Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation

Novikova, Mariia; Adams, Lucas J.; Fontana, Juan; Gres, Anna T.; Balasubramaniam, Muthukumar; Winkler, Dennis C.; Kudchodkar, Sagar B.; Soheilian, Ferri; Sarafianos, Stefan G.; Steven, Alasdair C.; Freed, Eric O.; Goff, Stephen P.

doi:10.1128/mBio.01567-18

Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation

Journal Article · Tue Oct 16 04:00:00 EDT 2018 · mBio (Online)

DOI:https://doi.org/10.1128/mBio.01567-18· OSTI ID:1502210

Novikova, Mariia; Adams, Lucas J.; ; Gres, Anna T.; Balasubramaniam, Muthukumar; Winkler, Dennis C.; Kudchodkar, Sagar B.; Soheilian, Ferri; Sarafianos, Stefan G.; Steven, Alasdair C.; Freed, Eric O.; Goff, Stephen P.

ABSTRACT

Late in the HIV-1 replication cycle, the viral structural protein Gag is targeted to virus assembly sites at the plasma membrane of infected cells. The capsid (CA) domain of Gag plays a critical role in the formation of the hexameric Gag lattice in the immature virion, and, during particle release, CA is cleaved from the Gag precursor by the viral protease and forms the conical core of the mature virion. A highly conserved Pro-Pro-Ile-Pro (PPIP) motif (CA residues 122 to 125) [PPIP(122–125)] in a loop connecting CA helices 6 and 7 resides at a 3-fold axis formed by neighboring hexamers in the immature Gag lattice. In this study, we characterized the role of this PPIP(122–125) loop in HIV-1 assembly and maturation. While mutations P123A and P125A were relatively well tolerated, mutation of P122 and I124 significantly impaired virus release, caused Gag processing defects, and abolished infectivity. X-ray crystallography indicated that the P122A and I124A mutations induce subtle changes in the structure of the mature CA lattice which were permissive forin vitroassembly of CA tubes. Transmission electron microscopy and cryo-electron tomography demonstrated that the P122A and I124A mutations induce severe structural defects in the immature Gag lattice and abrogate conical core formation. Propagation of the P122A and I124A mutants in T-cell lines led to the selection of compensatory mutations within CA. Our findings demonstrate that the CA PPIP(122–125) loop comprises a structural element critical for the formation of the immature Gag lattice.

IMPORTANCECapsid (CA) plays multiple roles in the HIV-1 replication cycle. CA-CA domain interactions are responsible for multimerization of the Gag polyprotein at virus assembly sites, and in the mature virion, CA monomers assemble into a conical core that encapsidates the viral RNA genome. Multiple CA regions that contribute to the assembly and release of HIV-1 particles have been mapped and investigated. Here, we identified and characterized a Pro-rich loop in CA that is important for the formation of the immature Gag lattice. Changes in this region disrupt viral production and abrogate the formation of infectious, mature virions. Propagation of the mutants in culture led to the selection of second-site compensatory mutations within CA. These results expand our knowledge of the assembly and maturation steps in the viral replication cycle and may be relevant for development of antiviral drugs targeting CA.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: NIH

OSTI ID:: 1502210

Journal Information:: mBio (Online), Journal Name: mBio (Online) Journal Issue: 5 Vol. 9; ISSN 2150-7511

Publisher:: American Society for Microbiology

Country of Publication:: United States

Language:: ENGLISH

References (59)

Crystal structure of an HIV assembly and maturation switch Wagner, Jonathan M.; Zadrozny, Kaneil K.; Chrustowicz, Jakub eLife, Vol. 5 https://doi.org/10.7554/eLife.17063	journal	July 2016
Structural Changes in Influenza Virus at Low pH Characterized by Cryo-Electron Tomography Fontana, J.; Cardone, G.; Heymann, J. B. Journal of Virology, Vol. 86, Issue 6 https://doi.org/10.1128/JVI.06698-11	journal	January 2012
Homology-based Identification of Capsid Determinants That Protect HIV1 from Human TRIM5α Restriction Maillard, Pierre V.; Zoete, Vincent; Michielin, Olivier Journal of Biological Chemistry, Vol. 286, Issue 10 https://doi.org/10.1074/jbc.M110.187609	journal	December 2010
A Consensus View of ESCRT-Mediated Human Immunodeficiency Virus Type 1 Abscission Lippincott-Schwartz, J.; Freed, E. O.; van Engelenburg, S. B. Annual Review of Virology, Vol. 4, Issue 1 https://doi.org/10.1146/annurev-virology-101416-041840	journal	September 2017
Virus Budding and the ESCRT Pathway Votteler, Jörg; Sundquist, Wesley I. Cell Host & Microbe, Vol. 14, Issue 3 https://doi.org/10.1016/j.chom.2013.08.012	journal	September 2013
X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability Gres, Anna T.; Kirby, Karen A.; KewalRamani, Vineet N. Science, Vol. 349, Issue 6243 https://doi.org/10.1126/science.aaa5936	journal	June 2015
Computational resources for cryo-electron tomography in Bsoft Bernard Heymann, J.; Cardone, Giovanni; Winkler, Dennis C. Journal of Structural Biology, Vol. 161, Issue 3 https://doi.org/10.1016/j.jsb.2007.08.002	journal	March 2008
Retrovirus maturation—an extraordinary structural transformation Mattei, Simone; Schur, Florian KM; Briggs, John AG Current Opinion in Virology, Vol. 18 https://doi.org/10.1016/j.coviro.2016.02.008	journal	June 2016
Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells Wright, Elizabeth R.; Schooler, Jordan B.; Ding, H. Jane The EMBO Journal, Vol. 26, Issue 8 https://doi.org/10.1038/sj.emboj.7601664	journal	March 2007
X-Ray Structures of the Hexameric Building Block of the HIV Capsid Pornillos, Owen; Ganser-Pornillos, Barbie K.; Kelly, Brian N. Cell, Vol. 137, Issue 7 https://doi.org/10.1016/j.cell.2009.04.063	journal	June 2009
Extreme Genetic Fragility of the HIV-1 Capsid Rihn, Suzannah J.; Wilson, Sam J.; Loman, Nick J. PLoS Pathogens, Vol. 9, Issue 6 https://doi.org/10.1371/journal.ppat.1003461	journal	June 2013
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics Zhao, Gongpu; Perilla, Juan R.; Yufenyuy, Ernest L. Nature, Vol. 497, Issue 7451 https://doi.org/10.1038/nature12162	journal	May 2013
Atomic-level modelling of the HIV capsid Pornillos, Owen; Ganser-Pornillos, Barbie K.; Yeager, Mark Nature, Vol. 469, Issue 7330 https://doi.org/10.1038/nature09640	journal	January 2011
Structural basis for targeting HIV-1 Gag proteins to the plasma membrane for virus assembly Saad, J. S.; Miller, J.; Tai, J. Proceedings of the National Academy of Sciences, Vol. 103, Issue 30 https://doi.org/10.1073/pnas.0602818103	journal	July 2006
Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein Lemke, C. T.; Titolo, S.; von Schwedler, U. Journal of Virology, Vol. 86, Issue 12 https://doi.org/10.1128/JVI.00493-12	journal	April 2012
Scaling and assessment of data quality Evans, Philip Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82 https://doi.org/10.1107/S0907444905036693	journal	December 2005
A Strongly Transdominant Mutation in the Human Immunodeficiency Virus Type 1 gag Gene Defines an Achilles Heel in the Virus Life Cycle Lee, S. -K.; Harris, J.; Swanstrom, R. Journal of Virology, Vol. 83, Issue 17 https://doi.org/10.1128/JVI.00317-09	journal	June 2009
Structural and Functional Insights into the HIV-1 Maturation Inhibitor Binding Pocket Waki, Kayoko; Durell, Stewart R.; Soheilian, Ferri PLoS Pathogens, Vol. 8, Issue 11 https://doi.org/10.1371/journal.ppat.1002997	journal	November 2012
Automated electron microscope tomography using robust prediction of specimen movements Mastronarde, David N. Journal of Structural Biology, Vol. 152, Issue 1 https://doi.org/10.1016/j.jsb.2005.07.007	journal	October 2005
How HIV-1 Gag assembles in cells: Putting together pieces of the puzzle Lingappa, Jaisri R.; Reed, Jonathan C.; Tanaka, Motoko Virus Research, Vol. 193 https://doi.org/10.1016/j.virusres.2014.07.001	journal	November 2014
The Mechanism of HIV-1 Core Assembly: Insights from Three-Dimensional Reconstructions of Authentic Virions Briggs, John A. G.; Grünewald, Kay; Glass, Bärbel Structure, Vol. 14, Issue 1 https://doi.org/10.1016/j.str.2005.09.010	journal	January 2006
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data Davey, Norman E.; Satagopam, Venkata P.; Santiago-Mozos, Salvador PLoS Computational Biology, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pcbi.1003951	journal	December 2014
Alkyl Amine Bevirimat Derivatives Are Potent and Broadly Active HIV-1 Maturation Inhibitors Urano, Emiko; Ablan, Sherimay D.; Mandt, Rebecca Antimicrobial Agents and Chemotherapy, Vol. 60, Issue 1 https://doi.org/10.1128/AAC.02121-15	journal	October 2015
HIV-1 assembly, release and maturation Freed, Eric O. Nature Reviews Microbiology, Vol. 13, Issue 8 https://doi.org/10.1038/nrmicro3490	journal	June 2015
Image reconstructions of helical assemblies of the HIV-1 CA protein Li, Su; Hill, Christopher P.; Sundquist, Wesley I. Nature, Vol. 407, Issue 6802 https://doi.org/10.1038/35030177	journal	September 2000
Susceptibility and adaptation to human TRIM5α alleles at positive selected sites in HIV-1 capsid Rahm, Nadia; Gfeller, David; Snoeck, Joke Virology, Vol. 441, Issue 2 https://doi.org/10.1016/j.virol.2013.03.021	journal	July 2013
Structure of the Carboxyl-Terminal Dimerization Domain of the HIV-1 Capsid Protein Gamble, T. R. Science, Vol. 278, Issue 5339 https://doi.org/10.1126/science.278.5339.849	journal	October 1997
Averaging of Electron Subtomograms and Random Conical Tilt Reconstructions through Likelihood Optimization Scheres, Sjors H. W.; Melero, Roberto; Valle, Mikel Structure, Vol. 17, Issue 12 https://doi.org/10.1016/j.str.2009.10.009	journal	December 2009
Suboptimal inhibition of protease activity in human immunodeficiency virus type 1: Effects on virion morphogenesis and RNA maturation Moore, Michael D.; Fu, William; Soheilian, Ferri Virology, Vol. 379, Issue 1 https://doi.org/10.1016/j.virol.2008.06.030	journal	September 2008
The capsid-spacer peptide 1 Gag processing intermediate is a dominant-negative inhibitor of HIV-1 maturation Checkley, Mary Ann; Luttge, Benjamin G.; Soheilian, Ferri Virology, Vol. 400, Issue 1 https://doi.org/10.1016/j.virol.2010.01.028	journal	April 2010
In Vitro Resistance to the Human Immunodeficiency Virus Type 1 Maturation Inhibitor PA-457 (Bevirimat) Adamson, C. S.; Ablan, S. D.; Boeras, I. Journal of Virology, Vol. 80, Issue 22 https://doi.org/10.1128/JVI.01369-06	journal	September 2006
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
HIV-1 Assembly, Budding, and Maturation Sundquist, W. I.; Krausslich, H. -G. Cold Spring Harbor Perspectives in Medicine, Vol. 2, Issue 7 https://doi.org/10.1101/cshperspect.a006924	journal	March 2012
PHENIX : building new software for automated crystallographic structure determination Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11 https://doi.org/10.1107/S0907444902016657	journal	October 2002
HIV-1 Gag Processing Intermediates Trans-dominantly Interfere with HIV-1 Infectivity Müller, Barbara; Anders, Maria; Akiyama, Hisashi Journal of Biological Chemistry, Vol. 284, Issue 43 https://doi.org/10.1074/jbc.M109.027144	journal	August 2009
Antiviral Inhibition of the HIV-1 Capsid Protein Tang, Chun; Loeliger, Erin; Kinde, Isaac Journal of Molecular Biology, Vol. 327, Issue 5 https://doi.org/10.1016/S0022-2836(03)00289-4	journal	April 2003
Functional Surfaces of the Human Immunodeficiency Virus Type 1 Capsid Protein von Schwedler, U. K.; Stray, K. M.; Garrus, J. E. Journal of Virology, Vol. 77, Issue 9 https://doi.org/10.1128/JVI.77.9.5439-5450.2003	journal	May 2003
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Quenching protein dynamics interferes with HIV capsid maturation Wang, Mingzhang; Quinn, Caitlin M.; Perilla, Juan R. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01856-y	journal	November 2017
An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation Schur, Florian K. M.; Obr, Martin; Hagen, Wim J. H. Science, Vol. 353, Issue 6298 https://doi.org/10.1126/science.aaf9620	journal	July 2016
Second site reversion of a mutation near the amino terminus of the HIV-1 capsid protein López, Claudia S.; Tsagli, Seyram M.; Sloan, Rachel Virology, Vol. 447, Issue 1-2 https://doi.org/10.1016/j.virol.2013.08.023	journal	December 2013
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
A Two-Pronged Structural Analysis of Retroviral Maturation Indicates that Core Formation Proceeds by a Disassembly-Reassembly Pathway Rather than a Displacive Transition Keller, P. W.; Huang, R. K.; England, M. R. Journal of Virology, Vol. 87, Issue 24 https://doi.org/10.1128/JVI.01408-13	journal	October 2013
Noise Reduction in Electron Tomographic Reconstructions Using Nonlinear Anisotropic Diffusion Frangakis, Achilleas S.; Hegerl, Reiner Journal of Structural Biology, Vol. 135, Issue 3 https://doi.org/10.1006/jsbi.2001.4406	journal	September 2001
Identification of an HIV-1 Mutation in Spacer Peptide 1 That Stabilizes the Immature CA-SP1 Lattice Fontana, Juan; Keller, Paul W.; Urano, Emiko Journal of Virology, Vol. 90, Issue 2 https://doi.org/10.1128/JVI.02204-15	journal	November 2015
Protease Cleavage Leads to Formation of Mature Trimer Interface in HIV-1 Capsid Meng, Xin; Zhao, Gongpu; Yufenyuy, Ernest PLoS Pathogens, Vol. 8, Issue 8 https://doi.org/10.1371/journal.ppat.1002886	journal	August 2012
In Vitro Assembly Properties of Purified Bacterially Expressed Capsid Proteins of Human Immunodeficiency Virus Gross, Ingolf; Hohenberg, Heinz; Krausslich, Hans-Georg European Journal of Biochemistry, Vol. 249, Issue 2 https://doi.org/10.1111/j.1432-1033.1997.t01-1-00592.x	journal	October 1997
Maturation of the HIV-1 core by a non-diffusional phase transition Frank, Gabriel A.; Narayan, Kedar; Bess, Julian W. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms6854	journal	January 2015
The structure and flexibility of conical HIV-1 capsids determined within intact virions Mattei, Simone; Glass, Bärbel; Hagen, Wim J. H. Science, Vol. 354, Issue 6318 https://doi.org/10.1126/science.aah4972	journal	December 2016
Proteolytic refolding of the HIV-1 capsid protein amino-terminus facilitates viral core assembly von Schwedler, U. K. The EMBO Journal, Vol. 17, Issue 6 https://doi.org/10.1093/emboj/17.6.1555	journal	March 1998
HIV-1 Maturation Inhibitor Bevirimat Stabilizes the Immature Gag Lattice Keller, P. W.; Adamson, C. S.; Heymann, J. B. Journal of Virology, Vol. 85, Issue 4 https://doi.org/10.1128/JVI.01926-10	journal	November 2010
Assembly and Analysis of Conical Models for the HIV-1 Core Ganser, B. K. Science, Vol. 283, Issue 5398 https://doi.org/10.1126/science.283.5398.80	journal	January 1999
In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13689	journal	December 2016
PA-457: A potent HIV inhibitor that disrupts core condensation by targeting a late step in Gag processing Li, F.; Goila-Gaur, R.; Salzwedel, K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 23 https://doi.org/10.1073/pnas.2234683100	journal	October 2003
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution Schur, Florian K. M.; Hagen, Wim J. H.; Rumlová, Michaela Nature, Vol. 517, Issue 7535 https://doi.org/10.1038/nature13838	journal	November 2014
The structural biology of HIV assembly Ganser-Pornillos, Barbie K.; Yeager, Mark; Sundquist, Wesley I. Current Opinion in Structural Biology, Vol. 18, Issue 2 https://doi.org/10.1016/j.sbi.2008.02.001	journal	April 2008
Small-Molecule Inhibition of Human Immunodeficiency Virus Type 1 Replication by Specific Targeting of the Final Step of Virion Maturation Zhou, J.; Yuan, X.; Dismuke, D. Journal of Virology, Vol. 78, Issue 2 https://doi.org/10.1128/JVI.78.2.922-929.2004	journal	December 2003
Species-Specific Tropism Determinants in the Human Immunodeficiency Virus Type 1 Capsid Hatziioannou, T.; Cowan, S.; von Schwedler, U. K. Journal of Virology, Vol. 78, Issue 11 https://doi.org/10.1128/JVI.78.11.6005-6012.2004	journal	May 2004

Similar Records

Inositol phosphates are assembly co-factors for HIV-1

Journal Article · Tue Jul 31 20:00:00 EDT 2018 · Nature (London) · OSTI ID:1474170

Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies

Journal Article · Tue Nov 26 23:00:00 EST 2013 · Journal of the American Chemical Society, 135(47):17793-17803 · OSTI ID:1114095

Crystal structure of an HIV assembly and maturation switch

Journal Article · Wed Jul 13 20:00:00 EDT 2016 · eLife · OSTI ID:1267471

Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation

Citation Formats

References (59)

Similar Records

Related Subjects