title: Natural variants of the HIV-1 long terminal repeat: analysis of promoters with duplicated DNA regulatory motifs.
abstract: Sequence variation in the long terminal repeat (LTR) region of HIV-1 was analyzed in viral isolates of 17 infected individuals. Two classes of LTR size variants were found. One HIV-1 variant was detected containing an additional binding site for the transcription factor Sp1. Another LTR size variation was observed in four patients in a region just upstream of the NF-kappa B enhancer. This variation was the result of a duplication of a short DNA sequence (CTG-motif). Cell culture experiments demonstrated that the natural variant with four Sp1 sites had a slightly higher promoter activity and viral replication rate than the isogenic control LTR with three Sp1 sites. No positive effect of the duplicated CTG-motif could be detected. In order to measure small differences in virus production more accurately, equal amounts of a size variant and the wild-type plasmid were cotransfected into T-cells. The virus with four Sp1 sites did outgrow the three Sp1 virus in 35 days of culture and CTG-monomer virus outcompeted the CTG-dimer virus in 42 days. Based on these results we estimate a 5-10% difference in virus production of the LTR variants when compared to that of wild-type.
authors.affiliation: Department of Virology, University of Amsterdam, The Netherlands.
authors.forename: S E
authors.initials: SE
authors.lastname: Koken
authors.forename: J L
authors.initials: JL
authors.lastname: van Wamel
authors.forename: J
authors.initials: J
authors.lastname: Goudsmit
authors.forename: B
authors.initials: B
authors.lastname: Berkhout
authors.forename: J L
authors.initials: JL
authors.lastname: Geelen
mesh_terms: D001483:Base Sequence; D014644:Genetic Variation; D015658:HIV Infections / Q000235:genetics*; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000254:growth & development; D006801:Humans; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment; D016329:Sp1 Transcription Factor / Q000235:genetics; D013601:T-Lymphocytes / Q000382:microbiology; D014162:Transfection
chemical_list: D016328:NF-kappa B; D016329:Sp1 Transcription Factor