Investigating protein–protein interactions in multisubunit proteins: the case of eukaryotic RNA polymerases

The physiological functions executed by eukaryotic cells are often catalyzed by large multiprotein complexes. Very few complexes have been analyzed at a detailed structural level, and one therefore strongly relies on generic but indirect methods to establish protein–protein interaction maps between the polypeptide subunits of these complexes, and to delineate the relevant interacting domains. Currently, the two more popular approaches are based on protein “pull-down” assays, where the ability of two partner polypeptides is measured by fast copurification tests, and by two-hybrid interaction mapping, where interacting proteins reconstitute a functional heterodimeric transcriptional activator in vivo. If carefully implemented, both provide important insight into the organization of multiprotein complexes. The predictive power of these approaches will be assessed at the light of our current knowledge of eukaryotic DNA-dependent RNA polymerases. Keywords: protein–protein interactions; transcription; DNA-dependent RNA polymerase; multisubunit protein complexes; Saccharomyces cerevisiae