RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro

Adaptation of bacterial cells to diverse habitats relies on the ability of RNA polymerase to respond to various regulatory signals. Some of these sign als are conserved throughout evolution, whereas others are species specific . In this study we present a comprehensive comparative analysis of RNA poly merases from two distantly related bacterial species, Escherichia coli and Bacillus subtilis, using a panel of in vitro transcription assays. We found substantial species-specific differences in the ability of these enzymes t o escape from the promoter and to recognize certain types of elongation sig nals. Both enzymes responded similarly to other pause and termination signa ls and to the general E. coli elongation factors NusA and GreA. We also dem onstrate that, although promoter recognition depends largely on the a subun it, promoter discrimination exhibited in species-specific fashion by both R NA polymerases resides in the core enzyme. We hypothesize that differences in signal recognition are due to the changes in contacts made between the b eta and beta' subunits and the downstream DNA duplex.