RNA Polymerases: Subunits and Functional Domains


RNA polymerase is a multisubunit enzyme that catalyses the synthesis of RNA. Although there is a striking degree of structural and functional conservation among all RNA polymerases, there are also many distinguishing features that reflect the specific requirements of individual organisms.

Keywords: transcription; RNA polymerase; holoenzyme; subunit

Figure 1.

Subunit complexity of RNA polymerases. The sizes of the subunits are approximate; the diagram is a generalization and is not intended to accurately display precise subunit interactions or enzyme structure.

Figure 2.

Reconstitution of selective transcription assays with RNA polymerases I, II, and III. The three types of RNA polymerases are shown with the respective protein fractions required to achieve promoter‐selective transcription in vitro. Many of the activities represented in the protein fractions contain multiple polypeptides. Alternate names are shown in parentheses.

Figure 3.

Evolutionary conservation of RNA polymerase. Relative subunit sizes are approximate; Saccharomyces cerevisiae represents eukaryotic RNA polymerase subunit structure, Escherichia coli represents bacterial subunit structure and Sulfolobus (Sulfolobus acidocaldarius) represents archaebacterial subunit structure.

Figure 4.

Nuclear RNA polymerases are structurally and functionally similar. Subunits of yeast Saccharomyces cerevisiae are used as an example.

Figure 5.

C‐terminal domain (CTD) length and sequence in RNA polymerase II. Each open box represents one CTD heptapeptide, the black rectangles (not drawn to scale) represent RNA polymerase II large subunit amino acids in front of the CTD. The sequence of the Saccharomyces cerevisiaeCTD (bold‐faced residues display deviation from the canonical consensus sequence) from a commonly used laboratory strain is shown. The yeast CTD shows strain variability, comprising either 26 or 27 repeats.

Figure 6.

RNA polymerase II structure. Saccharomyces cerevisiae RNA polymerase II/4/7 structure. The position of the 25 Å DNA‐binding cleft is indicated (white asterisk), and individual subunits are represented in different colours. Figure courtesy of Richard H. Ebright, HHMI and Rutgers University.


Further Reading

Buratowski S (2000) Snapshots of RNA polymerase II transcription initiation. Current Opinion in Cell Biology 12: 320–325.

Chao DM and Young RA (1991) Tailored tails and transcription initiation: the carboxyl terminal domain of RNA polymerase II. Gene Expression 1: 1–4.

Chedin S, Ferri ML, Peyroche G et al. (1998) The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation. Cold Spring Harbor Symposia on Quantitative Biology 63: 381–389.

Conaway JW, Shilatifard A, Dvir A and Conaway RC (2000) Control of elongation by RNA polymerase II. Trends in Biochemical Sciences 25: 375–380.

Greenblatt J (1997) RNA polymerase II holoenzyme and transcriptional regulation. Current Opinion in Cell Biology 9: 310–319.

Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiology and Molecular Biology Reviews 62: 465–503.

Ishihama A, Kimura M and Mitsuzawa H (1998) Subunits of yeast RNA polymerases: structure and function. Current Opinion in Microbiology 1: 190–196.

Lee TI and Young RA (2000) Transcription of eukaryotic protein‐coding genes. Annual Review of Genetics 34: 77–137.

Malik S and Roeder RG (2000) Transcriptional regulation through Mediator‐like coactivators in yeast and metazoan cells. Trends in Biochemical Science 25: 277–283.

Myers LC and Kornberg RD (2000) Mediator of transcriptional regulation. Annual Review of Biochemistry 69: 729–749.

Myer VE and Young RA (1998) RNA polymerase II holoenzymes and subcomplexes. Journal of Biological Chemistry 273: 27757–27760.

Orphanides G, Lagrange T and Reinberg D (1996) The general transcription factors of RNA polymerase II. Genes and Development 10: 2657–2683.

Paule MR and White RJ (2000) Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Research 28: 1283–1298.

Proudfoot N (2000) Connecting transcription to messenger RNA processing. Trends in Biochemical Sciences 25: 290–293.

Severinov K (2000) RNA polymerase structure–function: insights into points of transcriptional regulation. Current Opinion in Microbiology 3: 118–125.

Uptain SM, Kane CM and Chamberlin MJ (1997) Basic mechanisms of transcript elongation and its regulation. Annual Review of Biochemistry 66: 117–172.

Woychik NA (1998) Fractions to functions: RNA polymerase II thirty years later. Cold Spring Harbor Symposia on Quantitative Biology 63: 311–317.

Young RA (1991) RNA polymerase II. Annual Review of Biochemistry 60: 689–715.

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Woychik, Nancy A, and Reinberg, Danny(Apr 2001) RNA Polymerases: Subunits and Functional Domains. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003302]