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Open Access Research article

A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

Nicolas Lenfant1, Jolanta Polanowska13, Sophie Bamps12, Shizue Omi13, Jean-Paul Borg1 and Jérôme Reboul13*

Author affiliations

1 Inserm, U891, CRCM, Marseille, F-13009, France; Institut Paoli-Calmettes, Marseille, F-13009, France; Univ Méditerranée, F-13007, Marseille, France

2 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT, UK

3 CIML, Parc Scientifique et Technologique de Luminy Case 906 - 13288 Marseille - Cedex 9, France

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Citation and License

BMC Genomics 2010, 11:671  doi:10.1186/1471-2164-11-671

Published: 26 November 2010

Abstract

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 webcite) consortium through IntAct (PMID: 19850723) and assigned the identifier IM-14654]