Protein Interaction Maps  - PIMs

Many biological processes are controlled by networks of interacting proteins. These networks constitute the regulatory pathways that control cellular behavior; i.e., they determine whether a cell grows, divides, dies, differentiates, and how it communicates with other cells. Groups of interacting proteins also form the basis for the molecular machines that carry out fundamental processes such as DNA replication and transcription. An initial understanding of how most biological processes work, therefore, would be gained by knowing how the various proteins interact with each othe; i.e., by mapping the interactome. Since the early 1990s we have been developing two-hybrid technology to enable us to sample all possible binary interactions among large sets of proteins (e.g., see Finley and Brent 1994 and list of papers). We set out to use this technology to construct a map of the interactions among most of the ~14,000 proteins from the fruit fly, Drosophila.

MAPPING THE PROTEIN-PROTEIN INTERACTIONS ENCODED BY THE DROSOPHILA GENOME 

In collaboration with the Finley lab, scientists at Curagen Corp., amplified 12,278 Drosophila open reading frames (ORFs) and subcloned them into the Gal4-based yeast two-hybrid system. Results from the interaction screens with these clones, in which 20,405 interactions were detected among ~7,048 proteins, have been published (Giot et al. 2003, Science 302, 1727-1726).

The Finley lab subcloned the same amplified ORFs into a modified LexA-based two-hybrid system. Initial screening with the LexA two-hybrid arrays has shown that interactions found in common with the Gal4 screens are enriched for high confidence interactions, but that the overlap between the LexA and Gal4 data is small, owing largely to the incomplete nature of both high throughput screens (Stanyon et al, 2004, Genome Biology 5, R96). In an effort to construct more comprehensive interaction maps, we continued to screen the LexA arrays using a novel screening approach (Zhong et al., 2003, Genome Research 13, 2691-2699). Results from these screens appear in DroID prior to, or immediately after they are published.

Our Drosophila protein interaction data is being made available to the public through the following databases.

DroID - The Drosophila Interactions Database www.DroIDb.org

Flybase.org (which provides links to DroID)

EMBL-EBI Intact

BioGRID

This project has been supported in part by grants to the Finley lab from the National Institutes of Health, National Human Genome Research Institute (Grant Number HG01536) and by previous support from the Merck Genome Research Institute.

Finley lab, Center for Molecular Medicine & Genetics, Wayne State University School of Medicine

Return to Projects