Exploitation of the Low Fidelity of Human Immunodeficiency Virus Type 1 (HIV-1) Reverse Transcriptase and the Nucleotide Composition Bias in the HIV-1 Genome To Alter the Drug Resistance Development of HIV

Balzarini, Jan; Camarasa, Marı́a-José; Pérez‐Pérez, María‐Jesús; San‐Félix, Ana; Velázquez, Sonsoles; Perno, Carlo Federico; Clercq, Erik De; Anderson, J.C.; Karlsson, Anna

doi:10.1128/jvi.75.13.5772-5777.2001

Cited by 22 publications

(13 citation statements)

References 36 publications

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“…5). These dinucleotide contexts are quite similar to other reports (50,51 (52)(53)(54). If this is true in our case, the G to A transition should happen during minus strand synthesis and would be observed in both LTRs.…”

Section: Table III Mutations That Occurred In Both Ltrssupporting

confidence: 77%

Mutational Analysis of HIV-1 Long Terminal Repeats to Explore the Relative Contribution of Reverse Transcriptase and RNA Polymerase II to Viral Mutagenesis

O'Neil¹,

Sun²,

Yu³

et al. 2002

Journal of Biological Chemistry

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HIV-1 evolves rapidly, which is thought to result from one or more error-prone steps in the virus life cycle. Because HIV-1 reverse transcriptase (RT) does not possess 3-to 5-exonucleolytic proofreading activity and because RT has been shown to be error-prone in cell free systems, it should be an important contributor to the high rate of HIV-1 mutation. However, because RNA polymerase II (pol II) synthesizes viral RNA, it might also contribute significantly to HIV-1 mutagenesis. To assess the relative contributions of RT and RNA pol II to HIV-1 mutagenesis, a system was established to study the rate and nature of mutations in HIV-1 long terminal repeats (LTRs). Owing to the unique nature of replication at the ends of the viral genome, mutational analysis of retroviral LTRs provides an opportunity to evaluate the relative contribution of HIV-1 RT and RNA pol II to viral mutagenesis. Mutational analysis was performed on both LTRs of 215 proviruses, restricted to a single cycle of replication, employing single-stranded conformational polymorphism and DNA sequencing allowing direct identification of mutations in the absence of selection and within autologous viral sequences. A total of 21 independent mutations was identified. Ten mutations were observed in both LTRs, which could have been introduced by either RT or RNA pol II, whereas the other eleven mutations were only present in a single LTR and could only have been introduced by RT. This provides the first direct evidence that HIV-1 RT contributes significantly to HIV-1 mutagenesis and is likely to be the primary engine for HIV-1 mutagenesis. Moreover, mutations were observed at the U3-R border, but the nature of the mutations and their frequency differed from experiments performed using cell-free systems suggesting that other viral and/or cellular factors contribute to fidelity at the ends of the viral genome.

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Section: Table III Mutations That Occurred In Both Ltrssupporting

confidence: 77%

Mutational Analysis of HIV-1 Long Terminal Repeats to Explore the Relative Contribution of Reverse Transcriptase and RNA Polymerase II to Viral Mutagenesis

O'Neil¹,

Sun²,

Yu³

et al. 2002

Journal of Biological Chemistry

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“…The WT virus did not generate the E138K mutation in MT2 cells, which may also be related to the dNTP pool imbalance, since changing the intracellular dCTP/dTTP ratio can alter the evolutionary pattern at E138 under TSAO pressure (7). Possibly, the different sizes of intracellular dNTP pools in MT2 cells and CBMCs also impact the dNTP imbalance bias.…”

Section: Discussionmentioning

confidence: 99%

“…Intracellular dNTP pools play an important role in impacting HIV-1 replication kinetics and mutation rates (6,7,24,27,36,37). The cellular dNTP concentrations of two different types of HIV-1 target cells, activated/dividing CD4 ϩ T cells and terminally differentiated/nondividing macrophages, were recently determined, and the latter cells contain very low dNTP concentrations (16).…”

Section: Discussionmentioning

confidence: 99%

Subunit-Selective Mutational Analysis and Tissue Culture Evaluations of the Interactions of the E138K and M184I Mutations in HIV-1 Reverse Transcriptase

Oliveira

Quashie

et al. 2012

J Virol

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The emergence of HIV-1 drug resistance remains a major obstacle in antiviral therapy. M184I/V and E138K are signature mutations of clinical relevance in HIV-1 reverse transcriptase (RT) for the nucleoside reverse transcriptase inhibitors (NRTIs) lamivudine (3TC) and emtricitabine (FTC) and the second-generation (new) nonnucleoside reverse transcriptase inhibitor (NNRTI) rilpivirine (RPV), respectively, and the E138K mutation has also been shown to be selected by etravirine in cell culture. The E138K mutation was recently shown to compensate for the low enzyme processivity and viral fitness associated with the M184I/V mutations through enhanced deoxynucleoside triphosphate (dNTP) usage, while the M184I/V mutations compensated for defects in polymerization rates associated with the E138K mutations under conditions of high dNTP concentrations. The M184I mutation was also shown to enhance resistance to RPV and ETR when present together with the E138K mutation. These mutual compensatory effects might also enhance transmission rates of viruses containing these two mutations. Therefore, we performed tissue culture studies to investigate the evolutionary dynamics of these viruses. Through experiments in which E138K-containing viruses were selected with 3TC-FTC and in which M184I/V viruses were selected with ETR, we demonstrated that ETR was able to select for the E138K mutation in viruses containing the M184I/V mutations and that the M184I/V mutations consistently emerged when E138K viruses were selected with 3TC-FTC. We also performed biochemical subunit-selective mutational analyses to investigate the impact of the E138K mutation on RT function and interactions with the M184I mutation. We now show that the E138K mutation decreased rates of polymerization, impaired RNase H activity, and conferred ETR resistance through the p51 subunit of RT, while an enhancement of dNTP usage as a result of the simultaneous presence of both mutations E138K and M184I occurred via both subunits.

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“…Using exogenously provided deoxycytidine (dC) and tetrahydrouridine (THU) to artificially increase the concentration of dCTPs in cells lead to the selection of E138G instead of E138K by TSAO derivatives (42). This was interpreted to be the result of an augmented dCTP/dTTP ratio that skewed the RT mutational bias.…”

Section: E138k and Hiv-1 Mutational Biasmentioning

confidence: 99%

Basis for Early and Preferential Selection of the E138K Mutation in HIV-1 Reverse Transcriptase

McCallum

Oliveira

Ibanescu

et al. 2013

Antimicrob Agents Chemother

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dE138K, a G¡A mutation in HIV-1 reverse transcriptase (RT), is preferentially selected by etravirine (ETR) and rilpivirine over other substitutions at position E138 that offer greater drug resistance. We hypothesized that there was a mutational bias for the E138K substitution and designed an allele-specific PCR to monitor the emergence of E138A/G/K/Q/R/V during ETR selection experiments. We also performed competition experiments using mutated viruses and quantified the prevalence of E138 minority species in drug-naive patients. E138K, as well as E138G, consistently emerged first during ETR selection experiments, followed by E138A and E138Q; E138R was never selected. Surprisingly, E138K was identified as a tiny minority in 23% of drug-naive subtype B patients, a result confirmed by ultradeep sequencing (UDS). This result could reflect a low fitness cost of E138K; however, E138K was one of the least fit substitutions at codon E138, even after taking into account the deoxynucleoside triphosphate pools of the cells used in competition experiments. Further UDS analysis revealed other minority species in a pattern consistent with the mutational bias of HIV RT. There was no evidence of APOBEC3-hypermutation in these selection experiments or in patients. Our results confirm the mutational bias of HIV-1 in patients and highlight the importance of G¡A mutations in HIV-1 drug resistance evolution.

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Exploitation of the Low Fidelity of Human Immunodeficiency Virus Type 1 (HIV-1) Reverse Transcriptase and the Nucleotide Composition Bias in the HIV-1 Genome To Alter the Drug Resistance Development of HIV

Cited by 22 publications

References 36 publications

Mutational Analysis of HIV-1 Long Terminal Repeats to Explore the Relative Contribution of Reverse Transcriptase and RNA Polymerase II to Viral Mutagenesis

Mutational Analysis of HIV-1 Long Terminal Repeats to Explore the Relative Contribution of Reverse Transcriptase and RNA Polymerase II to Viral Mutagenesis

Subunit-Selective Mutational Analysis and Tissue Culture Evaluations of the Interactions of the E138K and M184I Mutations in HIV-1 Reverse Transcriptase

Basis for Early and Preferential Selection of the E138K Mutation in HIV-1 Reverse Transcriptase

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