| ||
| ||
|
|
|
Transcription in prokaryotes and eukaryotes differ in very unique ways. Although the protein has to be homologous enough to have the components needed for polymerizing transcripts as described in the overview. Since the components are for the most part are similar between the two RNA polymerases, elongation is fairly similar. Initiation and termination, however, differ greatly. There is considerable sequence and structural homology between prokaryotic and eukaryotic polymerases. However, RNA polymerase for prokaryotes has five subunits, while eukaryotic RNA polymerase has twelve (1). Initiation: Prokaryotic transcription initiation is done by the holoenzyme. The holoenzyme is composed of the RNA polymerase, called the core, and an initiation specific subunit called a sigma factor. Although the core shares significant homology to RNA polymerase II, sigma factor shares almost no homology to the eukaryotic counterparts, the transcription factors (1). Prokaryotic initiation first starts when the holoenzyme recognizes two conserved hexamers in the promoters. These two hexamers are located at the -10 and -35 position. Along with RNA polymerase, the three subunits of the sigma factor bind to both the DNA and to the core enzyme to form an extremely stable complex (1). After the open complex is formed and the transcription bubble is created, the introduction of ribonucleotides is possible. Polymerization starts during this part if initiation, and goes into elongation as soon as the sigma subunit dissociates from the core polymerase (1). The end of transcription initiation is vaguer in eukaryotes. Instead of a sigma unit forming the initiation complex, the complex of a eukaryotic system is created by the polymerase and multiple transcription factors as described in the Eukaryotic Transcription page. The end of initiation is sometimes described as polymerase escaping from the promoter and away from the +1 site (3). Other times initiation ends when certain transcription factors are removed from the complex. Elongation: For the most part the mechanism for elongation is similar between prokaryotic and eukaryotic RNA polymerase. The majority of the polymerization of NTP molecules to form a long, single stranded RNA molecule occurs during this stage. As described in the Eukaryotic Transcription page, by simple guess and check, RNA polymerase allows the NTPs to hybridize to the DNA template through simple base pairing (4). At transcription termination the mechanisms for prokaryotic and eukaryotic transcription differ. Termination: For prokaryotes the simplest form of transcription initiation involves the formation of hairpin loops. This is formed by a long string of uridine residues that comes after a cytosine and guanine sequence in dyad symmetry (3). This simply means that there is a sequence of C and G residues that are then repeated in the reverse order. This will then create a C-G self base pair in order to form a hairpin loop. The uridine residues form weak hydrogen bonds. Since the hydrogen bonds between the DNA template and the mRNA strand are weak, the transcript can escape from the template. Transcription termination by polymerase II is not very well known. In higher level organisms the formation of a hairpin-like structure is seen. This loop is needed to terminate transcription. Another protein independent part of termination includes attenuators. Prokaryotes use attenuators to weaken the polymerizing RNA strand from the DNA template. As far as studies report eukaryotes only use the hairpin-like structure to help facilitate termination (3). All that is known for sure is that there are parts in gene that are necessary for transcription termination. Another large difference between prokaryotic and eukaryotic transcription termination are the different factors that are involved in it. A big player in termination for prokaryotes is rho factor. This particular protein binds to a sequence on the building transcript. In conjuncture with a pause site on the gene where the polymerase stops temporarily, the rho protein can facilitate termination (5). It has been suggested that a rho-like factor is involved in termination. Other parameters might also facilitate in the termination of transcription. Attenuation is not possible due to the compartmentalization of eukaryotic cells. In higher organisms, chromatin conformation may play a part in termination, but the mechanism has not been worked out (3).
|