A Drosophila protein-interaction map centered on cell-cycle regulators

Clement A Stanyon¹ , Guozhen Liu¹ , Bernardo A Mangiola¹ , Nishi Patel¹ , Loic Giot² , Bing Kuang² , Huamei Zhang¹ , Jinhui Zhong¹ and Russell L Finley Jr¹^,3

¹Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA

²CuraGen Corporation, 555 Long Warf Drive, New Haven, CT 06511, USA

³Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA

author email corresponding author email

Genome Biology 2004, 5:R96doi:10.1186/gb-2004-5-12-r96


Published:	26 November 2004

Subject areas: Molecular biology, Development

Abstract

Background

Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detect over 20,000 interactions among Drosophila proteins. Although these data are a valuable resource for insights into protein networks, they cover only a fraction of the expected number of interactions.

Results

To complement the Gal4-based interaction data, we used the same set of Drosophila open reading frames to construct arrays for a LexA-based two-hybrid system. We screened the arrays using a novel pooled mating approach, initially focusing on proteins related to cell-cycle regulators. We detected 1,814 reproducible interactions among 488 proteins. The map includes a large number of novel interactions with potential biological significance. Informative regions of the map could be highlighted by searching for paralogous interactions and by clustering proteins on the basis of their interaction profiles. Surprisingly, only 28 interactions were found in common between the LexA- and Gal4-based screens, even though they had similar rates of true positives.

Conclusions

The substantial number of new interactions discovered here supports the conclusion that previous interaction mapping studies were far from complete and that many more interactions remain to be found. Our results indicate that different two-hybrid systems and screening approaches applied to the same proteome can generate more comprehensive datasets with more cross-validated interactions. The cell-cycle map provides a guide for further defining important regulatory networks in Drosophila and other organisms.