX 78712, USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
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6
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Zhang X, Zhang R, Yu J. New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation. Front Cell Dev Biol 2020; 8:657. [PMID: 32850797 PMCID: PMC7426637 DOI: 10.3389/fcell.2020.00657] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1) retrotransposition is a major hallmark of cancer accompanied by global chromosomal instability, genomic instability, and genetic heterogeneity and has become one indicator for the occurrence, development, and poor prognosis of many diseases. LINE-1 also modulates the immune system and affects the immune microenvironment in a variety of ways. Aberrant expression of LINE-1 retrotransposon can provide strong stimuli for an innate immune response, activate the immune system, and induce autoimmunity and inflammation. Therefore, inhibition the activity of LINE-1 has become a potential treatment strategy for various diseases. In this review, we discussed the components and regulatory mechanisms involved with LINE-1, its correlations with disease and immunity, and multiple inhibitors of LINE-1, providing a new understanding of LINE-1.
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Affiliation(s)
- Xiao Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Rui Zhang
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center of Caner, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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7
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Sokolowski M, Chynces M, deHaro D, Christian CM, Belancio VP. Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans. Nucleic Acids Res 2017; 45:5294-5308. [PMID: 28431148 PMCID: PMC5605252 DOI: 10.1093/nar/gkx211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/12/2017] [Indexed: 01/15/2023] Open
Abstract
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed. We demonstrate that introduction of equivalent stop codons in the full-length human L1 sequence leads to the expression of truncated ORF1 proteins. When supplied in trans some truncated human ORF1 proteins suppress human L1 retrotransposition. This effect requires the N-terminus and coiled-coil domain (C-C) as mutations within the ORF1p C-C domain abolish the suppressive effect of truncated proteins on L1 retrotransposition. We demonstrate that the expression levels and length of truncated ORF1 proteins influence their ability to suppress L1 retrotransposition. Taken together these findings suggest that L1 retrotransposition may be influenced by coexpression of defective L1 loci and that these L1 loci may reduce accumulation of de novo L1 integration events.
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Affiliation(s)
- Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - May Chynces
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Dawn deHaro
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Claiborne M Christian
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
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