The overall process of transcription is conserved between prokaryotes and eukaryotes, but a number of the details of this process are remarkably different. The first major difference is the RNA polymerase itself. In eukaryotes, it is a 4 subunit complex, and one polymerase is responsible for the transcription of all types of RNA. In eukaryotes, the RNA polymerase is a large 12 subunit complex, and three separate RNA polymerases are found. RNA polymerase I is responsible for transcribing rRNA, RNA pol. II transcribes mRNA and snRNA, and RNA pol. III transcribes tRNA and rRNA.
The promoter regions that are upstream of genes are also different in eukaryotes and prokaryotes. There are two key regions that are found within a prokaryotic promoter are located -10 and -35 base pairs upstream from the first transcribed nucleotide. The -10 site has a consensus nucleotide sequence of TATAAT and the -35 consensus sequence is TTGACA (Vassylyev, et al, 2002). These key promoter regions are recognized by the σ subunit of RNA polymerase. The eukaryotic promoter is far more complex and variable than the prokaryotic promoter. Several conserved regions do exist, however. A conserved TATA sequence is located at approximately the -25 position upstream of the start site. An initiator element is located between the -3 and +5 region. Eukaryotic promoters may contain this combination of recognition sites, but it is not a necessity. Other promoter elements are found in different eukaryotic promoter regions. The binding of various promoter regions to the transcription factors associated with RNA polymerase allows for greater regulation of transcription regulation.
As mentioned, only one additional subunit, or transcription factor, is required for promoter recognition in prokaryotes. The sigma factor binds to promoter regions and to bacterial RNA polymerase to initiate transcription (Vassylyev, et al, 2002). Eukaryotes require the assembly of a number of transcription factors, including TFIIB, -D, -E, -F, and -H as well as a mediator complex to begin transcription (Armache, et al, 2003).
Unlike the process in eukaryotes, the transcription initiation factor dissociates from RNA polymerase following the start of the elongation phase (Vassylyev, et al, 2002). This leads to a conformational change in the transcribing RNA polymerase. Eukaryotes maintain an association with the transcription factors, with the exception of the mediator complex, throughout elongation as these are necessary for an actively transcribing enzyme.
As a result of only binding one transcription factor, the bacterial enzyme must perfom many of the common actions of transcription without the aid of additional subunits used by eukaryotes. The processes of binding to the template strand and unwinding the double stranded DNA to form a transcription bubble (from about -12 to +2) is performed by the RNA polymerase holoenzyme (Vassylyev, et al, 2002). This same process in eukaryotes creates a slightly larger bubble (about -12 to +4) and is completed by the associated TFIIH and its helicase activity in eukaryotes (Gnatt, et al, 2001).
The elongation process itself is fairly well conserved between the two cell types. Several conserved aspartate residues and Mg ions are located at the active site, where nucleotides will enter and base pair to the DNA template strand (Vassylyev, et al, 2002). The translocation of the RNA polymerase following the formation of a phosphodiester bond is also similar. A bridge helix spanning the cleft between the two largest subunits exists in both types of RNA polymerase. The bending of this helix causes the translocation of the polymerase (Vassylyev, et al, 2002) (Cramer, et al, 2001).
Termination also differs between prokaryotes and eukaryotes. In eukaryotes, the release of the mRNA transcript is facilitated by the transcription factor TFIIS (Kettenberger, 2003). In prokaryotes, two common methods of termination are seen. First, G-C rich regions at the end of a transcript may form a stem loop structure that will pause the RNA polymerase and allow the RNA strand to dissociate from RNA polymerase in rho-independent termination. Rho-dependent termination involves the activity of the Rho factor, which recognizes C-rich regions of the transcript and cleaves it through ATPase activity (Henkin, 1996).
Other factors relating to the processing of transcribed mRNA are unique to eukaryotes. A eukaryotic transcript contains introns, which are non-coding sequences that are spliced out of the message before it is translated. Eukaryotic mRNA is also modified by a 5’ methyl cap and a 3’ polyA tail, both of which do not exist in prokaryotes.