The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription

  1. Eva Torreira
  2. Jaime Alegrio Louro
  3. Irene Pazos
  4. Noelia González-Polo
  5. David Gil-Carton
  6. Ana Garcia Duran
  7. Sébastien Tosi
  8. Oriol Gallego  Is a corresponding author
  9. Olga Calvo  Is a corresponding author
  10. Carlos Fernández-Tornero  Is a corresponding author
  1. Centro de Investigaciones Biológicas, Spain
  2. The Barcelona Institute of Science and Technology, Spain
  3. Instituto de Biología Funcional y Genómica, Spain
  4. Cooperative Center for Research in Biosciences CIC bioGUNE, Spain

Abstract

Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.

Article and author information

Author details

  1. Eva Torreira

    Centro de Investigaciones Biológicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Jaime Alegrio Louro

    Centro de Investigaciones Biológicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2800-923X
  3. Irene Pazos

    Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Noelia González-Polo

    Instituto de Biología Funcional y Genómica, Salamanca, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. David Gil-Carton

    Structural Biology Unit, Cooperative Center for Research in Biosciences CIC bioGUNE, Derio, Spain
    Competing interests
    The authors declare that no competing interests exist.
  6. Ana Garcia Duran

    Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. Sébastien Tosi

    Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  8. Oriol Gallego

    Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
    For correspondence
    oriol.gallego@irbbarcelona.org
    Competing interests
    The authors declare that no competing interests exist.
  9. Olga Calvo

    Instituto de Biología Funcional y Genómica, Salamanca, Spain
    For correspondence
    ocalvo@usal.es
    Competing interests
    The authors declare that no competing interests exist.
  10. Carlos Fernández-Tornero

    Centro de Investigaciones Biológicas, Madrid, Spain
    For correspondence
    cftornero@cib.csic.es
    Competing interests
    The authors declare that no competing interests exist.

Funding

Ministerio de Economía y Competitividad (BFU2013-48374-P)

  • Carlos Fernández-Tornero

Fundación Ramón Areces (-)

  • Carlos Fernández-Tornero

Ministerio de Economía y Competitividad (RYC-2011-07967)

  • Oriol Gallego

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

Reviewing Editor

  1. Alan G Hinnebusch, National Institutes of Health, United States

Version history

  1. Received: August 21, 2016
  2. Accepted: March 6, 2017
  3. Accepted Manuscript published: March 6, 2017 (version 1)
  4. Accepted Manuscript updated: March 8, 2017 (version 2)
  5. Version of Record published: March 22, 2017 (version 3)
  6. Version of Record updated: March 24, 2017 (version 4)

Copyright

© 2017, Torreira 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

  • 4,211
    views
  • 766
    downloads
  • 57
    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. Eva Torreira
  2. Jaime Alegrio Louro
  3. Irene Pazos
  4. Noelia González-Polo
  5. David Gil-Carton
  6. Ana Garcia Duran
  7. Sébastien Tosi
  8. Oriol Gallego
  9. Olga Calvo
  10. Carlos Fernández-Tornero
(2017)
The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription
eLife 6:e20832.
https://doi.org/10.7554/eLife.20832

Share this article

https://doi.org/10.7554/eLife.20832

Further reading

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

    1. Chromosomes and Gene Expression
    Marwan Anoud, Emmanuelle Delagoutte ... Jean-Paul Concordet
    Research Article

    Tardigrades are microscopic animals renowned for their ability to withstand extreme conditions, including high doses of ionizing radiation (IR). To better understand their radio-resistance, we first characterized induction and repair of DNA double- and single-strand breaks after exposure to IR in the model species Hypsibius exemplaris. Importantly, we found that the rate of single-strand breaks induced was roughly equivalent to that in human cells, suggesting that DNA repair plays a predominant role in tardigrades’ radio-resistance. To identify novel tardigrade-specific genes involved, we next conducted a comparative transcriptomics analysis across three different species. In all three species, many DNA repair genes were among the most strongly overexpressed genes alongside a novel tardigrade-specific gene, which we named Tardigrade DNA damage Response 1 (TDR1). We found that TDR1 protein interacts with DNA and forms aggregates at high concentration suggesting it may condensate DNA and preserve chromosome organization until DNA repair is accomplished. Remarkably, when expressed in human cells, TDR1 improved resistance to Bleomycin, a radiomimetic drug. Based on these findings, we propose that TDR1 is a novel tardigrade-specific gene conferring resistance to IR. Our study sheds light on mechanisms of DNA repair helping cope with high levels of DNA damage inflicted by IR.