Transcription Mechanisms in Prokaryotes

In prokaryotes, binding of the polymerase's s factor to promoter can catalyze unwinding of the DNA double helix.  The most important s factor is Sigma 70, whose structure has been determined by x-ray crystallography.

(a)

      

(b)

Figure 4-D-1.  The structure of Sigma 70 and its DNA binding site.  (a) Structure of Sigma 70, residues 114 to 448.  PDB ID = 1SIG.  (b) A model for the binding between Sigma 70 and the promoter, based on biochemical studies.  Residues Y425, Y430, W433 and W434 are directly involved in the unwinding (melting) of the double helix.

Note that the promoter is rich in A and T.  The AT pair involves two hydrogen bonds whereas the CG pair involves three hydrogen bonds.  Therefore, AT pairs are easier to separate.  The DNA replication origin is also rich in A and T. 

After the DNA strands are separated at the promoter region, the core polymerase (aabb') can then start to synthesize RNA based on the sequence of the DNA template strand (see .  Since the role of the s factor is mainly to initiate transcription, it will be released after about 10 ribonucleotides have been polymerized.

Elongation of the RNA strand continues until the core polymerase reaches the termination site 

Regulation by Transcription Factors

Regulation of the lac operon transcription by
Catabolite Activator Protein (CAP) and lac Repressor

Activation of the glnA transcription by
Nitrogen Regulatory Protein C (NTRC)
(Example of DNA looping)