title: Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels.
abstract: We previously found that natural single-nucleotide variations located within a proximal region of splicing acceptor 1 (SA1prox) in the HIV-1 genome could alter the viral replication potential and mRNA expression pattern, especially the vif mRNA level. Here, we studied the virological and molecular basis of nucleotide sequence variations in SA1prox for alterations of viral replication ability. Consistent with our previous findings, variant clones indeed expressed Vif at different levels and grew distinctively in cells with various APOBEC3G expression levels. Similar effects were observed for natural variations found in HIV-2 SA1prox, suggesting the importance of the SA1prox sequence. To define nucleotides critical for the regulation of HIV-1 Vif expression, effects of natural SA1prox variations newly found in the HIV Sequence Compendium database on vif mRNA/Vif protein levels were examined. Seven out of nine variations were found to produce Vif at lower, higher, or more excessive levels than wild-type NL4-3. Combination experiments of variations giving distinct Vif levels suggested that the variations mutually affected vif transcript production. While low and high producers of Vif grew in an APOBEC3G-dependent manner, excessive expressers always showed an impeded growth phenotype due to defects in single-cycle infectivity and/or virion production levels. The phenotype of excessive expressers was not due primarily to inadequate expression of Tat or Rev, although SA1prox variations altered the overall HIV-1 mRNA expression pattern. Collectively, our results demonstrate that HIV SA1prox regulates Vif expression levels and suggest a relationship between SA1prox and viral adaptation/evolution given that variations occurred naturally.
  
  
  OBJECTIVE
  While human cells possess restriction factors to inhibit HIV-1 replication, HIV-1 encodes antagonists to overcome these barriers. Conflicts between host restriction factors and viral counterparts are critical driving forces behind mutual evolution. The interplay of cellular APOBEC3G and viral Vif proteins is a typical example. Here, we demonstrate that naturally occurring single-nucleotide variations in the proximal region of splicing acceptor 1 (SA1prox) of the HIV-1 genome frequently alter Vif expression levels, thereby modulating viral replication potential in cells with various ABOBEC3G levels. The results of the present study reveal a previously unidentified and important way for HIV-1 to compete with APOBEC3G restriction by regulating its Vif expression levels. We propose that SA1prox plays a regulatory role in Vif counteraction against APOBEC3G in order to contribute to HIV-1 replication and evolution, and this may be applicable to other primate lentiviruses.
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.
authors.forename: Masako
authors.initials: M
authors.lastname: Nomaguchi
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Doi
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Sakai
authors.affiliation: Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan.
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Ode
authors.affiliation: Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan.
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Iwatani
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Kumamoto, Japan.|International Research Center of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan.
authors.forename: Takamasa
authors.identifier: http://orcid.org/0000-0003-4852-4236
authors.initials: T
authors.lastname: Ueno
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.
authors.forename: Yui
authors.initials: Y
authors.lastname: Matsumoto
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan.
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Miyazaki
authors.affiliation: Department of Immunotherapeutics, Graduate School of Medicine and Dentistry, Tokyo Medical and Dental University, Tokyo, Japan.
authors.forename: Takao
authors.initials: T
authors.lastname: Masuda
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Tokushima, Japan adachi@tokushima-u.ac.jp.
authors.forename: Akio
authors.initials: A
authors.lastname: Adachi
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D001483:Base Sequence; D002460:Cell Line; D003062:Codon; D015967:Gene Expression Regulation, Viral; D023061:Gene Order; D016679:Genome, Viral; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide; D022821:RNA Splice Sites; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D014158:Transcription, Genetic; D014779:Virus Replication / Q000235:genetics; D054320:vif Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D003062:Codon; D022821:RNA Splice Sites; D012367:RNA, Viral; D054320:vif Gene Products, Human Immunodeficiency Virus