Prokaryotic transcription

Prokaryotic transcription occurs in the cytoplasm alongside translation.

Initiation

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The following steps occur, in order, for transcription initiation:

• RNA polymerase (RNAP) recognizes and specifically binds to the promoter region on DNA. At this stage, the DNA is double-stranded ("closed"). This RNAP/wound-DNA structure is referred to as the closed complex.
• The DNA is unwound and becomes single-stranded ("open") in the vicinity of the initiation site (defined as +1). This RNAP/unwound-DNA structure is called the open complex.
• The RNA polymerase transcribes the DNA, but produces about 10 abortive (short, non-productive) transcripts which are unable to leave the RNA polymerase because the exit channel is blocked by the σ-factor.
• The σ-factor eventually dissociates from the holoenzyme, and elongation proceeds.

Promoters can differ in "strength"; that is, how actively they promote transcription of their adjacent DNA sequence. Promoter strength is in many (but not all) cases, a matter of how tightly RNA polymerase and its associated accessory proteins bind to their respective DNA sequences. The more similar the sequences are to a consensus sequence, the stronger the binding is.

Most transcripts originate using adenosine-5'-triphosphate (ATP) and, to a lesser extent, guanosine-5'-triphosphate (GTP) (purine nucleoside triphosphates) at the +1 site. Uridine-5'-triphosphate (UTP) and cytidine-5'-triphosphate (CTP) (pyrimidine nucleoside triphosphates) are disfavoured at the initiation site.

Termination

Two termination mechanisms are well known:

• Intrinsic termination (also called Rho-independent transcription termination) involves terminator sequences within the RNA that signal the RNA polymerase to stop. The terminator sequence is usually a palindromic sequence that forms a stem-loop hairpin structure that leads to the dissociation of the RNAP from the DNA template.

• Rho-dependent termination uses a termination factor called ρ factor(rho factor) which is a protein to stop RNA synthesis at specific sites. This protein binds at a rho ultilisation site on the nascent RNA strand and runs along the mRNA towards the RNAP. A stem loop structure upstream of the terminator region pauses the RNAP, when ρ-factor reaches the RNAP, it causes RNAP to dissociate from the DNA, terminating transcription.

Other termination mechanisms include where RNAP comes across a region with repetitious thymidine residues in the DNA template, or where a GC-rich inverted repeat followed by 4 A residues. The inverted repeat forms a stable stem loop structure in the RNA, which causes the RNA to dissociate from the DNA template.

The -35 region and the -10 ("Pribnow box") region comprise the basic prokaryotic promoter, and |T| stands for the terminator. The DNA on the template strand between the +1 site and the terminator is transcribed into RNA, which is then translated into protein..