Reconstitution of an Infectious Human Endogenous Retrovirus

The human genome represents a fossil record of ancient retroviruses that once replicated in the ancestors of contemporary humans. Indeed, approximately 8% of human DNA is composed of sequences that are recognizably retroviral. Despite occasional reports associating human endogenous retrovirus (HERV) expression with human disease, almost all HERV genomes contain obviously inactivating mutations, and none are thought to be capable of replication. Nonetheless, one family of HERVs, namely HERV-K(HML-2), may have replicated in human ancestors less than 1 million years ago. By deriving a consensus sequence, we reconstructed a proviral clone (HERV-KCON) that likely resembles the progenitor of HERV-K(HML-2) variants that entered the human genome within the last few million years. We show that HERV-KCON Gag and protease proteins mediate efficient assembly and processing into retrovirus-like particles. Moreover, reporter genes inserted into the HERV-KCON genome and packaged into HERV-K particles are capable of infectious transfer and stable integration in a manner that requires reverse transcription. Additionally, we show that HERV-KCON Env is capable of pseudotyping HIV-1 particles and mediating entry into human and nonhuman cell lines. Furthermore, we show that HERV-KCON is resistant to inhibition by the human retrovirus restriction factors tripartite motif 5α and apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) 3G but is inhibited by APOBEC 3F. Overall, the resurrection of this extinct infectious agent in a functional form from molecular fossils should enable studies of the molecular virology and pathogenic potential of this ancient human retrovirus.

[1]  Francis Harper,et al.  Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. , 2006, Genome research.

[2]  P. Bieniasz,et al.  Comparative analysis of the antiretroviral activity of APOBEC3G and APOBEC3F from primates. , 2006, Virology.

[3]  P. Bieniasz,et al.  HIV-1 Vpu Promotes Release and Prevents Endocytosis of Nascent Retrovirus Particles from the Plasma Membrane , 2006, PLoS pathogens.

[4]  M. Emerman,et al.  Adaptive Evolution and Antiviral Activity of the Conserved Mammalian Cytidine Deaminase APOBEC3H , 2006, Journal of Virology.

[5]  S. E. Barker,et al.  Effective gene therapy with nonintegrating lentiviral vectors , 2006, Nature Medicine.

[6]  B. Cullen.  Role and Mechanism of Action of the APOBEC3 Family of Antiretroviral Resistance Factors , 2006, Journal of Virology.

[7]  T. Heidmann,et al.  Identification of a Functional Envelope Protein from the HERV-K Family of Human Endogenous Retroviruses , 2005, Journal of Virology.

[8]  David E. Swayne,et al.  Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus , 2005, Science.

[9]  Robert Belshaw,et al.  Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity , 2005, Journal of Virology.

[10]  J. Sodroski,et al.  The B30.2(SPRY) Domain of the Retroviral Restriction Factor TRIM5α Exhibits Lineage-Specific Length and Sequence Variation in Primates , 2005, Journal of Virology.

[11]  Jan Paces,et al.  High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection. , 2005, Molecular biology and evolution.

[12]  Michael Emerman,et al.  Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Neuberger,et al.  Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. , 2005, Molecular biology and evolution.

[14]  P. Bieniasz.  Intrinsic immunity: a front-line defense against viral attack , 2004, Nature Immunology.

[15]  D. Pérez-Caballero,et al.  APOBEC3G Incorporation into Human Immunodeficiency Virus Type 1 Particles , 2004, Journal of Virology.

[16]  N. Bannert,et al.  Retroelements and the human genome: New perspectives on an old relation , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  S. Nisole,et al.  A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  W. Brown,et al.  APOBEC3F Properties and Hypermutation Preferences Indicate Activity against HIV-1 In Vivo , 2004, Current Biology.

[19]  M. Malim,et al.  Cytidine Deamination of Retroviral DNA by Diverse APOBEC Proteins , 2004, Current Biology.

[20]  M. Malim,et al.  APOBEC-Mediated Editing of Viral RNA , 2004, Science.

[21]  M. Emerman,et al.  Ancient Adaptive Evolution of the Primate Antiviral DNA-Editing Enzyme APOBEC3G , 2004, PLoS biology.

[22]  J. Luban,et al.  Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 , 2004, Nature.

[23]  A. Burt,et al.  Long-term reinfection of the human genome by endogenous retroviruses. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Holmes,et al.  Unintegrated Lentivirus DNA Persistence and Accessibility to Expression in Nondividing Cells: Analysis with Class I Integrase Mutants , 2004, Journal of Virology.

[25]  C. M. Owens,et al.  The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys , 2004, Nature.

[26]  Jennifer F Hughes,et al.  Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  F. Mallet,et al.  [Retroviral inheritance in man]. , 2004, Journal de la Societe de biologie.

[28]  Hui Zhang,et al.  The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA , 2003, Nature.

[29]  Gersende Caron,et al.  Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts , 2003, Nature.

[30]  M. Malim,et al.  DNA Deamination Mediates Innate Immunity to Retroviral Infection , 2003, Cell.

[31]  F. Clavel,et al.  Hypermutation of HIV-1 DNA in the Absence of the Vif Protein , 2003, Science.

[32]  M. Malim,et al.  Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein , 2002, Nature.

[33]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[34]  J. Costas.  Characterization of the intragenomic spread of the human endogenous retrovirus family HERV-W. , 2002, Molecular biology and evolution.

[35]  K. Kidd,et al.  Insertional polymorphisms of full-length endogenous retroviruses in humans , 2001, Current Biology.

[36]  D. Derse,et al.  Examining Human T-Lymphotropic Virus Type 1 Infection and Replication by Cell-Free Infection with Recombinant Virus Vectors , 2001, Journal of Virology.

[37]  Yuntao Wu,et al.  Selective Transcription and Modulation of Resting T Cell Activity by Preintegrated HIV DNA , 2001, Science.

[38]  K. Boller,et al.  Phenotypic heterogeneity of human endogenous retrovirus particles produced by teratocarcinoma cell lines. , 2001, The Journal of general virology.

[39]  C. L. Hill,et al.  Differential Susceptibility of Retroviruses to Nucleoside Analogues , 2001, Antiviral chemistry & chemotherapy.

[40]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[41]  S. Le,et al.  The human endogenous retrovirus K Rev response element coincides with a predicted RNA folding region. , 2000, RNA.

[42]  R. Löwer,et al.  Corf, the Rev/Rex homologue of HTDV/HERV-K, encodes an arginine-rich nuclear localization signal that exerts a trans-dominant phenotype when mutated. , 2000, Virology.

[43]  Bette T. Korber,et al.  Detecting hypermutations in viral sequences with an emphasis on G A hypermutation , 2000, Bioinform..

[44]  A. Boese,et al.  A Rev‐like NES mediates cytoplasmic localization of HERV‐K cORF , 2000, FEBS letters.

[45]  B. Cullen,et al.  An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Kenneth K. Kidd,et al.  Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans , 1999, Current Biology.

[47]  B. Berkhout,et al.  Identification of an Active Reverse Transcriptase Enzyme Encoded by a Human Endogenous HERV-K Retrovirus , 1999, Journal of Virology.

[48]  T. Bhat,et al.  Functional characterization of the protease of human endogenous retrovirus, K10: can it complement HIV-1 protease? , 1998, Biochemistry.

[49]  R. Plasterk,et al.  Molecular Reconstruction of Sleeping Beauty , a Tc1-like Transposon from Fish, and Its Transposition in Human Cells , 1997, Cell.

[50]  R. Haynes,et al.  A consensus sequence for a functional human endogenous retrovirus K (HERV-K) dUTPase. , 1997, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[51]  T. Kanda,et al.  Human endogenous retrovirus K10 encodes a functional integrase , 1996, Journal of virology.

[52]  C. Limbach,et al.  HERV-K: the biologically most active human endogenous retrovirus family. , 1996, Journal of acquired immune deficiency syndromes and human retrovirology : official publication of the International Retrovirology Association.

[53]  R. Kurth,et al.  Evidence that HERV-K is the endogenous retrovirus sequence that codes for the human teratocarcinoma-derived retrovirus HTDV. , 1993, Virology.

[54]  F. Grässer,et al.  Human endogenous retroviral element K10 (HERV-K10) encodes a full-length gag homologous 73-kDa protein and a functional protease. , 1993, AIDS research and human retroviruses.

[55]  E. Hunter,et al.  A single amino acid substitution within the matrix protein of a type D retrovirus converts its morphogenesis to that of a type C retrovirus , 1990, Cell.