title: Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding.
abstract: Retroviruses favor target-DNA (tDNA) distortion and particular bases at sites of integration, but the mechanism underlying HIV-1 selectivity is unknown. Crystal structures revealed a network of prototype foamy virus (PFV) integrase residues that distort tDNA: Ala188 and Arg329 interact with tDNA bases, while Arg362 contacts the phosphodiester backbone. HIV-1 integrase residues Ser119, Arg231, and Lys258 were identified here as analogs of PFV integrase residues Ala188, Arg329 and Arg362, respectively. Thirteen integrase mutations were analyzed for effects on integrase activity in vitro and during virus infection, yielding a total of 1610 unique HIV-1 integration sites. Purine (R)/pyrimidine (Y) dinucleotide sequence analysis revealed HIV-1 prefers the tDNA signature (0)RYXRY(4), which accordingly favors overlapping flexible dinucleotides at the center of the integration site. Consistent with roles for Arg231 and Lys258 in sequence specific and non-specific binding, respectively, the R231E mutation altered integration site nucleotide preferences while K258E had no effect. S119A and S119T integrase mutations significantly altered base preferences at positions -3 and 7 from the site of viral DNA joining. The S119A preference moreover mimicked wild-type PFV selectivity at these positions. We conclude that HIV-1 IN residue Ser119 and PFV IN residue Ala188 contact analogous tDNA bases to effect virus integration.
authors: Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA, Division of Infectious Diseases, Imperial College London, St-Mary's Campus, Norfolk Place, London W2 1PG, UK and Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire EN6 3LD, UK.
authors: Erik
authors: E
authors: Serrao
authors: Lavanya
authors: L
authors: Krishnan
authors: Ming-Chieh
authors: MC
authors: Shun
authors: Xiang
authors: X
authors: Li
authors: Peter
authors: P
authors: Cherepanov
authors: Alan
authors: A
authors: Engelman
authors: Goedele N
authors: GN
authors: Maertens
mesh_terms: D000595:Amino Acid Sequence; D002460:Cell Line; D004247:DNA / Q000737:chemistry*; D019427:HIV Integrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015497:HIV-1 / Q000235:genetics*; D019426:Integrases / Q000737:chemistry / Q000378:metabolism; D009154:Mutation; D009711:Nucleotides / Q000032:analysis; D011485:Protein Binding; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D016092:Spumavirus / Q000201:enzymology; D016662:Virus Integration
chemical_list: D009711:Nucleotides; D004247:DNA; D019427:HIV Integrase; D019426:Integrases; C514801:p31 integrase protein, Human immunodeficiency virus 1