title: Genetic and functional diversity of human immunodeficiency virus type 1 subtype B Nef primary isolates.
abstract: We have characterized the functional integrity of seven primary Nef isolates: five from a long-term nonprogressing human immunodeficiency virus (HIV)-infected individual and one each from two patients with AIDS. One of the seven Nefs was defective for CD4 downregulation, two others were defective for PAK-2 activation, and one Nef was defective for PAK-2 activation and major histocompatibility complex (MHC) class I downregulation. Five of the Nefs were tested and found to be functional for the enhancement of virus particle infectivity. The structural basis for each of the functional defects has been analyzed by constructing a consensus nef, followed by mutational analysis of the variant amino acid residues. Mutations A29V and F193I were deleterious to CD4 downregulation and PAK-2 activation, respectively, while S189R rendered Nef defective for both MHC class I downregulation and PAK-2 activation. A search of the literature identified HIVs from five patients with Nefs predominantly mutated at F193 and from one patient with Nefs predominantly mutated at A29. A29 is highly conserved in all HIV subtypes except for subtype E. F193 is conserved in subtype B (and possibly in the closely related subtype D), but none of the other HIV group M subtypes. Our results suggest that functional distinctions may exist between HIV subtypes.
authors.affiliation: Department of Internal Medicine, Division of Infectious Diseases, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA.
authors.forename: J L
authors.initials: JL
authors.lastname: Foster
authors.forename: R P
authors.initials: RP
authors.lastname: Molina
authors.forename: T
authors.initials: T
authors.lastname: Luo
authors.forename: V K
authors.initials: VK
authors.lastname: Arora
authors.forename: Y
authors.initials: Y
authors.lastname: Huang
authors.forename: D D
authors.initials: DD
authors.lastname: Ho
authors.forename: J V
authors.initials: JV
authors.lastname: Garcia
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000821:virology; D000595:Amino Acid Sequence; D002460:Cell Line; D015693:Gene Products, nef / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015754:Genes, nef / Q000235:genetics*; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology; D020276:HIV Long-Term Survivors; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology*; D006801:Humans; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010957:Plasmids / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D014162:Transfection; D054311:nef Gene Products, Human Immunodeficiency Virus
chemical_list: D015693:Gene Products, nef; D054311:nef Gene Products, Human Immunodeficiency Virus; D017346:Protein Serine-Threonine Kinases