An experimental evolution approach to studying horizontal transfer of antiviral defences between bacterial species
Lead Research Organisation:
University of Bath
Department Name: Biology and Biochemistry
Abstract
CRISPR-Cas is akin to a bacterial immune system. It allows bacteria to 'remember' foreign invading DNA (e.g. from viruses), ultimately targeting them for destruction. The ability of CRISPR-Cas systems to specifically recognise certain sequences has led to the development of this system as a tool for gene editing, revolutionising molecular biology. Despite this, relatively little research has centred on the long-term stability and viability of transferring CRISPR-Cas systems between bacteria.
Studies that have examined the sequence similarities of CRISPR-Cas genes between different species have suggested that in nature bacteria may have exchanged these genes between species by horizontal gene transfer (HGT). However, the evolutionary effects of gaining new CRISPR-Cas systems are yet to be investigated experimentally.
Aim: The overarching aim of this project is to investigate how CRISPR-Cas transcription regulation evolves when transferred to a naïve host. In addition, this project aims to identify the selective pressures that favour such horizontal gene transfer events and enable bacteria expressing an acquired CRISPR-Cas system to rise to dominance in a population. This research will inform the future production and maintenance of functional synthetic CRISPR-Cas systems in naïve bacterial species. The results generated will model the potential pre-requisites and evolutionary consequences of the horizontal gene transfer events that are proposed to have contributed to the evolutionary history of CRISPR-Cas systems.
Objective 1: To understand under what environmental conditions CRISPR-Cas systems produce a selective advantage to bacteria competing within a population otherwise lacking CRISPR-Cas. This will use P. aeruginosa as a model system that already possess a native CRISPR-Cas system.
Objective 2: To transfer a functional synthetic version of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa to a naïve host - Pseudomonas fluorescens. The consequences of this event on the fitness of the host will then be followed.
Objective 3: To understand what selection pressures will favour the P. fluorescens that have acquired this CRISPR-Cas system and allow them to reach fixation in a population of wild type P. fluorescens.
Objective 4: To describe the regulatory changes and compensatory mutations that allow P. fluorescens to maintain expression of an acquired CRISPR-Cas system. As well as how these mutations influence the new system conferring a selective advantage to the host
Studies that have examined the sequence similarities of CRISPR-Cas genes between different species have suggested that in nature bacteria may have exchanged these genes between species by horizontal gene transfer (HGT). However, the evolutionary effects of gaining new CRISPR-Cas systems are yet to be investigated experimentally.
Aim: The overarching aim of this project is to investigate how CRISPR-Cas transcription regulation evolves when transferred to a naïve host. In addition, this project aims to identify the selective pressures that favour such horizontal gene transfer events and enable bacteria expressing an acquired CRISPR-Cas system to rise to dominance in a population. This research will inform the future production and maintenance of functional synthetic CRISPR-Cas systems in naïve bacterial species. The results generated will model the potential pre-requisites and evolutionary consequences of the horizontal gene transfer events that are proposed to have contributed to the evolutionary history of CRISPR-Cas systems.
Objective 1: To understand under what environmental conditions CRISPR-Cas systems produce a selective advantage to bacteria competing within a population otherwise lacking CRISPR-Cas. This will use P. aeruginosa as a model system that already possess a native CRISPR-Cas system.
Objective 2: To transfer a functional synthetic version of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa to a naïve host - Pseudomonas fluorescens. The consequences of this event on the fitness of the host will then be followed.
Objective 3: To understand what selection pressures will favour the P. fluorescens that have acquired this CRISPR-Cas system and allow them to reach fixation in a population of wild type P. fluorescens.
Objective 4: To describe the regulatory changes and compensatory mutations that allow P. fluorescens to maintain expression of an acquired CRISPR-Cas system. As well as how these mutations influence the new system conferring a selective advantage to the host
Organisations
People |
ORCID iD |
R Brady (Primary Supervisor) | |
Josie Elliott (Student) |
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/T008741/1 | 30/09/2020 | 29/09/2028 | |||
2445260 | Studentship | BB/T008741/1 | 30/09/2020 | 29/09/2024 | Josie Elliott |
Description | Microbiology Society Travel Grant 2022 |
Amount | £274 (GBP) |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 11/2022 |
End | 11/2022 |
Description | Santander Mobility Award |
Amount | £230 (GBP) |
Organisation | University of Bath |
Sector | Academic/University |
Country | United Kingdom |
Start | 04/2022 |
End | 05/2022 |
Description | Society Conference Grant |
Amount | £206 (GBP) |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 03/2023 |
End | 04/2023 |
Description | Society Conference Grant |
Amount | £360 (GBP) |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 03/2022 |
End | 04/2022 |
Title | Created functional, synthetic, modular version of the CRISPR-Cas system of Pseudomonas aeruginosa PA14 |
Description | Designed and validated a functional, synthetic, modular version of the CRISPR-Cas system of Pseudomonas aeruginosa PA14 |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | Tool is newly created and unpublished, impacts thus limited. |
Description | Interactive exhibit at Somerscience festival |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Somerscience is a free local science festival based in Castle Cary Somerset, UK with the aim to get the general public interested in science and scientific careers. I created and presented an interactive exhibit of activities designed to teach children and adults about CRISPR-Cas immunity and genetic engineering. We interested with hundreds of family groups over the day, introducing the concepts of gene editing in a fun and friendly way to children and sparking discussion and discourse with adults about the ethic of gene editing. |
Year(s) Of Engagement Activity | 2023 |
URL | https://somerscience.co.uk/ |
Description | Outreach activity at Futures researchers night Schools Fair, Bristol |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Created and presented a series of activities to teach school children about CRISPR and genetic engineering at an outreach event - Futures research night, Bristol UK |
Year(s) Of Engagement Activity | 2022 |
Description | Outreach activity at Futures researchers night UpLate event, Bristol |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Attended the FUTURES research night free science festival in Bristol, UK. Over an evening families and other groups visited our interactive exhibit which introduces concepts of CRISPR-Cas immunity and genetic editing to a general audience in order to de-mystify these terms of adults, and create a positive first point of contact for the concept to children. |
Year(s) Of Engagement Activity | 2023 |
URL | https://futuresnight.co.uk/ |
Description | Talk at EMPSEB 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presented research at European Meeting for PhD Students in Evolutionary Biology in Espoo, Finland. Presented to other PhD students. |
Year(s) Of Engagement Activity | 2022 |
Description | Talk at Jacques Monod Conference "A matter of scale: within-host and between-host processes driving coevolution with parasites" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Presented my research to an international audience of scientists at the conference in Roscoff, France. The intended purpose what to spark discussion, make new connections and potential collaborations as well as receive feedback on my research from scientific peers. |
Year(s) Of Engagement Activity | 2023 |
Description | Talk at Microbial Ecology and Evolution, Communities and Coevolution Conference 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Research presentation at Microbial Ecology and Evolution, Communities and Coevolution Conference 2022 at the Max Planck Institute of Evolutionary Biology, Plon, Germany. Presented to other scientific professionals. |
Year(s) Of Engagement Activity | 2022 |
Description | Talk at Microbiology Society Annual Conference 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Presented research during a short talk at the Microbiology Society Annual Conference in Belfast, UK to an audience of science professionals. |
Year(s) Of Engagement Activity | 2022 |