1. Biochemistry and Chemical Biology
Download icon

Coupling between the DEAD-box RNA helicases Ded1p and eIF4A

  1. Zhaofeng Gao
  2. Andrea A Putnam
  3. Heath A Bowers
  4. Ulf-Peter Guenther
  5. Xuan Ye
  6. Audrey Kindsfather
  7. Angela K Hilliker
  8. Eckhard Jankowsky  Is a corresponding author
  1. Case Western Reserve University, United States
  2. University of Richmond, United States
Research Article
  • Cited 31
  • Views 2,462
  • Annotations
Cite this article as: eLife 2016;5:e16408 doi: 10.7554/eLife.16408

Abstract

Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p. Here we show that S. cerevisiae eIF4A and Ded1p directly interact with each other and simultaneously with the scaffolding protein eIF4G. We delineate a comprehensive thermodynamic framework for the interactions between Ded1p, eIF4A, eIF4G, RNA and ATP, which indicates that eIF4A, with and without eIF4G, acts as modulator for activity and substrate preferences of Ded1p, which is the RNA remodeling unit in all complexes. Our results reveal and characterize an unexpected interdependence between the two RNA helicases and eIF4G, and suggest that Ded1p is an integral part of eIF4F, the complex comprising eIF4G, eIF4A, and eIF4E.

Article and author information

Author details

  1. Zhaofeng Gao

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Andrea A Putnam

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Heath A Bowers

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Ulf-Peter Guenther

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Xuan Ye

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3157-7537

  6. Audrey Kindsfather

    Department of Biology, University of Richmond, Richmond, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Angela K Hilliker

    Department of Biology, University of Richmond, Richmond, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Eckhard Jankowsky

    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, United States
    For correspondence
    exj13@case.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7677-7412

Funding

National Institute of General Medical Sciences (GM118088)

  • Zhaofeng Gao
  • Andrea A Putnam
  • Heath A Bowers
  • Ulf-Peter Guenther
  • Xuan Ye
  • Eckhard Jankowsky

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 Institute of Child Health and Human Development, United States

Publication history

  1. Received: March 26, 2016
  2. Accepted: August 4, 2016
  3. Accepted Manuscript published: August 5, 2016 (version 1)
  4. Version of Record published: August 18, 2016 (version 2)

Copyright

© 2016, Gao 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

  • 2,462
    Page views
  • 588
    Downloads
  • 31
    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)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Research organism

    1. Of interest

    Witnessing the structural evolution of an RNA enzyme

    Xavier Portillo et al.
  2. Further reading

Further reading

    1. Biochemistry and Chemical Biology

    Witnessing the structural evolution of an RNA enzyme

    Xavier Portillo et al.
    Research Article Updated

    An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

    1. Biochemistry and Chemical Biology

    A universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation

    Gajanan S Patil et al.
    Research Article Updated

    Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4′-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show that FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3′,5′-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organizations. The universal distribution of FAALs suggests that they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.

    1. Biochemistry and Chemical Biology

    Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins

    Urszula Nowicka et al.
    Research Article Updated

    Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that are translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in the mitochondrial uptake of these nuclear-encoded proteins can cause proteotoxic stress and identify response mechanisms that may counteract it. Here, we report that upon impairments in mitochondrial protein import, high-risk precursor and immature forms of mitochondrial proteins form aberrant deposits in the cytosol. These deposits then cause further cytosolic accumulation and consequently aggregation of other mitochondrial proteins and disease-related proteins, including α-synuclein and amyloid β. This aggregation triggers a cytosolic protein homeostasis imbalance that is accompanied by specific molecular chaperone responses at both the transcriptomic and protein levels. Altogether, our results provide evidence that mitochondrial dysfunction, specifically protein import defects, contributes to impairments in protein homeostasis, thus revealing a possible molecular mechanism by which mitochondria are involved in neurodegenerative diseases.