Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly
Autoři:
Robert A. Dick aff001; Chaoyi Xu aff002; Dustin R. Morado aff003; Vladyslav Kravchuk aff004; Clifton L. Ricana aff005; Terri D. Lyddon aff005; Arianna M. Broad aff001; J. Ryan Feathers aff001; Marc C. Johnson aff005; Volker M. Vogt aff001; Juan R. Perilla aff002; John A. G. Briggs aff003; Florian K. M. Schur aff004
Působiště autorů:
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
aff001; Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
aff002; Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
aff003; Institute of Science and Technology Austria, Klosterneuburg, Austria
aff004; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
aff005; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
aff006
Vyšlo v časopise:
Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLoS Pathog 16(1): e32767. doi:10.1371/journal.ppat.1008277
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.ppat.1008277
Souhrn
Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.
Klíčová slova:
HIV – HIV-1 – Lentivirus – Lysine – Molecular dynamics – Monomers – Retroviruses – Viral structure
Zdroje
1. Mattei S, Schur FKM, Briggs JA. Retrovirus maturation—An extraordinary structural transformation. Curr Opin Virol. 2016 Jun;18:27–35. doi: 10.1016/j.coviro.2016.02.008 27010119
2. Pornillos O, Ganser-Pornillos BK. Maturation of retroviruses. Curr Opin Virol. 2019 Jun;36:47–55. doi: 10.1016/j.coviro.2019.05.004 31185449
3. Leroux C, Cadoré JL, Montelaro RC. Equine Infectious Anemia Virus (EIAV): What has HIV’s country cousin got tell us? Vet Res. 2004 Jul;35(4):485–512. doi: 10.1051/vetres:2004020 15236678
4. Gross I, Hohenberg H, Wilk T, Wiegers K, Grättinger M, Müller B, et al. A conformational switch controlling HIV-1 morphogenesis. EMBO J. 2000 Jan;19(1):103–13. doi: 10.1093/emboj/19.1.103 10619849
5. Datta SAK, Temeselew LG, Crist RM, Soheilian F, Kamata A, Mirro J, et al. On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch? J Virol. 2011 May;85(9):4111–21. doi: 10.1128/JVI.00006-11 21325421
6. Schur FKM, Dick RA, Hagen WJH, Vogt VM, Briggs JAG. The Structure of Immature Virus-Like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the p10 Domain in Assembly. Sundquist WI, editor. J Virol. 2015 Oct;89(20):10294–302. doi: 10.1128/JVI.01502-15 26223638
7. Goh BC, Perilla JR, England MR, Heyrana KJ, Craven RC, Schulten K. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. Structure. 2015 Aug;23(8):1414–1425. doi: 10.1016/j.str.2015.05.017 26118533
8. Bush DL, Monroe EB, Bedwell GJ, Prevelige PE, Phillips JM, Vogt VM. Higher-Order Structure of the Rous Sarcoma Virus SP Assembly Domain. J Virol. 2014 May;88(10):5617–29. doi: 10.1128/JVI.02659-13 24599998
9. Dick RA, Barros M, Jin D, Lösche M, Vogt VM. Membrane Binding of the Rous Sarcoma Virus Gag Protein Is Cooperative and Dependent on the Spacer Peptide Assembly Domain. J Virol. 2016 Mar;90(5):2473–85.
10. Keller PW, Johnson MC, Vogt VM. Mutations in the Spacer Peptide and Adjoining Sequences in Rous Sarcoma Virus Gag Lead to Tubular Budding. J Virol. 2008 Jul;82(14):6788–97. doi: 10.1128/JVI.00213-08 18448521
11. Qu K, Glass B, Doležal M, Schur FKM, Murciano B, Rein A, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proc Natl Acad Sci. 2018 Dec;115(50):E11751–60. doi: 10.1073/pnas.1811580115 30478053
12. Accola MA, Höglund S, Göttlinger HG. A Putative α-Helical Structure Which Overlaps the Capsid-p2 Boundary in the Human Immunodeficiency Virus Type 1 Gag Precursor Is Crucial for Viral Particle Assembly. J Virol. 1998 Mar;72(3):2072–8. 9499062
13. Liang C, Hu J, Russell RS, Roldan A, Kleiman L, Wainberg MA. Characterization of a putative a-helix across the capsid-SP1 boundary that is critical for the multimerization of human immunodeficiency virus type 1 Gag. J Virol. 2002 Nov;76:11729–11737. doi: 10.1128/JVI.76.22.11729-11737.2002 12388733
14. Mattei S, Tan A, Glass B, Müller B, Kräusslich H-G, Briggs JAG. High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation. Proc Natl Acad Sci. 2018 Oct;115(40):E9401–10. doi: 10.1073/pnas.1811237115 30217893
15. Schur FKM, Obr M, Hagen WJH, Wan W, Jakobi AJ, Kirkpatrick JM, et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science 2016 Jul;353(6298):506–508. doi: 10.1126/science.aaf9620 27417497
16. Adamson CS, Salzwedel K, Freed EO. Virus maturation as a new HIV-1 therapeutic target. Expert Opin Ther Targets. 2009 Aug;13(8):895–908. doi: 10.1517/14728220903039714 19534569
17. Dick RA, Zadrozny KK, Xu C, Schur FKM, Lyddon TD, Ricana CL, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018 Aug;560:509–512. doi: 10.1038/s41586-018-0396-4 30069050
18. Dick RA, Mallery DL, Vogt VM, James LC. IP6 Regulation of HIV Capsid Assembly, Stability, and Uncoating. Viruses. 2018 Nov;10(11):640.
19. Mallery DL, Márquez CL, McEwan WA, Dickson CF, Jacques DA, Anandapadamanaban M, et al. IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis. Elife. 2018 May;7:e35335. doi: 10.7554/eLife.35335 29848441
20. Bush DL, Vogt VM. In Vitro Assembly of Retroviruses. Annu Rev Virol. 2014 Nov;1(1):561–80. doi: 10.1146/annurev-virology-031413-085427 26958734
21. Schur FKM, Hagen WJH, Rumlová M, Ruml T, Müller B, Kraüsslich HG, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 2015 Jan;517(7535):505–8. doi: 10.1038/nature13838 25363765
22. Campbell S, Fisher RJ, Towler EM, Fox S, Issaq HJ, Wolfe T, et al. Modulation of HIV-like particle assembly in vitro by inositol phosphates. Proc Natl Acad Sci. 2001 Sep;98(19):10875–9. doi: 10.1073/pnas.191224698 11526217
23. de Marco A, Davey NE, Ulbrich P, Phillips JM, Lux V, Riches JD, et al. Conserved and variable features of Gag structure and arrangement in immature retrovirus particles. J Virol. 2010 Nov;84(22):11729–36. doi: 10.1128/JVI.01423-10 20810738
24. Bharat TAM, Davey NE, Ulbrich P, Riches JD, de Marco A, Rumlova M, et al. Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Nature. 2012 Jul;487(7407):385–9. doi: 10.1038/nature11169 22722831
25. Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 2013 May;497(7451):643–6. doi: 10.1038/nature12162 23719463
26. Schur FKM. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Curr Opin Struct Biol. 2019 Oct;58:1–9. doi: 10.1016/j.sbi.2019.03.018 31005754
27. Obr M & Schur FKM. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. Advances in Virus Research. 2019;105:117–159. doi: 10.1016/bs.aivir.2019.07.008 31522703
28. Loewus FA, Murthy PPN. myo-Inositol metabolism in plants. Plant Sci. 2000 Jan 14;150(1):1–19.
29. Ganser-Pornillos BK, Cheng A, Yeager M. Structure of Full-Length HIV-1 CA: A Model for the Mature Capsid Lattice. Cell. 2007 Oct 5;131(1):70–9. doi: 10.1016/j.cell.2007.08.018 17923088
30. Jaballah SA, Bailey GD, Desfosses A, Hyun J, Mitra AK, Kingston RL. In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature. Sci Rep. 2017 Dec;7(1):2913. doi: 10.1038/s41598-017-02060-0 28588198
31. Wagner JM, Zadrozny KK, Chrustowicz J, Purdy MD, Yeager M, Ganser-Pornillos BK, et al. Crystal structure of an HIV assembly and maturation switch. Elife. 2016 Jul;5:e17063. doi: 10.7554/eLife.17063 27416583
32. Chen K, Piszczek G, Carter C, Tjandra N. The maturational refolding of the β-hairpin motif of equine infectious anemia virus capsid protein extends its helix α1 at capsid assembly locus. J Biol Chem. 2013 Jan;288(3):1511–20. doi: 10.1074/jbc.M112.425140 23184932
33. Melamed D, Mark-Danieli M, Kenan-Eichler M, Kraus O, Castiel A, Laham N, et al. The Conserved Carboxy Terminus of the Capsid Domain of Human Immunodeficiency Virus Type 1 Gag Protein Is Important for Virion Assembly and Release. J Virol. 2004 Sep;78(18):9675–88. doi: 10.1128/JVI.78.18.9675-9688.2004 15331700
34. Monroe EB, Kang S, Kyere SK, Li R, Prevelige PE. Hydrogen/Deuterium Exchange Analysis of HIV-1 Capsid Assembly and Maturation. Structure. 2010 Nov;18(11):1483–91. doi: 10.1016/j.str.2010.08.016 21070947
35. Bharat TAM, Castillo Menendez LR, Hagen WJH, Lux V, Igonet S, Schorb M, et al. Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. Proc Natl Acad Sci. 2014 Jun;111(22):8233–8. doi: 10.1073/pnas.1401455111 24843179
36. Borsetti A, Öhagen Å, Göttlinger HG. The C-Terminal Half of the Human Immunodeficiency Virus Type 1 Gag Precursor Is Sufficient for Efficient Particle Assembly. J Virol. 1998 Nov;72(11):9313–7. 9765481
37. Novikova M, Adams LJ, Fontana J, Gres AT, Balasubramaniam M, Winkler DC, et al. Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation. MBio. 2018 Nov;9(5):e01567–18. doi: 10.1128/mBio.01567-18 30327442
38. Bartonova V, Igonet S, Sticht J, Glass B, Habermann A, Vaney MC, et al. Residues in the HIV-1 capsid assembly inhibitor binding site are essential for maintaining the assembly-competent quaternary structure of the capsid protein. J Biol Chem. 2008 Nov;283(46):32024–33. doi: 10.1074/jbc.M804230200 18772135
39. Bailey GD, Hyun JK, Mitra AK, Kingston RL. Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly. Structure. 2009 May;17(5):737–48. doi: 10.1016/j.str.2009.03.010 19446529
40. Mitrophanous K, Yoon S, Rohll J, Patil D, Wilkes F, Kim V, et al. Stable gene transfer to the nervous system using a non-primate lentiviral vector. Gene Ther. 1999 Nov;6(11):1808–18. doi: 10.1038/sj.gt.3301023 10602376
41. Malakhov MP, Mattern MR, Malakhova OA, Drinker M, Weeks SD, Butt TR. SUMO fusions and SUMO-specific protease for efficient expression and purification of proteins. J Struct Funct Genomics. 2004 Mar;5(1/2):75–86.
42. Phillips JM, Murray PS, Murray D, Vogt VM. A molecular switch required for retrovirus assembly participates in the hexagonal immature lattice. EMBO J. 2008 May;27(9):1411–20. doi: 10.1038/emboj.2008.71 18401344
43. Corcoran J, So P-L, Barber RD, Vincent KJ, Mazarakis ND, Mitrophanous KA, et al. Retinoic acid receptor beta2 and neurite outgrowth in the adult mouse spinal cord in vitro. J Cell Sci. 2002 Oct;115(Pt 19):3779–86. doi: 10.1242/jcs.00046 12235288
44. Chang LJ, Urlacher V, Iwakuma T, Cui Y, Zucali J. Efficacy and safety analyses of a recombinant human immunodeficiency virus type 1 derived vector system. Gene Ther. 1999 May;6(5):715–28. doi: 10.1038/sj.gt.3300895 10505094
45. Song YE, Olinger GY, Janaka SK, Johnson MC. Sequence Determinants in Gammaretroviral Env Cytoplasmic Tails Dictate Virus-Specific Pseudotyping Compatibility. J Virol. 2019;93.
46. Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol. 2005 Oct;152(1):36–51. doi: 10.1016/j.jsb.2005.07.007 16182563
47. Vulović M, Franken E, Ravelli RBG, van Vliet LJ, Rieger B. Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy. Ultramicroscopy. 2012 May;116:115–34.
48. Hagen WJH, Wan W, Briggs JAG. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J Struct Biol. 2017 Feb;197(2):191–8. doi: 10.1016/j.jsb.2016.06.007 27313000
49. Rohou A, Grigorieff N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015 Nov;192(2):216–21. doi: 10.1016/j.jsb.2015.08.008 26278980
50. Grant T, Grigorieff N. Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. Sundquist WI, editor. Elife. 2015 May;4:e06980. doi: 10.7554/eLife.06980 26023829
51. Kremer JR, Mastronarde DN, McIntosh JR. Computer Visualization of Three-Dimensional Image Data Using IMOD. J Struct Biol. 1996 Jan-Feb;116(1):71–6. doi: 10.1006/jsbi.1996.0013 8742726
52. Xiong Q, Morphew MK, Schwartz CL, Hoenger AH, Mastronarde DN. CTF determination and correction for low dose tomographic tilt series. J Struct Biol. 2009 Dec;168(3):378–87. doi: 10.1016/j.jsb.2009.08.016 19732834
53. Turoňová B, Schur FKM, Wan W, Briggs JAG. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å. J Struct Biol. 2017 Sep;199(3):187–95. doi: 10.1016/j.jsb.2017.07.007 28743638
54. Pruggnaller S, Mayr M, Frangakis AS. A visualization and segmentation toolbox for electron microscopy. J Struct Biol. 2008 Oct;164(1):161–5. doi: 10.1016/j.jsb.2008.05.003 18691905
55. Förster F, Medalia O, Zauberman N, Baumeister W, Fass D. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc Natl Acad Sci. 2005 Mar;102(13):4729–34. doi: 10.1073/pnas.0409178102 15774580
56. Nickell S, Förster F, Linaroudis A, Del Net W, Beck F, Hegerl R, et al. TOM software toolbox: Acquisition and analysis for electron tomography. J Struct Biol. 2005 Mar;149(3):227–34. doi: 10.1016/j.jsb.2004.10.006 15721576
57. Castano-Diez D, Kudryashev M, Arheit M, Stahlberg H. Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biol. 2012 May;178(2):139–51. doi: 10.1016/j.jsb.2011.12.017 22245546
58. Wan W, Kolesnikova L, Clarke M, Koehler A, Noda T, Becker S, et al. Structure and assembly of the Ebola virus nucleocapsid. Nature. 2017 Nov;551(7680):394–7. doi: 10.1038/nature24490 29144446
59. Rosenthal PB, Henderson R. Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy. J Mol Biol. 2003 Oct;333(4):721–45. doi: 10.1016/j.jmb.2003.07.013 14568533
60. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct;25(13):1605–12. doi: 10.1002/jcc.20084 15264254
61. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D. 2004 Dec;60(12 Part 1):2126–32.
62. Schrodinger LLC. The PyMOL Molecular Graphics System, Version 1.3r1. 2010.
63. Jin Z, Jin L, Peterson DL, Lawson CL. Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26. J Mol Biol. 1999 Feb;286(1):83–93. doi: 10.1006/jmbi.1998.2443 9931251
64. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr Sect D. 2010 Feb;66(2):213–21.
65. Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr Sect D. 2010 Jan;66(1):12–21.
66. Fletcher R, Reeves CM. Function minimization by conjugate gradients. Comput J. 1964 Feb;7(2):149–54.
67. Sun W, Yuan Y-X. Optimization Theory and Methods : Nonlinear Programming. Springer Science+Business Media, LLC; 2006.
68. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005 Dec;26(16):1781–802. doi: 10.1002/jcc.20289 16222654
69. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017 Jan;14(1):71–3. doi: 10.1038/nmeth.4067 27819658
70. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984 Oct;81(8):3684–90.
71. Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994 Sep;101(5):4177–89.
72. Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: The Langevin piston method. J Chem Phys. 1995 Sep;103(11):4613–21.
73. Ryckaert J-P, Ciccotti G, Berendsen HJ. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977 Mar;23(3):327–41.
74. Shan Y, Klepeis JL, Eastwood MP, Dror RO, Shaw DE. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. J Chem Phys. 2005 Feb;122(5):054101.
75. Füzik T, Píchalová R, Schur FKM, Strohalmová K, Křížová I, Hadravová R, et al. Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging. J Virol. 2016 May;90(9):4593–603. doi: 10.1128/JVI.03197-15 26912613
Článek vyšel v časopise
PLOS Pathogens
2020 Číslo 1
- Případ Bulovka: Jak postupují jiné nemocnice, aby podobným tragédiím zabránily?
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Vědci vytvořili první funkční mozkovou tkáň pomocí 3D tisku
- Státní zdravotní ústav: Čeká nás „pertusový rok“
- Jak souvisí postcovidový syndrom s poškozením mozku?
Nejčtenější v tomto čísle
- Chromatin maturation of the HIV-1 provirus in primary resting CD4+ T cells
- Norovirus infection results in eIF2α independent host translation shut-off and remodels the G3BP1 interactome evading stress granule formation
- Modular Mimicry and Engagement of the Hippo Pathway by Marburg Virus VP40: Implications for Filovirus Biology and Budding
- Broad dengue neutralization in mosquitoes expressing an engineered antibody