Similar subunit architecture of archaeal and eukaryal RNA polymerases

Protein interactions among RNA polymerase small subunits from the archaeon Methanococcus jannaschii were investigated using affinity pulldown assays i n pairwise and higher-order combinations. In the most extensive study of ar chaeal RNA polymerase subunit interactions to dare. including 37 pairs of p roteins. 10 ternary combinations, and three quaternary combinations, we fou nd evidence for pairwise interactions of subunit D with subunits L and N. a nd a ternary complex of subunits D, L and N. No other small subunit interac tions occurred. These results are consistent with interactions observed in a crystal structure of eukaryotic RNA polymerase II and support a common ar chaeal/eukaryal RNA polymerase architecture. We further propose that subuni t E-n is not an integral member of archaeal RNA polymerases. Finally, we di scuss the relative accuracy of the various methods that have been used to p redict protein-protein interactions in RNA polymerase. (C) 2001 Federation of European Microbiological Societies, Published by Elsevier Science B.V. A ll rights reserved.