Macromolecular interactions, of which protein interactions constitute a major part, form the basis of most or all biological activity. Our long term goal is to further our knowledge of the molecular interactions that underlie multicellular development. Recent genome wide RNAi screens have identified 740 C. elegans genes required for early embryogenesis. These genes form an ideal starting point for a systems level approach to understanding embryonic development. We will use a novel application of the yeast two-hybrid (Y2H) system based on screening a library of fragments to identify the minimal domains mediating interactions between the early embryogenesis proteins. Current interaction networks do not take into account that many proteins consist of multiple independently folding domains. By explicitly considering the modular nature of proteins, the network we will generate more accurately represents the underlying biology, and can yield more detailed hypotheses. In addition to identifying interaction domains, using a fragment library increases the coverage of the interaction network by lowering the false negative rate. To further increase the predictive value of the network we will integrate the protein interactions with existing phenotypic characterizations and expression data. To generate the interaction network, we will generate a prey library containing multiple (~40) fragments for each of the 740 early embryogenesis genes, and query this library using ~200 of the 740 proteins as bait. We will focus on proteins involved in the core mitotic machinery, polarity establishment, and human disease. However, as the library already contains fragments of all 740 genes, the network can easily be expanded to encompass all early embryogenesis genes in the future. The 740 early embryogenesis genes are involved in highly conserved processes, as indicated by the fact that 545 have homologs in human of which 59 are implicated in disease. The integrated interaction network generated will therefore be very valuable to both C. elegans researchers and others studying animal development. ? ? ?
| Boxem, Mike; Maliga, Zoltan; Klitgord, Niels et al. (2008) A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134:534-45 |
