MAPPING OF RNA-POLYMERASE BINDING-SITES IN THE H A GENE REGION OF BACTERIOPHAGE-S13 BY FOOTPRINTING AND EXONUCLEASE-III ANALYSIS/

The H/A gene region of the bacteriophage S13 genome (map positions 459 7 to 289) was analyzed for Escherichia coli RNA polymerase-binding sit es by combined DNase I footprinting, exonuclease III analysis and DNA sequencing. Two high-affinity binding sites were identified, one corre sponding to the A gene promoter at position 5384 to 56, overlapping th e H/A intergenic region at position 1 to 63, the other at position 517 1 to 5230, at the 3'-end of the H gene. A medium-affinity RNA polymera se binding site was mapped at position 4810 to 4850 in the middle of t he H gene upstream of a low-affinity site at position 5280 to 5330. Th e studies complete footprinting analyses of the S13 genome from positi on 4597 to 2198 and in combination with previous studies on transcript ion provide definitive evidence on the position of the A gene promoter in S13 and the closely related phage phi X174.