Functional topology of the bacterial RNA polymerase. Multipoint monitoring by a fluorescent probe

Abstract

In bacterial transcription exchangeable G-subunits are responsible for interaction with core promoter DNA while C-terminal domain (CTD) of α-subunit may form additional contacts with more distal region, designated as UP-element. The αCTD is also involved in interaction with regulatory factors including well studied cAMP receptor protein (CRP) if its binding site is located in the upstream region. Genetic studies revealed amino acid residues of αCTD mostly important for UP-dependent transcription (L262, R265, N268, K297) which are also crucial for CRP-dependent activation [1]. To compare the topology of conformational changes during these two, different in nature, complex formations we used a fluorescent label which was positioned at various sites within the αCTD.