Genome-wide protein interaction maps using two-hybrid systems

Automated sequence technology has rendered functional biology amenable to g enomic scale analysis. Among genome-wide exploratory approaches, the two-hy brid system in yeast (Y2H) has outranked other techniques because it is the system of choice to detect protein-protein interactions. Deciphering the c ascade of binding events in a whole cell helps define signal transduction a nd metabolic pathways or enzymatic complexes, The function of proteins is e ventually attributed through whole cell protein interaction maps where tota lly unknown proteins are partnered with fully annotated proteins belonging to the same functional category. Since its first description in the late 19 80's, several versions of the Y2H have been developed in order to overcome the major limitations of the system, namely false positives and false negat ives. Optimized versions have been recently applied at multi-molecular and genomic scale. These genome-wide surveys can be methodologically divided in to two types of approaches: one either tests combinations of predefined pol ypeptides (the so-called matrix approach) using various short-cuts to speed up the process, or one screens with a given polypeptide (bait) for potenti al partners (preys) present in complex libraries of genomic or complementar y DNA (library screening). In the former strategy, one tests what one knows , for example pair-wise interactions between full-length open reading frame s from recently sequenced and annotated genomes. Although based on a one-by -one scheme, this method is reported to be amenable to large-scale genomics thanks to multicloning strategies and to the use of small robotics worksta tions. In the latter, highly complex cDNA or genomic libraries of protein d omains can be screened to saturation with high-throughput screening systems allowing the discovery of yet unidentified proteins. Both approaches have strengths and drawbacks that will be discussed here, None yields a full pro teome-wide screening since certain proteins (e.g. some transcription factor s) are not usable in Y2H, Novel two-hybrid assays have been recently descri bed in bacteria. Applications of these time- and cost-effective assays to g enomic screening will be discussed and compared to the Y2H technology. (C) 2000 Federation of European Biochemical Societies. Published by Elsevier Sc ience B.V. All rights reserved.