Prokaryotes and eukaryotes have incredible similarities and differences in transcription. Both have considerably conserved areas of transcription, but both have several mechanisms that have diverged from each other.
There are several characteristics of transcription that are similar between prokaryotes and eukaryotes. The core is very conserved between the species from E. coli to humans (9). The active site is also quite conserved, both polymerases using magnesium ions to facilitate transcription, and a bridge helix to facilitate translocation of the enzyme. The “clamp”, and the “rudder” regions are structurally conserved between prokaryotes and eukaryotes (1). Abortive transcripts are also found in both prokaryotes and eukaryotes. The respective polymerases also bind to promoters, and have upstream elements that can enhance transcription.
While there are similarities between prokaryotes and eukaryotes, there are many differences between them. Prokaryotes have only one RNA Polymerase, while eukaryotes have three (RNA Polymerases I, which transcribes rRNA; II, which transcribes mRNA; and III, which transcribes tRNA). The difference in molecular weight between the prokaryotic polymerase and Pol II in eukaryotes is 100 kDa (400 kDa to 500 kDa). Prokaryotes have six subunits in their main polymerase (two alphas, a beta, a beta’, an omega, and a sigma), while eukaryotic polymerase II has twelve subunits (Rpb1-Rpb12) and seven transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, TFIIS). A small difference is present in the bridge helix of the active site; the prokaryotic active site has an always bent bridge helix, while the eukaryotic active site has a straight bridge helix that bends to facilitate translocation.
There are differences in initiation between prokaryotes and eukaryotes. There are different promoters each polymerase binds to. Prokaryotes bind to two promoters, one at the -10 position (the Pribnow box) and one at the -35 position. The eukaryotes bind at the -25 position, also known as the TATA box. There are different upstream enhancers between the polymerases, with UP elements and Fis sites in the prokaryotes, and a multitude of different upstream elements in the eukarytes, like the CAAT box and GC boxeswhich are bound to the polymerase by mediators (which are not known to occur in prokaryotes). The transcription bubble is created differently by each polymerase, with TFIIH using its helicase activity to “melt” the duplex DNA apart in eukaryotes, where the helicase activity is not required in prokaryotes.
After transcription, there are differences in termination and processing. Prokaryotes terminate transcription by either a Rho-dependent or Rho-independent pathway, which uses the instability of the hairpin loop. Eukaryotes use TFIIS cleavage after transcribing either pause sites or CoTC sites, followed by 5’-3’ degradation of the backtracked transcript. Eukaryotic transcripts are processed during and after elongation to preserve the transcript. This process includes capping and polyadenylation. Prokaryotes protect their transcript by coupling translation with transcription.