Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli

Citation

Belliveau, Nathan Maurice (2018) Quantitative Dissection of the Allosteric and Sequence-Dependent Regulatory Genome in E. coli. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9DN438T. https://resolver.caltech.edu/CaltechTHESIS:01052018-221609680

Abstract

Transcriptional regulation of gene expression is one of the most ubiquitous processes in biology. But 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. One of the ways genes are regulated is through external signals. To that end, we begin by presenting a general theory of allosteric transcriptional regulation using a statistical formulation of the Monod-Wyman-Changeux model, which we rigorously test using the ubiquitous simple repression motif in Escherichia coli. We then move to consider the consequence of the regulatory sequences themselves on gene expression. Here we apply a massively parallel reporter assay, Sort-Seq, to build models that describe the sequence-dependent binding energies of transcription factors and RNA polymerase to DNA. By coupling such models to our thermodynamic models of regulation, we construct a genotype to phenotype mapping that predicts gene expression as a function of regulatory sequence. We first demonstrate this approach in the context of the allosteric simple repression motif, and then show how it can be applied broadly across a bacterial genome, in conjunction with mass spectrometry, to uncover how genes are regulated.

Thesis Files