Though transcription is the same process in both eukaryotes and prokaryotes, the process in eukaryotes is much more complicated. Some overall differences are that in eukaryotes, transcription and translation take place is separate cellular compartments while in prokaryotes, RNA is usually translated while it is being transcribed. A second major difference is that eukaryotic mRNA is usually still complicated and must be modified by capping and intron splicing before it can be used to make protein. However, in prokaryotes, the mRNA usually doesn’t need much modification and thus is able to undergo translation before transcription is done.
There are also structural and functional differences of RNAP of eukaryotes and prokaryotes and yet among these differences, there are also many aspects in common. One major difference is the fact that prokaryotic RNAP is made up of fewer subunits that eukaryotic. Eukaryotic RNAPII, as stated previously, has 12 subunits (Rpb1-Rpb 12) while prokaryotic core RNAP contains only one subunit but has multiple domains (alpha, beta, beta prime, and omega). Also, while promoter specific initiation in eukaryotes requires more than a dozen basal initiation factors, only a single polypeptide in bacteria, the sigma subunit, is required to bind to the core RNAP and forms the holoenzyme (Subunit Difference) [1].
Like eukaryotic RNAPII, the holoenzyme will bind to specific promoters and it will melt the DNA to form the transcription bubble [1]. Both RNAPII and the bacterial holoenzyme are able to bind to both promoter and nonpromoter DNA fragments. This shows that in the absence of additional promoters, RNAPII and the holoenzyme are able to interact stably and nonspecifically with free DNA [3]. Another difference is that in RNAPII, there is a fork loop in the Rpb2 subunit which is absent from the holoenzyme which would suggest that promoter melting in eukaryotes requires general transcription factors while prokaryotes do not [2].
The holoenzyme, like RNAPII, contains an active site channel which allows for DNA entrance and also has an RNA exit (Active Site Comparison). There are also some conserved structural features such as the beta prime zipper and beta prime lid. The structure of the beta prime lid is very similar to the RNAPII Rpb1 lid [1]. There are also other structural similarities between RNAPII and the holoenzyme. Both have a swinging clamp where motions due to this clamp cause large conformational changes in the core to allow proper association with DNA [1]. Specific structures such as the bridge helix and the E and A sites are conserved between RNAPII and the holoenzyme but have slightly different functions. The bridge helix is a highly conserved sequence but in RNAPII, the helix is straight, while in the holoenzyme, the helix is bent and partially unfolded [4].
The A and E sites described in the eukaryotic overview are also conserved between RNAPII and the holoenzyme. The difference is their mechanism of NTP selection by the template DNA base. As stated earlier, in RNAPII, NTPs will enter beneath the active center and bind in the E site, rotate to the A site where they pair with the template and a fixed by interaction with the bridge helix [5]. In contrast to the holoenzyme, NTPs will enter through the side and bind to a pre-initiation site (E site) in the correct orientation, which means that only translation is required to bind the nucleotide to the addition site (A site) [5]. Additional factors that show the active site is conserved between eukaryotes and prokaryotes is the fact that both have Mg2+ ions in their active sites that play a crucial role in the stabilization of the active site[1].
The catalytic core of eukaryotic RNAP is very homologous in structure and function with the bacterial enzyme. Despite details of initiation being quite different, the overall task of the general initiation apparatus are the same. They recognize the promoter on DNA, recruit RNAP to the specific start site and melt the DNA to create the transcription bubble [1]. Of course both structures will lead to the formation of cellular mRNA.
[1] Murakami, K.S.; Masuda, S.; Darst, S.A. Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme a 4 Å Resolution. Science. 17 May 2002. 296, 1280-1284.
[2] Gnatt, A.L; Cramer, P.; Fu, J.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 8 June 2001. 292, 1876-1882.
[3] Conaway, J.W.; Conaway, R.C. An RNA Polymerase II Transcription Factor Shares Functional Properties with Escherichia coli σ70. Science. 22 June 1990. 248, 1550-1553.
[4] Cramer, P.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 8 June 2001. 292, 1863-1876.
[5] Westover, K.D.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center. Cell. 12 November 2004. 119, 481-489.