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 5 August 1994:
Vol. 265. no. 5173, pp. 793 - 796
DOI: 10.1126/science.8047884
Prev | Table of Contents | Next

Articles

Science, Vol 265, Issue 5173, 793-796
Copyright © 1994 by American Association for the Advancement of Science

articles

Discontinuous mechanism of transcription elongation

E Nudler, A Goldfarb, and M Kashlev

Public Health Research Institute, New York, NY 10016.

During transcription elongation, three flexibly connected parts of RNA polymerase of Escherichia coli advance along the template so that the front-end domain is followed by the catalytic site which in turn is followed by the RNA product binding site. The advancing enzyme was found to maintain the same conformation throughout extended segments of the transcribed region. However, when the polymerase traveled across certain DNA sites that seemed to briefly anchor the front-end domain, cyclic shifting of the three parts, accompanied by buildup and relief of internal strain, was observed. Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro.
A. Hirtreiter, D. Grohmann, and F. Werner (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex.
J. Andrecka, B. Treutlein, M. A. I. Arcusa, A. Muschielok, R. Lewis, A. C. M. Cheung, P. Cramer, and J. Michaelis (2009)
Nucleic Acids Res. 37, 5803-5809
   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 »
Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.
E. Sosunova, V. Sosunov, M. Kozlov, V. Nikiforov, A. Goldfarb, and A. Mustaev (2003)
PNAS 100, 15469-15474
   Abstract »    Full Text »    PDF »
Analysis of the Open Region and of DNA-Protein Contacts of Archaeal RNA Polymerase Transcription Complexes during Transition from Initiation to Elongation.
P. Spitalny and M. Thomm (2003)
J. Biol. Chem. 278, 30497-30505
   Abstract »    Full Text »    PDF »
The initiation-elongation transition: Lateral mobility of RNA in RNA polymerase II complexes is greatly reduced at +8/+9 and absent by +23.
M. Pal and D. S. Luse (2003)
PNAS 100, 5700-5705
   Abstract »    Full Text »    PDF »
RNA Polymerase II Transcription Complexes May Become Arrested If the Nascent RNA Is Shortened to Less than 50 Nucleotides.
A. Ujvari, M. Pal, and D. S. Luse (2002)
J. Biol. Chem. 277, 32527-32537
   Abstract »    Full Text »    PDF »
Translocation after Synthesis of a Four-Nucleotide RNA Commits RNA Polymerase II to Promoter Escape.
J. F. Kugel and J. A. Goodrich (2002)
Mol. Cell. Biol. 22, 762-773
   Abstract »    Full Text »    PDF »
Promoter Clearance by RNA Polymerase II Is an Extended, Multistep Process Strongly Affected by Sequence.
M. Pal, D. McKean, and D. S. Luse (2001)
Mol. Cell. Biol. 21, 5815-5825
   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 »
Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.
U. Fiedler and H. Th. M. Timmers (2001)
Nucleic Acids Res. 29, 2706-2714
   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 »
The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition.
T. Kusakabe, A. V. Hine, S. G. Hyberts, and C. C. Richardson (1999)
PNAS 96, 4295-4300
   Abstract »    Full Text »    PDF »
Functional topography of nascent RNA in elongation intermediates of RNA polymerase.
N. Komissarova and M. Kashlev (1998)
PNAS 95, 14699-14704
   Abstract »    Full Text »    PDF »
Template End-to-End Transposition by RNA Polymerase II.
M. G. Izban, M. A. Parsons, and R. R. Sinden (1998)
J. Biol. Chem. 273, 27009-27016
   Abstract »    Full Text »    PDF »
Mutations in and Monoclonal Antibody Binding to Evolutionary Hypervariable Region of Escherichia coli RNA Polymerase beta ' Subunit Inhibit Transcript Cleavage and Transcript Elongation.
N. Zakharova, I. Bass, E. Arsenieva, V. Nikiforov, and K. Severinov (1998)
J. Biol. Chem. 273, 24912-24920
   Abstract »    Full Text »    PDF »
Structural Changes in the RNA Polymerase II Transcription Complex during Transition from Initiation to Elongation.
I. Samkurashvili and D. S. Luse (1998)
Mol. Cell. Biol. 18, 5343-5354
   Abstract »    Full Text »
Recognition of a Human Arrest Site Is Conserved between RNA Polymerase II and Prokaryotic RNA Polymerases.
J. Mote Jr. and D. Reines (1998)
J. Biol. Chem. 273, 16843-16852
   Abstract »    Full Text »    PDF »
Information Processing by RNA Polymerase: Recognition of Regulatory Signals during RNA Chain Elongation.
R. A. Mooney, I. Artsimovitch, and R. Landick (1998)
J. Bacteriol. 180, 3265-3275
   Full Text »
Disruption of Escherichia coli HepA, an RNA Polymerase-associated Protein, Causes UV Sensitivity.
O. Muzzin, E. A. Campbell, L. Xia, E. Severinova, S. A. Darst, and K. Severinov (1998)
J. Biol. Chem. 273, 15157-15161
   Abstract »    Full Text »    PDF »
The Transition from Initiation to Elongation by RNA Polymerase II.
D.S. LUSE and I. SAMKURASHVILI (1998)
Cold Spring Harb Symp Quant Biol 63, 289-300
   Abstract »    PDF »
Mechanistic Model of the Elongation Complex of Escherichia coli RNA Polymerase.
N. KORZHEVA, A. MUSTAEV, E. NUDLER, V. NIKIFOROV, and A. GOLDFARB (1998)
Cold Spring Harb Symp Quant Biol 63, 337-346
   Abstract »    PDF »
Escherichia coli RNA polymerase terminates transcription efficiently at rho-independent terminators on single-stranded DNA templates.
S. M. Uptain and M. J. Chamberlin (1997)
PNAS 94, 13548-13553
   Abstract »    Full Text »    PDF »
Formation and Crystallization of Yeast RNA Polymerase II Elongation Complexes.
A. Gnatt, J. Fu, and R. D. Kornberg (1997)
J. Biol. Chem. 272, 30799-30805
   Abstract »    Full Text »    PDF »
The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coli RNA polymerase without abolishing its catalytic activities.
S. C. Hung and M. E. Gottesman (1997)
Genes & Dev. 11, 2670-2678
   Abstract »    Full Text »    PDF »
RNA Polymerase Switches between Inactivated and Activated States By Translocating Back and Forth along the DNA and the RNA.
N. Komissarova and M. Kashlev (1997)
J. Biol. Chem. 272, 15329-15338
   Abstract »    Full Text »    PDF »
Transcription Elongation through DNA Arrest Sites. A MULTISTEP PROCESS INVOLVING BOTH RNA POLYMERASE II SUBUNIT RPB9 AND TFIIS.
D. E. Awrey, R. G. Weilbaecher, S. A. Hemming, S. M. Orlicky, C. M. Kane, and A. M. Edwards (1997)
J. Biol. Chem. 272, 14747-14754
   Abstract »    Full Text »    PDF »
RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates.
K. Fredrick and J. D. Helmann (1997)
PNAS 94, 4982-4987
   Abstract »    Full Text »    PDF »
Nuclease Activity of T7 RNA Polymerase and the Heterogeneity of Transcription Elongation Complexes.
S. S. Sastry and B. M. Ross (1997)
J. Biol. Chem. 272, 8644-8652
   Abstract »    Full Text »    PDF »
Domain Organization of Escherichia coli Transcript Cleavage Factors GreA and GreB.
D. Koulich, M. Orlova, A. Malhotra, A. Sali, S. A. Darst, and S. Borukhov (1997)
J. Biol. Chem. 272, 7201-7210
   Abstract »    Full Text »    PDF »
Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded.
N. Komissarova and M. Kashlev (1997)
PNAS 94, 1755-1760
   Abstract »    Full Text »    PDF »
Nuclease Cleavage of the Upstream Half of the Nontemplate Strand DNA in an Escherichia coli Transcription Elongation Complex Causes Upstream Translocation and Transcriptional Arrest.
D. Wang and R. Landick (1997)
J. Biol. Chem. 272, 5989-5994
   Abstract »    Full Text »    PDF »
A novel RNA polymerase I-dependent RNase activity that shortens nascent transcripts from the 3' end.
H. Tschochner (1996)
PNAS 93, 12914-12919
   Abstract »    Full Text »    PDF »
Structural Modules of the Large Subunits of RNA Polymerase. INTRODUCING ARCHAEBACTERIAL AND CHLOROPLAST SPLIT SITES IN THE beta AND beta prime SUBUNITS OF ESCHERICHIA COLI RNA POLYMERASE.
K. Severinov, A. Mustaev, A. Kukarin, O. Muzzin, I. Bass, S. A. Darst, and A. Goldfarb (1996)
J. Biol. Chem. 271, 27969-27974
   Abstract »    Full Text »    PDF »
Translocation and Transcriptional Arrest during Transcript Elongation by RNA Polymerase II.
I. Samkurashvili and D. S. Luse (1996)
J. Biol. Chem. 271, 23495-23505
   Abstract »    Full Text »    PDF »
Factor-dependent Release of Nascent RNA by Ternary Complexes of Vaccinia RNA Polymerase.
L. Deng, J. Hagler, and S. Shuman (1996)
J. Biol. Chem. 271, 19556-19562
   Abstract »    Full Text »    PDF »
Amino Acid Substitutions in the Two Largest Subunits of Escherichia coli RNA Polymerase That Suppress a Defective Rho Termination Factor Affect Different Parts of the Transcription Complex.
L. M. Heisler, G. Feng, D. J. Jin, C. A. Gross, and R. Landick (1996)
J. Biol. Chem. 271, 14572-14583
   Abstract »    Full Text »    PDF »
Identification of a Group of Cellular Cofactors That Stimulate the Binding of RNA Polymerase II and TRP-185 to Human Immunodeficiency Virus 1 TAR RNA.
F. Wu-Baer, W. S. Lane, and R. B. Gaynor (1996)
J. Biol. Chem. 271, 4201-4208
   Abstract »    Full Text »    PDF »
Transcription Against an Applied Force.
H. Yin, M. D. Wang, K. Svoboda, R. Landick, S. M. Block, and J. Gelles (1995)
Science 270, 1653-1657
   Abstract »
Action of alpha-Amanitin during Pyrophosphorolysis and Elongation by RNA Polymerase II.
D. R. Chafin, H. Guo, and D. H. Price (1995)
J. Biol. Chem. 270, 19114-19119
   Abstract »    Full Text »    PDF »
Studies of the Functional Topography of the Catalytic Center of Escherichia coli Primase.
A. A. Mustaev and G. N. Godson (1995)
J. Biol. Chem. 270, 15711-15718
   Abstract »    Full Text »    PDF »
Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation..
R Weilbaecher, C Hebron, G Feng, and R Landick (1994)
Genes & Dev. 8, 2913-2927
   Abstract »    PDF »


To Advertise     Find Products

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