Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain

  1. Atefeh Rafiei
  2. Sofia Cruz Tetlalmatzi
  3. Claire H Edrington
  4. Linda Lee
  5. D Alex Crowder
  6. Daniel J Saltzberg
  7. Andrej Sali
  8. Gary Brouhard
  9. David C Schriemer  Is a corresponding author
  1. University of Calgary, Canada
  2. McGill University, Canada
  3. University of California, San Francisco, United States

Abstract

Doublecortin (DCX) is a microtubule (MT) associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX-MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-EM and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its-tail, our study shows that lattice-driven self-assembly is an important property of DCX.

Data availability

The DCX-MT integrative models, including final structures, modeling details, and input experimental data, were deposited into the PDB-dev repository for integrative models (www.pdb-dev.com) as follows: Dimeric DCX-MT (diagonal1): PDBDEV_00000071 Dimeric DCX-MT (lateral): PDBDEV_00000072 Dimeric DCX-MT (longitudinal): PDBDEV_00000073 Dimeric DCX-MT (diagonal2): PDBDEV_00000074 All LC-MS/MS data generated to support the findings of this study have been deposited with the ProteomeXchange Consortium with the dataset identifier PXD033167.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Atefeh Rafiei

    Department of Chemistry, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Sofia Cruz Tetlalmatzi

    Department of Biology, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Claire H Edrington

    Department of Biology, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Linda Lee

    Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. D Alex Crowder

    Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Daniel J Saltzberg

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Andrej Sali

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0435-6197
  8. Gary Brouhard

    Department of Biology, 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:" 0000-0001-9101-1247
  9. David C Schriemer

    Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
    For correspondence
    dschriem@ucalgary.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5202-1618

Funding

Canarie (RS-326)

  • David C Schriemer

Natural Sciences and Engineering Research Council of Canada (RGPIN-2017-04879)

  • David C Schriemer

Natural Sciences and Engineering Research Council of Canada (RGPIN-2020-04876)

  • Gary Brouhard

Canadian Institutes of Health Research (PJT-148702)

  • Gary Brouhard

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

Copyright

© 2022, Rafiei 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

  • 1,041
    views
  • 159
    downloads
  • 10
    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. Atefeh Rafiei
  2. Sofia Cruz Tetlalmatzi
  3. Claire H Edrington
  4. Linda Lee
  5. D Alex Crowder
  6. Daniel J Saltzberg
  7. Andrej Sali
  8. Gary Brouhard
  9. David C Schriemer
(2022)
Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain
eLife 11:e66975.
https://doi.org/10.7554/eLife.66975

Share this article

https://doi.org/10.7554/eLife.66975

Further reading

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Ting Liu, Xing Shen ... Zhihong Xue
    Research Article

    The interplay between G4s and R-loops are emerging in regulating DNA repair, replication, and transcription. A comprehensive picture of native co-localized G4s and R-loops in living cells is currently lacking. Here, we describe the development of HepG4-seq and an optimized HBD-seq methods, which robustly capture native G4s and R-loops, respectively, in living cells. We successfully employed these methods to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). We discovered that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes. We further demonstrated the helicase Dhx9 as a direct and major regulator that modulates the formation and resolution of co-localized G4s and R-loops. Depletion of Dhx9 impaired the self-renewal and differentiation capacities of mESCs by altering the transcription of co-localized G4s and R-loops -associated genes. Taken together, our work established that the endogenous co-localized G4s and R-loops are prevalently persisted in the regulatory regions of active genes and are involved in the transcriptional regulation of their linked genes, opening the door for exploring broader roles of co-localized G4s and R-loops in development and disease.

    1. Biochemistry and Chemical Biology
    Emily L Dearlove, Chatrin Chatrin ... Danny T Huang
    Research Article

    Ubiquitination typically involves covalent linking of ubiquitin (Ub) to a lysine residue on a protein substrate. Recently, new facets of this process have emerged, including Ub modification of non-proteinaceous substrates like ADP-ribose by the DELTEX E3 ligase family. Here, we show that the DELTEX family member DTX3L expands this non-proteinaceous substrate repertoire to include single-stranded DNA and RNA. Although the N-terminal region of DTX3L contains single-stranded nucleic acid binding domains and motifs, the minimal catalytically competent fragment comprises the C-terminal RING and DTC domains (RD). DTX3L-RD catalyses ubiquitination of the 3’-end of single-stranded DNA and RNA, as well as double-stranded DNA with a 3’ overhang of two or more nucleotides. This modification is reversibly cleaved by deubiquitinases. NMR and biochemical analyses reveal that the DTC domain binds single-stranded DNA and facilitates the catalysis of Ub transfer from RING-bound E2-conjugated Ub. Our study unveils the direct ubiquitination of nucleic acids by DTX3L, laying the groundwork for understanding its functional implications.