Transcriptional control is mediated by batteries of transcription factors that interact with DNA, each other and with the transcription apparatus itself. In many of these cases, proteins bound to regulatory regions hundreds to thousands of basepairs away from the basal transcription apparatus perform a kind of biological action at a distance by binding at more than one site on the DNA simultaneously resulting in wholesale rearrangements of the genomic DNA (e.g. DNA looping). However, the mechanistic underpinnings of transcriptional control, especially that involving large-scale deformations of the DNA, and the quantitative consequences of this control largely remain to be elucidated. The work proposed here builds upon three distinct but related pillars to analyze the formation of these complexes: i) the use of statistical mechanics models to compute the relation between regulatory architecture and the level of gene expression, ii) the use of single-molecule tethered particle experiments to measure the stability and kinetics of formation of transcription factor-DNA complexes and iii) the measurement of level of gene expression in living cells. In all three of these cases, DNA sequence (flexibility), binding site strength and number of operators are used as dials to tune the level of gene expression.
Transcriptional regulation is at the heart of processes in biology ranging from the formation of biofilms to cell differentiation to evolution. In its role as one of the central threads in the study of genes and how they are regulated, transcriptional control is relevant to biology and medicine alike. The work proposed here aims to strengthen our understanding of transcription in microbes in a way that will have applications from synthetic biology to the study of pathogens.
|Belliveau, Nathan M; Barnes, Stephanie L; Ireland, William T et al. (2018) Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A 115:E4796-E4805|
|Razo-Mejia, Manuel; Barnes, Stephanie L; Belliveau, Nathan M et al. (2018) Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction. Cell Syst 6:456-469.e10|
|Chure, Griffin; Lee, Heun Jin; Rasmussen, Akiko et al. (2018) Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution. J Bacteriol :|
|Phillips, Rob (2017) Musings on mechanism: quest for a quark theory of proteins? FASEB J 31:4207-4215|
|Einav, Tal; Phillips, Rob (2017) Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants. J Phys Chem B 121:3813-3824|
|Mohapatra, Lishibanya; Goode, Bruce L; Jelenkovic, Predrag et al. (2016) Design Principles of Length Control of Cytoskeletal Structures. Annu Rev Biophys 45:85-116|
|Garcia, Hernan G; Brewster, Robert C; Phillips, Rob (2016) Using synthetic biology to make cells tomorrow's test tubes. Integr Biol (Camb) 8:431-50|
|Einav, Tal; Mazutis, Linas; Phillips, Rob (2016) Statistical Mechanics of Allosteric Enzymes. J Phys Chem B 120:6021-37|
|Kreamer, Naomi N; Phillips, Rob; Newman, Dianne K et al. (2015) Predicting the impact of promoter variability on regulatory outputs. Sci Rep 5:18238|
|Mulligan, Peter J; Chen, Yi-Ju; Phillips, Rob et al. (2015) Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics. Biophys J 109:618-29|
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