Towards engineering microbial consortia using RNA-based genetic controllers
File(s)
Author(s)
Boo, Alice
Type
Thesis
Abstract
In nature, quorum sensing is a mechanism used by microbes to communicate and coordinate behaviours at the population level. Over the last two decades, synthetic biologists have used the unique property of quorum sensing to sense population density for coordinating cellular behaviours of single and mixed cultures. This gave rise to the development of multicellular biosynthesis systems for metabolic engineering and of spatially distributed systems for synthetic biology. However, robustly controlling the composition of multicellular systems remains a challenge and limits its wide adoption by the metabolic engineering community. Current strategies for controlling synthetic microbial communities vastly rely on engineer- ing metabolic dependencies between microbial species in a process called syntrophy. While syntrophy guarantees the survival of all strains in the coculture, it does not provide a way to control community composition. Existing genetic circuits that can dynamically control community composition often impose too much burden on their hosts for division of labour to be a viable solution to improve yields and titers of valuable metabolic products. Here we investigate the potential of using RNA-based gene circuits to reduce the cost of express- ing heterologous genes for the control of community composition in a two-member E. coli coculture. In this work, we present the development of three genetic modules that rely on RNA species to detect changes in population density and to regulate growth rate when community composition becomes unstable. Together, the modules work in concert to stabilise community composition around a ratio set by the intrinsic properties of the circuit’s genetic components. We identify the key parameters of the circuits that enable tuning of the composition ratio. We characterise the cost of expressing each module of the genetic controller by measuring its impact on the host growth rate and on consumption of free cellular resources. Together these findings highlight the importance of developing host-aware circuits to control community composition so as to enable their wide adoption by metabolic engineers.
Version
Open Access
Date Issued
2022-01
Date Awarded
2022-05
Copyright Statement
Creative Commons Attribution NonCommercial Licence
License URL
Advisor
Stan, Guy-Bart
Ledesma Amaro, Rodrigo
Sponsor
Imperial College London
Publisher Department
Bioengineering
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)