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

  title={An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing},
  author={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… 
Control of Transcription Termination and Antitermination
The regulatory molecules that are known to influence the elongation/termination decision by RNA polymerase (RNAP) are described, with the emphasis on the most recent findings and on the mechanism of ‘‘active’’ regulators whose actions are not limited to changes in RNA folding.
Transcription elongation: structural basis and mechanisms.
  • E. Nudler
  • Biology
    Journal of molecular biology
  • 1999
A structure-function model of the ternary elongation complex ofRNAP is suggested, if not at a defined structural level, then at least as a conceptual view, such that key components of RNAP are defined operationally on the basis of compelling biochemical, protein chemical, and genetic data.
Transcription termination and anti‐termination in E. coli
Basic principles are reviewed and attempt to unify into basic principles the remarkable recent progress in understanding transcription termination and anti‐termination in Escherichia coli.
Determinants of the stability of transcription elongation complexes: interactions of the nascent RNA with the DNA template and the RNA polymerase.
It is shown that the formation of a stable elongation complex at any particular template position can be treated as an equilibrium process, and that semi-quantitative dissociation constants can be estimated for the complex by using a gel band-shift assay to monitor the binding of the RNA oligomer to the complex.


Transcript elongation and termination are competitive kinetic processes.
A kinetic approach to predict the efficiency of termination at intrinsic (factor independent) terminators of Escherichia coli and related organisms and suggests that termination efficiency can readily be modulated by protein factors and environmental variables that shift the kinetic competition toward either elongation or termination.
Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription.
The transcription cleavage factor GreA increased the fidelity of transcription by preferential cleavage of transcripts containing misincorporated residues in the unactivated state of the elongation complex, which may prevent the formation of "dead-end" transcription complexes in vivo.
A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli.
A thermodynamic analysis of the elongation phase of transcription in Escherichia coli closely predicts the exact sites of termination at a number of intrinsic terminators (and attenuators) in the E. coli genome.
Structure of transcription elongation complexes in vivo.
The opening of duplex DNA in the elongation phase of transcription by Escherichia coli RNA polymerase in vivo was detected at a regulatory site where a prolonged pause in transcription occurs.
Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded.
It is demonstrated that the loss of catalytic activity upon arrest of Escherichia coli RNAP is accompanied by an isomerization of the ternary complex in which the enzyme disengages from the 3' end of the transcript and moves backward along the DNA with concomitant reverse threading of the intact RNA through the enzyme.
Structural Organization of Transcription Termination Factor Rho (*)
  • J. Richardson
  • Biology, Chemistry
    The Journal of Biological Chemistry
  • 1996
The current understanding of the structure and function of transcription termination factor Rho is summarized based on indirect approaches, such as biochemical characterization of the protein, phylogenetic comparative analyses, and the functional properties of mutants with known amino acid changes.
Two conformations of RNA polymerase II revealed by electron crystallography.
A new two-dimensional crystal form of yeast RNA polymerase II was obtained in which the conformation of the enzyme appears "open", allowing entry of DNA, as required for the initiation of transcription, prompting the conclusion that the open to closed transition is a crucial step in the transcription initiation process.