PT  - JOURNAL ARTICLE
AU  - Guillaume Urtecho
AU  - Arielle D. Tripp
AU  - Kimberly D. Insigne
AU  - Hwangbeom Kim
AU  - Sriram Kosuri
TI  - Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in <em>E. coli</em>
AID  - 10.1101/207332
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 207332
4099  - http://biorxiv.org/content/early/2018/01/28/207332.short
4100  - http://biorxiv.org/content/early/2018/01/28/207332.full
AB  - Promoters are the key drivers of gene expression and are largely responsible for the regulation of cellular responses to time and environment. In E. coli, decades of studies have revealed most, if not all, of the sequence elements necessary to encode promoter function. Despite our knowledge of these motifs, it is still not possible to predict the strength and regulation of a promoter from primary sequence alone. Here we develop a novel multiplexed assay to study promoter function in E. coli by building a site-specific genomic recombination-mediated cassette exchange (RMCE) system that allows for the facile construction and testing of large libraries of genetic designs integrated into precise genomic locations. We build and test a library of 10,898 σ70 promoter variants consisting of all combinations of a set of eight ‐35 elements, eight ‐10 elements, three UP elements, eight spacers, and eight backgrounds. We find that the ‐35 and ‐10 sequence elements can explain approximately 74% of the variance in promoter strength within our dataset using a simple log-linear statistical model. Simple neural network models explain greater than 95% of the variance in our dataset by capturing nonlinear interactions with the spacer, background, and UP elements.