Effect of guanosine tetraphosphate (ppGpp) on the conformational state ofE. coli RNA polymerase and transcription directed by tyrT, T7D, and T7A1 promoters

Abstract

Guanosine tetraphosphate (ppGpp) is an allosteric regulator of DNA-dependent RNA polymerase. It selectively inhibits transcription from some promoters containing the GC-rich sequence near the starting point of transcription. Using the method of the fluorescent label it was shown that interacting with the β-subunit of the enzyme ppGpp induces essential conformational transitions of the RNA polymerase. The mutation in the enzyme β-subunit that increases the polymerase affinity for T7D promoter affects ppGpp-induced conformational changes. The rate of the abortive RNA synthesis directed by the mutant enzyme from this promoter, which contains no GC-rich sequences near the starting point appeared to be ppGpp-dependent. ppGpp has no effect on T7D activity in the system containing the native enzyme. Thus, the regulatory function of ppGpp depends on the structure of the RNA polymerase and could be realized by the enzyme not only by recognition of the GC-rich block in the promoter.