6.2 Prokaryotic transcription

The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant plasmids , which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance.

Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand    . The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand    . The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A–T pairing in a DNA double helix.

The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site    . Nucleotides preceding the initiation site are given negative numbers and are designated upstream    . Conversely, nucleotides following the initiation site are denoted with “+” numbering and are called downstream    nucleotides.

Initiation of transcription in prokaryotes

Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.

Our discussion here will exemplify transcription by describing this process in Escherichia coli , a well-studied bacterial species. Although some differences exist between transcription in E. coli and transcription in archaea, an understanding of E. coli transcription can be applied to virtually all bacterial species.

Prokaryotic rna polymerase

Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli , the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted α , α , β , and β ' comprise the polymerase core enzyme    . These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two α -subunits are necessary to assemble the polymerase on the DNA; the β -subunit binds to the ribonucleoside triphosphate that will become part of the nascent “recently born” mRNA molecule; and the β ' binds the DNA template strand. The fifth subunit, σ , is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without σ , the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme    .