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Biochemistry, RNA Polymerase

Editor: Judith Borger Updated: 7/17/2023 9:10:30 PM


Essential and fundamental to all organisms, transcription is the process for RNA synthesis from template DNA. At the heart of this activity is the large multisubunit enzyme called RNA polymerase. RNA polymerase, abbreviated RNAP and officially known as DNA-directed RNA polymerase, is found in all living organisms as well as many viruses. Present in bacteria, archaea, and even eukaryotes, these RNAPs all share similar protein core structures as well as mechanisms.


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RNAP is the multisubunit enzyme that transcribes template DNA into RNA. While bacteria (prokaryotes) and archaea contain only one RNAP, eukaryotes contain three RNAPs: RNAP I, RNAP II, and RNAP III. Though there are drastic differences between these multisubunit RNAPs, they are also many significant similarities. Clearly related and forming a family, these RNAPs have three highly conserved subunits. Though archaea RNAP is more complex than bacterial RNAP and is more closely related to eukaryotic RNAP II, about 50% of the enzyme is still conserved.[1] Thus, scientists have been able to glean many of RNAP’s important structure and function by studying the simpler bacterial RNAP. Because bacterial RNAP is most heavily researched and has the most significant clinical relevance, most of this activity will focus on this RNAP.

All RNAPs contain a core. This RNA-synthesizing core generates 5’ to 3’ RNA chains by hydrolyzing pyrophosphate from nucleoside triphosphates. Bacterial core RNAP is the simplest, comprised of five subunits: beta, beta prime, two alphas, and omega. Together, the large beta and beta prime subunits form a claw with the reactive magnesium ion.[2] In the center of the claw is a catalytically active site. The initiation of the core assembly occurs by the dimerization of the N-terminal domain of the alpha subunits, followed by beta and with omega subsequently serving as the chaperone for beta prime. A flexible linker tethers the C-terminal domains of alphas and serves important regulatory roles. Archaea and eukaryotic core subunits are also highly homologous to bacterial RNAP. Bacterial, archaeal, and eukaryotic RNAPs all resemble a crab claw with an enzyme active site located at the bottom cleft of the claw.[3][4] Here, a catalytic metal magnesium ion as well as an absolutely-conserved motif of NADFDGD and three invariant residues are found.[3][4] The architecture surrounding the cleft is also highly conserved among all three domains of life, suggesting that this mechanism of RNA synthesis gets conserved from bacteria to humans.

Issues of Concern

Issues of concern arise when RNAP mistranscribes, also known as transcription infidelity. However, this area of research has been difficult to study since the error of translation is significantly higher, obscuring phenotypic results.[5][6] Along with misincorporation of nucleotides, another mechanism of transcription infidelity involves bacterial RNAP elongation slippage on homopolymeric A/T tracks, disrupting open reading frames.[7]

Cellular Level

RNAP is a highly abundant enzyme which catalyzes the formation of phosphodiester bonds linking nucleotides together, subsequently producing linear chain. The growing RNA chain is extended by one nucleotide at a time in the 5’ to 3’ direction using nucleoside triphosphates (ATP, CTP, UTP, and GTP) as substrates. Estimates are that about 20 nucleotides undergo synthesis for each gene with over a thousand transcripts formed in an hour from one gene. Unlike DNA polymerase, RNAP has increased infidelity. One mistake is made every 10,000 nucleotides while DNA polymerase makes one mistake every 10,000,000 nucleotides. Despite lower accuracy, RNAP does have a proofreading mechanism. RNAP can back up, excise the misincorporated ribonucleotide, and insert the proper ribonucleotide.

Molecular Level

RNAP is a multisubunit enzyme that contains both protein-protein as well as protein-DNA interactions. The specificity factors of bacterial RNAP, sigma, contain four distinct regions: region 1, region 2, region 3, and region 4. Except for sigma factors belonging to the sigma54 family, all sigma factors contain a highly conserved region 2 and region 4 while some also additionally contain a conserved region 3.[2] These regions are vital because they allow the core to recognize specific promoters, allowing for differential upregulation and or downregulation during particular times. These promoter elements include the following: UP elements, -35 element, and the extended -10 motif.  The tethered C-terminal domains of the alpha subunits interact with the UP elements which are AT-rich sequences located from -40 to -60 relative to the +1 transcriptional start site.[8][9] Region 4.2 of sigma interacts with the -35 element, which is a highly conserved -35 TTGACA-30 sequence.[10] Region 3.0 interacts with the extended -10 sequence which is a -15TGn-13 as well as the most upstream basepair, the -12 T of the -10 element.[11] Region 2.4 interacts with the -10 element, which is a highly conserved sequence comprised of -12 TATAAT -7.[11]

Along with sigma-DNA interactions, sigma also makes various extensive protein contacts with core RNAP. Important interactions include residues within Regions 2.1 and 2.2 with the beta prime subunit as well as residues with region 3.2 threading through a channel comprised of beta and beta prime.[12] Regions in 4.1 and 4.2 interact with the beta-flap, a domain within the beta subunit, while the beta-flap tip makes contact by the very C-terminus (known as helix 5) of the sigma factor.[13] Interestingly, primary sigma factors contain a highly charged region 1.1, which interacts with the beta and beta prime cleft and acts as a DNA mimic, helping hold DNA that is downstream of the transcription start site.[14]

The overall structure of RNAP resembles that of a crab claw. The beta and beta prime subunits form two opposing pincer-like structures, bordering the main channel.[15][16] The larger of the pincer, the beta prime subunit, contains a highly mobile domain that can hinge around a flexible region; this is known as the switch region and has five discrete elements SW1-SW5.[17] A cleft between the two pincers houses the RNAP catalytic site which contains a magnesium ion.[18] Leading to this catalytic active site are two channels. The primary channel contains the DNA-RNA hybrid as well as the downstream DNA while the secondary channel proves access for NTP substrates as well as the nascent RNA.[19]


RNAP’s function is to transcribe DNA into RNA. The template stranded DNA is read from 3’ to 5’ fashion while RNA synthesis occurs in a 5’ to 3’ manner. Many different kinds of RNA get produced: mRNA, tRNA, rRNA, sRNA, snoRNA, and other noncoding RNAs.


RNAP’s mechanism of transcribing DNA into RNA is highly conserved across prokaryotes, archaea, and eukaryotes. To begin the process of bacterial transcription, along with core polymerase, an additional specificity factor is also necessary. These specificity proteins recognize certain elements in the promoter DNA and determine the start site of transcription. In bacteria, these specificity factors have the name of sigma subunits. Sigma, together with core, form the bacterial RNAP. Though research has now identified hundreds of sigma, the main sigma factor, sigma70 in Escherichia coli or sigma A in other bacteria, is responsible for exponential growth and regulation of housekeeping genes.[20] Other alternate sigma factors are used during times of stress and/or different growth conditions.[20]

To initiate the process of bacterial transcription, sigma and core together first binds to double-stranded DNA.[21][2] C-terminal domains of the alpha subunits both interact with the UP elements, Region 4.2 interactions with the -35, and Region 3.0 interacts with the extended -10.[2] These interactions between core and promoter DNA are very unstable and short-lived, forming a product called the unstable closed complex (RPc).[21] The thinking is that the double-stranded DNA lies across the face of the RNAP. RPc quickly transitions to the stable open complex (RPo) where the DNA unzips, bends about 90 degrees, and forms a bubble from -11/12 to about +5 relative to the +1 transcriptional start site.[21][22] Along with DNA changes, there are also major protein conformational changes within polymerase: Region 1.1 moves downstream to enter that beta and beta prime channel and beta prime clamp undergoes large conformational changes, allowing the downstream DNA to be fully secured.[22] Nucleotide triphosphates then enter through the secondary channel of the core, leading to the synthesis of RNA and forming a complex called the initiating complex (RPi). These RNA products are very short and are also known as abortives. Once the abortives reach a certain size, they can ultimately push Region 3.2 out of its current position within the RNA exit channel.[23] This change thus opens up the RNA exit channel, leading to the release of both the sigma factor as well as RNA. Core polymerase continues moving along the template stranded DNA until it reaches the termination site. In Rho-dependent termination, a factor called Rho is responsible for disrupting the complex of RNAP/RNA/template DNA while in Rho-independent termination, a loop forms at the end of the RNA molecule, allowing for RNAP to fall off.[24]


Antibodies to RNAP can be commercially purchased and are routinely used in the laboratories to detect the presence of RNAP subunits. Furthermore, anti-RNAP III antibodies are considered to be highly sensitive and specific for systemic sclerosis or scleroderma and are also associated with diffuse cutaneous scleroderma and scleroderma renal crisis.[25] Within the diffuse cutaneous scleroderma population, the presence of anti-RNAP III antibodies correlates with a decrease in time of onset of initial symptoms and skin thickening peak.[26] Thus, patients with anti-RNAP III antibodies are at a higher risk of developing sclerodermal renal crisis.[27] Patients who are positive for anti-RNAP III antibodies had higher incidences of systemic scleroderma disease, ranging from 14% to 51%.[27]


Though mutations in eukaryotic RNAP have not been solely implicated in disease, dysregulation of ribosomal RNA synthesis via RNAP I has lead to a variety of different diseases. The most well-recognized diseases result from a loss of function mutations in ribosomes or factors associated with Pol I.[28] These diseases are known as ribosomopathies and include Diamond-Blackfan anemia, 5q minus syndrome, Treacher Collins syndrome, and Blooms and Werner syndrome.[28] There are also other ribosomopathies which are associated with mutations affecting RNA processing and modification; these diseases include Shwachman-Diamond syndrome, dyskeratosis congenita, cartilage hair hypoplasia, North American Indian childhood cirrhosis, Bowen-Conradi syndrome, and alopecia, neurological defect and endocrinopathy (ANE) syndrome. Unfortunately, ribosomopathies are rare, and treatment is typically palliative rather than curative.[28]

Clinical Significance

Prevention of gene expression is one way in which antibiotics can kill bacteria. Since transcription is an essential process for all organisms, the transcription machinery is an extremely attractive target for the development of new antibiotics. Rifampicin is a commonly used antibiotic against Mycobacterium tuberculosis. Belonging to the ansamycin class of antibiotics, rifampicin binds to the beta subunit of RNAP within the DNA/RNA channel and prevents the formation of the second or third phosphodiester bond, inducing the release of short abortives and subsequently blocking nascent RNA extension.[29][30][31] Interestingly, bacteria have quickly evolved to develop resistance to rifampicin. Mutations within the beta subunit of RNAP (S531L, H526Y, and D516V) account for about for 41, 36, and 9% of resistant tuberculosis strains, respectively.[31] Other antibiotics that block nascent RNA extension include sorangicin and GE23077.[32] Another commonly used antibiotic, fidaxomicin, also binds to Clostridium difficile RNAP. Instead of the beta subunit, fidaxomicin binds to the switch region of RNAP.[33] This binding prevents RPo formation. The proposed mechanism is that fidaxomicin prevents the correct spatial orientation of Region 2 and Region 4 for recognition of the -10 and -35 core promoter elements, respectively.[33][34] Other antibiotics that also target the RNAP switch region include squaramides, myxopyronin, corallopyronin, and ripostatin.[32] Though only very few antibiotics have reached the clinical market, there are also other many antibiotics which inhibit transcription by varying processes. The SB-2 series disrupt holoenzyme assembly, pseudoridmycin is a nucleoside analog, and salinamides targets the mobile elements of the primary channel.[32]

Along with prokaryotic transcription inhibition, researchers have discovered several compounds that target eukaryotic RNAP. Actinomycin D is a bacterial antibiotic used as an antitumor reagent. It intercalates DNA, thereby preventing the progression of both bacterial and eukaryotic RNAP I.[35][36] Along with actinomycin D, other chemicals also inhibit eukaryotic transcription. Alpha-amanitin binds to the bridge helix and trigger loop of RNAP II and III, preventing the incorporation of nascent RNA chains,[37][38] while 8-hydroxyquinoline chelates bivalent cations, manganese, and magnesium, within the active site of RNAP.[39]



Hirata A, Murakami KS. Archaeal RNA polymerase. Current opinion in structural biology. 2009 Dec:19(6):724-31. doi: 10.1016/ Epub 2009 Oct 31     [PubMed PMID: 19880312]

Level 3 (low-level) evidence


Decker KB, Hinton DM. Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases. Annual review of microbiology. 2013:67():113-39. doi: 10.1146/annurev-micro-092412-155756. Epub 2013 Jun 13     [PubMed PMID: 23768203]

Level 3 (low-level) evidence


Jun SH, Reichlen MJ, Tajiri M, Murakami KS. Archaeal RNA polymerase and transcription regulation. Critical reviews in biochemistry and molecular biology. 2011 Feb:46(1):27-40. doi: 10.3109/10409238.2010.538662. Epub     [PubMed PMID: 21250781]


Ebright RH. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. Journal of molecular biology. 2000 Dec 15:304(5):687-98     [PubMed PMID: 11124018]

Level 3 (low-level) evidence


Strathern JN, Jin DJ, Court DL, Kashlev M. Isolation and characterization of transcription fidelity mutants. Biochimica et biophysica acta. 2012 Jul:1819(7):694-9. doi: 10.1016/j.bbagrm.2012.02.005. Epub 2012 Feb 16     [PubMed PMID: 22366339]


Reynolds NM, Lazazzera BA, Ibba M. Cellular mechanisms that control mistranslation. Nature reviews. Microbiology. 2010 Dec:8(12):849-56. doi: 10.1038/nrmicro2472. Epub     [PubMed PMID: 21079633]

Level 3 (low-level) evidence


Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M. Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. The Journal of biological chemistry. 2013 Jan 25:288(4):2700-10. doi: 10.1074/jbc.M112.429464. Epub 2012 Dec 5     [PubMed PMID: 23223236]


Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH. Structural organization of the RNA polymerase-promoter open complex. Cell. 2000 Jun 9:101(6):601-11     [PubMed PMID: 10892647]

Level 3 (low-level) evidence


Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science (New York, N.Y.). 1993 Nov 26:262(5138):1407-13     [PubMed PMID: 8248780]


Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Molecular cell. 2002 Mar:9(3):527-39     [PubMed PMID: 11931761]


Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science (New York, N.Y.). 2002 May 17:296(5571):1285-90     [PubMed PMID: 12016307]


Murakami KS, Darst SA. Bacterial RNA polymerases: the wholo story. Current opinion in structural biology. 2003 Feb:13(1):31-9     [PubMed PMID: 12581657]

Level 3 (low-level) evidence


Kuznedelov K, Minakhin L, Niedziela-Majka A, Dove SL, Rogulja D, Nickels BE, Hochschild A, Heyduk T, Severinov K. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science (New York, N.Y.). 2002 Feb 1:295(5556):855-7     [PubMed PMID: 11823642]


Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 2002 Mar 8:108(5):599-614     [PubMed PMID: 11893332]


Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature. 2002 Jun 13:417(6890):712-9     [PubMed PMID: 12000971]


Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife. 2015 Sep 8:4():. doi: 10.7554/eLife.08504. Epub 2015 Sep 8     [PubMed PMID: 26349032]


Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH. The RNA polymerase "switch region" is a target for inhibitors. Cell. 2008 Oct 17:135(2):295-307. doi: 10.1016/j.cell.2008.09.033. Epub     [PubMed PMID: 18957204]


Steitz TA, Steitz JA. A general two-metal-ion mechanism for catalytic RNA. Proceedings of the National Academy of Sciences of the United States of America. 1993 Jul 15:90(14):6498-502     [PubMed PMID: 8341661]


Nudler E. RNA polymerase backtracking in gene regulation and genome instability. Cell. 2012 Jun 22:149(7):1438-45. doi: 10.1016/j.cell.2012.06.003. Epub     [PubMed PMID: 22726433]


Gruber TM, Gross CA. Multiple sigma subunits and the partitioning of bacterial transcription space. Annual review of microbiology. 2003:57():441-66     [PubMed PMID: 14527287]


Hook-Barnard IG, Hinton DM. Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters. Gene regulation and systems biology. 2007:1():275-93     [PubMed PMID: 19119427]


Saecker RM, Record MT Jr, Dehaseth PL. Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. Journal of molecular biology. 2011 Oct 7:412(5):754-71. doi: 10.1016/j.jmb.2011.01.018. Epub 2011 Mar 1     [PubMed PMID: 21371479]


Hsu LM. Promoter clearance and escape in prokaryotes. Biochimica et biophysica acta. 2002 Sep 13:1577(2):191-207     [PubMed PMID: 12213652]


Platt T. Transcription termination and the regulation of gene expression. Annual review of biochemistry. 1986:55():339-72     [PubMed PMID: 3527045]

Level 3 (low-level) evidence


Kuwana M, Kaburaki J, Mimori T, Tojo T, Homma M. Autoantibody reactive with three classes of RNA polymerases in sera from patients with systemic sclerosis. The Journal of clinical investigation. 1993 Apr:91(4):1399-404     [PubMed PMID: 8473491]


Wirz EG, Jaeger VK, Allanore Y, Riemekasten G, Hachulla E, Distler O, Airò P, Carreira PE, Tikly M, Vettori S, Balbir Gurman A, Damjanov N, Müller-Ladner U, Distler J, Li M, Häusermann P, Walker UA, EUSTAR coauthors. Incidence and predictors of cutaneous manifestations during the early course of systemic sclerosis: a 10-year longitudinal study from the EUSTAR database. Annals of the rheumatic diseases. 2016 Jul:75(7):1285-92. doi: 10.1136/annrheumdis-2015-207271. Epub 2015 Jul 31     [PubMed PMID: 26232495]


Kuwana M. A To-Do List at Diagnosis of Systemic Sclerosis with Positive Anti-RNA Polymerase III Antibodies. The Journal of rheumatology. 2017 May:44(5):550-552. doi: 10.3899/jrheum.170037. Epub     [PubMed PMID: 28461517]


Hannan KM, Sanij E, Rothblum LI, Hannan RD, Pearson RB. Dysregulation of RNA polymerase I transcription during disease. Biochimica et biophysica acta. 2013 Mar-Apr:1829(3-4):342-60. doi: 10.1016/j.bbagrm.2012.10.014. Epub 2012 Nov 12     [PubMed PMID: 23153826]

Level 3 (low-level) evidence


Severinov K, Mustaev A, Severinova E, Kozlov M, Darst SA, Goldfarb A. The beta subunit Rif-cluster I is only angstroms away from the active center of Escherichia coli RNA polymerase. The Journal of biological chemistry. 1995 Dec 8:270(49):29428-32     [PubMed PMID: 7493980]


Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA. Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell. 2001 Mar 23:104(6):901-12     [PubMed PMID: 11290327]


McClure WR, Cech CL. On the mechanism of rifampicin inhibition of RNA synthesis. The Journal of biological chemistry. 1978 Dec 25:253(24):8949-56     [PubMed PMID: 363713]


Mosaei H, Harbottle J. Mechanisms of antibiotics inhibiting bacterial RNA polymerase. Biochemical Society transactions. 2019 Feb 28:47(1):339-350. doi: 10.1042/BST20180499. Epub 2019 Jan 15     [PubMed PMID: 30647141]


Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular cell. 2018 Apr 5:70(1):60-71.e15. doi: 10.1016/j.molcel.2018.02.026. Epub 2018 Mar 29     [PubMed PMID: 29606590]


Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA. Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife. 2018 Feb 26:7():. doi: 10.7554/eLife.34823. Epub 2018 Feb 26     [PubMed PMID: 29480804]


Perry RP, Kelley DE. Inhibition of RNA synthesis by actinomycin D: characteristic dose-response of different RNA species. Journal of cellular physiology. 1970 Oct:76(2):127-39     [PubMed PMID: 5500970]


Sobell HM. Actinomycin and DNA transcription. Proceedings of the National Academy of Sciences of the United States of America. 1985 Aug:82(16):5328-31     [PubMed PMID: 2410919]

Level 3 (low-level) evidence


Rudd MD, Luse DS. Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes. The Journal of biological chemistry. 1996 Aug 30:271(35):21549-58     [PubMed PMID: 8702941]


Brueckner F, Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nature structural & molecular biology. 2008 Aug:15(8):811-8. doi: 10.1038/nsmb.1458. Epub 2008 Jun 13     [PubMed PMID: 18552824]


Fraser RS, Creanor J. The mechanism of inhibition of ribonucleic acid synthesis by 8-hydroxyquinoline and the antibiotic lomofungin. The Biochemical journal. 1975 Jun:147(3):401-10     [PubMed PMID: 810137]