This resource presents promoter activities and characteristics of 1076 Escherichia coli operons as measured using a multiplexed reporter assay. Briefly, we have measured the promoter activity of over 300,000 genomic DNA fragments spanning the entire E. coli genome and report our measurements after summarizing promoter activity to single-nucleotide resolution. In addition, we performed a scanning mutagenesis of 2,057 previously reported promoters in order to identify regulatory regions that control the expression of these sequences. The following page provides summary reports of these findings for 1076 E. coli operons.

Manuscript

The full manuscript describing the method of data acquisition can can be found here (Urtecho & Insigne et al.BioRxiv. 2020. https://doi.org/10.1101/2020.01.04.894907)

Acknowledgements

This work was supported by the National Science Foundation Graduate Research Fellowship 2015210106 to G.U., National Institutes of Health New Innovator Award DP2GM114829 to S.K., Searle Scholars Program (to S.K.), U.S. Department of Energy (DE-FC02-02ER63421 to S.K.), UCLA, and Linda and Fred Wudl. We thank the UCLA BSCRC high throughput sequencing core and Technology Center for Genomics and Bioinformatics for technical assistance; Robert B. Phillips, Reid C. Johnson, and Jeffery H. Miller for thoughtful feedback throughout this project; Matteo Pellegrini for computational advice; Christina P. Burghard for advice on bioinformatics analysis; and all past and present members of the Kosuri lab for technical feedback. Furthermore, we would also like to thank David Gray and Lisa M. Golden for manuscript feedback. We would also like to thank the invaluable resources of RegulonDB and EcoCyc as well as all contributors to these collections. Lastly, we thank the UCLA Molecular Biology Interdepartmental Graduate Program and UCLA Bioinformatics Interdepartmental Graduate Program.

Contact information

Please refer all questions to Guillaume Urtecho (Twitter: @GoGurtecho, email: gurtecho@g.ucla.edu).

Code availability

Code used for the manuscript can be accessed at: https://github.com/KosuriLab/ecoli_promoter_mpra

Code used for the website can be accessed at: https://github.com/ecopromotersite/EcoPromoters