Direct interaction between Escherichia coli RNA polymerase and the zinc ribbon domains of DNA topoisomerase I

Bokun Cheng, Chang Xi Zhu, Chengling Ji, Adriana Ahumada, Yuk Ching Tse-Dinh

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


Escherichia coli DNA topoisomerase I (encoded by the topa gene) is important for maintaining steady-state DNA supercoiling and has been shown to influence vital cellular processes including transcription. Topoisomerase I activity is also needed to remove hypernegative supercoiling generated on the DNA template by the progressing RNA polymerase complex during transcription elongation. The accumulation of hypernegative supercoiling in the absence of topoisomerase I can lead to R-loop formation by the nascent transcript and template strand, leading to suppression of transcription elongation. Here we show by affinity chromatography and overlay blotting that E. coli DNA topoisomerase I interacts directly with the RNA polymerase complex. The protein-protein interaction involves the β′ subunit of RNA polymerase and the C-terminal domains of E. coli DNA topoisomerase I, which are homologous to the zinc ribbon domains in a number of transcription factors. This direct interaction can bring the topoisomerase I relaxing activity to the site of transcription where its activity is needed. The zinc ribbon C-terminal domains of other type IA topoisomerases, including mammalian topoisomerase III, may also help link the enzyme activities to their physiological functions, potentially including replication, transcription, recombination, and repair.

Original languageEnglish (US)
Pages (from-to)30705-30710
Number of pages6
JournalJournal of Biological Chemistry
Issue number33
StatePublished - Aug 15 2003
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


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