In vitro assembly of an archaeal D-L-N RNA polymerase subunit complex reveals a eukaryote-like structural arrangement

Archaeal RNA polymerases (RNAPs) resemble the eukaryotic nuclear RNAPs in c omplexity, and many of their subunits display a high degree of sequence sim ilarity to their eukaryotic counterparts. Here we describe specific protein -protein contacts present between individual recombinant RNAP subunits from the archaeon Methanococcus jannaschii, Subunits D and L interact specifica lly with each other in two-hybrid assays. D also interacts under the same c onditions with the RPB11 and AC19 subunits from the yeast Saccharomyces cer evisiae, suggesting that essential elements of the binding surface between these proteins have been conserved across the archaeal/eukaryotic evolution ary domain boundary. Interactions between L and RPB3 or AC40 were, however, not detectable. Recombinant D and L subunits associate under in vitro cond itions and copurify with each other during size-exclusion chromatography, A ddition of an another recombinant subunit (N) to the D-L complex results in the formation of a triple complex. This D-L-N complex resembles the RPBB-R PB11-RPB10 or AC40-AC19-RPB10 complexes in eukaryotic RNAP(II) and RNAP(I)/ RNAP(III) respectively. Our data provide evidence for a close similarity in the quaternary arrangement of a subset of archaeal and eukaryotic RNA poly merase subunits and the conservation of the protein-protein contacts formed between them.