A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria

Abstract

Organisms across all domains of life must make regulatory decisions in response to changing environments. The decision about when and where to turn on transcription in bacteria is mainly controlled through the binding of transcription factors to promoter regions of the DNA. However, while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. Even for the organism Escherichia coli, whose regulation is arguably best understood, we still have no indication if or how more than half of the genes are regulated. Here we show how a combination of massively-parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect bacterial promoters. We use the approach to recover nucleotide-resolution models of promoter mechanism for a variety of well-characterized and previously unannotated promoters in E. coli. We believe this approach opens up the possibility of quantitatively dissecting the mechanisms of promoter function across the genome of E. coli and other bacteria as well.

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