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The Molecular Biophysics of Evolutionary and Physiological Adaptation

Citation

Chure, Griffin Daniel (2020) The Molecular Biophysics of Evolutionary and Physiological Adaptation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/q8h6-xr92. https://resolver.caltech.edu/CaltechTHESIS:06022020-102020436

Abstract

Central to any definition of Life is the ability to sense changes in one’s environment and respond in kind. Adaptive phenomena can be found across the biological scales ranging from the nanosecond-scale conformational changes of proteins, to temporary rewiring of metabolic networks, to the 3.5 billion years of evolution that produced the enormous biodiversity we see today. This thesis presents a body of work which attempts to examine the overlap between these three scales of adaptation through the quantitative lens of statistical physics. Namely, we examine how molecular, physiological, and evolutionary adaptation governs a feature common to all life – the regulation of gene expression.

We begin by examining the phenomenon of molecular adaptation in the context of allostery, specifically in the context of allosteric transcriptional repressors. Using simple tools of quasi-equilibrium thermodynamics, we derive and experimentally dissect a quantitative model of how such a repressor adapts to different concentrations of an extracellular inducer molecule, modulating the repressors activity and thereby gene expression. While the model is relatively simple, it is remarkably powerful in its ability to draw concrete, quantitative predictions about not only the level of gene expression at a given concentration of inducer, but details of how the repressor responds to changes in the inducer concentration. With a few lines of simple mathematics, we are able to use this model to derive a state variable of the simple repression motif which we term the free energy of the regulatory architecture. This permits us to collapse nearly 500 distinct measurements of the level of gene expression onto a master curve defined by this free energy.

We leverage this feature of the model and use data collapse as a method to identify the effects of mutation, a strong evolutionary force responsible for much of the genetic diversity in bacteria. In Chapter 3, we examine how mutations within the allosteric repressor itself can be mapped to changes in the free energy. The precise value of these free energy shifts and their dependence on the inducer concentration reveal different classes of mutations with one class affecting only the DNA-repressor interaction and another class governing the allosteric nature of the repressor. We test these pen-and-paper predictions experimentally and illustrate that given sufficient knowledge of how single mutants behave, the complete phenotypic response of pairwise double mutants can be predicted with quantitative accuracy.

With this framework in hand, we turn to exploring how changes in the physiological state of the cell influence the molecular biophysics of the regulatory architecture. We hypothesize that changes in the source of carbon in the growth medium or changes in the growth temperature can be accounted for by the existing model without any additional parameters. We experimentally show that the parameter values determined in one physiological state are inherited when the available carbon source is verified, but changes in the growth temperature require some additional considerations. Chapter 4 as a whole reveals that, while there remains work to be done both theoretically and experimentally when it comes to temperature variation, thermodynamic models can remain powerful tools to draw predictions of gene expression in different physiological contexts.

Finally, in Chapter 5, we explore physiological adaptation and cellular decision making where it counts – in the survival of cells to environmental insults. We turn our focus beyond transcriptional regulation and consider the relationship between osmotic shocks, the abundance of mechanosensitive channels, and cellular survival with single cell resolution. Using a combination of quantitative microscopy and tricks of statistical inference, we infer how the probability of a cell surviving an osmotic shock scales as a function of the cell’s number of mechanosensitive channels.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Biophysics, Transcriptional Regulation, Statistical Mechanics, Thermodynamics, Molecular and Cellular Biology
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biochemistry and Molecular Biophysics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Phillips, Robert B.
Thesis Committee:
  • Leadbetter, Jared R. (chair)
  • Newman, Dianne K.
  • Elowitz, Michael B.
  • Phillips, Robert B.
Defense Date:1 June 2020
Non-Caltech Author Email:griffinchure (AT) gmail.com
Funders:
Funding AgencyGrant Number
National Institutes of Health (NIH) 1R35 GM118043
Templeton Foundation51250
Templeton Foundation60973
National Institutes of Health (NIH)DP1 OD000217
Record Number:CaltechTHESIS:06022020-102020436
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:06022020-102020436
DOI:10.7907/q8h6-xr92
Related URLs:
URLURL TypeDescription
https://gchure.github.io/phd/OtherDigital version of the complete thesis.
https://doi.org/10.1016/j.cels.2018.02.004DOIPublication associated with chapters 2 and 6.
https://doi.org/10.1073/pnas.1907869116DOIPublication associated with chapters 3 and 7.
https://doi.org/10.1101/2019.12.19.878462 DOIPublication associated with chapters 4 and 8.
https://doi.org/10.1128/JB.00460-18DOIPublication associated with chapters 5 and 9.
ORCID:
AuthorORCID
Chure, Griffin Daniel0000-0002-2216-2057
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:13767
Collection:CaltechTHESIS
Deposited By: Griffin Chure
Deposited On:08 Jun 2020 22:27
Last Modified:16 Jan 2021 01:09

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