Transcription is a part of the central dogma of biology and describes the copying of a gene from the DNA to a messenger RNA (mRNA) which will then be translated to the protein. The copying process is very well understood, but differs in prokaryotic to eukaryotic organisms.

Within bacterial cells the circular chromosome contains elements that are sites for a multi-subunit enzyme, RNA polymerase, which catalyzes the transcription. The RNA polymerase is composed of five main subunits: Two α, β, β’, and ω subunits which are held together as a dimer. Additionally each of the core enzymes contain a sigma factor, σ, which is required to recognize and bind the DNA promoter region.

How does transcription initiate in E.Coli and other prokaryotic organisms?

The far right box designates the start to of the gene and the other parts make up the promoter region. The -10 region is known as the Pribnow box; it is required for prokaryotic transcription and is AT rich. The -35 region is upstream by 35 nucleotides from the gene start site and is not required for transcription, but genes with this sequence are transcribed faster. The sigma factor, σ, recognizes specific sequences in the promoter and facilitates the RNA polymerase to find and bind the promoter. There are many sigma factors that regulate different genes. In species of bacteria that survive many environmental factors so they can regulate different genes with the different sigma factors. σ70 is known as the housekeeping sigma factor which is responsible for basic functions, σ32transcribes heat-shock genes, σF signals flagellar proteins. So the sigma factors guide the RNA polymerase to the start of a specific operator sequence with the gene needed to be transcribed. When the RNA polymerase binds the promoter region it forms a halo enzyme.  To initiate transcription an open complex has to be formed for RNA nucleotides to bond with the template strand of DNA via Watson-Crick base pairing. The -10 regions, or Pribnow box, is AT rich because the bonding between the A-T residues is weaker than the C-G bonds. The open complex ion prokaryotic cells also forms without any energy input because the DNA is negatively supercoiled which provides the physical energy to open the stand.  The Pribnow box exists to allow the DNA to be melted and for the open complex to be formed so transcription can be initiates. The sigma factor is released when the RNA polymerase clears the promoter region allowing it to find another free RNA polymerase and guide it again to a specific promoter. The RNA polymerase enzyme contains an active site between the β’ subunits which forms a transcription bubble by separating the template strand from the non-coding strand of DNA. Transcription can then continue as free RNA nucleotides will bind to the 3’end of the mRNA sequence being generated and will use the template strand of DNA as a guide. The RNA bound to template DNA forms a heteroduplex  until transcription is ultimately terminated.

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