1. Biochemistry and Chemical Biology
  2. Cell Biology
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Pat1 promotes processing body assembly by enhancing the phase separation of the DEAD-box ATPase Dhh1 and RNA

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Cite this article as: eLife 2019;8:e41415 doi: 10.7554/eLife.41415

Abstract

Processing bodies (PBs) are cytoplasmic mRNP granules that assemble via liquid-liquid phase separation and are implicated in the decay or storage of mRNAs. How PB assembly is regulated in cells remains unclear. Previously, we identified the ATPase activity of the DEAD-box protein Dhh1 as a key regulator of PB dynamics and demonstrated that Not1, an activator of the Dhh1 ATPase and member of the CCR4-NOT deadenylase complex inhibits PB assembly in vivo (Mugler et al., 2016). Here, we show that the PB component Pat1 antagonizes Not1 and promotes PB assembly via its direct interaction with Dhh1. Intriguingly, in vivo PB dynamics can be recapitulated in vitro, since Pat1 enhances the phase separation of Dhh1 and RNA into liquid droplets, whereas Not1 reverses Pat1-Dhh1-RNA condensation. Overall, our results uncover a function of Pat1 in promoting the multimerization of Dhh1 on mRNA, thereby aiding the assembly of large multivalent mRNP granules that are PBs.

Article and author information

Author details

  1. Ruchika Sachdev

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  2. Maria Hondele

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2733-2561
  3. Miriam Linsenmeier

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  4. Pascal Vallotton

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  5. Christopher F Mugler

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8258-1192
  6. Paolo Arosio

    ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  7. Karsten Weis

    ETH Zurich, Zurich, Switzerland
    For correspondence
    karsten.weis@bc.biol.ethz.ch
    Competing interests
    Karsten Weis, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7224-925X

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_159731)

  • Karsten Weis

National Institute of General Medical Sciences (R01GM058065)

  • Karsten Weis

National Institute of General Medical Sciences (R01GM101257)

  • Karsten Weis

Human Frontier Science Program (LT000914/2015)

  • Maria Hondele

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_179275)

  • Karsten Weis

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, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Publication history

  1. Received: August 28, 2018
  2. Accepted: January 15, 2019
  3. Accepted Manuscript published: January 16, 2019 (version 1)
  4. Version of Record published: February 7, 2019 (version 2)

Copyright

© 2019, Sachdev 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.

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Further reading

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    La-related protein 4 (LARP4) directly binds both poly(A) and poly(A)-binding protein (PABP). LARP4 was shown to promote poly(A) tail (PAT) lengthening and stabilization of individual mRNAs presumably by protection from deadenylation (Mattijssen et al., 2017). We developed a nucleotide resolution transcriptome-wide, single molecule SM-PAT-seq method. This revealed LARP4 effects on a wide range of PAT lengths for human mRNAs and mouse mRNAs from LARP4 knockout (KO) and control cells. LARP4 effects are clear on long PAT mRNAs but become more prominent at 30–75 nucleotides. We also analyzed time courses of PAT decay transcriptome-wide and for ~200 immune response mRNAs. This demonstrated accelerated deadenylation in KO cells on PATs < 75 nucleotides and phasing consistent with greater PABP dissociation in the absence of LARP4. Thus, LARP4 shapes PAT profiles throughout mRNA lifespan with impact on mRNA decay at short lengths known to sensitize PABP dissociation in response to deadenylation machinery.

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