Evolution of multisubunit RNA polymerases in the three domains of life
Abstract
RNA polymerases (RNAPs) carry out transcription in all living organisms. All multisubunit RNAPs are derived from a common ancestor, a fact that becomes apparent from their amino acid sequence, subunit composition, structure, function and molecular mechanisms. Despite the similarity of these complexes, the organisms that depend on them are extremely diverse, ranging from microorganisms to humans. Recent findings about the molecular and functional architecture of RNAPs has given us intriguing insights into their evolution and how their activities are harnessed by homologous and analogous basal factors during the transcription cycle. We provide an overview of the evolutionary conservation of and differences between the multisubunit polymerases in the three domains of life, and introduce the 'elongation first' hypothesis for the evolution of transcriptional regulation.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The last common ancestor may have had RNA and phosphodiester-based energy coupling.
“Specifically, the last common ancestor may have had a cell membrane (Jékely 2006;Koga 2011;Lombard et al. 2012;Sojo et al. 2014;Coleman et al. 2019), RNA and phosphodiester-based energy coupling (e.g.Werner and Grohmann 2011), as well as thioester-based intermediary metabolism (Goldford et al. 2017;Weiss et al. 2018), but may not have used a strictly DNA genome (Mushegian and Koonin 1996;Leipe et”
From The Emergence of Life (2019) · cites this paper as Werner and Grohmann 2011
Cites
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works
Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution
Cramer, P., Bushnell, D. A., & Kornberg, R. D. (2001) · Science · doi:10.1126/science.1059493 · Cited by 1,247 · see citing works
Multiple Sigma Subunits and the Partitioning of Bacterial Transcription Space
Gruber, T. M., & Gross, C. A. (2003) · Annual Review of Microbiology · doi:10.1146/annurev.micro.57.030502.090913 · Cited by 937 · see citing works
Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution
Gnatt, A., Cramer, P., Fu, J.-L., Bushnell, D., & Kornberg, R. (2001) · Science · doi:10.1126/science.1059495 · Cited by 921 · see citing works
Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution
Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., & Darst, S. A. (1999) · Cell · doi:10.1016/s0092-8674(00)81515-9 · Cited by 813 · see citing works
Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex
Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., & Darst, S. A. (2002) · Science · doi:10.1126/science.1069595 · Cited by 642 · see citing works
Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation
Proshkin, S., Rahmouni, A. R., Mironov, A. S., & Nudler, E. (2010) · Science · doi:10.1126/science.1184939 · Cited by 565 · see citing works
Structure of the Bacterial RNA Polymerase Promoter Specificity σ Subunit
Campbell, E. A., Muzzin, O., Chlenov, M., Sun, J. L., Olson, C. A., Weinman, O., Trester-Zedlitz, M., & Darst, S. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00470-7 · Cited by 492 · see citing works
Bacterial RNA polymerases: the wholo story
Murakami, K. S., & Darst, S. A. (2003) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00005-2 · Cited by 489 · see citing works
Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., & Ebright, R. H. (2006) · Science · doi:10.1126/science.1131399 · Cited by 453 · see citing works
Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS
Kettenberger, H., Armache, K., & Cramer, P. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.11.040 · Cited by 437 · see citing works
Structural basis for transcription elongation by bacterial RNA polymerase
Vassylyev, D. G., Vassylyeva, M. N., Perederina, A. A., Tahirov, T. H., & Artsimovitch, I. (2007) · Nature · doi:10.1038/nature05932 · Cited by 409 · see citing works
The archaebacterial origin of eukaryotes
Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R., & Embley, T. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810647105 · Cited by 381 · see citing works
Transcription factories: gene expression in unions?
Sutherland, H. G. E., & Bickmore, W. A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2592 · Cited by 380 · see citing works
Prokaryotic and eukaryotic RNA polymerases have homologous core subunits.
Sweetser, D. B., Nonet, M. L., & Young, R. A. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.5.1192 · Cited by 354 · see citing works
A NusE:NusG Complex Links Transcription and Translation
Burmann, B. M., Schweimer, K., Luo, X., Wahl, M. C., Stitt, B. L., Gottesman, M. E., & ROSCH, P. J. (2010) · Science · doi:10.1126/science.1184953 · Cited by 352 · see citing works
Control of rRNA transcription in Escherichia coli
Condon, C., Squires, C., & Squires, C. L. (1995) · Microbiological Reviews · doi:10.1128/mr.59.4.623-645.1995 · Cited by 349 · see citing works
Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms
Bushnell, D. A., Westover, K. D., Davis, R., & Kornberg, R. D. (2004) · Science · doi:10.1126/science.1090838 · Cited by 343 · see citing works
RNA polymerase II–TFIIB structure and mechanism of transcription initiation
Kostrewa, D., Zeller, M. E., Armache, K., Seizl, M., Leike, K., Thomm, M., & Cramer, P. (2009) · Nature · doi:10.1038/nature08548 · Cited by 317 · see citing works
TATA element recognition by the TATA box-binding protein has been conserved throughout evolutionPreprint
Patikoglou, G. A., Kim, J. L., Sun, L., Yang, S., Kodadek, T. J., & Burley, S. K. (1999) · Genes & Development · doi:10.1101/gad.13.24.3217 · Cited by 307 · see citing works
Structure of Eukaryotic RNA Polymerases
Cramer, P., Armache, K., Baumli, S., Benkert, S., Brueckner, F., Buchen, C., Damsma, G. E., Dengl, S., Geiger, S. R., Jasiak, A. J., et al. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.130008 · Cited by 305 · see citing works
Mechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH
Kim, T.-K., Ebright, R. H., & Reinberg, D. (2000) · Science · doi:10.1126/science.288.5470.1418 · Cited by 262 · see citing works
Iyer, L. M., Koonin, E. V., & Aravind, L. (2003) · BMC Structural Biology · doi:10.1186/1472-6807-3-1 · Cited by 261 · see citing works
Holstege, F. C. P., van der Vliet, P. C., & Timmers, H. T. M. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00512.x · Cited by 257 · see citing works
The regulatory roles and mechanism of transcriptional pausing
Landick, R. C. (2006) · Biochemical Society Transactions · doi:10.1042/bst0341062 · Cited by 251 · see citing works
Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7
Armache, K., Mitterweger, S., Meinhart, A., & Cramer, P. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413038200 · Cited by 246 · see citing works
Regulator Trafficking on Bacterial Transcription Units In Vivo
Mooney, R. A., Davis, S. E., Peters, J. M., Rowland, J. L., Ansari, A. Z., & Landick, R. C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2008.12.021 · Cited by 243 · see citing works
DNA curvature and flexibility in vitro and in vivo
Peters, J. P., & Maher, L. J. (2010) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583510000077 · Cited by 228 · see citing works
The X-ray crystal structure of RNA polymerase from Archaea
Hirata, A., Klein, B. J., & Murakami, K. S. (2008) · Nature · doi:10.1038/nature06530 · Cited by 220 · see citing works
Transcriptional antitermination
Greenblatt, J., Nodwell, J. R., & Mason, S. W. (1993) · Nature · doi:10.1038/364401a0 · Cited by 219 · see citing works
Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase
Opalka, N., Chlenov, M., Chacón, P., Rice, W. J., Wriggers, W. R., & Darst, S. A. (2003) · Cell · doi:10.1016/s0092-8674(03)00600-7 · Cited by 207 · see citing works
Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase
Laptenko, O., Lee, J., Lomakin, I. B., & Borukhov, S. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg610 · Cited by 200 · see citing works
Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism
Liu, X., Bushnell, D. A., Wang, D., Calero, G. A., & Kornberg, R. D. (2009) · Science · doi:10.1126/science.1182015 · Cited by 198 · see citing works
Belogurov, G. A., Vassylyeva, M. N., Svetlov, V. V., Klyuyev, S., Grishin, N. V., Vassylyev, D. G., & Artsimovitch, I. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.02.021 · Cited by 195 · see citing works
Transcription through the roadblocks: the role of RNA polymerase cooperation
Epshtein, V., Toulmé, F., Rahmouni, A. R., Borukhov, S., & Nudler, E. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg452 · Cited by 194 · see citing works
Makeyev, E. V., & Bamford, D. H. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00780-3 · Cited by 191 · see citing works
Mooney, R. A., Schweimer, K., ROSCH, P. J., Gottesman, M. E., & Landick, R. C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.05.078 · Cited by 187 · see citing works
Molecular Evolution of Multisubunit RNA Polymerases: Sequence Analysis
Lane, W. J., & Darst, S. A. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.10.062 · Cited by 182 · see citing works
Flores, O. A., Lu, H., Killeen, M. T., Greenblatt, J., Burton, Z. F., & Reinberg, D. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.22.9999 · Cited by 179 · see citing works
Transcript Elongation by RNA Polymerase II
Selth, L. A., Sigurðsson, S., & Svejstrup, J. Q. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.062807.091425 · Cited by 176 · see citing works
Synthesis-Mediated Release of a Small RNA Inhibitor of RNA Polymerase
Wassarman, K. M., & Saecker, R. M. (2006) · Science · doi:10.1126/science.1134830 · Cited by 174 · see citing works
Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif
Hirtreiter, A., Damsma, G., Cheung, A., Klose, D., Grohmann, D., Vojnic, E., Martin, A. C. R., Cramer, P., & Werner, F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq135 · Cited by 172 · see citing works
Self-citationMissra, A., & Gilmour, D. S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000681107 · Cited by 165 · see citing works
Zhou, K., Kuo, W. H. W., Fillingham, J., & Greenblatt, J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806302106 · Cited by 162 · see citing works
Bacterial transcription elongation factors: new insights into molecular mechanism of action
Borukhov, S. I., Lee, J., & Laptenko, O. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04481.x · Cited by 157 · see citing works
Thinking quantitatively about transcriptional regulation
Greive, S. J., & von Hippel, P. H. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1588 · Cited by 155 · see citing works
A Recombinant RNA Polymerase II-like Enzyme Capable of Promoter-Specific Transcription
Werner, F., & Weinzierl, R. O. J. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00629-9 · Cited by 144 · see citing works
Self-citationSigurðsson, S., Dirac-Svejstrup, A. B., & Svejstrup, J. Q. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.026 · Cited by 141 · see citing works
Revisited gene regulation in bacteriophage λ
Dodd, I. B., Shearwin, K. E., & Egan, J. B. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.02.001 · Cited by 140 · see citing works
Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases
Cheetham, G. M. T., & Steitz, T. A. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(99)00058-5 · Cited by 139 · see citing works
Regulation of bacterial RNA polymerase σ factor activity: a structural perspective
Campbell, E. A., Westblade, L. F., & Darst, S. A. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.02.016 · Cited by 137 · see citing works
Mapping the Location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex
Chen, H., & Hahn, S. (2004) · Cell · doi:10.1016/j.cell.2004.09.028 · Cited by 136 · see citing works
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure
Korkhin, Y., Ünligil, U. M., Littlefield, O., Nelson, P. J., Stuart, D. I., Sigler, P. B., Bell, S. D., & Abrescia, N. G. A. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000102 · Cited by 134 · see citing works
Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis
Lane, W. J., & Darst, S. A. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.10.063 · Cited by 134 · see citing works
Molecular basis of RNA-dependent RNA polymerase II activity
Lehmann, E., Brueckner, F., & Cramer, P. (2007) · Nature · doi:10.1038/nature06290 · Cited by 129 · see citing works
Herbert, K. M., Zhou, J., Mooney, R. A., Porta, A. L., Landick, R. C., & Block, S. M. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.03.051 · Cited by 128 · see citing works
RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex
Geiger, S. R., Lorenzen, K., Schreieck, A., Hanecker, P., Kostrewa, D., Heck, A. J. R., & Cramer, P. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.07.028 · Cited by 125 · see citing works
Modus operandi of the bacterial RNA polymerase containing the σ54 promoter‐specificity factor
Wigneshweraraj, S., Bose, D. A., Burrows, P. C., Joly, N., Schumacher, J., Rappas, M., Pape, T., Zhang, X., Stockley, P. G., Severinov, K., et al. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06181.x · Cited by 125 · see citing works
Direct Detection of Abortive RNA Transcripts in Vivo
Goldman, S. R., Ebright, R. H., & Nickels, B. E. (2009) · Science · doi:10.1126/science.1169237 · Cited by 124 · see citing works
Structure of a Mycobacterium tuberculosis NusA–RNA complex
Beuth, B., Pennell, S., Arnvig, K. B., Martin, S. R., & Taylor, I. A. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600829 · Cited by 120 · see citing works
Binding of TFIIB to RNA Polymerase II
Chen, H., & Hahn, S. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00306-x · Cited by 118 · see citing works
Direct Modulation of RNA Polymerase Core Functions by Basal Transcription Factors
Werner, F., & Weinzierl, R. O. J. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.18.8344-8355.2005 · Cited by 116 · see citing works
Self-citationFunctional topography of nascent RNA in elongation intermediates of RNA polymerase
Komissarova, N. V., & Kashlev, M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14699 · Cited by 110 · see citing works
Structure and function of archaeal RNA polymerases
Werner, F. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05876.x · Cited by 108 · see citing works
Self-citationOhkuma, Y., Sumimoto, H., Hoffmann, A., Shimasaki, S., Horikoshi, M., & Roeder, R. G. (1991) · Nature · doi:10.1038/354398a0 · Cited by 100 · see citing works
A movie of the RNA polymerase nucleotide addition cycle
Brueckner, F., Ortiz, J. O., & Cramer, P. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.04.005 · Cited by 93 · see citing works
Andrecka, J., Treutlein, B., Arcusa, M. A. I., Muschielok, A., Lewis, R., Cheung, A. C. M., Cramer, P., & Michaelis, J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp601 · Cited by 93 · see citing works
The Structure of an RNAi Polymerase Links RNA Silencing and Transcription
Salgado, P. S., Koivunen, M. R. L., Makeyev, E. V., Bamford, D. H., Stuart, D. I., & Grimes, J. M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040434 · Cited by 92 · see citing works
Stability, Flexibility, and Dynamic Interactions of Colliding RNA Polymerase II Elongation Complexes
Saeki, H., & Svejstrup, J. Q. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.009 · Cited by 92 · see citing works
Orlicky, S., Tran, P., Sayre, M. H., & Edwards, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m003165200 · Cited by 92 · see citing works
Bridge helix and trigger loop perturbations generate superactive RNA polymerases
Tan, L., Wiesler, S. C., Trzaska, D., Carney, H. C., & Weinzierl, R. O. J. (2008) · Journal of Biology · doi:10.1186/jbiol98 · Cited by 91 · see citing works
Transcription Factor S, a Cleavage Induction Factor of the Archaeal RNA Polymerase
Hausner, W., Lange, U., & Musfeldt, M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.17.12393 · Cited by 91 · see citing works
Kulbachinskiy, A. V., & MUSTAEV, A. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.c600060200 · Cited by 91 · see citing works
Ha, K. S., Toulokhonov, I., Vassylyev, D. G., & Landick, R. C. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.06.036 · Cited by 90 · see citing works
The structural changes of T7 RNA polymerase from transcription initiation to elongation
Steitz, T. A. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.09.001 · Cited by 90 · see citing works
Eichner, J., Chen, H., Warfield, L., & Hahn, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.386 · Cited by 89 · see citing works
Conserved sequence motifs in the small subunit of human general transcription factor TFIIE
Sumimoto, H., Ohkuma, Y., Sinn, E., Kato, H., Shimasaki, S., Horikoshi, M., & Roeder, R. G. (1991) · Nature · doi:10.1038/354401a0 · Cited by 85 · see citing works
The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter
Nickels, B. E., Mukhopadhyay, J., Garrity, S. J., Ebright, R. H., & Hochschild, A. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb757 · Cited by 85 · see citing works
Structural Modules of the Large Subunits of RNA Polymerase
Severinov, K., MUSTAEV, A. A., Kukarin, A., Muzzin, O., Bass, I. A., Darst, S. A., & Goldfarb, A. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.44.27969 · Cited by 85 · see citing works
Dual Roles for Transcription Factor IIF in Promoter Escape by RNA Polymerase II
Yan, Q., Moreland, R. J., Conaway, J. W., & Conaway, R. C. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.50.35668 · Cited by 84 · see citing works
Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II
Walmacq, C., Kireeva, M. L., Irvin, J. D., Nedialkov, Y. A., Lubkowska, L., Malagón, F., Strathern, J. N., & Kashlev, M. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.006908 · Cited by 82 · see citing works
Runner, V. M., Podolny, V., & Buratowski, S. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01714-07 · Cited by 79 · see citing works
Jeon, C., Yoon, H. S., & Agarwal, K. L. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.19.9106 · Cited by 77 · see citing works
Allosteric control of the RNA polymerase by the elongation factor RfaH
Svetlov, V. V., Belogurov, G. A., Shabrova, E. V., Vassylyev, D. G., & Artsimovitch, I. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm600 · Cited by 76 · see citing works
Naji, S., Grünberg, S., & Thomm, M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m611674200 · Cited by 75 · see citing works
Batada, N. N., Westover, K. D., Bushnell, D. A., Levitt, M., & Kornberg, R. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408168101 · Cited by 72 · see citing works
Structural evolution of multisubunit RNA polymerases
Werner, F. (2008) · Trends in Microbiology · doi:10.1016/j.tim.2008.03.008 · Cited by 71 · see citing works
Self-citationStructure–function analysis of RNA polymerases I and III
Werner, M., Thuriaux, P., & Soutourina, J. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.10.005 · Cited by 68 · see citing works
Sevostyanova, A., Svetlov, V. V., Vassylyev, D. G., & Artsimovitch, I. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708432105 · Cited by 67 · see citing works
A Fully Recombinant System for Activator-dependent Archaeal Transcription
Ouhammouch, M., Werner, F., Weinzierl, R. O. J., & Geiduschek, E. P. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.c400446200 · Cited by 66 · see citing works
Self-citationRenfrow, M. B., Naryshkin, N. A., Lewis, L. M., Chen, H., Ebright, R. H., & Scott, R. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311433200 · Cited by 63 · see citing works
Schwartz, E. C., Shekhtman, A. G., Dutta, K., Pratt, M. R., Cowburn, D., Darst, S. A., & Muir, T. W. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.09.008 · Cited by 59 · see citing works
Hirtreiter, A., Grohmann, D., & Werner, F. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp928 · Cited by 58 · see citing works
Self-citationArchaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12
Werner, F. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.21.4299 · Cited by 57 · see citing works
Self-citationTethering of the Large Subunits of Escherichia coli RNA Polymerase
Severinov, K., Mooney, R. A., Darst, S. A., & Landick, R. C. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.39.24137 · Cited by 56 · see citing works
Topography of the Euryarchaeal Transcription Initiation Complex
Bartlett, M. S., Thomm, M., & Geiduschek, E. P. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311429200 · Cited by 55 · see citing works
Garrett, K. P., Serizawa, H., Hanley, J. P., Bradsher, J., Tsuboi, A., Arai, N., Yokota, T., Arai, K., Conaway, R. C., & Conaway, J. W. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)35928-3 · Cited by 55 · see citing works
Cheng, B., & Price, D. H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn630 · Cited by 52 · see citing works
Transcription Factor E Is a Part of Transcription Elongation Complexes
Grünberg, S., Bartlett, M. S., Naji, S., & Thomm, M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m707371200 · Cited by 52 · see citing works
Spitalny, P., & Thomm, M. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.06084.x · Cited by 43 · see citing works
Partners of Rpb8p, a Small Subunit Shared by Yeast RNA Polymerases I, II, and III
Briand, J.-F., Navarro, F., Rematier, P., Boschiero, C., Labarre, S., Werner, M., Shpakovski, G. V., & Thuriaux, P. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.17.6056-6065.2001 · Cited by 41 · see citing works
Structure–function studies of the RNA polymerase II elongation complex
Brueckner, F., Armache, K., Cheung, A. C. M., Damsma, G. E., Kettenberger, H., Lehmann, E., Sydow, J. F., & Cramer, P. (2009) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444908039875 · Cited by 41 · see citing works
Grohmann, D., & Werner, F. (2010) · Research in Microbiology · doi:10.1016/j.resmic.2010.09.002 · Cited by 35 · see citing works
Self-citationMacLellan, S. R., Wecke, T., & Helmann, J. D. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06331.x · Cited by 35 · see citing works
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases
Ruprich‐Robert, G., & Thuriaux, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq201 · Cited by 34 · see citing works
Evolutionary Comparison of Ribosomal Operon Antitermination Function
Arnvig, K. B., Zeng, S. H., Quan, S., Papageorge, A. T., Zhang, N., Villapakkam, A. C., & Squires, C. L. (2008) · Journal of Bacteriology · doi:10.1128/jb.00760-08 · Cited by 32 · see citing works
Ziegler, L. M., Khaperskyy, D. A., Ammerman, M. L., & Ponticelli, A. S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m309656200 · Cited by 31 · see citing works
Fused and Overlapping rpoB and rpoC Genes in Helicobacters, Campylobacters, and Related Bacteria
Zakharova, N., Paster, B. J., Wesley, I. V., Dewhirst, F. E., Berg, D. E., & Severinov, K. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.12.3857-3859.1999 · Cited by 30 · see citing works
Elongation by RNA polymerase: a race through roadblocks
Vassylyev, D. G. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.10.004 · Cited by 26 · see citing works
Grohmann, D., Hirtreiter, A., & Werner, F. (2009) · Biochemical Journal · doi:10.1042/bj20090782 · Cited by 25 · see citing works
Self-citationFunctional Divergence in the Growing Family of RNA Polymerases
Landick, R. C. (2009) · Structure · doi:10.1016/j.str.2009.02.006 · Cited by 23 · see citing works
Crystal structure and RNA-binding analysis of the archaeal transcription factor NusA
Shibata, R., Bessho, Y., Shinkai, A., Nishimoto, M., Fusatomi, E., Terada, T., Shirouzu, M., & Yokoyama, S. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.01.119 · Cited by 22 · see citing works
Grohmann, D., & Werner, F. (2010) · RNA Biology · doi:10.4161/rna.7.3.11912 · Cited by 20 · see citing works
Self-citationReich, C., Zeller, M. E., Milkereit, P., Hausner, W., Cramer, P., Tschochner, H., & Thomm, M. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06577.x · Cited by 20 · see citing works
Structural, Biochemical, and Dynamic Characterizations of the hRPB8 Subunit of Human RNA Polymerases
Kang, X., Hu, Y., Li, Y., Guo, X., Jiang, X., Lai, L., Xia, B., & Jin, C. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m513241200 · Cited by 18 · see citing works
A two-subunit bacterial σ-factor activates transcription in Bacillus subtilis
MacLellan, S. R., Guariglia-Oropeza, V., Gaballa, A., & Helmann, J. D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910006106 · Cited by 14 · see citing works
Post‐initiation control by the initiation factor sigma
Artsimovitch, I. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06136.x · Cited by 13 · see citing works
Rearrangement of the RNA polymerase subunit H and the lower jaw in archaeal elongation complexes
Grünberg, S., Reich, C., Zeller, M. E., Bartlett, M. S., & Thomm, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1190 · Cited by 11 · see citing works
Conformational toggle triggers a modulator of RNA polymerase activity
Deighan, P., & Hochschild, A. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2006.06.004 · Cited by 10 · see citing works
Trypanosome RNA Polymerases and Transcription Factors: Sensible Trypanocidal Drug Targets?
Vanhamme, L. (2008) · Current Drug Targets · doi:10.2174/138945008786786064 · Cited by 7 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Organization and regulation of gene transcription
Cramer, P. (2019) · Nature · doi:10.1038/s41586-019-1517-4 · Cited by 732 · see citing works
Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing
Haag, J. R., & Pikaard, C. S. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3152 · Cited by 405 · see citing works
Structural basis of transcription initiation by RNA polymerase II
Sainsbury, S., Bernecky, C., & Cramer, P. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3952 · Cited by 397 · see citing works
Hahn, S., & Young, E. T. (2011) · Genetics · doi:10.1534/genetics.111.127019 · Cited by 341 · see citing works
Burmann, B. M., Knauer, S. H., Sevostyanova, A., Schweimer, K., Mooney, R. A., Landick, R. C., Artsimovitch, I., & ROSCH, P. J. (2012) · Cell · doi:10.1016/j.cell.2012.05.042 · Cited by 233 · see citing works
Kellinger, M. W., Song, C., Chong, J. P. C., Lu, X., He, C., & Wang, D. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2346 · Cited by 228 · see citing works
Viruses of archaea: Structural, functional, environmental and evolutionary genomics
Krupovìč, M., Cvirkaitė‐Krupovič, V., Iranzo, J., Prangishvili, D. A., & Koonin, E. V. (2017) · Virus Research · doi:10.1016/j.virusres.2017.11.025 · Cited by 222 · see citing works
Termination and antitermination: RNA polymerase runs a stop sign
Santangelo, T. J., & Artsimovitch, I. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2560 · Cited by 202 · see citing works
Haag, J. R., Ream, T. S., Marasco, M. R., Nicora, C., Norbeck, A. D., Paša‐Tolić, L., & Pikaard, C. S. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.09.027 · Cited by 201 · see citing works
X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme
Murakami, K. S. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.430900 · Cited by 186 · see citing works
RNA Polymerase II C-Terminal Domain: Tethering Transcription to Transcript and Template
Corden, J. L. (2013) · Chemical Reviews · doi:10.1021/cr400158h · Cited by 184 · see citing works
Bervoets, I., & Charlier, D. (2019) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuz001 · Cited by 180 · see citing works
Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters
Rhodius, V. A., Segall-Shapiro, T. H., Sharon, B. D., Ghodasara, A., Orlova, E., Tabakh, H., Burkhardt, D. H., Clancy, K., Peterson, T. C., Gross, C. A., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.58 · Cited by 168 · see citing works
Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators
Kang, J. Y., Mooney, R. A., Nedialkov, Y. A., Saba, J., Mishanina, T. V., Artsimovitch, I., Landick, R. C., & Darst, S. A. (2018) · Cell · doi:10.1016/j.cell.2018.05.017 · Cited by 162 · see citing works
Recent advances in understanding mitochondrial genome diversity
Zardoya, R. (2020) · F1000Research · doi:10.12688/f1000research.21490.1 · Cited by 159 · see citing works
A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria
Sojo, V., Pomiankowski, A., & Lane, N. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001926 · Cited by 154 · see citing works
Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes
Guglielmini, J., Woo, A. C., Krupovìč, M., Forterre, P., & Gaïa, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912006116 · Cited by 148 · see citing works
Grohmann, D., Nagy, J., Chakraborty, A., Klose, D., Fielden, D., Ebright, R. H., Michaelis, J., & Werner, F. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.030 · Cited by 146 · see citing works
Self-citationGrünberg, S., Warfield, L., & Hahn, S. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2334 · Cited by 144 · see citing works
The Spt4–Spt5 complex: A multi-faceted regulator of transcription elongation
Hartzog, G. A., & Fu, J. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.08.007 · Cited by 140 · see citing works
A Nexus for Gene Expression—Molecular Mechanisms of Spt5 and NusG in the Three Domains of Life
Werner, F. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.01.031 · Cited by 137 · see citing works
Self-citationPan, J., Meyers, R. M., Michel, B. C., Mashtalir, N., Sizemore, A. E., Wells, J. N., Cassel, S. H., Vázquez, F., Weir, B. A., Hahn, W. C., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.04.011 · Cited by 132 · see citing works
Bacterial Transcription as a Target for Antibacterial Drug Development
Ma, C., Yang, X., & Lewis, P. J. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00055-15 · Cited by 126 · see citing works
Nuclear Organization and Genome Function
Bortle, K. V., & Corces, V. G. (2012) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-101011-155824 · Cited by 119 · see citing works
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Zamft, B., Bintu, L., Ishibashi, T., & Bustamante, C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205063109 · Cited by 117 · see citing works
Biogenesis of multisubunit RNA polymerases
Wild, T., & Cramer, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.12.001 · Cited by 116 · see citing works
A Movie of RNA Polymerase II Transcription
Cheung, A. C. M., & Cramer, P. (2012) · Cell · doi:10.1016/j.cell.2012.06.006 · Cited by 115 · see citing works
Transcription termination by the eukaryotic RNA polymerase III
Arimbasseri, G. A., Rijal, K., & Maraia, R. J. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.006 · Cited by 115 · see citing works
The replication machinery of LUCA: common origin of DNA replication and transcription
Koonin, E. V., Krupovìč, M., Ishino, S., & Ishino, Y. (2020) · BMC Biology · doi:10.1186/s12915-020-00800-9 · Cited by 110 · see citing works
The LUCA and its complex virome
Krupovìč, M., Dolja, V. V., & Koonin, E. V. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0408-x · Cited by 110 · see citing works
Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean
Mihara, T., Koyano, H., Hingamp, P., Grimsley, N. H., Goto, S., & Ogata, H. (2018) · Microbes and Environments · doi:10.1264/jsme2.me17203 · Cited by 109 · see citing works
Diverse and unified mechanisms of transcription initiation in bacteria
Chen, J., Boyaci, H., & Campbell, E. A. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00450-2 · Cited by 106 · see citing works
The interplay between nucleoid organization and transcription in archaeal genomes
Peeters, E., Driessen, R. P. C., Werner, F., & Dame, R. T. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3467 · Cited by 104 · see citing works
Self-citationUnfolding the Mysteries of Protein Metamorphosis
Dishman, A. F., & Volkman, B. F. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00276 · Cited by 104 · see citing works
Insulated transcriptional elements enable precise design of genetic circuits
Zong, Y., Zhang, H. M., Lyu, C., Ji, X., Hou, J., Guo, X., Ouyang, Q., & Lou, C. (2017) · Nature Communications · doi:10.1038/s41467-017-00063-z · Cited by 99 · see citing works
The evolution of the ribosome biogenesis pathway from a yeast perspective
Ebersberger, I., Simm, S., Leisegang, M. S., Schmitzberger, P., Mirus, O., von Haeseler, A., Bohnsack, M. T., & Schleiff, E. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1137 · Cited by 99 · see citing works
RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules
Zhou, M., & Law, J. A. (2015) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2015.07.005 · Cited by 97 · see citing works
Structural basis of transcription elongation
Martínez-Rucobo, F. W., & Cramer, P. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.09.002 · Cited by 96 · see citing works
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
Martinez-Gutierrez, C. A., & Aylward, F. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab254 · Cited by 95 · see citing works
Structure of RNA polymerase bound to ribosomal 30S subunit
Demo, G., Rasouly, A., Vasilyev, N., Svetlov, V. V., Loveland, A. B., Díaz-Avalos, R., Grigorieff, N., Nudler, E., & Korostelev, A. A. (2017) · eLife · doi:10.7554/elife.28560 · Cited by 93 · see citing works
Transcription control engineering and applications in synthetic biology
Engstrom, M. D., & Pfleger, B. F. (2017) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2017.09.003 · Cited by 92 · see citing works
Bird, J. G., Basu, U., Kuster, D., Ramachandran, A., Grudzien‐Nogalska, E., Towheed, A., Wallace, D. C., Kiledjian, M., Temiakov, D., Patel, S. S., et al. (2018) · eLife · doi:10.7554/elife.42179 · Cited by 85 · see citing works
Camprubí, E., de Leeuw, J. W., House, C. H., Raulin, F., Russell, M. J., Spang, A., Tirumalai, M. R., & Westall, F. (2019) · Space Science Reviews · doi:10.1007/s11214-019-0624-8 · Cited by 84 · see citing works
Mechanisms of σ54-Dependent Transcription Initiation and Regulation
Danson, A. E., Jovanovic, M., Buck, M., & Zhang, X. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.04.022 · Cited by 84 · see citing works
RNA polymerase motions during promoter melting
Feklístov, A., Bae, B., Hauver, J., Lass, A., Kalesse, M., Glaus, F., Altmann, K., Heyduk, T., Landick, R. C., & Darst, S. A. (2017) · Science · doi:10.1126/science.aam7858 · Cited by 83 · see citing works
Structures of the RNA polymerase-σ 54 reveal new and conserved regulatory strategies
Yang, Y., Darbari, V. C., Zhang, N., Lü, D., Glyde, R., Wang, Y., Winkelman, J. T., Gourse, R. L., Murakami, K. S., Buck, M., et al. (2015) · Science · doi:10.1126/science.aab1478 · Cited by 80 · see citing works
Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates
Turowski, T. W., Petfalski, E., Goddard, B. D., French, S. L., Helwak, A., & Tollervey, D. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.002 · Cited by 75 · see citing works
Haag, J. R., Brower‐Toland, B. D., Krieger, E. K., Sidorenko, L. V., Nicora, C., Norbeck, A. D., Irsigler, A., Larue, H., Brzeski, J., McGinnis, K. M., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.08.067 · Cited by 74 · see citing works
Mirón-García, M. C., Garrido-Godino, A. I., García-Molinero, V., Hernández‐Torres, F., Rodríguez‐Navarro, S., & Navarro, F. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003297 · Cited by 72 · see citing works
Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II
Engel, C., Neyer, S., & Cramer, P. (2018) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070317-033058 · Cited by 72 · see citing works
Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase
Lerner, E., Chung, S., Allen, B. L., Wang, S., Lee, J., Lu, W., Grimaud, L., Ingargiola, A., Michalet, X., Alhadid, Y. K., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1605038113 · Cited by 70 · see citing works
Time-resolved comparative molecular evolution of oxygenic photosynthesis
Oliver, T. J., Sánchez‐Baracaldo, P., Larkum, A. W. D., Rutherford, A. W., & Cardona, T. (2021) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2021.148400 · Cited by 70 · see citing works
Klose, D., Klare, J. P., Grohmann, D., Kay, C. W. M., Werner, F., & Steinhoff, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039492 · Cited by 70 · see citing works
Self-citationThe Spt5 C-Terminal Region Recruits Yeast 3′ RNA Cleavage Factor I
Mayer, A., Schreieck, A., Lidschreiber, M., Leike, K., Martin, D. E., & Cramer, P. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06310-11 · Cited by 68 · see citing works
TAF1B Is a TFIIB-Like Component of the Basal Transcription Machinery for RNA Polymerase I
Naidu, S., Friedrich, J. K., Russell, J., & Zomerdijk, J. C. B. M. (2011) · Science · doi:10.1126/science.1207656 · Cited by 67 · see citing works
Li, W., Giles, C., & Li, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku333 · Cited by 67 · see citing works
Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea
Dar, D., Prasse, D., Schmitz, R. A., & Sorek, R. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.143 · Cited by 67 · see citing works
Zhang, Z., English, B. P., Grimm, J. B., Kazane, S. A., Hu, W., Tsai, A., Inouye, C. J., You, C., Piehler, J., Schultz, P. G., et al. (2016) · Genes & Development · doi:10.1101/gad.285395.116 · Cited by 67 · see citing works
TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle
Schulz, S., Gietl, A., Smollett, K. L., Tinnefeld, P., Werner, F., & Grohmann, D. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1515817113 · Cited by 65 · see citing works
Self-citationComplete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS
Nagy, J., Grohmann, D., Cheung, A. C. M., Schulz, S., Smollett, K. L., Werner, F., & Michaelis, J. (2015) · Nature Communications · doi:10.1038/ncomms7161 · Cited by 62 · see citing works
Self-citationRecent advances in the understanding of archaeal transcription
Grohmann, D., & Werner, F. (2011) · Current Opinion in Microbiology · doi:10.1016/j.mib.2011.04.012 · Cited by 61 · see citing works
Self-citationDomiński, Z., Carpousis, A. J., & Clouet-d’Orval, B. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2013.01.010 · Cited by 59 · see citing works
Gene duplication and neofunctionalization: POLR3G and POLR3GLPreprint
Renaud, M., Praz, V., Vieu, E., Florens, L. A., Washburn, M. P., Lhôte, P., & Hernandez, N. (2013) · Genome Research · doi:10.1101/gr.161570.113 · Cited by 57 · see citing works
NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication
Tomar, S. K., & Artsimovitch, I. (2013) · Chemical Reviews · doi:10.1021/cr400064k · Cited by 56 · see citing works
Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA
Fujita, K., Iwaki, M., & Yanagida, T. (2016) · Nature Communications · doi:10.1038/ncomms13788 · Cited by 56 · see citing works
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes
Medvedeva, S., Sun, J., Yutin, N., Koonin, E. V., Nunoura, T., Rinke, C., & Krupovìč, M. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01144-6 · Cited by 55 · see citing works
Automated Structural Comparisons Clarify the Phylogeny of the Right-Hand-Shaped Polymerases
Mönttinen, H. A. M., Ravantti, J., Stuart, D. I., & Poranen, M. M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu219 · Cited by 55 · see citing works
Sauguet, L., Raia, P., Henneke, G., & Delarue, M. H. (2016) · Nature Communications · doi:10.1038/ncomms12227 · Cited by 53 · see citing works
A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage
Yakunina, M. V., Артамонова, Т. О., Borukhov, S. I., Makarova, K. S., Severinov, K., & Станиславович, М. Л. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1095 · Cited by 52 · see citing works
Architecture of the Yeast RNA Polymerase II Open Complex and Regulation of Activity by TFIIF
Fishburn, J., & Hahn, S. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.06242-11 · Cited by 52 · see citing works
DNA-Dependent RNA Polymerase Detects Hidden Giant Viruses in Published Databanks
Sharma, V., Colson, P., Giorgi, R., Pontarotti, P., & Raoult, D. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu128 · Cited by 51 · see citing works
DNA origami as biocompatible surface to match single-molecule and ensemble experiments
Gietl, A., Holzmeister, P., Grohmann, D., & Tinnefeld, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks326 · Cited by 51 · see citing works
Self-citationArchaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/39
Blombach, F., Salvadori, E., Fouqueau, T., Yan, J., Reimann, J., Sheppard, C., Smollett, K. L., Albers, S., Kay, C. W. M., Thalassinos, K., et al. (2015) · eLife · doi:10.7554/elife.08378 · Cited by 51 · see citing works
Self-citationTranscriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks
Martínez-Pastor, M., Tonner, P. D., Darnell, C. L., & Schmid, A. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-023413 · Cited by 51 · see citing works
Teichmann, M., Dumay‐Odelot, H., & Fribourg, S. (2012) · Transcription · doi:10.4161/trns.3.1.18917 · Cited by 50 · see citing works
Kramm, K., Schröder, T., Gouge, J., Vera, A. M., Gupta, K., Heiss, F. B., Liedl, T., Engel, C., Berger, I., Vannini, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16702-x · Cited by 50 · see citing works
Self-citationWinkelman, J. T., Winkelman, B. T., Boyce, J., Maloney, M. F., Chen, A. Y., Ross, W., & Gourse, R. L. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.037 · Cited by 49 · see citing works
Glyde, R., Ye, F., Chandran, V., Zhang, N., Buck, M., & Zhang, X. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.010 · Cited by 49 · see citing works
An updated structural classification of replicative DNA polymerases
Raia, P., Delarue, M. H., & Sauguet, L. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180579 · Cited by 49 · see citing works
Archaeal β-CASP ribonucleases of the aCPSF1 family are orthologs of the eukaryal CPSF-73 factor
Phung, D. K., Rinaldi, D., Langendijk-Genevaux, P. S., Quentin, Y., Carpousis, A. J., & Clouet-d’Orval, B. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1237 · Cited by 48 · see citing works
Ravarani, C. N. J., Flock, T., Chavali, S., Anandapadamanaban, M., Babu, M. M., & Santhanam, B. (2020) · Nature Communications · doi:10.1038/s41467-020-16182-z · Cited by 47 · see citing works
Singh, A. P., Grover, S., Sinha, S., Das, M., Somvanshi, P., & Grover, A. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.26124 · Cited by 47 · see citing works
RNA polymerase III subunit architecture and implications for open promoter complex formation
Wu, C. C., Herzog, F., Jennebach, S., Lin, Y., Pai, C.-Y., Aebersold, R. H., Cramer, P., & Chen, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211665109 · Cited by 45 · see citing works
Structural insights into transcriptional regulation of human RNA polymerase III
Wang, Q., Li, S., Wan, F., Xu, Y., Wu, Z., Mi, C., Lan, P., Lei, M., & Wu, J. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00557-x · Cited by 45 · see citing works
Structure and function of virion RNA polymerase of a crAss-like phage
Drobysheva, A. V., Panafidina, S. A., Kolesnik, M. V., Klimuk, E. I., Minakhin, L., Yakunina, M. V., Borukhov, S., Nilsson, E., Holmfeldt, K., Yutin, N., et al. (2021) · Nature · doi:10.1038/s41586-020-2921-5 · Cited by 44 · see citing works
Transcription is regulated by NusA:NusG interaction
Strauß, M., Vitiello, C. L., Schweimer, K., Gottesman, M. E., ROSCH, P. J., & Knauer, S. H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw423 · Cited by 44 · see citing works
Monitoring RNA dynamics in native transcriptional complexes
Chauvier, A., St-Pierre, P., Nadon, J., Hien, E. D. M., Pérez‐González, C., Eschbach, S. H., Lamontagne, A.-M., Penedo, J. C., & Lafontaine, D. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106564118 · Cited by 44 · see citing works
Sub1/PC4, a multifaceted factor: from transcription to genome stability
Garavís, M., & Calvo, O. (2017) · Current Genetics · doi:10.1007/s00294-017-0715-6 · Cited by 43 · see citing works
Key Concepts and Challenges in Archaeal Transcription
Blombach, F., Matelska, D., Fouqueau, T., Cackett, G., & Werner, F. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.06.020 · Cited by 43 · see citing works
Self-citationTranscription initiation factor TBP: old friend new questions
Kramm, K., Engel, C., & Grohmann, D. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180623 · Cited by 42 · see citing works
Self-citationEukaryotic RNA Polymerases: The Many Ways to Transcribe a Gene
Barba‐Aliaga, M., Alepuz, P. M., & Pérez-Ortín, J. E. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.663209 · Cited by 42 · see citing works
Smollett, K. L., Blombach, F., Reichelt, R., Thomm, M., & Werner, F. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.21 · Cited by 41 · see citing works
Self-citationThe RNA polymerase trigger loop functions in all three phases of the transcription cycle
Fouqueau, T., Zeller, M. E., Cheung, A. C. M., Cramer, P., & Thomm, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt433 · Cited by 40 · see citing works
Tetone, L. E., Friedman, L. J., Osborne, M. L., Ravi, H., Kyzer, S., Stumper, S. K., Mooney, R. A., Landick, R. C., & Gelles, J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616525114 · Cited by 40 · see citing works
Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation
Gao, F., Danson, A. E., Ye, F., Jovanovic, M., Buck, M., & Zhang, X. (2020) · Biomolecules · doi:10.3390/biom10030351 · Cited by 40 · see citing works
Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use
Maraia, R. J., & Arimbasseri, G. A. (2017) · Biomolecules · doi:10.3390/biom7010026 · Cited by 39 · see citing works
Salvo, M. D., Pinatel, E., Talà, A., Fondi, M., Peano, C., & Alifano, P. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2049-x · Cited by 39 · see citing works
Yue, L., Li, J., Zhang, B., Qi, L., Li, Z., Zhao, F., Li, L., Zheng, X., & Dong, X. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa702 · Cited by 39 · see citing works
Multisubunit RNA Polymerases of Jumbo Bacteriophages
Sokolova, M. L., Misovetc, I., & Severinov, K. (2020) · Viruses · doi:10.3390/v12101064 · Cited by 39 · see citing works
Rymen, B., Ferrafiat, L., & Blevins, T. (2020) · Transcription · doi:10.1080/21541264.2020.1825906 · Cited by 39 · see citing works
- Authors
- Werner, F., & Grohmann, D.
- Affiliations
- Institute of Structural and Molecular Biology (GB)
- Corresponding author
- Werner, Finn
- Venue
- Nature Reviews Microbiology
- Published
- 2011-01-13
- Volume
- 9
- Issue
- 2
- Pages
- 85-98
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W1992223935
- Cited by
- 431
- References
- 120
- Citations by year
- 2026: 18 · 2025: 19 · 2024: 28 · 2023: 26 · 2022: 25 · 2021: 38 · 2020: 39 · 2019: 35 · 2018: 28 · 2017: 36 · 2016: 21 · 2015: 24 · 2014: 21 · 2013: 30 · 2012: 28
- FWCI
- 2.72
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/H019332/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- three domains of life, transcriptional regulation, basal transcription factors, subunit composition, eukaryotic RNA polymerase, archaeal RNA polymerase, bacterial RNA polymerase
- MeSH terms
- Archaea, Bacteria, Models, Molecular, Phylogeny, DNA-Directed RNA Polymerases, Saccharomyces cerevisiae, Gene Expression Regulation, Enzymologic, Conserved Sequence, Evolution, Molecular, Protein Structure, Quaternary, Transcriptional Elongation Factors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review