Structure of the human core transcription-export complex reveals a hub for multivalent interactions

  1. Thomas Pühringer
  2. Ulrich Hohmann
  3. Laura Fin
  4. Belén Pacheco-Fiallos
  5. Ulla Schellhaas
  6. Julius Brennecke
  7. Clemens Plaschka  Is a corresponding author
  1. Research Institute of Molecular Pathology (IMP), Austria
  2. Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Austria

Abstract

The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO–UAP56/DDX39B–ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1–NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here we report the cryo-electron microscopy structure of the human THO–UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO–UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX–mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.

Data availability

Three-dimensional cryo-EM density maps A, B, C, D, and E have been deposited in the Electron Microscopy Data Bank under the accession numbers EMD-11853, EMD-11857, EMD-11854, EMD-11855, EMD-11856, respectively. The coordinate file of the human THO-UAP56 complex has been deposited in the Protein Data Bank under the accession number 7APK.

The following data sets were generated

Article and author information

Author details

  1. Thomas Pühringer

    Research Institute of Molecular Pathology (IMP), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9127-9120
  2. Ulrich Hohmann

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2124-1439
  3. Laura Fin

    Research Institute of Molecular Pathology (IMP), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  4. Belén Pacheco-Fiallos

    Research Institute of Molecular Pathology (IMP), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  5. Ulla Schellhaas

    Research Institute of Molecular Pathology (IMP), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9684-9839
  6. Julius Brennecke

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
    Competing interests
    The authors declare that no competing interests exist.
  7. Clemens Plaschka

    Research Institute of Molecular Pathology (IMP), Vienna, Austria
    For correspondence
    clemens.plaschka@imp.ac.at
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6020-9514

Funding

Boehringer Ingelheim

  • Clemens Plaschka

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (P2GEP3_188343)

  • Ulrich Hohmann

H2020 European Research Council (ERC-2015-CoG 682181)

  • Julius Brennecke

Austrian Science Fund (F4303 and W1207)

  • Julius Brennecke

Österreichischen Akademie der Wissenschaften

  • Julius Brennecke

H2020 European Research Council (ERC-2020-STG 949081)

  • Clemens Plaschka

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

Copyright

© 2020, Pühringer 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

  • 7,921
    views
  • 1,025
    downloads
  • 60
    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. Thomas Pühringer
  2. Ulrich Hohmann
  3. Laura Fin
  4. Belén Pacheco-Fiallos
  5. Ulla Schellhaas
  6. Julius Brennecke
  7. Clemens Plaschka
(2020)
Structure of the human core transcription-export complex reveals a hub for multivalent interactions
eLife 9:e61503.
https://doi.org/10.7554/eLife.61503

Share this article

https://doi.org/10.7554/eLife.61503

Further reading

    1. Chromosomes and Gene Expression
    2. Evolutionary Biology
    Gülnihal Kavaklioglu, Alexandra Podhornik ... Christian Seiser
    Research Article

    Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.

    1. Chromosomes and Gene Expression
    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.