The primary aim of this project was to use five model systems to understand how genes and proteins cooperate locally and globally within the cell. The model systems included the prokaryote E. coli, the baker’s yeast S. cerevisiae, the nematode C. elegans, the mouse M. musculus and cultured mammalian cells.

The investigators used molecular tags and mass spectrometry to study protein-protein interactions in E. coli. In yeast, the group purified protein complexes to generate a protein-protein interaction network and used synthetic gene array technology to generate a genetic interaction network. The C. elegans project developed a new system that exploits yeast homologous recombination to subclone worm genes and generate a protein interaction network. In the mouse model system, gene expression was examined using mouse ES cells and gene-trap technology; ultimately, the investigators sought to identify regions of the genome involved in gene expression and normal mouse development. And finally, the investigators developed proteomics technologies for high-throughput cell-based protein-protein interaction screens and mass spectrometry-based analysis to understand how proteins communicate in human cells.

This project developed system-wide models of cell dynamics for five model systems: bacteria, yeast, worms, mice and cultured mammalian cells. It resulted in the first view of a prokaryotic protein interaction network and yielded the first genome-wide eukaryotic genetic network. Members of the yeast group also generated the largest dataset of yeast protein-protein interactions obtained using affinity chromatography/mass spectrometry. Members of the C. elegans project developed a new system that exploits yeast homologous recombination to enable efficient subcloning of worm genes. The murine system was used to study regulatory regions of the mouse genome and to develop mouse models of human disease. Large-scale mutagenesis screens generated more than 2000 abnormal mouse strains, 279 of which are carrying inherited mutations. Many of these strains are now being used to model human diseases such as osteoporosis. New tools for understanding protein interaction networks in mammalian culture models were also developed including a high-throughput cell-based assay, which has uncovered approximately 900 protein-protein interactions involved in a major intracellular signaling pathway.

This project lays the framework for studying protein and genetic networks in clinically relevant bacterial and eukaryotic systems, and for the study of digenic diseases in humans.