Systemic biological analysis of the mutations in two distinct HIV-1mt genomes occurred during replication in macaque cells

Nomaguchi, Masako; Doi, Naoya; Fujiwara, Sachi; Saito, Akatsuki; Akari, Hirofumi; Nakayama, Emi E.; Shioda, Tatsuo; Yokoyama, Masahiro; Sato, Hironori; Adachi, Akio

doi:10.1016/j.micinf.2013.01.005

Cited by 23 publications

(56 citation statements)

References 32 publications

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“…Improvement of HIV-1rmt clones carrying 66SR in the virion production level may lead to generation of new viral clones with better growth potentials. In this regard, we already gained a number of growthenhanced viral clones by long-term cultures of virus-infected cells (18). Adaptation of 66SR+ 5gtu to M1.3S cells in a similar way is in progress.…”

Section: Resultsmentioning

confidence: 99%

“…HIV -1 NL4 -3 (15) (GenBank accession number AF324493), SIVmac239 MA239 (19) (GenBank accession number M33262), HIV -1 SF162 (GenBank accession number M65024), and SIVgsn166 (GenBank accession number AF468659) sequences are indicated by white, gray, stripe, and black areas, respectively. Arrows represent the sites of growthenhancing adaptive mutations (18). Clone 5gtu carries four single -amino acid mutations around the two gray areas in the Gag -CA region (11,20).…”

Section: Resultsmentioning

confidence: 99%

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Single-amino acid mutation 66SR in Gag-matrix enhances viral single-cycle infectivity of R5-tropic HIV-1rmt

et al. 2015

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Single-amino acid mutation 66SR in Gag-matrix enhances viral single-cycle infectivity of R5-tropic HIV-1rmt

et al. 2015

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“…In addition, we constructed a series of CCR5-tropic viruses (MN5Rh-3, MN5/SD, MN5/SDQ, and MN5/LSDQ) (Fig. 2D), which carry the Env sequence derived from NF462 and a growth-enhancing Env S304G mutation (47). The growth potential of these viruses in M1.3S cells was analyzed.…”

Section: Resultsmentioning

confidence: 99%

“…The sequence of RhM tetherin from M1.3S cells was identical to that of an RhM (71), and SIVgsn166 (GenBank accession number AF468659) sequences are indicated by white, black, and red areas, respectively. Green arrows show adaptive mutations that enhance viral growth potential (47). Orange arrows show the CA-Q110D mutation that augments viral growth in macaque cells/monkeys (19,24).…”

Section: Methodsmentioning

confidence: 99%

Generation of Rhesus Macaque-Tropic HIV-1 Clones That Are Resistant to Major Anti-HIV-1 Restriction Factors

Nomaguchi

Yokoyama

Kono

et al. 2013

J Virol

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h Human immunodeficiency virus type 1 (HIV-1) replication in macaque cells is restricted mainly by antiviral cellular APOBEC3, TRIM5␣/TRIM5CypA, and tetherin proteins. For basic and clinical HIV-1/AIDS studies, efforts to construct macaque-tropic HIV-1 (HIV-1mt) have been made by us and others. Although rhesus macaques are commonly and successfully used as infection models, no HIV-1 derivatives suitable for in vivo rhesus research are available to date. In this study, to obtain novel HIV-1mt clones that are resistant to major restriction factors, we altered Gag and Vpu of our best HIV-1mt clone described previously. First, by sequence-and structure-guided mutagenesis, three amino acid residues in Gag-capsid (CA) (M94L/R98S/G114Q) were found to be responsible for viral growth enhancement in a macaque cell line. Results of in vitro TRIM5␣ susceptibility testing of HIV-1mt carrying these substitutions correlated well with the increased viral replication potential in macaque peripheral blood mononuclear cells (PBMCs) with different TRIM5 alleles, suggesting that the three amino acids in HIV-1mt CA are involved in the interaction with TRIM5␣. Second, we replaced the transmembrane domain of Vpu of this clone with the corresponding region of simian immunodeficiency virus SIVgsn166 Vpu. The resultant clone, MN4/LSDQgtu, was able to antagonize macaque but not human tetherin, and its Vpu effectively functioned during viral replication in a macaque cell line. Notably, MN4/ LSDQgtu grew comparably to SIVmac239 and much better than any of our other HIV-1mt clones in rhesus macaque PBMCs. In sum, MN4/LSDQgtu is the first HIV-1 derivative that exhibits resistance to the major restriction factors in rhesus macaque cells.

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“…Antagonism between host restriction factors and viral counterparts drives them to coevolve under mutual selective pressure (1)(2)(3)(4). We previously performed HIV-1 adaptation experiments and showed that growth-enhancing mutations were clustered in a narrow region of the C-terminal domain of Pol-integrase (IN) (5). Virological analysis of these mutations and comparative analysis of HIV-1 sequences revealed that naturally occurring single-nucleotide variations in a proximal region of splicing acceptor 1 (SA1prox) (Fig.…”

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confidence: 99%

Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels

Nomaguchi

Doi

Sakai

et al. 2016

J Virol

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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. IMPORTANCEWhile 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.

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Systemic biological analysis of the mutations in two distinct HIV-1mt genomes occurred during replication in macaque cells

Cited by 23 publications

References 32 publications

Single-amino acid mutation 66SR in Gag-matrix enhances viral single-cycle infectivity of R5-tropic HIV-1rmt

Single-amino acid mutation 66SR in Gag-matrix enhances viral single-cycle infectivity of R5-tropic HIV-1rmt

Generation of Rhesus Macaque-Tropic HIV-1 Clones That Are Resistant to Major Anti-HIV-1 Restriction Factors

Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels

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