A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding.
BACKGROUND
Proteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and signaling complexes, and are generally thought to interact with their protein partners through a C-terminal consensus sequence. We undertook a comprehensive search for protein partners of all individual PDZ domains in C. elegans to characterize their function and mode of interaction.


RESULTS
Coupling high-throughput yeast two-hybrid screens with extensive validation by co-affinity purification, we defined a domain-orientated interactome map. This integrates PDZ domain proteins in numerous cell-signaling pathways and shows that PDZ domain proteins are implicated in an unexpectedly wide range of cellular processes. Importantly, we uncovered a high frequency of non-canonical interactions, not involving the C-terminus of the protein partner, which were directly confirmed in most cases. We completed our study with the generation of a yeast array representing the entire set of PDZ domains from C. elegans and provide a proof-of-principle for its application to the discovery of PDZ domain targets for any protein or peptide of interest.


CONCLUSIONS
We provide an extensive domain-centered dataset, together with a clone resource, that will help future functional study of PDZ domains. Through this unbiased approach, we revealed frequent non-canonical interactions between PDZ domains and their protein partners that will require a re-evaluation of this domain's molecular function.[The protein interactions from this publication have been submitted to the IMEx (http://www.imexconsortium.org) consortium through IntAct (PMID: 19850723) and assigned the identifier IM-14654].
Inserm, U891, CRCM, Marseille, F-13009, France.
Nicolas
N
Lenfant
Jolanta
J
Polanowska
Sophie
S
Bamps
Shizue
S
Omi
Jean-Paul
JP
Borg
Jérôme
J
Reboul
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D016384:Consensus Sequence / Q000235:genetics; D016678:Genome / Q000235:genetics*; D047468:Immunoprecipitation; D054731:PDZ Domains / Q000235:genetics*; D011485:Protein Binding / Q000235:genetics; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D015203:Reproducibility of Results; D020798:Two-Hybrid System Techniques
D029742:Caenorhabditis elegans Proteins; D020543:Proteome