Key Points
-
The transcription elongation complex is composed of a multisubunit RNA polymerase (RNAP), a DNA template and a nascent RNA. This complex is normally extremely stable but can be efficiently disassembled by the action of select proteins, called termination factors, or specific sequences, called intrinsic terminators.Regulated transcription termination is the underlying mechanism of attenuation, riboswitch function and polar repression of downstream expression. Efficient termination is also necessary to halt transcription elongation complexes at the end of genes in order to block unproductive or aberrant expression of downstream genes.Expression of many genes, most notably those encoding ribosomal RNA, is critically dependent on antitermination mechanisms that modify RNAP into a termination-resistant state.
-
Antitermination factors can modulate or block the activity of termination factors, override intrinsic terminators in leader sequences under conditions necessitating downstream expression, and modify the activity of RNAP to provide expression of select genes (for example, upon phage infection).
-
Many antitermination factors act just once during mRNA synthesis by blocking the formation of an RNA hairpin structure that is necessary for intrinsic termination. These factors usually employ direct binding to RNA, and structures as large as translating ribosomes are used to determine the RNA fold.
-
Processive antitermination factors bind to, and modify the activity of, elongating RNAP such that the modified complex is resistant to multiple or tandem downstream termination signals. Studies of antitermination factors provide important insights into mechanisms of processive RNA synthesis in all domains. These factors provide stability to the transcription complex, either by shielding the encapsulated nucleic acids or preventing structural changes in RNAP necessary for RNA release and complex disassembly.
Abstract
Termination signals induce rapid and irreversible dissociation of the nascent transcript from RNA polymerase. Terminators at the end of genes prevent unintended transcription into the downstream genes, whereas terminators in the upstream regulatory leader regions adjust expression of the structural genes in response to metabolic and environmental signals. Premature termination within an operon leads to potentially deleterious defects in the expression of the downstream genes, but also provides an important surveillance mechanism. This Review discusses the actions of bacterial and phage antiterminators that allow RNA polymerase to override a terminator when the circumstances demand it.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Mooney, R. A., Artsimovitch, I. & Landick, R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180, 3265–3275 (1998).
Grachev, M. A. et al. Oligonucleotides complementary to a promoter over the region -8+2 as transcription primers for E. coli RNA polymerase. Nucleic Acids Res. 12, 8509–8524 (1984).
Yin, H. et al. Transcription against an applied force. Science 270, 1653–1657 (1995).
Ring, B. Z., Yarnell, W. S. & Roberts, J. W. Function of E. coli RNA polymerase s factor s 70 in promoter-proximal pausing. Cell 86, 485–493 (1996).
Artsimovitch, I. & Landick, R. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell 109, 193–203 (2002).
Landick, R., Carey, J. & Yanofsky, C. Translation activates the paused transcription complex and restores transcription of the trp operon leader region. Proc. Natl Acad. Sci. USA 82, 4663–4667 (1985).
Komissarova, N. & Kashlev, M. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272, 15329–15338 (1997).
Toulme, F., Mosrin-Huaman, C., Artsimovitch, I. & Rahmouni, A. R. Transcriptional pausing in vivo: a nascent RNA hairpin restricts lateral movements of RNA polymerase in both forward and reverse directions. J. Mol. Biol. 351, 39–51 (2005).
Cramer, P. Multisubunit RNA polymerases. Curr. Opin. Struct. Biol. 12, 89–97 (2002).
Schmidt, M. C. & Chamberlin, M. J. NusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites. J. Mol. Biol. 195, 809–818 (1987).
Gusarov, I. & Nudler, E. The mechanism of intrinsic transcription termination. Mol. Cell 3, 495–504 (1999).
Toulokhonov, I., Artsimovitch, I. & Landick, R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292, 730–733 (2001).
Artsimovitch, I. & Landick, R. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev. 12, 3110–3122 (1998).
Yarnell, W. S. & Roberts, J. W. Mechanism of intrinsic transcription termination and antitermination. Science 284, 611–615 (1999).
Santangelo, T. J. & Roberts, J. W. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell 14, 117–126 (2004).
Shankar, S., Hatoum, A. & Roberts, J. W. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol. Cell 27, 914–927 (2007).
Peters, J. M. et al. Rho directs widespread termination of intragenic and stable RNA transcription. Proc. Natl Acad. Sci. USA 106, 15406–15411 (2009).
Sevostyanova, A. & Artsimovitch, I. Functional analysis of Thermus thermophilus transcription factor NusG. Nucleic Acids Res. 38, 7432–7445 (2010).
Santangelo, T. J., Cubonova, L., Skinner, K. M. & Reeve, J. N. Archaeal intrinsic transcription termination in vivo. J. Bacteriol. 191, 7102–7108 (2009).
Roberts, J. W. Termination factor for RNA synthesis. Nature 224, 1168–1174 (1969).
Richardson, J. P., Grimley, C. & Lowery, C. Transcription termination factor Rho activity is altered in Escherichia coli with suA gene mutations. Proc. Natl Acad. Sci. USA 72, 1725–1728 (1975).
Cardinale, C. J. et al. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320, 935–938 (2008).
Harinarayanan, R. & Gowrishankar, J. Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J. Mol. Biol. 332, 31–46 (2003).
Klumpp, S. & Hwa, T. Stochasticity and traffic jams in the transcription of ribosomal RNA: intriguing role of termination and antitermination. Proc. Natl Acad. Sci. USA 105, 18159–18164 (2008).
Washburn, R. S. & Gottesman, M. E. Transcription termination maintains chromosome integrity. Proc. Natl Acad. Sci. USA 108, 792–797 (2011).
Richardson, J. & Greenblatt, J. in Escherichia coli and Salmonella Vol. 1 (eds F.C. Neidhardt et al.) 822–848 (ASM Press, Washington DC, 1996).
Ciampi, M. S. Rho-dependent terminators and transcription termination. Microbiology 152, 2515–2528 (2006).
Epshtein, V., Dutta, D., Wade, J. & Nudler, E. An allosteric mechanism of Rho-dependent transcription termination. Nature 463, 245–249 (2010).
Mooney, R. A. et al. Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33, 97–108 (2009).
Morgan, W. D., Bear, D. G. & von Hippel, P. H. Specificity of release by Escherichia coli transcription termination factor Rho of nascent mRNA transcripts initiated at the l PR . J. Biol. Chem. 259, 8664–8671 (1984).
Gutierrez, P. et al. Solution structure of YaeO, a Rho-specific inhibitor of transcription termination. J. Biol. Chem. 282, 23348–23353 (2007).
Pani, B. et al. Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu. J. Biol. Chem. 281, 26491–26500 (2006).
Weisberg, R. A. & Gottesman, M. E. Processive antitermination. J. Bacteriol. 181, 359–367 (1999).
Stewart, V., Landick, R. & Yanofsky, C. Rho-dependent transcription termination in the tryptophanase operon leader region of Escherichia coli K-12. J. Bacteriol. 166, 217–223 (1986).
Henkin, T. M. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev. 22, 3383–3390 (2008).
Merino, E. & Yanofsky, C. Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet. 21, 260–264 (2005).
Smith, A. M., Fuchs, R. T., Grundy, F. J. & Henkin, T. M. Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal. RNA Biol. 7, 104–110 (2010).
Amster-Choder, O. The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination. Curr. Opin. Microbiol. 8, 127–134 (2005).
Phadtare, S. & Severinov, K. RNA remodeling and gene regulation by cold shock proteins. RNA Biol. 7, 788–795 (2010).
Kumarevel, T., Mizuno, H. & Kumar, P. K. Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand. Nature 434, 183–191 (2005).
Schmalisch, M. H., Bachem, S. & Stulke, J. Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation. Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278, 51108–51115 (2003).
Demene, H. et al. Structural mechanism of signal transduction between the RNA-binding domain and the phosphotransferase system regulation domain of the LicT antiterminator. J. Biol. Chem. 283, 30838–30849 (2008).
Gopinath, S. C. et al. Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP. Nucleic Acids Res. 36, 3463–3473 (2008).
van Tilbeurgh, H. & Declerck, N. Structural insights into the regulation of bacterial signalling proteins containing PRDs. Curr. Opin. Struct. Biol. 11, 685–693 (2001).
Raveh, H., Lopian, L., Nussbaum-Shochat, A., Wright, A. & Amster-Choder, O. Modulation of transcription antitermination in the bgl operon of Escherichia coli by the PTS. Proc. Natl Acad. Sci. USA 106, 13523–13528 (2009).
Galperin, M. Y. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol. 188, 4169–4182 (2006).
Fox, K. A. et al. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc. Natl Acad. Sci. USA 106, 4435–4440 (2009).
Chai, W. & Stewart, V. RNA sequence requirements for NasR-mediated, nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader. J. Mol. Biol. 292, 203–216 (1999).
Yanofsky, C. Attenuation in the control of expression of bacterial operons. Nature 289, 751–758 (1981).
Gong, F. & Yanofsky, C. Analysis of tryptophanase operon expression in vitro: accumulation of TnaC-peptidyl-tRNA in a release factor 2-depleted S-30 extract prevents Rho factor action, simulating induction. J. Biol. Chem. 277, 17095–17100 (2002).
Gong, M., Cruz-Vera, L. R. & Yanofsky, C. Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli. J. Bacteriol. 189, 3147–3155 (2007).
Grundy, F. J., Winkler, W. C. & Henkin, T. M. tRNA-mediated transcription antitermination in vitro: codon–anticodon pairing independent of the ribosome. Proc. Natl Acad. Sci. USA 99, 11121–11126 (2002).
Grundy, F. J. & Henkin, T. M. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 74, 475–482 (1993).
Green, N. J., Grundy, F. J. & Henkin, T. M. The T box mechanism: tRNA as a regulatory molecule. FEBS Lett. 584, 318–324 (2010).
Murray, K. D. & Bremer, H. Control of SpoT-dependent ppGpp synthesis and degradation in Escherichia coli. J. Mol. Biol. 259, 41–57 (1996).
Winkler, W. C., Cohen-Chalamish, S. & Breaker, R. R. An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci. USA 99, 15908–15913 (2002).
Park, S. Y., Cromie, M. J., Lee, E. J. & Groisman, E. A. A bacterial mRNA leader that employs different mechanisms to sense disparate intracellular signals. Cell 142, 737–748 (2010).
Montange, R. K. & Batey, R. T. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 37, 117–133 (2008).
Epshtein, V., Mironov, A. S. & Nudler, E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci. USA 100, 5052–5056 (2003).
McDaniel, B. A., Grundy, F. J., Artsimovitch, I. & Henkin, T. M. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl Acad. Sci. USA 100, 3083–3088 (2003).
Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E. & Breaker, R. R. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nature Struct. Biol. 10, 701–707 (2003).
Mandal, M. & Breaker, R. R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Struct. Mol. Biol. 11, 29–35 (2004).
French, S. L., Santangelo, T. J., Beyer, A. L. & Reeve, J. N. Transcription and translation are coupled in Archaea. Mol. Biol. Evol. 24, 893–895 (2007).
Miller, O. L. Jr, Hamkalo, B. A. & Thomas, C. A. Jr Visualization of bacterial genes in action. Science 169, 392–395 (1970).
Santangelo, T. J. et al. Polarity in archaeal operon transcription in Thermococcus kodakaraensis. J. Bacteriol. 190, 2244–2248 (2008).
Peters, J. M., Vangeloff, A. D. & Landick, R. Bacterial transcription terminators: the RNA 3′-end chronicles. J. Mol. Biol. 23 Mar 2011 (doi:10.1016/j.jmb.2011.03.036)
Burns, C. M. & Richardson, J. P. NusG is required to overcome a kinetic limitation to Rho function at an intragenic terminator. Proc. Natl Acad. Sci. USA 92, 4738–4742 (1995).
Sullivan, S. & Gottesman, M. Requirement for E. coli NusG protein in factor-dependent transcription termination. Cell 68, 989–994 (1992).
Burmann, B. M. et al. A NusE:NusG complex links transcription and translation. Science 328, 501–504 (2010).
Proshkin, S., Rahmouni, A. R., Mironov, A. & Nudler, E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328, 504–508 (2010).
Torres, M., Condon, C., Balada, J. M., Squires, C. & Squires, C. L. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination. EMBO J. 20, 3811–3820 (2001).
Campbell, A. Comparative molecular biology of lambdoid phages. Annu. Rev. Microbiol. 48, 193–222 (1994).
Artsimovitch, I. & Landick, R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl Acad. Sci. USA 97, 7090–7095 (2000).
Toulokhonov, I., Zhang, J., Palangat, M. & Landick, R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 27, 406–419 (2007).
Barik, S., Ghosh, B., Whalen, W., Lazinski, D. & Das, A. An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site. Cell 50, 885–899 (1987).
Mogridge, J., Mah, T. & Greenblatt, J. A protein-RNA interaction network facilitates the template-independent cooperative assembly on RNA polymerase of a stable antitermination complex containing the lambda N protein. Genes Dev. 9, 2831–2845 (1995).
Rees, W. A., Weitzel, S. E., Das, A. & von Hippel, P. H. Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage l. J. Mol. Biol. 273, 797–813 (1997).
Gusarov, I. & Nudler, E. Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell 107, 437–449 (2001).
Vieu, E. & Rahmouni, A. R. Dual role of boxB RNA motif in the mechanisms of termination/antitermination at the lambda tR1 terminator revealed in vivo. J. Mol. Biol. 339, 1077–1087 (2004).
Nickels, B. E., Roberts, C. W., Sun, H. I., Roberts, J. W. & Hochschild, A. The s70 subunit of RNA polymerase is contacted by the l Q antiterminator during early elongation. Mol. Cell 10, 611–622 (2002).
Roberts, J. W. et al. Antitermination by bacteriophage l Q protein. Cold Spring Harb. Symp. Quant. Biol. 63, 319–325 (1998).
Deighan, P., Diez, C. M., Leibman, M., Hochschild, A. & Nickels, B. E. The bacteriophage l Q antiterminator protein contacts the b-flap domain of RNA polymerase. Proc. Natl Acad. Sci. USA 105, 15305–15310 (2008).
Kaczanowska, M. & Ryden-Aulin, M. Ribosome biogenesis and the translation process in Escherichia coli. Microbiol. Mol. Biol. Rev. 71, 477–494 (2007).
Condon, C., Squires, C. & Squires, C. L. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59, 623–645 (1995).
Greive, S. J., Lins, A. F. & von Hippel, P. H. Assembly of an RNA-protein complex. Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in Escherichia coli. J. Biol. Chem. 280, 36397–36408 (2005).
Sen, R., King, R. A. & Weisberg, R. A. Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA. Mol. Cell 7, 993–1001 (2001).
King, R. A., Markov, D., Sen, R., Severinov, K. & Weisberg, R. A. A conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex. J. Mol. Biol. 342, 1143–1154 (2004).
Komissarova, N. et al. Inhibition of a transcriptional pause by RNA anchoring to RNA polymerase. Mol. Cell 31, 683–694 (2008).
Irnov, I. & Winkler, W. C. A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol. Microbiol. 76, 559–575 (2010).
Bailey, M. J., Hughes, C. & Koronakis, V. RfaH and the ops element, components of a novel system controlling bacterial transcription elongation. Mol. Microbiol. 26, 845–851 (1997).
Belogurov, G. A., Mooney, R. A., Svetlov, V., Landick, R. & Artsimovitch, I. Functional specialization of transcription elongation factors. EMBO J. 28, 112–122 (2009).
Belogurov, G. A. et al. Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol. Cell 26, 117–129 (2007).
Mooney, R. A., Schweimer, K., Rosch, P., Gottesman, M. & Landick, R. Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J. Mol. Biol. 391, 341–358 (2009).
Chalissery, J. et al. Interaction surface of the transcription terminator Rho required to form a complex with the C-terminal domain of the antiterminator NusG. J. Mol. Biol. 405, 49–64 (2011).
Sevostyanova, A., Svetlov, V., Vassylyev, D. G. & Artsimovitch, I. The elongation factor RfaH and the initiation factor s bind to the same site on the transcription elongation complex. Proc. Natl Acad. Sci. USA 105, 865–870 (2008).
Svetlov, V., Belogurov, G. A., Shabrova, E., Vassylyev, D. G. & Artsimovitch, I. Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res. 35, 5694–5705 (2007).
Bailey, M. J., Hughes, C. & Koronakis, V. In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element. Mol. Gen. Genet. 262, 1052–1059 (2000).
Nudler, E., Avetissova, E., Markovtsov, V. & Goldfarb, A. Transcription processivity: protein-DNA interactions holding together the elongation complex. Science 273, 211–217 (1996).
Sidorenkov, I., Komissarova, N. & Kashlev, M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2, 55–64 (1998).
Nudler, E. RNA polymerase active center: the molecular engine of transcription. Ann. Rev. Biochem. 78, 335–361 (2009).
Epshtein, V., Cardinale, C. J., Ruckenstein, A. E., Borukhov, S. & Nudler, E. An allosteric path to transcription termination. Mol. Cell 28, 991–1001 (2007).
Park, J. S. & Roberts, J. W. Role of DNA bubble rewinding in enzymatic transcription termination. Proc. Natl Acad. Sci. USA 103, 4870–4875 (2006).
Potter, K. D., Merlino, N. M., Jacobs, T. & Gollnick, P. TRAP binding to the Bacillus subtilis trp leader region RNA causes efficient transcription termination at a weak intrinsic terminator. Nucleic Acids Res. 39, 2092–2102 (2011).
Komissarova, N., Becker, J., Solter, S., Kireeva, M. & Kashlev, M. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10, 1151–1162 (2002).
Larson, M. H., Greenleaf, W. J., Landick, R. & Block, S. M. Applied force reveals mechanistic and energetic details of transcription termination. Cell 132, 971–982 (2008).
Datta, K. & von Hippel, P. H. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J. Biol. Chem. 283, 3537–3549 (2008).
Ha, K. S., Toulokhonov, I., Vassylyev, D. G. & Landick, R. The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase. J. Mol. Biol. 401, 708–725 (2010).
Yuzenkova, Y., Zenkin, N. & Severinov, K. Mapping of RNA polymerase residues that interact with bacteriophage Xp10 transcription antitermination factor p7. J. Mol. Biol. 375, 29–35 (2008).
Sydow, J. F. et al. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol. Cell 34, 710–721 (2009).
Belogurov, G. A., Sevostyanova, A., Svetlov, V. & Artsimovitch, I. Functional regions of the N-terminal domain of the antiterminator RfaH. Mol. Microbiol. 76, 286–301 (2010).
Werner, F. & Grohmann, D. Evolution of multisubunit RNA polymerases in the three domains of life. Nature Rev. Microbiol. 9, 85–98 (2011).
Hirtreiter, A. et al. Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res. 38, 4040–4051 (2010).
Klein, B. J. et al. RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc. Natl Acad. Sci. USA 108, 546–550 (2011).
Martinez-Rucobo, F. W., Sainsbury, S., Cheung, A. C. & Cramer, P. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 8 Mar 2011 (doi:10.1038/emboj.2011.64).
Steinmetz, E. J. & Platt, T. Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor. Proc. Natl Acad. Sci. USA 91, 1401–1405 (1994).
Rabhi, M. et al. Mutagenesis-based evidence for an asymmetric configuration of the ring-shaped transcription termination factor Rho. J. Mol. Biol. 405, 497–518 (2011).
Thomsen, N. D. & Berger, J. M. Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell 139, 523–534 (2009).
Rees, W., Weitzel, S., Yager, T., Das, A. & von Hippel, P. Bacteriophage l N protein alone can induce transcription antitermination in vitro. Proc. Natl Acad. Sci. USA 93, 342–346 (1996).
Sloan, S., Rutkai, E., King, R. A., Velikodvorskaya, T. & Weisberg, R. A. Protection of antiterminator RNA by the transcript elongation complex. Mol. Microbiol. 63, 1197–1208 (2007).
Acknowledgements
We thank N. Ruiz and the anonymous referees for their help in improving the manuscript. This work was supported by the US National Institutes of Health grants GM67153 (to I.A.) and F32-GM073336 (to T.J.S.).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Related links
Glossary
- Pause site
-
A signal that causes the elongation complex to stall temporarily.
- Arrest site
-
A signal at which the elongation complex comes to a complete halt but does not dissociate.
- Polarity
-
A quality control mechanism in which Rho terminates the transcription of mRNAs that are not translated.
- R-loops
-
DNA loops behind RNA polymerase that are created when the nascent RNA invades the DNA duplex and pairs with the template DNA strand.
- rrn operons
-
The operons that contain ribosomal RNA and tRNA genes.
- Leader regions
-
Regions of DNA that separate promoters from structural genes. Leaders play diverse regulatory roles as riboswitches, attenuators and targets for auxiliary factors.
- RF2
-
Release factor 2. A release factor that mediates hydrolysis of the peptidyl-tRNA ester bond at UAA and UGA stop codons.
- Zinc-finger
-
A small protein motif in which the structure is stabilized by a bound Zn2+ ion.
- Transcription bubble
-
A 12–14-nucleotide region in which the template and the non-template DNA strands are separated by the RNA polymerase.
Rights and permissions
About this article
Cite this article
Santangelo, T., Artsimovitch, I. Termination and antitermination: RNA polymerase runs a stop sign. Nat Rev Microbiol 9, 319–329 (2011). https://doi.org/10.1038/nrmicro2560
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrmicro2560
This article is cited by
-
Comprehensive transcription terminator atlas for Bacillus subtilis
Nature Microbiology (2022)
-
Enhancing transcription in Escherichia coli and Pseudomonas putida using bacteriophage lambda anti-terminator protein Q
Biotechnology Letters (2022)
-
Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator
Nature Communications (2021)
-
Promoter-proximal elongation regulates transcription in archaea
Nature Communications (2021)
-
Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine
Nature Communications (2021)