Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 31 July 1998:
Vol. 281. no. 5377, pp. 660 - 665
DOI: 10.1126/science.281.5377.660
Prev | Table of Contents | Next

Review

An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing

Peter H. von Hippel

Recent findings now allow the development of an integrated model of the thermodynamic, kinetic, and structural properties of the transcription complex in the elongation, termination, and editing phases of transcript formation. This model provides an operational framework for placing known facts and can be extended and modified to incorporate new advances. The most complete information about transcriptional mechanisms and their control continues to come from the Escherichia coli system, upon which most of the explicit descriptions provided here are based. The transcriptional machinery of higher organisms, despite its greater inherent complexity, appears to use many of the same general principles. Thus, the lessons of E. coli continue to be relevant.

The author is at the Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA. E-mail: petevh{at}molbio.uoregon.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Derailing the Locomotive: Transcription Termination.
D. S. Gilmour and R. Fan (2008)
J. Biol. Chem. 283, 661-664
   Full Text »    PDF »
Analysis of Promoter Targets for Escherichia coli Transcription Elongation Factor GreA In Vivo and In Vitro.
E. Stepanova, J. Lee, M. Ozerova, E. Semenova, K. Datsenko, B. L. Wanner, K. Severinov, and S. Borukhov (2007)
J. Bacteriol. 189, 8772-8785
   Abstract »    Full Text »    PDF »
The Site of Action of the Antiterminator Protein N from the Lambdoid Phage H-19B.
A. Cheeran, N. R. Kolli, and R. Sen (2007)
J. Biol. Chem. 282, 30997-31007
   Abstract »    Full Text »    PDF »
Ribosome Biogenesis and the Translation Process in Escherichia coli.
M. Kaczanowska and M. Ryden-Aulin (2007)
Microbiol. Mol. Biol. Rev. 71, 477-494
   Abstract »    Full Text »    PDF »
A new connection of mRNP biogenesis and export with transcription-coupled repair.
H. Gaillard, R. E. Wellinger, and A. Aguilera (2007)
Nucleic Acids Res. 35, 3893-3906
   Abstract »    Full Text »    PDF »
Characterization of a Novel 5' Subgenomic RNA3a Derived from RNA3 of Brome Mosaic Bromovirus.
R. Wierzchoslawski, A. Urbanowicz, A. Dzianott, M. Figlerowicz, and J. J. Bujarski (2006)
J. Virol. 80, 12357-12366
   Abstract »    Full Text »    PDF »
Dynamics of nascent mRNA folding and RNA-protein interactions: an alternative TAR RNA structure is involved in the control of HIV-1 mRNA transcription.
S. N. Richter, F. Belanger, P. Zheng, and T. M. Rana (2006)
Nucleic Acids Res. 34, 4278-4292
   Abstract »    Full Text »    PDF »
Observed Instability of T7 RNA Polymerase Elongation Complexes Can Be Dominated by Collision-induced "Bumping".
Y. Zhou and C. T. Martin (2006)
J. Biol. Chem. 281, 24441-24448
   Abstract »    Full Text »    PDF »
Thermodynamic and kinetic modeling of transcriptional pausing.
V. R. Tadigotla, D. O Maoileidigh, A. M. Sengupta, V. Epshtein, R. H. Ebright, E. Nudler, and A. E. Ruckenstein (2006)
PNAS 103, 4439-4444
   Abstract »    Full Text »    PDF »
Characterization of the Detachable Rho-Dependent Transcription Terminator of the fimE Gene in Escherichia coli K-12.
P. Hinde, P. Deighan, and C. J. Dorman (2005)
J. Bacteriol. 187, 8256-8266
   Abstract »    Full Text »    PDF »
Sequence Context Effects on Oligo(dT) Termination Signal Recognition by Saccharomyces cerevisiae RNA Polymerase III.
P. Braglia, R. Percudani, and G. Dieci (2005)
J. Biol. Chem. 280, 19551-19562
   Abstract »    Full Text »    PDF »
Functional Dissection of RNA Polymerase III Termination Using a Peptide Nucleic Acid as a Transcriptional Roadblock.
E. Guffanti, R. Corradini, S. Ottonello, and G. Dieci (2004)
J. Biol. Chem. 279, 20708-20716
   Abstract »    Full Text »    PDF »
Temperature-dependent processing of the cspA mRNA in Rhodobacter capsulatus.
S. Jager, E. Evguenieva-Hackenberg, and G. Klug (2004)
Microbiology 150, 687-695
   Abstract »    Full Text »    PDF »
Function and Assembly of the Bacteriophage T4 DNA Replication Complex: INTERACTIONS OF THE T4 POLYMERASE WITH VARIOUS MODEL DNA CONSTRUCTS.
E. Delagoutte and P. H. von Hippel (2003)
J. Biol. Chem. 278, 25435-25447
   Abstract »    Full Text »    PDF »
A Transcriptionally Active Subgenomic Promoter Supports Homologous Crossovers in a Plus-Strand RNA Virus.
R. Wierzchoslawski, A. Dzianott, S. Kunimalayan, and J. J. Bujarski (2003)
J. Virol. 77, 6769-6776
   Abstract »    Full Text »    PDF »
NTP-driven Translocation by Human RNA Polymerase II.
Y. A. Nedialkov, X. Q. Gong, S. L. Hovde, Y. Yamaguchi, H. Handa, J. H. Geiger, H. Yan, and Z. F. Burton (2003)
J. Biol. Chem. 278, 18303-18312
   Abstract »    Full Text »    PDF »
Cooperation Between RNA Polymerase Molecules in Transcription Elongation.
V. Epshtein and E. Nudler (2003)
Science 300, 801-805
   Abstract »    Full Text »    PDF »
Transcription Strategy in a Closterovirus: a Novel 5'-Proximal Controller Element of Citrus Tristeza Virus Produces 5'- and 3'-Terminal Subgenomic RNAs and Differs from 3' Open Reading Frame Controller Elements.
S. Gowda, M. A. Ayllon, T. Satyanarayana, M. Bar-Joseph, and W. O. Dawson (2002)
J. Virol. 77, 340-352
   Abstract »    Full Text »    PDF »
Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase.
Y. W. Yin and T. A. Steitz (2002)
Science 298, 1387-1395
   Abstract »    Full Text »    PDF »
RNA Recombination in Brome Mosaic Virus: Effects of Strand-Specific Stem-Loop Inserts.
R. C. L. Olsthoorn, A. Bruyere, A. Dzianott, and J. J. Bujarski (2002)
J. Virol. 76, 12654-12662
   Abstract »    Full Text »    PDF »
Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior.
K. Adelman, A. La Porta, T. J. Santangelo, J. T. Lis, J. W. Roberts, and M. D. Wang (2002)
PNAS 99, 13538-13543
   Abstract »    Full Text »    PDF »
Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase.
N. R. Forde, D. Izhaky, G. R. Woodcock, G. J. L. Wuite, and C. Bustamante (2002)
PNAS 99, 11682-11687
   Abstract »    Full Text »    PDF »
Transcription Termination: Primary Intermediates and Secondary Adducts.
M. Kashlev and N. Komissarova (2002)
J. Biol. Chem. 277, 14501-14508
   Abstract »    Full Text »    PDF »
Spt5 Cooperates with Human Immunodeficiency Virus Type 1 Tat by Preventing Premature RNA Release at Terminator Sequences.
C. F. Bourgeois, Y. K. Kim, M. J. Churcher, M. J. West, and J. Karn (2002)
Mol. Cell. Biol. 22, 1079-1093
   Abstract »    Full Text »    PDF »
Conserved economics of transcription termination in eubacteria.
S. Unniraman, R. Prakash, and V. Nagaraja (2002)
Nucleic Acids Res. 30, 675-684
   Abstract »    Full Text »    PDF »
Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria.
S. Unniraman, R. Prakash, and V. Nagaraja (2001)
J. Biol. Chem. 276, 41850-41855
   Abstract »    Full Text »    PDF »
Prediction of rho-independent transcriptional terminators in Escherichia coli.
E. A. Lesnik, R. Sampath, H. B. Levene, T. J. Henderson, J. A. McNeil, and D. J. Ecker (2001)
Nucleic Acids Res. 29, 3583-3594
   Abstract »    Full Text »    PDF »
TFIIS Enhances Transcriptional Elongation through an Artificial Arrest Site In Vivo.
D. Kulish and K. Struhl (2001)
Mol. Cell. Biol. 21, 4162-4168
   Abstract »    Full Text »    PDF »
RNA Sequences Involved in Transcriptional Termination of Respiratory Syncytial Virus.
S. B. Harmon, A. G. Megaw, and G. W. Wertz (2001)
J. Virol. 75, 36-44
   Abstract »    Full Text »
Saccharomyces cerevisiae Transcription Elongation Mutants Are Defective in PUR5 Induction in Response to Nucleotide Depletion.
R. J. Shaw and D. Reines (2000)
Mol. Cell. Biol. 20, 7427-7437
   Abstract »    Full Text »
3'-End Formation of Baculovirus Late RNAs.
J. Jin and L. A. Guarino (2000)
J. Virol. 74, 8930-8937
   Abstract »    Full Text »
The Functional Role of Basic Patch, a Structural Element of Escherichia coli Transcript Cleavage Factors GreA and GreB.
D. Kulish, J. Lee, I. Lomakin, B. Nowicka, A. Das, S. Darst, K. Normet, and S. Borukhov (2000)
J. Biol. Chem. 275, 12789-12798
   Abstract »    Full Text »    PDF »
Quality Control Mechanisms During Translation.
M. Ibba and a. D. Söll (1999)
Science 286, 1893-1897
   Abstract »    Full Text »
Nonequilibrium mechanism of transcription termination from observations of single RNA polymerase molecules.
H. Yin, I. Artsimovitch, R. Landick, and J. Gelles (1999)
PNAS 96, 13124-13129
   Abstract »    Full Text »    PDF »
Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences.
G. van Marle, J. C. Dobbe, A. P. Gultyaev, W. Luytjes, W. J. M. Spaan, and E. J. Snijder (1999)
PNAS 96, 12056-12061
   Abstract »    Full Text »    PDF »
Structural Characterization of RNA Polymerase II Complexes Arrested by a Cyclobutane Pyrimidine Dimer in the Transcribed Strand of Template DNA.
S. Tornaletti, D. Reines, and P. C. Hanawalt (1999)
J. Biol. Chem. 274, 24124-24130
   Abstract »    Full Text »    PDF »
Mapping Interactions of Escherichia coli GreB with RNA Polymerase and Ternary Elongation Complexes.
N. Loizos and S. A. Darst (1999)
J. Biol. Chem. 274, 23378-23386
   Abstract »    Full Text »    PDF »
Interactions of Escherichia coli sigma 70 within the transcription elongation complex.
S. S. Daube and P. H. von Hippel (1999)
PNAS 96, 8390-8395
   Abstract »    Full Text »    PDF »
The Versatility of Paramyxovirus RNA Polymerase Stuttering.
S. Hausmann, D. Garcin, C. Delenda, and D. Kolakofsky (1999)
J. Virol. 73, 5568-5576
   Abstract »    Full Text »
A Mutant Escherichia coli Primase Defective in Elongation of Primer RNA Chains.
W. Sun, J. Schoneich, and G. N. Godson (1999)
J. Bacteriol. 181, 3761-3767
   Abstract »    Full Text »
Escherichia coli DNA Topoisomerase I Inhibits R-loop Formation by Relaxing Transcription-induced Negative Supercoiling.
E. Masse and M. Drolet (1999)
J. Biol. Chem. 274, 16659-16664
   Abstract »    Full Text »    PDF »
Mechanism of Intrinsic Transcription Termination and Antitermination.
W. S. Yarnell and J. W. Roberts (1999)
Science 284, 611-615
   Abstract »    Full Text »
Tat-associated Kinase (P-TEFb): a Component of Transcription Preinitiation and Elongation Complexes.
Y.-H. Ping and T. M. Rana (1999)
J. Biol. Chem. 274, 7399-7404
   Abstract »    Full Text »    PDF »
Processive Antitermination.
R. A. Weisberg and M. E. Gottesman (1999)
J. Bacteriol. 181, 359-367
   Full Text »
DSIF and NELF Interact with RNA Polymerase II Elongation Complex and HIV-1 Tat Stimulates P-TEFb-mediated Phosphorylation of RNA Polymerase II and DSIF during Transcription Elongation.
Y.-H. Ping and T. M. Rana (2001)
J. Biol. Chem. 276, 12951-12958
   Abstract »    Full Text »    PDF »
Effect of Thymine Glycol on Transcription Elongation by T7 RNA Polymerase and Mammalian RNA Polymerase II.
S. Tornaletti, L. S. Maeda, D. R. Lloyd, D. Reines, and P. C. Hanawalt (2001)
J. Biol. Chem. 276, 45367-45371
   Abstract »    Full Text »    PDF »
Noise-based switches and amplifiers for gene expression.
J. Hasty, J. Pradines, M. Dolnik, and J. J. Collins (2000)
PNAS 97, 2075-2080
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)