HIV-1 nucleocapsid and ESCRT-component Tsg101 interplay prevents HIV from turning into a DNA-containing virus

HIV-1, the agent of the AIDS pandemic, is an RNA virus that reverse transcribes its RNA genome (gRNA) into DNA, shortly after its entry into cells. Within cells, retroviral assembly requires thousands of structural Gag proteins and two copies of gRNA as well as cellular factors, which converge to the plasma membrane in a finely regulated timeline. In this process, the nucleocapsid domain of Gag (GagNC) ensures gRNA selection and packaging into virions. Subsequent budding and virus release require the recruitment of the cellular ESCRT machinery. Interestingly, mutating GagNC results into the release of DNA-containing viruses, by promo-ting reverse transcription (RTion) prior to virus release, through an unknown mechanism. Therefore, we explored the biogenesis of these DNA-containing particles, combining live-cell total internal-reflection fluorescent microscopy, electron microscopy, trans-complementation assays and biochemical characterization of viral particles. Our results reveal that DNA virus production is the consequence of budding defects associated with Gag aggregation at the plasma membrane and deficiency in the recruitment of Tsg101, a key ESCRT-I component. Indeed, targeting Tsg101 to virus assembly sites restores budding, restricts RTion and favors RNA packaging into viruses. Altogether, our results highlight the role of GagNC in the spatiotemporal control of RTion, via an ESCRT-I-dependent mechanism.

[1]  Nathan H. Roy,et al.  HIV‐1 Assembly Differentially Alters Dynamics and Partitioning of Tetraspanins and Raft Components , 2010, Traffic.

[2]  Kunio Nagashima,et al.  The Nucleocapsid Region of HIV-1 Gag Cooperates with the PTAP and LYPXnL Late Domains to Recruit the Cellular Machinery Necessary for Viral Budding , 2009, PLoS pathogens.

[3]  D. Ott,et al.  The Nucleocapsid Region of Human Immunodeficiency Virus Type 1 Gag Assists in the Coordination of Assembly and Gag Processing: Role for RNA-Gag Binding in the Early Stages of Assembly , 2009, Journal of Virology.

[4]  W. Mothes,et al.  Assembly of the Murine Leukemia Virus Is Directed towards Sites of Cell–Cell Contact , 2009, PLoS biology.

[5]  Michael Emerman,et al.  HIV-1 accessory proteins--ensuring viral survival in a hostile environment. , 2008, Cell host & microbe.

[6]  C. Péchoux,et al.  Intracellular HIV-1 Gag localization is impaired by mutations in the nucleocapsid zinc fingers , 2007, Retrovirology.

[7]  D. Pérez-Caballero,et al.  Divergent retroviral late-budding domains recruit vacuolar protein sorting factors by using alternative adaptor proteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Kaplan,et al.  The activity of the protease of human immunodeficiency virus type 1 is initiated at the membrane of infected cells before the release of viral proteins and is required for release to occur with maximum efficiency , 1994, Journal of virology.

[9]  J. Darlix,et al.  The conserved N-terminal basic residues and zinc-finger motifs of HIV-1 nucleocapsid restrict the viral cDNA synthesis during virus formation and maturation , 2008, Nucleic acids research.

[10]  R. Gorelick,et al.  Vif is a RNA chaperone that could temporally regulate RNA dimerization and the early steps of HIV-1 reverse transcription , 2007, Nucleic acids research.

[11]  J. Darlix,et al.  When is it time for reverse transcription to start and go? , 2009, Retrovirology.

[12]  T. Hope,et al.  Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription , 2011, Proceedings of the National Academy of Sciences.

[13]  Michio Inoue,et al.  Human Immunodeficiency Virus Type 1 Gag Engages the Bro1 Domain of ALIX/AIP1 through the Nucleocapsid , 2007, Journal of Virology.

[14]  Bing Yu,et al.  MoMuLV and HIV-1 Nucleocapsid Proteins Have a Common Role in Genomic RNA Packaging but Different in Late Reverse Transcription , 2012, PloS one.

[15]  M. Mougel,et al.  Fully-spliced HIV-1 RNAs are reverse transcribed with similar efficiencies as the genomic RNA in virions and cells, but more efficiently in AZT-treated cells , 2007, Retrovirology.

[16]  T. Chang,et al.  Identification and characterization of human immunodeficiency virus type 1 gag-pol fusion protein in transfected mammalian cells , 1991, Journal of virology.

[17]  Roland Marquet,et al.  Dimerization of retroviral RNA genomes: an inseparable pair , 2004, Nature Reviews Microbiology.

[18]  K. Musier-Forsyth,et al.  Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription , 2010, RNA biology.

[19]  A. Saïb,et al.  Early Reverse Transcription Is Essential for Productive Foamy Virus Infection , 2010, PloS one.

[20]  W. Sundquist,et al.  The Protein Network of HIV Budding , 2003, Cell.

[21]  P. Bieniasz,et al.  HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress , 2001, Nature Medicine.

[22]  W. Weissenhorn,et al.  Essential ingredients for HIV-1 budding. , 2011, Cell host & microbe.

[23]  E. Freed,et al.  HIV type 1 Gag as a target for antiviral therapy. , 2012, AIDS research and human retroviruses.

[24]  Neil M. Bell,et al.  HIV Gag polyprotein: processing and early viral particle assembly. , 2013, Trends in microbiology.

[25]  A. Calistri,et al.  AIP1/ALIX Is a Binding Partner for HIV-1 p6 and EIAV p9 Functioning in Virus Budding , 2003, Cell.

[26]  J. Briggs,et al.  Structural Analysis of HIV-1 Maturation Using Cryo-Electron Tomography , 2010, PLoS pathogens.

[27]  S. Goff,et al.  The role of Gag in human immunodeficiency virus type 1 virion morphogenesis and early steps of the viral life cycle , 1996, Journal of virology.

[28]  A. Kaplan,et al.  Human immunodeficiency virus type 1 Gag proteins are processed in two cellular compartments. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[29]  M. Gullberg,et al.  Duolink-[ldquo]In-cell Co-IP[rdquo] for visualization of protein interactions in situ , 2011 .

[30]  H. Varmus,et al.  Characterization of ribosomal frameshifting in HIV-1 gag-pol expression , 1988, Nature.

[31]  Antony K. Chen,et al.  MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production , 2014, Proceedings of the National Academy of Sciences.

[32]  S. Neil,et al.  Host factors involved in retroviral budding and release , 2011, Nature Reviews Microbiology.

[33]  S. Breuer,et al.  Identification of HIV-1 inhibitors targeting the nucleocapsid protein. , 2012, Journal of medicinal chemistry.

[34]  E. Freed,et al.  p6Gag is required for particle production from full-length human immunodeficiency virus type 1 molecular clones expressing protease , 1995, Journal of virology.

[35]  J. Darlix,et al.  Flexible nature and specific functions of the HIV-1 nucleocapsid protein. , 2011, Journal of molecular biology.

[36]  R. Gorelick,et al.  Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein and Gag or Gag-derived proteins: biological implications. , 2010, Virology.

[37]  T. Spicer,et al.  Reverse transcription takes place within extracellular HIV-1 virions: potential biological significance. , 1993, AIDS research and human retroviruses.

[38]  R. Gorelick,et al.  Mutations in Human Immunodeficiency Virus Type 1 Nucleocapsid Protein Zinc Fingers Cause Premature Reverse Transcription , 2008, Journal of Virology.

[39]  J. Darlix,et al.  Nucleocapsid mutations turn HIV-1 into a DNA-containing virus , 2008, Nucleic acids research.

[40]  O. Bagasra,et al.  Intravirion reverse transcripts in the peripheral blood plasma on human immunodeficiency virus type 1-infected individuals , 1994, Journal of virology.

[41]  Sanford M. Simon,et al.  Imaging the biogenesis of individual HIV-1 virions in live cells , 2008, Nature.

[42]  Marc C. Johnson,et al.  Plasma Membrane Is the Site of Productive HIV-1 Particle Assembly , 2006, PLoS biology.

[43]  V. Dussupt,et al.  Identification of the HIV-1 NC Binding Interface in Alix Bro1 Reveals a Role for RNA , 2012, Journal of Virology.

[44]  Wesley I. Sundquist,et al.  Functional Surfaces of the Human Immunodeficiency Virus Type 1 Capsid Protein , 2003, Journal of Virology.

[45]  J. Gatell,et al.  A protein ballet around the viral genome orchestrated by HIV-1 reverse transcriptase leads to an architectural switch: from nucleocapsid-condensed RNA to Vpr-bridged DNA. , 2013, Virus research.

[46]  C. Tisné,et al.  Initiation of HIV-1 reverse transcription and functional role of nucleocapsid-mediated tRNA/viral genome interactions. , 2012, Virus research.

[47]  Michio Inoue,et al.  Human Immunodeficiency Virus Type 1 Gag Engages the Bro 1 Domain of ALIX / AIP 1 through the Nucleocapsid , 2008 .

[48]  W. Sundquist,et al.  Virus budding and the ESCRT pathway. , 2013, Cell host & microbe.

[49]  K. Tamura,et al.  Metabolic engineering of plant alkaloid biosynthesis. Proc Natl Acad Sci U S A , 2001 .

[50]  Kenneth A. Taylor,et al.  Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Katarzyna J Purzycka,et al.  A cis-acting element in retroviral genomic RNA links Gag-Pol ribosomal frameshifting to selective viral RNA encapsidation. , 2013, Cell host & microbe.

[52]  Karl Rohr,et al.  Dynamics of HIV-1 Assembly and Release , 2009, PLoS pathogens.

[53]  Y. Mély,et al.  Dynamics of Linker Residues Modulate the Nucleic Acid Binding Properties of the HIV-1 Nucleocapsid Protein Zinc Fingers , 2014, PloS one.

[54]  O. Nikolaitchik,et al.  Deciphering the Role of the Gag-Pol Ribosomal Frameshift Signal in HIV-1 RNA Genome Packaging , 2014, Journal of Virology.

[55]  W. Sundquist,et al.  The Human Endosomal Sorting Complex Required for Transport (ESCRT-I) and Its Role in HIV-1 Budding*♦ , 2004, Journal of Biological Chemistry.

[56]  C. Bräuchle,et al.  Live-cell visualization of dynamics of HIV budding site interactions with an ESCRT component , 2011, Nature Cell Biology.

[57]  L. Verplank,et al.  Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, binds the L domain in HIV type 1 Pr55Gag , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[58]  J. Briggs,et al.  Structural organization of authentic, mature HIV‐1 virions and cores , 2003, The EMBO journal.

[59]  K. Nagashima,et al.  Overexpression of the HIV-1 gag-pol polyprotein results in intracellular activation of HIV-1 protease and inhibition of assembly and budding of virus-like particles. , 1993, Virology.

[60]  S. Cohen,et al.  Tsg101 Control of Human Immunodeficiency Virus Type 1 Gag Trafficking and Release , 2003, Journal of Virology.

[61]  Prabuddha Sengupta,et al.  Distribution of ESCRT Machinery at HIV Assembly Sites Reveals Virus Scaffolding of ESCRT Subunits , 2014, Science.

[62]  M. Wainberg,et al.  The Role of Pr55gag in the Annealing of tRNA3Lys to Human Immunodeficiency Virus Type 1 Genomic RNA , 1999, Journal of Virology.

[63]  Michelle S Itano,et al.  Temporal and spatial organization of ESCRT protein recruitment during HIV-1 budding , 2014, Proceedings of the National Academy of Sciences.

[64]  C. Cheng‐Mayer,et al.  Human Immunodeficiency Virus Type 1 Nucleocapsid Inhibitors Impede trans Infection in Cellular and Explant Models and Protect Nonhuman Primates from Infection , 2009, Journal of Virology.

[65]  Wesley I. Sundquist,et al.  Tsg101 and the Vacuolar Protein Sorting Pathway Are Essential for HIV-1 Budding , 2001, Cell.

[66]  Marc C. Johnson,et al.  The stoichiometry of Gag protein in HIV-1 , 2004, Nature Structural &Molecular Biology.

[67]  K. Nagashima,et al.  Budding of Retroviruses Utilizing Divergent L Domains Requires Nucleocapsid , 2012, Journal of Virology.

[68]  K. Nagashima,et al.  Roles Played by Capsid-Dependent Induction of Membrane Curvature and Gag-ESCRT Interactions in Tetherin Recruitment to HIV-1 Assembly Sites , 2013, Journal of Virology.

[69]  L. Arthur,et al.  The two zinc fingers in the human immunodeficiency virus type 1 nucleocapsid protein are not functionally equivalent , 1993, Journal of virology.

[70]  R. Pomerantz,et al.  Endogenous reverse transcription of human immunodeficiency virus type 1 in physiological microenviroments: an important stage for viral infection of nondividing cells , 1996, Journal of virology.

[71]  P. Prevelige,et al.  Kinetic Analysis of the Role of Intersubunit Interactions in Human Immunodeficiency Virus Type 1 Capsid Protein Assembly In Vitro , 2002, Journal of Virology.

[72]  J. Renaud,et al.  The ESCRT-0 Component HRS is Required for HIV-1 Vpu-Mediated BST-2/Tetherin Down-Regulation , 2011, PLoS pathogens.

[73]  K. Nagashima,et al.  Functional role of Alix in HIV-1 replication. , 2009, Virology.

[74]  M. Piechaczyk,et al.  Effects of virion surface gp120 density on infection by HIV-1 and viral production by infected cells. , 2005, Virology.

[75]  P. Bieniasz The cell biology of HIV-1 virion genesis. , 2009, Cell host & microbe.

[76]  P. Bieniasz,et al.  Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu , 2008, Nature.