Identification of cellular proteins required for replication of human immunodeficiency virus type 1.

Cellular proteins are essential for human immunodeficiency virus type 1 (HIV-1) replication and may serve as viable new targets for treating infection. Using gene trap insertional mutagenesis, a high-throughput approach based on random inactivation of cellular genes, candidate genes were found that limit virus replication when mutated. Disrupted genes (N=87) conferring resistance to lytic infection with several viruses were queried for an affect on HIV-1 replication by utilizing small interfering RNA (siRNA) screens in TZM-bl cells. Several genes regulating diverse pathways were found to be required for HIV-1 replication, including DHX8, DNAJA1, GTF2E1, GTF2E2, HAP1, KALRN, UBA3, UBE2E3, and VMP1. Candidate genes were independently tested in primary human macrophages, toxicity assays, and/or Tat-dependent β-galactosidase reporter assays. Bioinformatics analyses indicated that several host factors present in this study participate in canonical pathways and functional processes implicated in prior genome-wide studies. However, the genes presented in this study did not share identity with those found previously. Novel antiviral targets identified in this study should open new avenues for mechanistic investigation.

[1]  J. Mcdougal,et al.  Binding of the human retrovirus HTLV-III/LAV/ARV/HIV to the CD4 (T4) molecule: conformation dependence, epitope mapping, antibody inhibition, and potential for idiotypic mimicry. , 1986, Journal of immunology.

[2]  J. Sodroski,et al.  Transcription directed by the HIV long terminal repeat in vitro. , 1987, AIDS research and human retroviruses.

[3]  Melchner,et al.  Identification of cellular promoters by using a retrovirus promoter trap , 1989, Journal of virology.

[4]  W. O'brien,et al.  Increased susceptibility of differentiated mononuclear phagocytes to productive infection with human immunodeficiency virus-1 (HIV-1). , 1992, The Journal of clinical investigation.

[5]  Paul E. Kennedy,et al.  HIV-1 Entry Cofactor: Functional cDNA Cloning of a Seven-Transmembrane, G Protein-Coupled Receptor , 1996, Science.

[6]  Y. Shimura,et al.  A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. , 1996, Genes & development.

[7]  Stephen C. Peiper,et al.  Identification of a major co-receptor for primary isolates of HIV-1 , 1996, Nature.

[8]  D. Reinberg,et al.  The human immunodeficiency virus transactivator Tat interacts with the RNA polymerase II holoenzyme , 1997, Molecular and cellular biology.

[9]  P. Worley,et al.  Huntingtin-associated protein 1 (HAP1) binds to a Trio-like polypeptide, with a rac1 guanine nucleotide exchange factor domain. , 1997, Human molecular genetics.

[10]  R. Gaynor,et al.  Purification of a Tat‐associated kinase reveals a TFIIH complex that modulates HIV‐1 transcription , 1997, The EMBO journal.

[11]  S. Bartz,et al.  Indicator cell lines for detection of primary strains of human and simian immunodeficiency viruses. , 1997, Virology.

[12]  H. Ruley,et al.  Functional genomics in mice by tagged sequence mutagenesis , 1997, Nature Genetics.

[13]  H. Kawasaki,et al.  A new NEDD8-ligating system for cullin-4A. , 1998, Genes & development.

[14]  A. Frankel,et al.  HIV-1: fifteen proteins and an RNA. , 1998, Annual review of biochemistry.

[15]  Involvement of TFIID and USA Components in Transcriptional Activation of the Human Immunodeficiency Virus Promoter by NF-κB and Sp1 , 1998, Molecular and Cellular Biology.

[16]  F. Kashanchi,et al.  Phosphorylation of the RAP74 subunit of TFIIF correlates with Tat-activated transcription of the HIV-1 long terminal repeat. , 2000, Virology.

[17]  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.

[18]  A. Levey,et al.  Huntingtin-associated Protein 1 Interacts with Hepatocyte Growth Factor-regulated Tyrosine Kinase Substrate and Functions in Endosomal Trafficking* , 2002, The Journal of Biological Chemistry.

[19]  R. Desrosiers,et al.  Envelope Glycoprotein Cytoplasmic Domains from Diverse Lentiviruses Interact with the Prenylated Rab Acceptor , 2002, Journal of Virology.

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

[21]  M. Foti,et al.  HIV‐1 Egress is Gated Through Late Endosomal Membranes , 2003, Traffic.

[22]  K. Jeang,et al.  A non-proteolytic role for ubiquitin in Tat-mediated transactivation of the HIV-1 promoter , 2003, Nature Cell Biology.

[23]  P. Bieniasz,et al.  Role of ESCRT-I in Retroviral Budding , 2003, Journal of Virology.

[24]  K. Wells,et al.  Mutations in the IGF-II pathway that confer resistance to lytic reovirus infection , 2004, BMC Cell Biology.

[25]  Jinsong Sheng,et al.  Discovery of mammalian genes that participate in virus infection , 2004, BMC Cell Biology.

[26]  J. Califano,et al.  Quantitative Detection of Promoter Hypermethylation of Multiple Genes in the Tumor, Urine, and Serum DNA of Patients with Renal Cancer , 2004, Cancer Research.

[27]  J. Lippincott-Schwartz,et al.  Rab9 GTPase Is Required for Replication of Human Immunodeficiency Virus Type 1, Filoviruses, and Measles Virus , 2005, Journal of Virology.

[28]  R. Roeder,et al.  TFII-I Regulates Induction of Chromosomally Integrated Human Immunodeficiency Virus Type 1 Long Terminal Repeat in Cooperation with USF , 2005, Journal of Virology.

[29]  Manish Kumar,et al.  Heat Shock Protein 40 Is Necessary for Human Immunodeficiency Virus-1 Nef-mediated Enhancement of Viral Gene Expression and Replication* , 2005, Journal of Biological Chemistry.

[30]  J. Caldwell,et al.  “UnPAKing” Human Immunodeficiency Virus (HIV) Replication: Using Small Interfering RNA Screening To Identify Novel Cofactors and Elucidate the Role of Group I PAKs in HIV Infection , 2006, Journal of Virology.

[31]  C. Chiang,et al.  The General Transcription Machinery and General Cofactors , 2006, Critical reviews in biochemistry and molecular biology.

[32]  Aaron Derdowski,et al.  The Pericentriolar Recycling Endosome Plays a Key Role in Vpu‐mediated Enhancement of HIV‐1 Particle Release , 2006, Traffic.

[33]  Amy S. Espeseth,et al.  Genome-scale RNAi screen for host factors required for HIV replication. , 2008, Cell host & microbe.

[34]  S. Ichinose,et al.  Statin-induced inhibition of HIV-1 release from latently infected U1 cells reveals a critical role for protein prenylation in HIV-1 replication. , 2008, Microbes and infection.

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

[36]  J. Lieberman,et al.  Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen , 2007, Science.

[37]  J. Murray,et al.  A critical role for CD63 in HIV replication and infection of macrophages and cell lines. , 2008, Virology.

[38]  L. Pintard,et al.  Regulation of cullin-RING E3 ubiquitin-ligases by neddylation and dimerization , 2009, Cellular and Molecular Life Sciences.

[39]  David J. Adams,et al.  The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus , 2009, Cell.

[40]  Amy S. Espeseth,et al.  Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies , 2009, PLoS pathogens.

[41]  K. Kok,et al.  siRNA and shRNA screens advance key understanding of host factors required for HIV-1 replication , 2009, Retrovirology.

[42]  Kuan-Teh Jeang,et al.  A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication* , 2009, The Journal of Biological Chemistry.

[43]  Qisheng Li,et al.  A genome-wide genetic screen for host factors required for hepatitis C virus propagation , 2009, Proceedings of the National Academy of Sciences.

[44]  G. Kukolj,et al.  Identification of a lipid kinase as a host factor involved in hepatitis C virus RNA replication. , 2009, Virology.

[45]  E. Freed,et al.  Novel approaches to inhibiting HIV-1 replication. , 2010, Antiviral research.

[46]  Nir Hacohen,et al.  Novel HIV-1 Knockdown Targets Identified by an Enriched Kinases/Phosphatases shRNA Library Using a Long-Term Iterative Screen in Jurkat T-Cells , 2010, PloS one.

[47]  H. Erfle,et al.  From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV‐1 replication , 2010, Biotechnology journal.

[48]  J. Murray,et al.  A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication , 2011, Retrovirology.

[49]  J. Snyder,et al.  Systematic Approaches towards the Development of Host-Directed Antiviral Therapeutics , 2011, International journal of molecular sciences.

[50]  Jinsong Sheng,et al.  Gene-Trap Mutagenesis Identifies Mammalian Genes Contributing to Intoxication by Clostridium perfringens ε-Toxin , 2011, PloS one.

[51]  Áine McKnight,et al.  A whole genome screen for HIV restriction factors , 2011, Retrovirology.

[52]  J. Murray,et al.  Host factors mediating HIV-1 replication. , 2011, Virus research.

[53]  K. Jeang,et al.  Insights into cellular factors that regulate HIV-1 replication in human cells. , 2011, Biochemistry.

[54]  John H. Morris,et al.  Global landscape of HIV–human protein complexes , 2011, Nature.