Model-driven design of minimal genomes

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

The advent of genome sequencing, genome editing and the ability to create synthetic genomes has spurred interest in minimal/reduced genomes. Finding minimal genomes should help us to understand relationships between genotype and phenotype, predict the effects of changes and, ultimately, design synthetic organisms.

While progress has been made in editing and creating genomes, very little has been made in rationally designing minimal genomes. Current methods for predicting minimal genomes compare essential gene sets (PNAS, 93, 10268-73, 1996) or disrupt single genes (Sciences, 286, 2165-69, 1999). Both approaches have been shown to be potentially misleading due to the complexity of the genotype to phenotype relationship (Nature, 407, 757-62, 2000).

I will develop robust and predictive methods for genome reduction, taking advantage of advances in computer models of both Escherichia coli (Nature protocols, 2, 727-38, 2007) and Mycoplasma genitalium (Cell, 150, 389-401, 2012). Such models have increased predictive powers but there is still a significant gap between computational predictions and experimental results.

I will mainly work on the experimental aspects of the project, involving characterisation of multiple in-vivo genetic disruptions in E. coli and Syn2.0/3.0. Resulting data will be used to quantify the accuracy of in-silico gene knockout models, refine them and discover reduced genomes.

Publications

10 25 50

publication icon
Rees-Garbutt J (2020) Designing minimal genomes using whole-cell models. in Nature communications

publication icon
Rees-Garbutt J (2020) Designing minimal genomes using whole-cell models. in Nature communications

Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/N509619/1 01/10/2016 30/09/2021
1793989 Studentship EP/N509619/1 19/09/2016 31/03/2020 Joshua Rees Rees
 
Description Created an analysis process for the M.genitalium whole-cell model
Created Minesweeper, a minimal genome design algorithm
Produced Minesweeper_256, an in-silico M.genitalium minimal genome, using Minesweeper
Discovered 10 low essential genes (genes which are essential in certain cellular situations), using Minesweeper
Tested, and reintroduced genes to, eight minimal gene sets from the literature to produce dividing in-silico M.genitalium cells
Tested 1418 single gene knockouts, for two generations of cells, in the E.coli whole-cell model
Exploitation Route We have preliminary data from the E.coli whole-cell model (Covert Group, Stanford, currently under review), and are attempting to produce in-silico E.coli minimal genomes using the Minesweeper algorithm. We are implementing the no-scar plasmid system (CRISPR-cas9 mediated homologous recombination) in the lab, to test our in-silico E.coli predictions in-vivo. This would be in-silico design and in-vivo editing at a greater scale and depth (number and size of genetic edits) than ever seen before.
Sectors Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL https://www.bristol.ac.uk/news/2020/february/genomes.html
 
Description Annual Conference Travel Grant
Amount £219 (GBP)
Funding ID Florence 2018 #219 
Organisation Society for Experimental Biology (SEB) 
Sector Academic/University
Country Global
Start 07/2018 
End 07/2018
 
Title Minesweeper Genome Design Algorithm 
Description Genome Design Algorithm for Minimal Genomes using whole-cell models. This code, in combination with the Mycoplasma genitalium whole-cell model https://github.com/CovertLab/WholeCell produces in-silico genome designs by knocking out modelled genes at scale. Requires a supercomputer to run the simulations. The Minesweeper algorithm can be manually run on a non-dedicated desktop, with its output determining what simulations to be run on the supercomputer. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact Resulted in publication (https://doi.org/10.1038/s41467-020-14545-0). I used Minesweeper in a series of computational design-simulate-test cycles to produce in silico M. genitalium minimal genomes (Minesweeper_256, 36% in silico reduction). If biologically correct, our subsequent in vivo minimal genome predictions are smaller than JCVI-syn3.0 (currently the smallest genome that can be grown in pure culture at 473 genes) and smaller than the most recent predictions for a reduced Mycoplasma genome (413 genes). In addition, we identified 10 low essential genes, and produced evidence for at least two minima for M. genitalium in silico. 
URL https://doi.org/10.1038/s41467-020-14545-0
 
Description BrisSynBio - MaxSynBio Bilateral Workshop (Poster Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation presenting research to international research audience as part of BrisSynBio - MaxSynBio Bilateral Workshop.
Year(s) Of Engagement Activity 2017
 
Description Bristol Biodesign Institute Conference, University of Bristol (Talk Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk Presentation presenting research to national research audience as part of Bristol Biodesign Institute Conference.
Year(s) Of Engagement Activity 2018
 
Description Cell Design 1 Course, DTC Centre, University of Oxford (Lecture presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Have given lectures annually to the PhD CDT students at the University of Oxford, as part of the Cell Design 1 Course.
Year(s) Of Engagement Activity 2018,2019
 
Description Cellular and Whole Cell Design Engineering Workshop, Bristol, UK (Talk Presentation) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented research talk and participated in the Cellular and Whole-Cell Design Engineering Workshop, Bristol, UK as part of an effort to re-develop and resubmit a Big Idea to the EPSRC.
Year(s) Of Engagement Activity 2019
 
Description Making New Life with CRISPR and Computers, University of Bristol (Lecture Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Lecture Presentation presenting research to the University of Bristol Biology Society undergraduates.
Year(s) Of Engagement Activity 2018
 
Description Society for Experimental Biology 2018, Florence, Italy (Talk Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk Presentation presenting research to international research audience as part of Society for Experimental Biology 2018, Florence. Titled 'Smart Minimal Gene Sets using Whole Cell Models'
Year(s) Of Engagement Activity 2018
URL http://www.sebiology.org/docs/default-source/Event-documents/cell-biology-abstracts-2.pdf
 
Description Synthetic Biology UK 2017, Manchester, UK (Talk Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk Presentation presenting research to international research audience as part of Synthetic Biology UK, in Manchester, UK.
Year(s) Of Engagement Activity 2017
 
Description Synthetic Biology UK 2018, Bristol, UK (Poster Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation presenting research to international research audience as part of Synthetic Biology UK 2018, Bristol.
Year(s) Of Engagement Activity 2018
 
Description Synthetic Biology: Engineering, Evolution & Design 2019, New York, USA (Poster Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation presenting research to international research audience as part of Synthetic Biology: Engineering, Evolution & Design 2019, New York. Poster #216 'Minimal Genomes: In-Silico using Whole-Cell Models, in-Vivo using CRISPR-cas9'
Year(s) Of Engagement Activity 2019
URL https://www.aiche.org/sites/default/files/docs/conferences/poster_grid_for_program_booklet_final_ver...
 
Description Three Minute Thesis - Understanding Bacterial Genomes to solve Global Crises 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Participated in the semi-final and final of the University of Bristol's Three Minute Thesis competition (a public presentation where you explain your PhD research to a lay audience in under three minutes). ~50 people attended the semi-final, >100 attended the final, which sparked questions and discussion afterward. Helped to cement the story told by our research group, and the structure of the introduction of our related paper.
Year(s) Of Engagement Activity 2019
URL https://youtu.be/_9Adiws779A