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

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 sigma factor. Rational engineering can be used to alter key promoter element nucleotides interacting with sigma 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-sigma factor structural relationship to disrupt sigma(70) 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.

Automated summary

Future applications of synthetic biology require refactored genetic sequences without internal regulatory elements. Rational engineering can alter nucleotides of promoter elements and eliminate transcriptional activity. This paper presents CORPSE and iCORPSE systems for removing and creating active promoters within gene sequences.