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Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity

Chen Qiu1, Robert C Dutcher1, Douglas F Porter2

  • 1Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

Nucleic Acids Research
|July 12, 2019
PubMed

Insights

Fungal Puf1/Puf2 proteins use distinct PUM-HD and RRM domains to bind UAAU motifs in RNA. Their combined action reveals a novel mechanism for RNA-binding specificity.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Mycology

Background:

  • PUF proteins regulate gene expression by binding specific mRNA sequences.
  • Classical PUF proteins utilize a PUM homology domain (PUM-HD) for RNA recognition.
  • Fungal Puf1 and Puf2 proteins represent a conserved subfamily with a unique domain combination.

Purpose of the Study:

  • To elucidate the structural basis of RNA recognition by fungal Puf1 proteins.
  • To investigate the cooperative function of the PUM-HD and RNA recognition motif (RRM) domains.
  • To understand the mechanism of specificity for UAAU motifs in RNA.

Main Methods:

  • Crystal structure determination of the Puf1 PUM-HD domain in complex with dual UAAU motif RNA.
  • Crystal structure determination of the Puf1 RRM domain.
  • Analysis of protein-RNA interactions and domain cooperation.

Main Results:

  • The Puf1 PUM-HD binds dual UAAU motifs in a 2:1 protein-to-RNA complex.
  • Crystal structures revealed a dimerization interface for the Puf1 RRM domain.
  • PUM-HD confers UAAU specificity, while RRM dimerization enhances binding to dual motifs.

Conclusions:

  • Fungal Puf1/Puf2 proteins employ a novel mechanism of RNA-binding specificity through domain cooperation.
  • The PUM-HD and RRM domains collaborate to achieve precise recognition of clustered RNA motifs.
  • This study provides structural insights into the functional synergy of multiple RNA-binding modules.

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