Figure comparing the basic cell structure of eukaryotes and prokaryotes.
Transcription occurs in both eukaryotes and certain prokaryotes through a DNA-dependent RNA polymerase (RNAP) which is involved in all the steps of the transcription cycle. This RNAP in both eukaryotes and prokaryotes are large, multisubunit enzymes. The transcription process in eukaryotes is highly regulated compared to prokaryotic transcription, allowing evolution of eukaryotes into multicellular organisms with distinct cell tissues and functions.
The polymerase II enzyme is the central core of the transcriptional machinery in eukaryotes consisting of 12 subunits. The largest subunit, Rpb1 contains the active site of the enzyme which is combined in a single fold of the polymerase with the second largest subunit, Rpb2. Rpb2 forms the hybrid-binding region, and both Rpb1 and Rpb2 form the active center of the enzyme which constitutes almost half of the total mass. The Rpb3, Rpb10, Rpb11, and Rpb12 are all involved in polymerase II assembly6. Rpb1, the “lobe” of Rpb2, and Rpb9 form the “upper jaw” region contained in the “jaw-lobe” component. The “shelf” module harbors the “lower jaw” which consists of Rpb5, Rpb6, and the “foot” and “cleft” regions of Rpb1. The Rpb4 and Rpb7 subunits are thought to be involved in a complex that recruits a dephosphorylation molecule, Fcp1, which dephosphorylates the carboxyl terminal domain of the polymerase II complex to end transcription allowing the RNAP to rejoin another initiation complex2.
Promoter specific initiation in eukaryotes requires more than a dozen basal initiation factors (see below), only a single polypeptide in bacteria, the sigma subunit, is required to bind to the core RNAP and forms the holoenzyme, which consists of just one subunit comprised of different domains12. The RNAP holoenzyme in bacteria consists of five subunits; alpha, alpha prime, beta, beta prime, and omega11.
These subunits have been found to have similar functions, structures, and sequences to specific subunits of eukaryotic polymerase II. Subunit beta prime, which is the largest subunit and has been found to be involved with catalysis, is correlated with the Rpb1 subunit. The bacterial RNAP beta subunit is the second largest subunit in the bacterial polymerase and has also been found to have catalytic activity, which has been compared to the Rpb2 subunit. The alpha and alpha prime subunits have the same sequence, but are located in different parts of the bacterial RNAP and each interacts with the different beta subunits11. These alpha subunits are found to be involved with transcription regulation and RNAP assembly, which correspond to the Rpb3 and Rpb11 subunits. The sigma subunit of bacterial RNAP is found to be similar to the eukaryotic Rpb6 subunit, and both of these subunits are found to promote RNAP assembly as well as increasing RNAP stability11. These findings suggest the eukaryotic and prokaryotic RNAPs share a core structure along with similar catalytic properties, but have different interactions with general transcription factors and regulatory factors due to the difference in peripheral and surface structure. The comparison between these two polymerases’ active sites can be seen with the corresponding button.
Transcription and Translation are completely separated processes in eukaryotes, transcription taking place in the nucleus and translation occurring in the cytoplasm. Prokaryotic cells do not have the spatial difference that eukaryotes have and the translation of the mRNA begins immediately as the transcript is being synthesized. This means that the mRNA being transcribed will not undergo much processing and modification. Eukaryotes have the ability to regulate and modify gene expression in much more complex and intricate ways due to the spatial separation of transcription and translation.
The complexity and number of subunits in the eukaryotic RNAP allow a much more complex regulation on all steps in transcription as compared to prokaryotic transcription. Prokaryotes contain three different promoter elements; -10, -35, and the upstream elements. Transcription factors are attracted by the sigma subunit of the bacterial RNAP, which will form the holoenzyme12. In eukaryotes, a variety of promoters has been found, including; the TATA-box, initiator elements, and downstream core promoter elements. These promoters all interact with various polymerase II transcriptional factors (TFIIA-H) in the assembly of the transcription apparatus. The ability of eukaryotic cells to have various promoter elements upstream and downstream of the start site along with various enhancers located on DNA allow for much more regulated/specialized transcription6.
Both enzymes will produce mRNA, however, mRNA produced from the eukaryotic and prokaryotic RNAP undergo different post-transcriptional modifications. Eukaryotes process the mRNA to a much higher extent. Prokaryotic modifications include the addition of CCA to the 3’ of some tRNA and rRNA, along with substantial cleaving and chemical modifications to rRNA and tRNA, but not to mRNA. mRNA usually undergoes translation before the entire strand is even transcribed, allowing little or no time for modifications. Eukaryotes undergo extensive splicing and modification processes before translation. This includes; splicing of introns, addition of a 5’ cap, and addition of a 3’ poly(A) tail8. These will help contribute to the increase in stability of the mRNA, enhancement of transcription efficiency, and protection from nucleases/phosphates. The variety of modification methods in eukaryotic RNAP allows for stability of the mRNA as well as increased transcription efficiency.