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Schiltz CJ, Wilson JR, Hosford CJ, Adams MC, Preising SE, DeBlasio SL, MacLeod HJ, Van Eck J, Heck ML, Chappie JS. Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids. Nat Commun 2022; 13:6368. [PMID: 36289207 PMCID: PMC9606263 DOI: 10.1038/s41467-022-33979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 12/25/2022] Open
Abstract
Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
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Affiliation(s)
- Carl J. Schiltz
- grid.5386.8000000041936877XDepartment of Molecular Medicine, Cornell University, Ithaca, NY 14853 USA ,grid.152326.10000 0001 2264 7217Present Address: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Jennifer R. Wilson
- grid.5386.8000000041936877XSection of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853 USA ,grid.508983.fPresent Address: USDA-Agricultural Research Service, Corn, Soybean & Wheat Quality Research Unit, Wooster, OH 44691 USA
| | - Christopher J. Hosford
- grid.5386.8000000041936877XDepartment of Molecular Medicine, Cornell University, Ithaca, NY 14853 USA ,Present Address: LifeMine Therapeutics, Cambridge, MA 02140 USA
| | - Myfanwy C. Adams
- grid.5386.8000000041936877XDepartment of Molecular Medicine, Cornell University, Ithaca, NY 14853 USA
| | - Stephanie E. Preising
- grid.5386.8000000041936877XSection of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853 USA
| | - Stacy L. DeBlasio
- grid.5386.8000000041936877XSection of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853 USA ,grid.508984.8USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY 14853 USA
| | - Hannah J. MacLeod
- grid.508984.8USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY 14853 USA ,Present Address: Accelevir Diagnostics, Baltimore, MD 21202 USA
| | - Joyce Van Eck
- grid.5386.8000000041936877XSection of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853 USA ,grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
| | - Michelle L. Heck
- grid.5386.8000000041936877XSection of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853 USA ,grid.508984.8USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY 14853 USA ,grid.5386.8000000041936877XBoyce Thompson Institute for Plant Research, Ithaca, NY 14853 USA
| | - Joshua S. Chappie
- grid.5386.8000000041936877XDepartment of Molecular Medicine, Cornell University, Ithaca, NY 14853 USA
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Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis. eLife 2022; 11:68677. [PMID: 35133274 PMCID: PMC8824475 DOI: 10.7554/elife.68677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage response mechanisms have meiotic roles that ensure successful gamete formation. While completion of meiotic double-strand break (DSB) repair requires the canonical RAD9A-RAD1-HUS1 (9A-1-1) complex, mammalian meiocytes also express RAD9A and HUS1 paralogs, RAD9B and HUS1B, predicted to form alternative 9-1-1 complexes. The RAD1 subunit is shared by all predicted 9-1-1 complexes and localizes to meiotic chromosomes even in the absence of HUS1 and RAD9A. Here, we report that testis-specific disruption of RAD1 in mice resulted in impaired DSB repair, germ cell depletion, and infertility. Unlike Hus1 or Rad9a disruption, Rad1 loss in meiocytes also caused severe defects in homolog synapsis, impaired phosphorylation of ATR targets such as H2AX, CHK1, and HORMAD2, and compromised meiotic sex chromosome inactivation. Together, these results establish critical roles for both canonical and alternative 9-1-1 complexes in meiotic ATR activation and successful prophase I completion.
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Affiliation(s)
| | | | - Matthew Z Guo
- Department of Biomedical Sciences, Cornell University
| | | | - Emma R Kelly
- Division of Mathematics and Natural Sciences, Elmira College
| | | | | | - Jennie R Sims
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University
| | - Vitor M Faca
- Department of Biochemistry and Immunology, FMRP, University of São Paulo
| | - Charlton Tsai
- Department of Biomedical Sciences, Cornell University
| | | | - Niek Wit
- Division of Immunology, The Netherlands Cancer Institute
| | - Heinz Jacobs
- Division of Immunology, The Netherlands Cancer Institute
| | | | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna
- Universidad Fernando Pessoa Canarias
| | - James Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute
| | - Amy M Lyndaker
- Division of Mathematics and Natural Sciences, Elmira College
| | - Miguel A Brieno-Enriquez
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University
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Adams MC, Schiltz CJ, Heck ML, Chappie JS. Crystal structure of the potato leafroll virus coat protein and implications for viral assembly. J Struct Biol 2021; 214:107811. [PMID: 34813955 DOI: 10.1016/j.jsb.2021.107811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/04/2021] [Accepted: 11/13/2021] [Indexed: 10/19/2022]
Abstract
Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michelle L Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Robert W. Holley Center for Agriculture and Health, Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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Thomason LC, Schiltz CJ, Court C, Hosford CJ, Adams MC, Chappie JS, Court DL. Bacteriophage λ RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth. Mol Microbiol 2021; 116:1044-1063. [PMID: 34379857 DOI: 10.1111/mmi.14792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Abstract
The CI and Cro repressors of bacteriophage λ create a bistable switch between lysogenic and lytic growth. In λ lysogens, CI repressor expressed from the PRM promoter blocks expression of the lytic promoters PL and PR to allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lytic PR promoter. Cro repressor blocks PRM transcription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from the PRM promoter in λ lysogens; RexB is also expressed from a second promoter, PLIT , embedded in rexA. Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lytic PL and PR promoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lytic PL and PR promoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, 21702.,RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Carolyn Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Christopher J Hosford
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,New England Biolabs, Inc, Ipswich, MA, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Donald L Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
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Bai G, Kermi C, Stoy H, Schiltz CJ, Bacal J, Zaino AM, Hadden MK, Eichman BF, Lopes M, Cimprich KA. HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis. Mol Cell 2020; 78:1237-1251.e7. [PMID: 32442397 PMCID: PMC7305998 DOI: 10.1016/j.molcel.2020.04.031] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
DNA replication stress can stall replication forks, leading to genome instability. DNA damage tolerance pathways assist fork progression, promoting replication fork reversal, translesion DNA synthesis (TLS), and repriming. In the absence of the fork remodeler HLTF, forks fail to slow following replication stress, but underlying mechanisms and cellular consequences remain elusive. Here, we demonstrate that HLTF-deficient cells fail to undergo fork reversal in vivo and rely on the primase-polymerase PRIMPOL for repriming, unrestrained replication, and S phase progression upon limiting nucleotide levels. By contrast, in an HLTF-HIRAN mutant, unrestrained replication relies on the TLS protein REV1. Importantly, HLTF-deficient cells also exhibit reduced double-strand break (DSB) formation and increased survival upon replication stress. Our findings suggest that HLTF promotes fork remodeling, preventing other mechanisms of replication stress tolerance in cancer cells. This remarkable plasticity of the replication fork may determine the outcome of replication stress in terms of genome integrity, tumorigenesis, and response to chemotherapy.
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Affiliation(s)
- Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Chames Kermi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Carl J Schiltz
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Julien Bacal
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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Schiltz CJ, Adams MC, Chappie JS. The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Nucleic Acids Res 2020; 48:2762-2776. [PMID: 32009148 PMCID: PMC7049728 DOI: 10.1093/nar/gkaa059] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/28/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC-Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS. Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Nucleic Acids Res 2019; 47:9448-9463. [PMID: 31400118 PMCID: PMC6755086 DOI: 10.1093/nar/gkz703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 Å and 1.86 Å resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - April Lee
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward A Partlow
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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