IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-03920-7.html
   My bibliography  Save this article

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition

Author

Listed:
  • Pooja Kumari

    (Friedrich Miescher Institute for Biomedical Research)

  • Florian Aeschimann

    (Friedrich Miescher Institute for Biomedical Research)

  • Dimos Gaidatzis

    (Friedrich Miescher Institute for Biomedical Research
    Swiss Institute of Bioinformatics)

  • Jeremy J. Keusch

    (Friedrich Miescher Institute for Biomedical Research)

  • Pritha Ghosh

    (International Institute of Molecular and Cell Biology in Warsaw)

  • Anca Neagu

    (Friedrich Miescher Institute for Biomedical Research)

  • Katarzyna Pachulska-Wieczorek

    (Institute of Bioorganic Chemistry, Polish Academy of Sciences)

  • Janusz M. Bujnicki

    (International Institute of Molecular and Cell Biology in Warsaw
    Institute of Biotechnology and Moleular Biology, Adam Mickiewicz University)

  • Heinz Gut

    (Friedrich Miescher Institute for Biomedical Research)

  • Helge Großhans

    (Friedrich Miescher Institute for Biomedical Research
    University of Basel)

  • Rafal Ciosk

    (Friedrich Miescher Institute for Biomedical Research
    Institute of Bioorganic Chemistry, Polish Academy of Sciences)

Abstract

RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity. Surprisingly, the mechanism of RNA recognition by LIN41 is drastically different from that of its more distant relative, the fly Brat. Our phylogenetic analysis suggests that this reflects a rapid evolution of the domain, presenting an interesting example of a conserved protein fold that acquired completely different solutions to RNA recognition.

Suggested Citation

  • Pooja Kumari & Florian Aeschimann & Dimos Gaidatzis & Jeremy J. Keusch & Pritha Ghosh & Anca Neagu & Katarzyna Pachulska-Wieczorek & Janusz M. Bujnicki & Heinz Gut & Helge Großhans & Rafal Ciosk, 2018. "Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03920-7
    DOI: 10.1038/s41467-018-03920-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-03920-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-03920-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Diego Esposito & Jane Dudley-Fraser & Acely Garza-Garcia & Katrin Rittinger, 2022. "Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03920-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.