Minimal Genome Design and Engineering
: Algorithms and whole-cell Models

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)

Abstract

Tailoring entire genomes to produce custom-made cells is now on the horizon. This level of control and understanding has been a goal for biologists since the publication of the first genome sequence in 1977. The field of genetics has expanded and grown since, advancing with the progress of genetic sequencing, synthesis, and editing, and with the discipline of synthetic biology emerging following the millennium. The editing and sequencing barriers to designing cells reduced dramatically in the early 2010s, with the publication of CRISPR-cas9 and the development of the MinION sequencer.

However, entire genome design still alludes us. Genome engineering progresses by systematic comparison of experimental results. The complexity and lack of knowledge of gene interactions still causes unexpected results. Libraries of genetic knockouts can only scale to encompass all possible double gene knockouts, before becoming economically infeasible, restricting data collection.

The publication of the first whole-cell model in 2012 (for Mycoplasma genitalium), combined with the availability and advancement of supercomputers from the mid-2000s, offers a way to tackle the complexity of gene interactions. It also allows genome engineers the possibility to emulate the work of metabolic engineers, who have an established cycle of in-silico design and in-vivo editing for their more constrained, sub-cellular systems.

In this thesis, I design entire genomes in-silico by producing a genome design algorithm to guide thousands of whole-cell model simulations running on supercomputers. I also simulate theoretical minimal genomes that have never been tested; and produce preliminary data from the second whole-cell model (for Escherichia coli).

This thesis aims to show that it is now possible to design entire genomes in-silico. The combination of in-silico (genome design algorithms, whole-cell models, supercomputers) and in-vivo (CRISPR-cas9 genetic editing, MinION genetic sequencing) components means the stage is now set for the in-vivo production of tailored genomes.
Date of Award26 Nov 2020
Original languageEnglish
Awarding Institution
  • University of Bristol
SponsorsEngineering and Physical Sciences Research Council
SupervisorLucia Marucci (Supervisor) & Claire S Grierson (Supervisor)

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