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.
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.
Organisations
People |
ORCID iD |
| Claire Grierson (Primary Supervisor) | |
| Joshua Rees (Student) |
Publications
Landon S
(2019)
Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering.
in Essays in biochemistry
Marucci L
(2020)
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.
in Frontiers in bioengineering and biotechnology
Rees-Garbutt J
(2021)
Minimal Genome Design Algorithms Using Whole-Cell Models.
in Methods in molecular biology (Clifton, N.J.)
Rees-Garbutt J
(2020)
Furthering genome design using models and algorithms
in Current Opinion in Systems Biology
Rees-Garbutt J
(2020)
Designing minimal genomes using whole-cell models.
in Nature communications
Rees-Garbutt J
(2020)
Testing theoretical minimal genomes using whole-cell models
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 | 01/10/2016 | 31/03/2020 | Joshua 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 | 21ENGBIO Reprogramming bacterial cells using whole-cell models |
| Amount | £100,677 (GBP) |
| Funding ID | BB/W012235/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2023 |
| End | 02/2024 |
| 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 |
| Description | Investigation and Development of a Whole-Cell Model for a Minimal Synthetic Organism |
| Amount | £80,000 (GBP) |
| Funding ID | 1953789 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2017 |
| End | 07/2021 |
| Description | Whole cell modelling for bacteria E.coli |
| Amount | £85,000 (GBP) |
| Funding ID | 2461985 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2020 |
| End | 06/2024 |
| 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 | BioInfoSummer 2022, plenary talk, Melbourne |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | International systems bio and informatics summer school; keynote talk given to students, research associates and academic staff members. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://bis.amsi.org.au/program/#1545180202079-177125ae-5543 |
| 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 | Invited Seminar, Sheffield University, January 2023 (in person) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk to the Department of Chemical and Biological Engineering; attended by PhD students, postdocs and academics. |
| Year(s) Of Engagement Activity | 2023 |
| 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 UK 2022, keynote talk, Newcastle (UK) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk to the major synthetic biology conference in the UK. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.eventsforce.net/biochemsoc/frontend/reg/thome.csp?pageID=65741&eventID=132&traceRedir=2 |
| 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 | Talk at "Computer-Aided Whole-Cell Design and Engineering" workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop, co-organised by Dr L. Marucci, was held on the 02-03 July 2019 at the University of Bristol, and funded by the Engineering and Physical Sciences Research Council (EPSRC) within the remits of the Big Ideas initiative. The workshop stimulated discussions about future research directions which combine whole-cell models and synthetic biology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://doi.org/10.3389/fbioe.2020.00942 |
| 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 |