Comparison of Prokaryotic and Eukaryotic transcription


Comparison

Eukaryotes and prokaryotes follow a common path through transcription. For instance both go through an initiation, elongation, and termination phase. There are some conserved domains that are found between prokaryotic polymerase and eukaryotic polymerase II. For instance the bridge helix, which is involved in translocation of the Polymerase in porkaryotes and eukaryotes, is conserved, however the bridge helix in prokaryotes is always bent where as the bridge helix is straight in eukaryotes6. Another conserved domain is the rudder (the loop that is closest to the active center). The active center is also conserved in both prokaryote and eukaryotes.

There are however some marked differences between the two.  Prokaryotic transcription is much simpler than eukaryotic transcription. For instance prokaryotes have only one RNA polymerase that carries out the complete process of transcription. Eukaryotes on the other hand have three polymerases (Pol I, Pol II, and Pol III) that carry out different processes involved in the synthesis of protiens1. Furthermore each eukaryotic polymerase carries out its necessary functions at different locations in the cell. Prokaryotic transcription is carried out in the cytoplasm, where transcription is coupled with translation1. This is probably due to the fact that it takes place in the cytoplasm and is subjected to nuclease degradation.

Another difference between prokaryotic and eukaryotic transcription are the subunits that make up the polymerases themselves. The prokaryotic polymerase is made up of four subunits alpha, beta, beta’, and omega subunits1. Eukaryotic Pol II is made up of 10 subunits. Rpb1 and Rpb2 make up the bulk of the complex6. Prokaryotes utilize a transcription factor sigma which is the smallest subunit of the structure that can easilty associate and dissociate from the core subunits. The sigma subunit is used to loosely bind the DNA and slide along the DNA backbone in search of a promoter. On the other hand Pol II in eukaryotes uses two small subunits Rpb4/Rpb7 to bind and scan the DNA. Promoter sequences vary as well between prokaryotes and eukaryotes. Prokaryotes contain a -10 (pribnow’s box) and -35 sequence that serves as a promoter for the polymerase to bind to and initiate transcription. In eukaryotes there is a TATA box that is -25 bp from the start site that Rpb4/Rpb7 use to initiate transcription1.

Termination is quite diiferent among prokaryotes and eukaryotes also. In prokaryotes there are two paths that can be taken for termination. One is the rho-independent pathway and the other is the rho-dependent pathway. The rho-independent pathway depends on a palindromic termination sequence that encodes a stem-loop structure and once the polymerase encodes this palindromic sequence it pauses and the weak interaction of the RNA-DNA hybrid allows it to dissociate from the polymerase1. In the rho-dependent pathway a protein known as rho binds to the newly transcribed mRNA and slides along it towards the polymerase. Once it reaches the polymerase it causes dissociation of the mRNA from the polymerase1. In eukaryotes termination is dependent upon two things a poly (A) signal and a downstream terminator sequence7. The poly (A) tail is encoded along with the mRNA transcript for protection from degradation. The terminator sequnce causes the polymerase to pause and then to ultimatley dissociate from the DNA and breakdown.

The figures used in this image are 1I50 and 1HQM
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