Archaeal RNA polymerase subunits e and F are not required for transcription in vitro, but a thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive

All archaeal genomes encode RNA polymerase (RNAP) subunits E and F that share a common ancestry with the eukaryotic RNAP subunits A43 and A14 (Pol I), Rpb7 and Rpb4 (Pol II), and C25 and C17 (Pol III). By gene replacement, we have isolated archaeal mutants of Thermococcus kodakarensis with the subunit F-encoding gene (rpoF) deleted, but we were unable to isolate mutants lacking the subunit E-encoding gene (rpoE). Wild-type T. kodakarensis grows at temperatures ranging from 60°C to 100°C, optimally at 85°C, and the ΔrpoF cells grew at the same rate as wild type at 70°C, but much slower and to lower cell densities at 85°C. The abundance of a chaperonin subunit, CpkB, was much reduced in the ΔrpoF strain growing at 85°C and increased expression of cpkB, rpoF or rpoE integrated at a remote site in the genome, using a nutritionally regulated promoter, improved the growth of ΔrpoF cells. RNAP preparations purified from ΔrpoF cells lacked subunit F and also subunit E and a transcription factor TFE that co-purifies with RNAP from wild-type cells, but in vitro, this mutant RNAP exhibited no discernible differences from wild-type RNAP in promoter-dependent transcription, abortive transcript synthesis, transcript elongation or termination.