A mechanism for the extension and unfolding of parallel G-quadruplexes by human telomerase at single-molecule resolution

  1. Bishnu P Paudel
  2. Aaron Lavel Moye
  3. Hala Abou Assi
  4. Roberto El-Khoury
  5. Scott Cohen
  6. Jessica K Holien
  7. Monica L Birrento
  8. Siritron Samosorn
  9. Kamthorn Intharapichai
  10. Christopher G Tomlinson
  11. Marie-Paule Teulade-Fichou
  12. Carlos González
  13. Jennifer L Beck
  14. Masad J Damha
  15. Antoine M van Oijen
  16. Tracy M Bryan  Is a corresponding author
  1. University of Wollongong, Australia
  2. Children's Medical Research Institute, Australia
  3. McGill University, Canada
  4. RMIT University, Australia
  5. Srinakharinwirot University, Thailand
  6. Kyoto Institute of Technology, Japan
  7. PSL Research University, France
  8. Instituto de Química Física 'Rocasolano', Spain

Abstract

Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for all summary graphs.

Article and author information

Author details

  1. Bishnu P Paudel

    School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3518-3882
  2. Aaron Lavel Moye

    Cell Biology Unit, Children's Medical Research Institute, Westmead, Australia
    Competing interests
    The authors declare that no competing interests exist.
  3. Hala Abou Assi

    Department of Chemistry, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1087-8805
  4. Roberto El-Khoury

    Department of Chemistry, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Scott Cohen

    Cell Biology Unit, Children's Medical Research Institute, Westmead, Australia
    Competing interests
    The authors declare that no competing interests exist.
  6. Jessica K Holien

    School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Australia
    Competing interests
    The authors declare that no competing interests exist.
  7. Monica L Birrento

    School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
    Competing interests
    The authors declare that no competing interests exist.
  8. Siritron Samosorn

    Department of Chemistry, Srinakharinwirot University, Bangkok, Thailand
    Competing interests
    The authors declare that no competing interests exist.
  9. Kamthorn Intharapichai

    Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  10. Christopher G Tomlinson

    Cell Biology Unit, Children's Medical Research Institute, Westmead, Australia
    Competing interests
    The authors declare that no competing interests exist.
  11. Marie-Paule Teulade-Fichou

    Institut Curie, PSL Research University, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  12. Carlos González

    Instituto de Química Física 'Rocasolano', Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  13. Jennifer L Beck

    School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
    Competing interests
    The authors declare that no competing interests exist.
  14. Masad J Damha

    Department of Chemistry, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  15. Antoine M van Oijen

    School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1794-5161
  16. Tracy M Bryan

    Cell Biology Unit, Children's Medical Research Institute, Westmead, Australia
    For correspondence
    tbryan@cmri.org.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7990-5501

Funding

Cancer Council NSW (RG 11-07,RG 16-10)

  • Tracy M Bryan

Cancer Institute NSW

  • Aaron Lavel Moye

Australian Research Council

  • Antoine M van Oijen

Ernest and Piroska Major Foundation

  • Scott Cohen

National Science and Engineering Council

  • Masad J Damha

Centre of Excellence for Innovation in Chemistry (PERCH-CIC)

  • Siritron Samosorn

Research Unit of Natural Products and Organic Synthesis for Drug Discovery (NPOS 405/2560)

  • Siritron Samosorn

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

Copyright

© 2020, Paudel 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

  • 3,487
    views
  • 523
    downloads
  • 47
    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. Bishnu P Paudel
  2. Aaron Lavel Moye
  3. Hala Abou Assi
  4. Roberto El-Khoury
  5. Scott Cohen
  6. Jessica K Holien
  7. Monica L Birrento
  8. Siritron Samosorn
  9. Kamthorn Intharapichai
  10. Christopher G Tomlinson
  11. Marie-Paule Teulade-Fichou
  12. Carlos González
  13. Jennifer L Beck
  14. Masad J Damha
  15. Antoine M van Oijen
  16. Tracy M Bryan
(2020)
A mechanism for the extension and unfolding of parallel G-quadruplexes by human telomerase at single-molecule resolution
eLife 9:e56428.
https://doi.org/10.7554/eLife.56428

Share this article

https://doi.org/10.7554/eLife.56428

Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Mai Nguyen, Elda Bauda ... Cecile Morlot
    Research Article

    Teichoic acids (TA) are linear phospho-saccharidic polymers and important constituents of the cell envelope of Gram-positive bacteria, either bound to the peptidoglycan as wall teichoic acids (WTA) or to the membrane as lipoteichoic acids (LTA). The composition of TA varies greatly but the presence of both WTA and LTA is highly conserved, hinting at an underlying fundamental function that is distinct from their specific roles in diverse organisms. We report the observation of a periplasmic space in Streptococcus pneumoniae by cryo-electron microscopy of vitreous sections. The thickness and appearance of this region change upon deletion of genes involved in the attachment of TA, supporting their role in the maintenance of a periplasmic space in Gram-positive bacteria as a possible universal function. Consequences of these mutations were further examined by super-resolved microscopy, following metabolic labeling and fluorophore coupling by click chemistry. This novel labeling method also enabled in-gel analysis of cell fractions. With this approach, we were able to titrate the actual amount of TA per cell and to determine the ratio of WTA to LTA. In addition, we followed the change of TA length during growth phases, and discovered that a mutant devoid of LTA accumulates the membrane-bound polymerized TA precursor.

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    Shinichi Kawaguchi, Xin Xu ... Toshie Kai
    Research Article

    Protein–protein interactions are fundamental to understanding the molecular functions and regulation of proteins. Despite the availability of extensive databases, many interactions remain uncharacterized due to the labor-intensive nature of experimental validation. In this study, we utilized the AlphaFold2 program to predict interactions among proteins localized in the nuage, a germline-specific non-membrane organelle essential for piRNA biogenesis in Drosophila. We screened 20 nuage proteins for 1:1 interactions and predicted dimer structures. Among these, five represented novel interaction candidates. Three pairs, including Spn-E_Squ, were verified by co-immunoprecipitation. Disruption of the salt bridges at the Spn-E_Squ interface confirmed their functional importance, underscoring the predictive model’s accuracy. We extended our analysis to include interactions between three representative nuage components—Vas, Squ, and Tej—and approximately 430 oogenesis-related proteins. Co-immunoprecipitation verified interactions for three pairs: Mei-W68_Squ, CSN3_Squ, and Pka-C1_Tej. Furthermore, we screened the majority of Drosophila proteins (~12,000) for potential interaction with the Piwi protein, a central player in the piRNA pathway, identifying 164 pairs as potential binding partners. This in silico approach not only efficiently identifies potential interaction partners but also significantly bridges the gap by facilitating the integration of bioinformatics and experimental biology.