Prokaryotes have only one type of RNA polymerase for the transcription of all types of genes (structural as well as RNA genes). But different sigma factors may associate with the same core enzyme at different times for expression of different genes. In E.coli, a70 is used in normal condition 832/ 8H under heat shock, o54 / cN under Nitrogen starvation and a28 for chemo taxis.
The transcription is initiated by the binding of the holocnzyme to the promoter. The o (sigma) polypeptide of the holocnzyme binds loosely to a sequence of the promoter even before the opening of the DNA double helix.
Thus a loose/ closed binary complex is formed. After this complcx is formed the adjaccnt sequence of the DNA denatures forming a transcription eye or bubble. The denaturing facilitated as the promoter region is AT rich. This transcription bubble along with the bound holoenzyme is called an open binary complex.
The transcription start point is a purine in 90% of cases. The first and the second nucleotide complementary to the first two nucleotides of the template strand binds at the elongation site of the enzyme. A phosphodiester bond is formed between these two ribonucleotides by a hydrophilic attack of the 3′ -OH group of the first ribonucleotide triphosphate on the first phosphate bond of the second nucleotide so that a pyrophosphate (P-P) is released in this reaction. Xow the complex consists of a partly denatured DNA bound with the holoenzyme having a di-ribonucleotide.
This complex is known as a ternary complex.More ribonucleotides are added without any movement of the holoenzyme so that a RNA chain of about nine nucleotides is synthesized. During the incorporation of the nucleotides in the initial stage, there is the possibility for the release of small RNA chains, a process described as abortive initiation.
A cycle of such abortive initiation occurs before the definitive initiation begins. Once the initiation succeeds, the sigma factor dissociates from RNA polymerase, leaving the core enzyme for the elongation of RNA chain. The dissociation of sigma facilitates promoter clearance of core enzyme so that another holoenzyme may bind to promoter for another round of transcription to begin.
Elongation of RNA chain takes placeby the addition of ribonucleotides to the 3′-end of the RNA so that the RNA chain grows in 5′-3′ direction.
In prokaryotes, termination of transcription is brought about by certain termination signals on DNA called terminators (these are DNA sequences). In E.coli the termination signals fall under two categories, such as:
1. Intrinsic terminators or protein factor rho (r) independent.
2. Extrinsic terminator or rho dependent
In the intrinsic termination, the RNA at its 3′-cnd contains a long stretch of U residues Hydrogen bonded to the long stretch of A residues of the template. In the stem of the RNA, there is a stretch of G-C reach segment. The G-C reach segment results in a hair-pin loop formation in the RNA stem. As a result the weak association between A-U in the long stretch of termination sequence break and the RNA is released.
This happens because the formation of hair-pin loop in the stem of RNA before the termination signal slows down transcription and as a result dA-rU bonds break at any one point releasing RNA from RNA-DNA hybrid.
In extrinsic termination rho protein is required. It is an important protein factor responsible for termination of transcription of many genes in E.coli. This protein is active as a hexamer (having six identical subunits). It has a molecular weight of 46,000 and also has ATP hydrolyzing activity. Rho factor binds to the 5′-end of nascent m-RNA and scans down along the length of m-RNA until it rcachcs the termination point. At termination point when the transcription slows down rho breaks ATP and utilizes that energy to denature the RNA-DNA hybrid so that the RNA is released from the bubble.
In prokaryotes, as many structural genes arc contiguously present and are transcribed together the transcribed mRNA is polycistronic.