Codon-Restrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters

ACS Synth Biol. 2022 Feb 18;11(2):689-699. doi: 10.1021/acssynbio.1c00359. Epub 2022 Jan 19.


Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters, which may constitute up to a third of the predicted Escherichia coli promoters. The promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present codon-restrained promoter silencing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ70 promoters embedded within gene coding sequences with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.

Keywords: internal regulation; refactoring; sigma factor; synthetic genomics; transcription initiation; σ factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Codon / genetics
  • DNA-Directed RNA Polymerases / genetics
  • Escherichia coli* / genetics
  • Escherichia coli* / metabolism
  • Promoter Regions, Genetic / genetics
  • Regulatory Sequences, Nucleic Acid
  • Sigma Factor* / genetics
  • Transcription, Genetic


  • Codon
  • Sigma Factor
  • DNA-Directed RNA Polymerases