The Bicoid mRNA Localization Factor Exuperantia Is an RNA-binding Pseudonuclease

Nat Struct Mol Biol. 2016 Aug;23(8):705-13. doi: 10.1038/nsmb.3254. Epub 2016 Jul 4.

Abstract

Anterior patterning in Drosophila is mediated by the localization of bicoid (bcd) mRNA at the anterior pole of the oocyte. Exuperantia (Exu) is a putative exonuclease (EXO) associated with bcd and required for its localization. We present the crystal structure of Exu, which reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The catalytic site is degenerate and inactive. Instead, the EXO-like domain mediates dimerization and RNA binding. We show that Exu binds RNA directly in vitro, that the SAM-like domain is required for RNA binding activity and that Exu binds a structured element present in the bcd 3' untranslated region with high affinity. Through structure-guided mutagenesis, we show that Exu dimerization is essential for bcd localization. Our data demonstrate that Exu is a noncanonical RNA-binding protein with EXO-SAM-like domain architecture that interacts with its target RNA as a homodimer.

MeSH terms

  • Animals
  • Catalytic Domain
  • Crystallography, X-Ray
  • Drosophila Proteins / chemistry*
  • Drosophila Proteins / physiology
  • Drosophila melanogaster / enzymology*
  • Egg Proteins / chemistry*
  • Egg Proteins / physiology
  • Exonucleases / chemistry*
  • Exonucleases / physiology
  • Female
  • Homeodomain Proteins / metabolism
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Transport
  • RNA / chemistry
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / physiology
  • Trans-Activators / metabolism

Substances

  • Drosophila Proteins
  • Egg Proteins
  • Homeodomain Proteins
  • RNA-Binding Proteins
  • Trans-Activators
  • bcd protein, Drosophila
  • exu protein, Drosophila
  • RNA
  • Exonucleases