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Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
CALTECH, Div Biol & Biol Engn, Pasadena, USA.ORCID iD: 0000-0002-1536-1963
CALTECH, Div Biol & Biol Engn, Pasadena, USA.
CALTECH, Dept Phys, Pasadena, USA.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 21, p. E4796-E4805Article in journal (Refereed) Published
Abstract [en]

Gene regulation is one of the most ubiquitous processes in biology. 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. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here, we take a first step toward multipromoter dissection and show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect multiple bacterial promoters in a systematic way. We show this approach on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases, we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input-output relationships. Given the generality of the approach presented here, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES , 2018. Vol. 115, no 21, p. E4796-E4805
Keywords [en]
gene regulation, massively parallel reporter assay, quantitative models, DNA affinity chromatography, mass spectrometry
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-357276DOI: 10.1073/pnas.1722055115ISI: 000432663000011PubMedID: 29728462OAI: oai:DiVA.org:uu-357276DiVA, id: diva2:1239647
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-12-05Bibliographically approved

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Jones, Daniel L.

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