1. Hybrigenics SA, 180 avenue Daumesnil, Paris 75012, France
2. Unité de Pathogénie Bactérienne des Muqueuses, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France

Correspondence to: Pierre Legrain¹ Correspondence and requests for materials should be addressed to P.L. (e-mail: Email: plegrain@hybrigenics.fr).

With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function¹. As elementary constituents of cellular protein complexes and pathways, protein–protein interactions are key determinants of protein function. Here we have built a large-scale protein–protein interaction map of the human gastric pathogen Helicobacter pylori. We have used a high-throughput strategy of the yeast two-hybrid assay to screen 261 H. pylori proteins against a highly complex library of genome-encoded polypeptides². Over 1,200 interactions were identified between H. pylori proteins, connecting 46.6% of the proteome. The determination of a reliability score for every single protein–protein interaction and the identification of the actual interacting domains permitted the assignment of unannotated proteins to biological pathways.