Transcription-coupled DNA supercoiling in defined protein systems and in E. coli topA mutant strains

IUBMB Life. 2013 Jul;65(7):615-22. doi: 10.1002/iub.1179. Epub 2013 Jun 12.


Transcription by RNA polymerases can stimulate (-) DNA supercoiling both in vitro and in Escherichia coli topA strains. This phenomenon has been successfully explained by a "twin-supercoiled-domain" model of transcription in which (+) supercoils are produced in front of the transcribing RNA polymerase and (-) supercoils behind it. Previously, it has been shown that certain sequence-specific DNA-binding proteins potently stimulate transcription-coupled DNA supercoiling (TCDS) in an in vitro protein system. These results are consistent with a topological barrier model where certain nucleoprotein complexes can form topological barriers that impede the diffusion and merger of independent chromosomal supercoil domains. Indeed, recent biochemical and single-molecule results demonstrated the existence of nucleoprotein-based DNA topological barriers, which are capable of dividing a DNA molecule into different topological domains. Additionally, recent in vivo studies showed that a transcriptional ensemble (including the transcribing RNA polymerase and the RNA transcript) alone is sufficient to cause a change in local DNA superhelicity. This topological change in local chromosome structure should have a great impact on the conformation and function of critical DNA sequence elements, such as promoters and DNA replication origins. In this article, we will also review recent progress by which TCDS is a critical stimulating force to activate transcription initiation from weak promoters, such as the Salmonella typhimurium leu-500 promoter.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA-Binding Proteins / genetics*
  • DNA-Directed RNA Polymerases / genetics*
  • Escherichia coli / genetics
  • Gene Expression Regulation, Bacterial*
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • Salmonella typhimurium / genetics
  • Transcription, Genetic*


  • DNA, Bacterial
  • DNA-Binding Proteins
  • DNA-Directed RNA Polymerases