PDZ domain proteins: 'dark matter' of the plant proteome?

PDZ domain proteins in metazoans function in diverse roles, and in conjunction with PDZ domain-binding proteins form macromolecular complexes for signaling at synapses and cell junctions. Bioinformatics approaches using the SMART tool indicate there are only a modest number of Arabidopsis PDZ proteins. However, there are hundreds of proteins predicted to possess PDZ domain-binding motifs, suggesting that there are many PDZ domain proteins not detectable by conventional bioinformatic approaches. Our Scansite analysis of PDZ domain-binding proteins indicates that PDZ domain proteins may play key roles in cytoskeletal organization including actin microfilaments, microtubules, and nuclear cytoskeletal proteins, and in the organization of macromolecular complexes involved in cell-to-cell signaling, transport, and cell wall formation.