Integrase Interacts with Nucleoporin NUP153 To Mediate the Nuclear Import of Human Immunodeficiency Virus Type 1

ABSTRACT The ability to traverse an intact nuclear envelope and productively infect nondividing cells is a salient feature of human immunodeficiency virus type 1 (HIV-1) and other lentiviruses, but the viral factors and mechanism of nuclear entry have not been defined. HIV-1 integrase (IN) is implicated to play a role in the nuclear import of the virus, but the cellular pathway for IN trafficking and the role of IN in mediating the nuclear import of viral particles are unknown. Using a semipermeabilized cell assay, we observed that the nuclear import of IN was not the result of passive diffusion but occurred independently of cytosolic factors, metabolic energy, and the classical receptor-mediated, Ran-dependent import pathways. To determine if IN enters the nucleus by interacting with the nucleopore complex (NPC), we found that IN bound directly with the FxFG-rich C-terminal domain of nucleoporin 153 (NUP153C). When added in excess to the import assay, NUP153C inhibited the nuclear import of IN. Known binding partners of NUP153C competed with IN for binding with NUP153 and also inhibited the nuclear import of IN. In cultured cells, overexpression of NUP153C reduced the infectivity of an HIV-derived vector by interfering with the nuclear translocation of the viral cDNA. These results support a functional role for the IN-NUP153 interaction in HIV-1 replication and suggest that HIV-1 subviral particles gain access to the nucleus by interacting directly with the NPC via the binding of particle-associated IN to NUP153C.

[1]  E. De Clercq,et al.  Nuclear localization of human immunodeficiency virus type 1 integrase expressed as a fusion protein with green fluorescent protein. , 1999, Virology.

[2]  C. Barbas,et al.  Fusion Proteins Consisting of Human Immunodeficiency Virus Type 1 Integrase and the Designed Polydactyl Zinc Finger Protein E2C Direct Integration of Viral DNA into Specific Sites , 2004, Journal of Virology.

[3]  M. Moore,et al.  Getting across the nuclear pore complex. , 1999, Trends in cell biology.

[4]  C. Shin,et al.  Role of the Nonspecific DNA-binding Region and α Helices within the Core Domain of Retroviral Integrase in Selecting Target DNA Sites for Integration* , 2001, The Journal of Biological Chemistry.

[5]  M. Malim,et al.  Reassessment of the Roles of Integrase and the Central DNA Flap in Human Immunodeficiency Virus Type 1 Nuclear Import , 2002, Journal of Virology.

[6]  F. Melchior,et al.  GTP hydrolysis by Ran occurs at the nuclear pore complex in an early step of protein import , 1995, The Journal of cell biology.

[7]  E. Kiseleva,et al.  The nuclear pore complex: structure, function, and dynamics. , 2000, Critical reviews in eukaryotic gene expression.

[8]  G. Lipowsky,et al.  NTF2 mediates nuclear import of Ran , 1998, The EMBO journal.

[9]  E. Nanak Metal affinity electrophoresis: An analytical tool , 1992 .

[10]  E. Griffis,et al.  Distinct functional domains within nucleoporins Nup153 and Nup98 mediate transcription-dependent mobility. , 2004, Molecular biology of the cell.

[11]  M S Lewis,et al.  Zn2+ promotes the self-association of human immunodeficiency virus type-1 integrase in vitro. , 1997, Biochemistry.

[12]  R. Craigie,et al.  Virology: HIV goes nuclear , 2006, Nature.

[13]  R. König,et al.  Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication , 2008, Cell.

[14]  M. Llano,et al.  LEDGF/p75 Determines Cellular Trafficking of Diverse Lentiviral but Not Murine Oncoretroviral Integrase Proteins and Is a Component of Functional Lentiviral Preintegration Complexes , 2004, Journal of Virology.

[15]  K. Ullman,et al.  The RNA binding domain within the nucleoporin Nup153 associates preferentially with single-stranded RNA. , 2004, RNA.

[16]  G. Blobel,et al.  Carrier-independent Nuclear Import of the Transcription Factor PU.1 via RanGTP-stimulated Binding to Nup153* , 2005, Journal of Biological Chemistry.

[17]  M. Emerman,et al.  The Cell Cycle Independence of HIV Infections Is Not Determined by Known Karyophilic Viral Elements , 2005, PLoS pathogens.

[18]  Maria Vanegas,et al.  Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering , 2005, Journal of Cell Science.

[19]  C. Pauza,et al.  Persistent human immunodeficiency virus type 1 infection of monoblastoid cells leads to accumulation of self-integrated viral DNA and to production of defective virions , 1989, Journal of virology.

[20]  A. Engelman,et al.  Class II Integrase Mutants with Changes in Putative Nuclear Localization Signals Are Primarily Blocked at a Postnuclear Entry Step of Human Immunodeficiency Virus Type 1 Replication , 2004, Journal of Virology.

[21]  Wulin Teo,et al.  An Essential Role for LEDGF/p75 in HIV Integration , 2006, Science.

[22]  S. A. Chow,et al.  Central Core Domain of Retroviral Integrase Is Responsible for Target Site Selection* , 1997, The Journal of Biological Chemistry.

[23]  U. Aebi,et al.  Nanomechanical Basis of Selective Gating by the Nuclear Pore Complex , 2007, Science.

[24]  C. Woodward,et al.  Subcellular Localization of Feline Immunodeficiency Virus Integrase and Mapping of Its Karyophilic Determinant , 2003, Journal of Virology.

[25]  Pamela A. Silver,et al.  Genome-Wide Localization of the Nuclear Transport Machinery Couples Transcriptional Status and Nuclear Organization , 2004, Cell.

[26]  A. Fassati,et al.  Nuclear Import of Viral DNA Genomes , 2003, Traffic.

[27]  C. Depienne,et al.  Characterization of the Nuclear Import Pathway for HIV-1 Integrase* , 2001, The Journal of Biological Chemistry.

[28]  H. Göttlinger,et al.  Lack of integrase can markedly affect human immunodeficiency virus type 1 particle production in the presence of an active viral protease , 1996, Journal of virology.

[29]  Zeger Debyser,et al.  HIV-1 Integrase Forms Stable Tetramers and Associates with LEDGF/p75 Protein in Human Cells* , 2003, The Journal of Biological Chemistry.

[30]  F. Bushman,et al.  Identification of discrete functional domains of HIV‐1 integrase and their organization within an active multimeric complex. , 1993, The EMBO journal.

[31]  E. De Clercq,et al.  LEDGF/p75 Is Essential for Nuclear and Chromosomal Targeting of HIV-1 Integrase in Human Cells* , 2003, Journal of Biological Chemistry.

[32]  U. Aebi,et al.  Domain-specific antibodies reveal multiple-site topology of Nup153 within the nuclear pore complex. , 2002, Journal of structural biology.

[33]  S. Adam,et al.  Nuclear protein import using digitonin-permeabilized cells. , 1992, Methods in enzymology.

[34]  K. Ullman,et al.  Versatility at the nuclear pore complex: lessons learned from the nucleoporin Nup153 , 2005, Chromosoma.

[35]  J. Church Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen , 2008, Pediatrics.

[36]  B. Fahrenkrog,et al.  Changes in nucleoporin domain topology in response to chemical effectors. , 2006, Journal of molecular biology.

[37]  Sarah Ng,et al.  The functionally conserved nucleoporins Nup124p from fission yeast and the human Nup153 mediate nuclear import and activity of the Tf1 retrotransposon and HIV-1 Vpr. , 2005, Molecular biology of the cell.

[38]  R. Reed,et al.  Splicing promotes rapid and efficient mRNA export in mammalian cells , 2008, Proceedings of the National Academy of Sciences.

[39]  Paul Shinn,et al.  A role for LEDGF/p75 in targeting HIV DNA integration , 2005, Nature Medicine.

[40]  I. Chen,et al.  Envelope Gene of the Human Endogenous Retrovirus HERV-W Encodes a Functional Retrovirus Envelope , 2001, Journal of Virology.

[41]  Andreas Marg,et al.  Nucleocytoplasmic shuttling by nucleoporins Nup153 and Nup214 and CRM1-dependent nuclear export control the subcellular distribution of latent Stat1 , 2004, The Journal of cell biology.

[42]  D. Görlich,et al.  A Saturated FG-Repeat Hydrogel Can Reproduce the Permeability Properties of Nuclear Pore Complexes , 2007, Cell.

[43]  K. Ullman,et al.  Sequence Preference in RNA Recognition by the Nucleoporin Nup153* , 2007, Journal of Biological Chemistry.

[44]  L. Gerace,et al.  Gradient of Increasing Affinity of Importin β for Nucleoporins along the Pathway of Nuclear Import , 2001, The Journal of cell biology.

[45]  M. Emerman,et al.  Evidence for Direct Involvement of the Capsid Protein in HIV Infection of Nondividing Cells , 2007, PLoS pathogens.

[46]  M. Bukrinsky,et al.  Association of integrase, matrix, and reverse transcriptase antigens of human immunodeficiency virus type 1 with viral nucleic acids following acute infection. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Kui Gao,et al.  Human immunodeficiency virus type 1 integrase: arrangement of protein domains in active cDNA complexes , 2001, The EMBO journal.

[48]  P. Tauc,et al.  Oligomeric states of the HIV-1 integrase as measured by time-resolved fluorescence anisotropy. , 2000, Biochemistry.

[49]  A. Engelman,et al.  Wild-Type Levels of Nuclear Localization and Human Immunodeficiency Virus Type 1 Replication in the Absence of the Central DNA Flap , 2002, Journal of Virology.

[50]  D. Newmeyer,et al.  Inhibition of in vitro nuclear transport by a lectin that binds to nuclear pores , 1987, The Journal of cell biology.

[51]  Elena Conti,et al.  Structural biology of nucleocytoplasmic transport. , 2007, Annual review of biochemistry.

[52]  Youichi Suzuki,et al.  The road to chromatin — nuclear entry of retroviruses , 2007, Nature Reviews Microbiology.

[53]  Zeger Debyser,et al.  Transportin-SR2 Imports HIV into the Nucleus , 2008, Current Biology.

[54]  M. Malim,et al.  HIV-1 infection requires a functional integrase NLS. , 2001, Molecular cell.

[55]  Jan Ellenberg,et al.  Nuclear pore complexes form immobile networks and have a very low turnover in live mammalian cells , 2001, The Journal of cell biology.

[56]  S. Guadagnini,et al.  HIV‐1 DNA Flap formation promotes uncoating of the pre‐integration complex at the nuclear pore , 2007, The EMBO journal.

[57]  D. Forbes,et al.  Separate nuclear import pathways converge on the nucleoporin Nup153 and can be dissected with dominant-negative inhibitors , 1998, Current Biology.

[58]  Ariberto Fassati,et al.  HIV infection of non-dividing cells: a divisive problem , 2006, Retrovirology.

[59]  A. Engelman,et al.  LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. , 2007, Genes & development.

[60]  G. Blobel,et al.  Nuclear protein import: Ran-GTP dissociates the karyopherin alphabeta heterodimer by displacing alpha from an overlapping binding site on beta. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[61]  H. Schuitemaker,et al.  Phenotype of HIV-1 lacking a functional nuclear localization signal in matrix protein of gag and Vpr is comparable to wild-type HIV-1 in primary macrophages. , 1999, Virology.

[62]  B. Burke,et al.  Targeting and function in mRNA export of nuclear pore complex protein Nup153 , 1996, The Journal of cell biology.

[63]  T. Ho,et al.  The mechanism of inhibition of Ran-dependent nuclear transport by cellular ATP depletion , 2002, The Journal of cell biology.

[64]  N. Yamamoto,et al.  Nuclear Import of the Preintegration Complex Is Blocked upon Infection by Human Immunodeficiency Virus Type 1 in Mouse Cells , 2006, Journal of Virology.

[65]  E. Wagner,et al.  Nuclear import of the stem-loop binding protein and localization during the cell cycle. , 2005, Molecular biology of the cell.

[66]  Frederic D. Bushman,et al.  A quantitative assay for HIV DNA integration in vivo , 2001, Nature Medicine.

[67]  K. Luby-Phelps,et al.  ERK2 enters the nucleus by a carrier-independent mechanism , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[68]  A. Skalka,et al.  Effects of cell cycle status on early events in retroviral replication , 2005, Journal of cellular biochemistry.

[69]  D. Jans,et al.  HIV-1 integrase is capable of targeting DNA to the nucleus via an Importin α/β-dependent mechanism , 2006 .

[70]  Myriam Witvrouw,et al.  Integrase Mutants Defective for Interaction with LEDGF/p75 Are Impaired in Chromosome Tethering and HIV-1 Replication* , 2005, Journal of Biological Chemistry.

[71]  F. Quiocho,et al.  Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2. , 2004, Journal of molecular biology.

[72]  W. Fischer,et al.  Novel vertebrate nucleoporins Nup133 and Nup160 play a role in mRNA export , 2001, The Journal of cell biology.

[73]  Ian F. Harrison,et al.  Nuclear import of HIV‐1 intracellular reverse transcription complexes is mediated by importin 7 , 2003, The EMBO journal.

[74]  J. Kappes,et al.  Human Immunodeficiency Virus Type 1 Integrase Protein Promotes Reverse Transcription through Specific Interactions with the Nucleoprotein Reverse Transcription Complex , 1999, Journal of Virology.

[75]  G. Blobel,et al.  Protein import into nuclei: association and dissociation reactions involving transport substrate, transport factors, and nucleoporins , 1995, Cell.

[76]  C. Dauguet,et al.  Extensive regions of pol are required for efficient human immunodeficiency virus polyprotein processing and particle maturation. , 1996, Virology.

[77]  Michael Emerman,et al.  Retroviral infection of non-dividing cells: old and new perspectives. , 2006, Virology.

[78]  B. Paschal,et al.  Identification of NTF2, a cytosolic factor for nuclear import that interacts with nuclear pore complex protein p62 , 1995, The Journal of cell biology.

[79]  J. Massagué,et al.  Smad2 nucleocytoplasmic shuttling by nucleoporins CAN/Nup214 and Nup153 feeds TGFbeta signaling complexes in the cytoplasm and nucleus. , 2002, Molecular cell.

[80]  J. Köser,et al.  Nucleoporin domain topology is linked to the transport status of the nuclear pore complex. , 2005, Journal of molecular biology.

[81]  G. Dreyfuss,et al.  Nup153 is an M9‐containing mobile nucleoporin with a novel Ran‐binding domain , 1999, The EMBO journal.

[82]  D. Jans,et al.  HIV-1 integrase is capable of targeting DNA to the nucleus via an importin alpha/beta-dependent mechanism. , 2006, The Biochemical journal.

[83]  C. Aiken,et al.  Evidence for a Functional Link between Uncoating of the Human Immunodeficiency Virus Type 1 Core and Nuclear Import of the Viral Preintegration Complex , 2006, Journal of Virology.

[84]  C. Barbas,et al.  Human Immunodeficiency Virus Type 1 Incorporated with Fusion Proteins Consisting of Integrase and the Designed Polydactyl Zinc Finger Protein E2C Can Bias Integration of Viral DNA into a Predetermined Chromosomal Region in Human Cells , 2006, Journal of Virology.

[85]  G. Blobel,et al.  The two steps of nuclear import, targeting to the nuclear envelope and translocation through the nuclear pore, require different cytosolic factors , 1992, Cell.

[86]  Takeshi Yoshida,et al.  Role of Nup98 in nuclear entry of human immunodeficiency virus type 1 cDNA. , 2004, Microbes and infection.

[87]  C. Depienne,et al.  Cellular distribution and karyophilic properties of matrix, integrase, and Vpr proteins from the human and simian immunodeficiency viruses. , 2000, Experimental cell research.

[88]  M. Willingham,et al.  Nuclear protein import: specificity for transport across the nuclear pore. , 1988, Experimental cell research.

[89]  A. Graessmann,et al.  A synthetic peptide bearing the HIV-1 integrase 161-173 amino acid residues mediates active nuclear import and binding to importin alpha: characterization of a functional nuclear localization signal. , 2004, Journal of molecular biology.

[90]  L. Gerace,et al.  Nuclear pore complexes: dynamics in unexpected places , 2001, The Journal of cell biology.

[91]  T. Masuda,et al.  Evaluation of the Functional Involvement of Human Immunodeficiency Virus Type 1 Integrase in Nuclear Import of Viral cDNA during Acute Infection , 2004, Journal of Virology.

[92]  D. Clapham,et al.  Real-time imaging of nuclear permeation by EGFP in single intact cells. , 2003, Biophysical journal.

[93]  F. Bushman,et al.  Human Immunodeficiency Virus cDNA Metabolism: Notable Stability of Two-Long Terminal Repeat Circles , 2002, Journal of Virology.

[94]  D. Görlich,et al.  The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion , 2002, The EMBO journal.

[95]  M. Emerman,et al.  HIV-1 infection of non-dividing cells , 1994, Nature.

[96]  S. Gasser,et al.  The nuclear envelope and transcriptional control , 2007, Nature Reviews Genetics.

[97]  R. Peters Translocation Through the Nuclear Pore Complex: Selectivity and Speed by Reduction‐of‐Dimensionality , 2005, Traffic.

[98]  S. A. Chow,et al.  Requirement for Integrase during Reverse Transcription of Human Immunodeficiency Virus Type 1 and the Effect of Cysteine Mutations of Integrase on Its Interactions with Reverse Transcriptase , 2004, Journal of Virology.

[99]  T. Masuda,et al.  Identification of Critical Amino Acid Residues in Human Immunodeficiency Virus Type 1 IN Required for Efficient Proviral DNA Formation at Steps prior to Integration in Dividing and Nondividing Cells , 2000, Journal of virology.

[100]  M. Lai,et al.  A Human Importin-β Family Protein, Transportin-SR2, Interacts with the Phosphorylated RS Domain of SR Proteins* , 2000, The Journal of Biological Chemistry.

[101]  M. Emerman,et al.  Capsid Is a Dominant Determinant of Retrovirus Infectivity in Nondividing Cells , 2004, Journal of Virology.

[102]  I. Macara Transport into and out of the Nucleus , 2001, Microbiology and Molecular Biology Reviews.

[103]  M. Fornerod,et al.  Nuclear import in viral infections. , 2005, Current topics in microbiology and immunology.

[104]  M. Fornerod,et al.  Import of adenovirus DNA involves the nuclear pore complex receptor CAN/Nup214 and histone H1 , 2001, Nature Cell Biology.

[105]  W. Greene,et al.  Slipping through the door: HIV entry into the nucleus. , 2002, Microbes and infection.

[106]  Richard Bayliss,et al.  Structural Basis for the Interaction between FxFG Nucleoporin Repeats and Importin-β in Nuclear Trafficking , 2000, Cell.