Locations and nucleotide sequences of three major class III promoters for bacteriophage T3 RNA polymerase on T3 DNA

The DNA sequences of three major class III T3 RNA polymerase promoters located at 45.0, 55.0, and 64.8% on the standard T3 genetic map have been determined. The precise RNA initiation sites were also determined by 5'-terminal RNA sequence analysis of the transcripts synthesized from the promoter-containing DNA fragments. Alignment of these three class III promoters and a previously determined T3 RNA polymerase promoter at 1.05% on T3 genetic map, with start points of transcription (+1) in register, indicates a high degree of sequence conservation among the four T3 RNA polymerase promoters. The sequences are identical between positions -12 and +4 and are uniformly A-T between -12 and -17. The conserved portion of the (-) strains sequence is 5'...AT-A-AT-T-TA-A-C-C-C-T-+1 C-A-C-T-A-A-A-G-G-G-A-...3'. Upstream from -17 and downstream from +4 the sequences diverge. Comparison of this sequence with a prototype 23-base pair promoter sequence for T7 RNA polymerase shows overall homology between positions-17 and +4 with conserved devergence at residues -1 and between -10 and -12. Furthermore, careful examination of the nucleotide sequences around 45.0 and 64.8 T3 map units shows that the putative RNA sequences arising from these regions by overlapping transcription from upstream promoters can be arranged into stable stemloop structures thought to be required for RNase III cleavage. This pattern is similar to those reported for the corresponding T7 RNA polymerase promoters on T7 DNA (Dunn, J.J., and Studier, F.W. (1983) J. Mol. Biol. 166, 477-535).