During transcription initiation, RNA polymerase binds tightly to the promoter DNA defining the start of transcription, transcribes comparatively slowly, and frequently releases short transcripts (3–8 nucleotides) in a process called abortive cycling. Transitioning to elongation, the second phase of transcription, the polymerase dissociates from the promoter while RNA synthesis continues. Elongation is characterized by higher rates of transcription and tight binding to the RNA transcript. The RNA polymerase from enterophage T7 (T7 RNAP) has been used as a model to understand the mechanism of transcription in general, and the transition from initiation to elongation specifically. This single-subunit enzyme undergoes dramatic conformational changes during this transition to support the changing requirements of nucleic acid interactions while continuously maintaining polymerase function. Crystal structures, available of multiple stages of the initiation complex and of the elongation complex, combined with biochemical and biophysical data, offer molecular detail of the transition. Some of the crystal structures contain a variant of T7 RNAP where proline 266 is substituted by leucine. This variant shows less abortive products and altered timing of transition, and is a valuable tool to study these processes. The structural transitions from early to late initiation are well understood and are consistent with solution data. The timing of events and the structural intermediates in the transition from late initiation to elongation are less well understood, but the available data allows one to formulate testable models of the transition to guide further research.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Tax calculation will be finalised during checkout.
Bandwar R P, Ma N, Emanuel S A, Anikin M, Vassylyev D G, Patel S S, and McAllister W T. 2007. The transition to an elongation complex by T7 RNA polymerase is a multistep process. J Biol Chem, 31: 22879–22886.
Cheetham G M, and Steitz T A. 1999. Structure of a transcribing T7 RNA polymerase initiation complex. Science, 286(5448):2305–2309.
Daube S S, and von Hippel P H. 1992. Functional transcription elongation complexes from synthetic RNA-DNA bubble duplexes. Science, 258(5086):1320–1324.
Durniak K J, Bailey S, and Steitz T A. 2008. The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science, 322(5901):553–557.
Gong P, Esposito E A, and Martin C T. 2004. Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase. J Biol Chem. 279(43): 44277–44285.
Guillerez J, Lopez P J, Proux F, Launay H, and Dreyfus M. 2005. A mutation in T7 RNA polymerase that facilitates promoter clearance. Proc Natl Acad Sci U S A, 102(17):5958–5963.
Liu X, and Martin C T. 2009. Transcription elongation complex stability: the topological lock. J Biol Chem, 284(52):36262–36270.
Martin C T, Esposito E A, Theis K, and Gong P. 2005. Structure and function in promoter escape by T7 RNA polymerase. Prog Nucleic Acid Res Mol Biol, 80: 323–347.
Milligan J F, Groebe D R, Witherell G W, and Uhlenbeck O C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res, 15(21): 8783–8798.
Ramírez-Tapia L E, and Martin C T. 2012. New Insights into the Mechanism of Initial Transcription. The T7 RNA polymerase mutant P266L transitions to elongation at longer RNA lengths than wild type. J Biol Chem, 287(44): 37352–37361.
Ritacco C J, Kamtekar S, Wang J, and Steitz T A. 2013. Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase. Nucleic Acids Res, 41(4):2673–82.
Schwinghammer K, Cheung A C, Morozov Y I, Agaronyan K, Temiakov D, and Cramer P. 2013. Structure of human mitochondrial RNA polymerase elongation complex. Nat Struct Mol Biol. 20(11):1298–1303.
Steitz T A. 2009. The structural changes of T7 RNA polymerase from transcription initiation to elongation. Curr Opin Struct Biol. 19(6):683–690.
Studier F W, and Moffatt B A. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol, 189(1): 113–130.
Tahirov T H, Temiakov D, Anikin M, Patlan V, McAllister W T, Vassylyev D G, and Yokoyama S. 2002. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature, 420(6911):43–50.
Tang G Q, Roy R, Bandwar R P, Ha T, and Patel S S. 2009. Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. Proc Natl Acad Sci U S A. 106(52):22175–22180.
Theis K, Gong P, and Martin C T. 2004. Topological and conformational analysis of the initiation and elongation complex of t7 RNA polymerase suggests a new twist. Biochemistry, 43(40):12709–12715.
Turingan R S, Liu C, Hawkins M E, and Martin C T. 2007. Structural confirmation of a bent and open model for the initiation complex of T7 RNA polymerase. Biochemistry, 46(7):1714–1723.
Vahia A V, and Martin C T. 2011. Direct tests of the energetic basis of abortive cycling in transcription. Biochemistry, 50(32):7015–7022.
Yin Y W, and Steitz T A. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science, 298(5597):1387–1395
About this article
Cite this article
Theis, K. Snapshots of a viral RNA polymerase switching gears from transcription initiation to elongation. Virol. Sin. 28, 337–344 (2013). https://doi.org/10.1007/s12250-013-3397-3
- RNA polymerase
- Crystal structure