1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease

Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance

  1. Ean Spielvogel
  2. Sook-Kyung Lee
  3. Shuntai Zhou
  4. Gordon J Lockbaum
  5. Mina Henes
  6. Amy Sondgeroth
  7. Klajdi Kosovrasti
  8. Ellen A Nalivaika
  9. Akbar Ali
  10. Nese Kurt Yilmaz
  11. Celia A Schiffer  Is a corresponding author
  12. Ronald Swanstrom  Is a corresponding author
  1. University of North Carolina at Chapel Hill, United States
  2. University of Massachusetts Medical School, United States
https://doi.org/10.7554/eLife.80328
Share this article
Cite this article
  1. Ean Spielvogel
  2. Sook-Kyung Lee
  3. Shuntai Zhou
  4. Gordon J Lockbaum
  5. Mina Henes
  6. Amy Sondgeroth
  7. Klajdi Kosovrasti
  8. Ellen A Nalivaika
  9. Akbar Ali
  10. Nese Kurt Yilmaz
  11. Celia A Schiffer
  12. Ronald Swanstrom
(2023)
Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance
eLife 12:e80328.
https://doi.org/10.7554/eLife.80328
  2. Download BibTeX
  3. Download .RIS

Abstract

Darunavir (DRV) is exceptional among potent HIV-1 protease inhibitors (PIs) in high drug concentrations that are achived in vivo. Little is known about the de novo resistance pathway for DRV. We selected for resistance to high drug concentrations against ten PIs and their structural precursor DRV. Mutations accumulated through two pathways (anchored by protease mutations I50V or I84V). Small changes in the inhibitor P1'-equivalent position led to preferential use of one pathway over the other. Changes in the inhbitor P2'-equivalent position determined differences in potency that were retained in the resistant viruses and that impacted the selected mutations. Viral variants from the two pathways showed differential selection of compensatory mutations in Gag cleavage sites. These results reveal the high level of selective pressure that is attainable with fifth generation PIs, and how features of the inhibitor affect both the resistance pathway and the residual potency in the face of resistance.

Data availability

The sequencing data (Figure 2, 3, and 4) is available at NIH Sequencing Read Archive (SRA) under BioProject ID PRJNA853351.All source data files for enzymatic Ki and Km (Table 1, Figure 2 and 5) have been uploaded to the Carolina Digital Repository: Swanstrom, Ron, and Ean Spielvogel. Km and Ki Dataset for Selection of Hiv-1 for Resistance to Fifth Generation Protease Inhibitors Reveals Two Independent Pathways to High-level Resistance. 2022.All source data files for EC50 inhibition curves (Figure 2 and 6) have been uploaded to the Carolina Digital Repository: Swanstrom, Ron, and Ean Spielvogel. Ec50 Dataset for Selection of Hiv-1 for Resistance to Fifth Generation Protease Inhibitors Reveals Two Independent Pathways to High-level Resistance. 2022.

The following data sets were generated

Article and author information

Author details

  1. Ean Spielvogel

    Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Sook-Kyung Lee

    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Shuntai Zhou

    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Gordon J Lockbaum

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Mina Henes

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Amy Sondgeroth

    Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Klajdi Kosovrasti

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Ellen A Nalivaika

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Akbar Ali

    Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Nese Kurt Yilmaz

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Celia A Schiffer

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
    For correspondence
    celia.schiffer@umassmed.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2270-6613

  12. Ronald Swanstrom

    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, United States
    For correspondence
    ron_swanstrom@med.unc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7777-0773

Funding

National Institute of General Medical Sciences (1P01GM109767-01A`)

  • Ean Spielvogel
  • Sook-Kyung Lee
  • Shuntai Zhou
  • Gordon J Lockbaum
  • Mina Henes
  • Amy Sondgeroth
  • Klajdi Kosovrasti
  • Ellen A Nalivaika
  • Akbar Ali
  • Nese Kurt Yilmaz
  • Celia A Schiffer
  • Ronald Swanstrom

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Owen Pornillos, University of Virginia, United States

Version history

  1. Preprint posted: November 9, 2019 (view preprint)
  2. Received: May 16, 2022
  3. Accepted: March 14, 2023
  4. Accepted Manuscript published: March 15, 2023 (version 1)
  5. Version of Record published: March 31, 2023 (version 2)
  6. Version of Record updated: April 5, 2023 (version 3)

Copyright

© 2023, Spielvogel et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 828
    views
  • 108
    downloads
  • 9
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ean Spielvogel
  2. Sook-Kyung Lee
  3. Shuntai Zhou
  4. Gordon J Lockbaum
  5. Mina Henes
  6. Amy Sondgeroth
  7. Klajdi Kosovrasti
  8. Ellen A Nalivaika
  9. Akbar Ali
  10. Nese Kurt Yilmaz
  11. Celia A Schiffer
  12. Ronald Swanstrom
(2023)
Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance
eLife 12:e80328.
https://doi.org/10.7554/eLife.80328

Share this article

https://doi.org/10.7554/eLife.80328

Categories and tags

Research organism

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Enrichment of rare codons at 5' ends of genes is a spandrel caused by evolutionary sequence turnover and does not improve translation

    Richard Sejour, Janet Leatherwood ... Bruce Futcher
    Research Article

    Previously, Tuller et al. found that the first 30–50 codons of the genes of yeast and other eukaryotes are slightly enriched for rare codons. They argued that this slowed translation, and was adaptive because it queued ribosomes to prevent collisions. Today, the translational speeds of different codons are known, and indeed rare codons are translated slowly. We re-examined this 5’ slow translation ‘ramp.’ We confirm that 5’ regions are slightly enriched for rare codons; in addition, they are depleted for downstream Start codons (which are fast), with both effects contributing to slow 5’ translation. However, we also find that the 5’ (and 3’) ends of yeast genes are poorly conserved in evolution, suggesting that they are unstable and turnover relatively rapidly. When a new 5’ end forms de novo, it is likely to include codons that would otherwise be rare. Because evolution has had a relatively short time to select against these codons, 5’ ends are typically slightly enriched for rare, slow codons. Opposite to the expectation of Tuller et al., we show by direct experiment that genes with slowly translated codons at the 5’ end are expressed relatively poorly, and that substituting faster synonymous codons improves expression. Direct experiment shows that slow codons do not prevent downstream ribosome collisions. Further informatic studies suggest that for natural genes, slow 5’ ends are correlated with poor gene expression, opposite to the expectation of Tuller et al. Thus, we conclude that slow 5’ translation is a ‘spandrel’--a non-adaptive consequence of something else, in this case, the turnover of 5’ ends in evolution, and it does not improve translation.

    1. Biochemistry and Chemical Biology

    Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy

    Boglarka Zambo, Evelina Edelweiss ... Gergo Gogl
    Research Article

    Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Human DDX6 regulates translation and decay of inefficiently translated mRNAs

    Ramona Weber, Chung-Te Chang
    Research Article

    Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.