A Tissue-Specific Protein Purification Approach in Caenorhabditis Elegans Identifies Novel Interaction Partners of DLG-1/Discs Large

BMC Biol. 2016 Aug 9;14:66. doi: 10.1186/s12915-016-0286-x.

Abstract

Background: Affinity purification followed by mass spectrometry (AP/MS) is a widely used approach to identify protein interactions and complexes. In multicellular organisms, the accurate identification of protein complexes by AP/MS is complicated by the potential heterogeneity of complexes in different tissues. Here, we present an in vivo biotinylation-based approach for the tissue-specific purification of protein complexes from Caenorhabditis elegans. Tissue-specific biotinylation is achieved by the expression in select tissues of the bacterial biotin ligase BirA, which biotinylates proteins tagged with the Avi peptide.

Results: We generated N- and C-terminal tags combining GFP with the Avi peptide sequence, as well as four BirA driver lines expressing BirA ubiquitously and specifically in the seam and hyp7 epidermal cells, intestine, or neurons. We validated the ability of our approach to identify bona fide protein interactions by identifying the known LGL-1 interaction partners PAR-6 and PKC-3. Purification of the Discs large protein DLG-1 identified several candidate interaction partners, including the AAA-type ATPase ATAD-3 and the uncharacterized protein MAPH-1.1. We have identified the domains that mediate the DLG-1/ATAD-3 interaction, and show that this interaction contributes to C. elegans development. MAPH-1.1 co-purified specifically with DLG-1 purified from neurons, and shared limited homology with the microtubule-associated protein MAP1A, a known neuronal interaction partner of mammalian DLG4/PSD95. A CRISPR/Cas9-engineered GFP::MAPH-1.1 fusion was broadly expressed and co-localized with microtubules.

Conclusions: The method we present here is able to purify protein complexes from specific tissues. We uncovered a series of DLG-1 interactors, and conclude that ATAD-3 is a biologically relevant interaction partner of DLG-1. Finally, we conclude that MAPH-1.1 is a microtubule-associated protein of the MAP1 family and a candidate neuron-specific interaction partner of DLG-1.

Keywords: Affinity purification; C. elegans; Discs large; Mass spectrometry; Microtubule-associated; Protein complex; Tissue-specific.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Biotinylation
  • Caenorhabditis elegans / metabolism*
  • Caenorhabditis elegans Proteins / isolation & purification*
  • Caenorhabditis elegans Proteins / metabolism
  • Fluorescent Antibody Technique
  • Guanylate Kinases / metabolism*
  • Multiprotein Complexes / isolation & purification
  • Neurons / metabolism
  • Organ Specificity*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping / methods*
  • Protein Transport
  • Reproducibility of Results

Substances

  • Caenorhabditis elegans Proteins
  • Multiprotein Complexes
  • DLG-1 protein, C elegans
  • Guanylate Kinases