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Research has been conducted on the bacterial RNA polymerase holoenzymes. The use of the fluorescence energy transfer and distance-constrained docking in identifying the tree-dimensional structure of this holoenzyme and the open complex of the bacterial RNA polymerase-promoter in solution is discussed.

Results demonstrate that the sigma(sup)70 in the transcription complexes largely are not released from RNA polymerase upon transition from initiation to elongation during genetic transcription in bacteria. Data indicate that sigma(sup)70 stays associated with and translocates with RNA polymerase.

Transcription activation by Escherichia coli Class II catabolite activator protein (CAP) involves a second activating region for Class II CAP-dependent promoters. Random mutagenesis of the gene encoding CAP did not alter the transcription activation of Class I CAP-dependent promoters and deoxyribonucleic acid binding. The activation of Class II-dependent CAP promoters is also characterized by the interaction of the ribonucleic acid polymerase alpha subunit N-terminal domain and specific amino acids in the Class II-specific activating region of CAP.

The RNA polymerase holoenzyme (RNAP) of Escherichia coli consists of a 613 amino acid-long sigma(70) region that recognizes the -35 hexamer and -10 hexamer promoter elements and a 329 amino acid-long alpha region that recognizes the upstream (UP) element present 20 bp upstream of the -35 element. RNAP contains two individual targets for the proteins activating transcription. Both targets are present in the DNA-binding domain of RNAP, and the transcription activators catabolite gene activator protein (CAP) and bacteriophage lambda-cl protein function synergistically during transcription activation. The transcription activators support protein-protein interactions and recruit the DNA-binding domains in RNAP.

An N-terminal domain consisting of amino acids 8-241, an unstructured and flexible interdomain linker, and a C-terminal domain with amino acids 249-329 constitute the RNA polymerase alpha subunit of Escherichia coli. Structure of the alpha subunit is obtained using limited proteolysis. A well defined secondary structure is exhibited by the alpha C-terminal domain, which is also a dimer exhibiting sequence specific DNA binding activity.

Escherichia coli catabolite gene activator protein (CAP) is a dimer with two identical subunits, each having two activating regions. CAP activates transcription at the lac promoter. Oriented heterodimers were used to determine which activating region is needed for transcription activation at the lac promoter. Results show that the promoter-proximal subunit is the only activating region needed for transcriptional activation.