Escherichia coli Promoters with Consistent Expression throughout the Murine Gut

Advanced microbial therapeutics have great potential as a novel modality to diagnose and treat a wide range of diseases. Yet, to realize this potential, robust parts for regulating gene expression and consequent therapeutic activity in situ are needed. In this study, we characterized the expression level of more than 8000 variants of the Escherichia coli sigma factor 70 (sigma 70) promoter in a range of different environmental conditions and growth states using fluorescence-activated cell sorting and deep sequencing. Sampled conditions indude aerobic and anaerobic culture in the laboratory as well as growth in several locations of the murine gastrointestinal tract. We found that sigma 70 promoters in E. colt generally maintain consistent expression levels across the murine gut (R-2: 0.55-0.85, p value < 1 x 10(-5)), suggesting a limited environmental influence but a higher variability between in vitro and in vivo expression levels, highlighting the challenges of translating in vitro promoter activity to in vivo applications. Based on these data, we design the Schantzetta library, composed of eight promoters spanning a wide expression range and displaying a high degree of robustness in both laboratory and in vivo conditions (R-2 = 0.98, p = 0.000827). This study provides a systematic assessment of the sigma 70 promoter activity in E. coli as it transits the murine gut leading to the definition of robust expression cassettes that could be a valuable tool for reliable engineering and development of advanced microbial therapeutics.

Automated summary

This study systematically evaluated the promoter activity of Escherichia coli in the murine gut, finding consistent expression levels but higher variability between in vitro and in vivo environments. The design of a library with robust gene combinations provides a valuable tool for reliable engineering and development of microbial therapeutics.