Oxazinomycin arrests RNA polymerase at the polythymidine sequences

Nucleic Acids Res. 2019 Nov 4;47(19):10296-10312. doi: 10.1093/nar/gkz782.


Oxazinomycin is a C-nucleoside antibiotic that is produced by Streptomyces hygroscopicus and closely resembles uridine. Here, we show that the oxazinomycin triphosphate is a good substrate for bacterial and eukaryotic RNA polymerases (RNAPs) and that a single incorporated oxazinomycin is rapidly extended by the next nucleotide. However, the incorporation of several successive oxazinomycins or a single oxazinomycin in a certain sequence context arrested a fraction of the transcribing RNAP. The addition of Gre RNA cleavage factors eliminated the transcriptional arrest at a single oxazinomycin and shortened the nascent RNAs arrested at the polythymidine sequences suggesting that the transcriptional arrest was caused by backtracking of RNAP along the DNA template. We further demonstrate that the ubiquitous C-nucleoside pseudouridine is also a good substrate for RNA polymerases in a triphosphorylated form but does not inhibit transcription of the polythymidine sequences. Our results collectively suggest that oxazinomycin functions as a Trojan horse substrate and its inhibitory effect is attributable to the oxygen atom in the position corresponding to carbon five of the uracil ring.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics
  • Escherichia coli / genetics
  • Oxygen / chemistry
  • Pseudomonas / chemistry
  • RNA / chemistry*
  • RNA / genetics
  • RNA Cleavage / drug effects
  • Streptomyces / chemistry
  • Substrate Specificity
  • Thymidine / chemistry
  • Thymidine / genetics
  • Transcription, Genetic / drug effects*
  • Transcription, Genetic / genetics
  • Transcriptional Elongation Factors / genetics
  • Uracil / chemistry
  • Uridine / analogs & derivatives*
  • Uridine / chemical synthesis
  • Uridine / chemistry
  • Uridine / pharmacology


  • Transcriptional Elongation Factors
  • minimycin
  • Uracil
  • RNA
  • DNA-Directed RNA Polymerases
  • Oxygen
  • Thymidine
  • Uridine