Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex

Abstract

The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent mRNPs and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4Å resolution structure of S. cerevisiae THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.

Data availability

Cryo-EM maps are available in the Electron Microscopy Data Bank (11859 and 11871). Atomic models are available in the Protein Data Bank (7APX and 7AQO).

The following data sets were generated

Article and author information

Author details

  1. Sandra K Schuller

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1800-8014
  2. Jan M Schuller

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9121-1764
  3. Jesuraj R Prabu

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Marc Baumgärtner

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Fabien Bonneau

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8787-7662
  6. Jérôme Basquin

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Elena Conti

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany
    For correspondence
    conti@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1254-5588

Funding

European Commission (EXORICO)

  • Elena Conti

Deutsche Forschungsgemeinschaft (201302640)

  • Elena Conti

Deutsche Forschungsgemeinschaft (369799452)

  • Elena Conti

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

Reviewing Editor

  1. Karsten Weis, ETH Zurich, Switzerland

Publication history

  1. Received: July 27, 2020
  2. Accepted: November 13, 2020
  3. Accepted Manuscript published: November 16, 2020 (version 1)
  4. Version of Record published: December 16, 2020 (version 2)

Copyright

© 2020, Schuller 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

  • 1,962
    Page views
  • 296
    Downloads
  • 6
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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. Sandra K Schuller
  2. Jan M Schuller
  3. Jesuraj R Prabu
  4. Marc Baumgärtner
  5. Fabien Bonneau
  6. Jérôme Basquin
  7. Elena Conti
(2020)
Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex
eLife 9:e61467.
https://doi.org/10.7554/eLife.61467

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Morgane Boone et al.
    Research Advance Updated

    In eukaryotic cells, stressors reprogram the cellular proteome by activating the integrated stress response (ISR). In its canonical form, stress-sensing kinases phosphorylate the eukaryotic translation initiation factor eIF2 (eIF2-P), which ultimately leads to reduced levels of ternary complex required for initiation of mRNA translation. Previously we showed that translational control is primarily exerted through a conformational switch in eIF2’s nucleotide exchange factor, eIF2B, which shifts from its active A-State conformation to its inhibited I-State conformation upon eIF2-P binding, resulting in reduced nucleotide exchange on eIF2 (Schoof et al. 2021). Here, we show functionally and structurally how a single histidine to aspartate point mutation in eIF2B’s β subunit (H160D) mimics the effects of eIF2-P binding by promoting an I-State like conformation, resulting in eIF2-P independent activation of the ISR. These findings corroborate our previously proposed A/I-State model of allosteric ISR regulation.

    1. Structural Biology and Molecular Biophysics
    SeCheol Oh et al.
    Research Article

    Structures of the human lysosomal K+ channel transmembrane protein 175 (TMEM175) in open and closed states revealed a novel architecture lacking the canonical K+ selectivity filter motif present in previously known K+ channel structures. A hydrophobic constriction composed of four isoleucine residues was resolved in the pore and proposed to serve as the gate in the closed state, and to confer ion selectivity in the open state. Here, we achieve higher-resolution structures of the open and closed states and employ molecular dynamics simulations to analyze the conducting properties of the putative open state, demonstrating that it is permeable to K+ and, to a lesser degree, also Na+. Both cations must dehydrate significantly to penetrate the narrow hydrophobic constriction, but ion flow is assisted by a favorable electrostatic field generated by the protein that spans the length of the pore. The balance of these opposing energetic factors explains why permeation is feasible, and why TMEM175 is selective for K+ over Na+, despite the absence of the canonical selectivity filter. Accordingly, mutagenesis experiments reveal an exquisite sensitivity of the channel to perturbations that mitigate the constriction. Together, these data reveal a novel mechanism for selective permeation of ions by TMEM175 that is unlike that of other K+ channels.