Exploring the role of diversity in bacteria-phage ecology and evolution.
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: Biosciences
Abstract
Bacteria in the rhizosphere can benefit agriculture by making nutrients available to plants. However, their beneficial effect is thought to be limited by viruses (phage) in soil. CRISPR-Cas adaptive immune systems of bacteria provide phage resistance but it is frequently very difficult to have bacteria evolve this type of phage resistance, and when it evolves, phage can readily escape CRISPR-Cas by point mutation. Recent studies suggest phage resistance may be improved when the adaptive immune system is integrated with an innate immune system, known as restriction-modification (RM). However, synergism between CRISPR and RM has not been clearly demonstrated yet, and because RM systems are highly diverse, it is also unclear whether such synergism would apply to all or only some RM systems. The key aim of this project is therefore to investigate the existence of synergy between different types of RM and CRISPR-Cas, and examine how this synergistic interaction affects bacteria-phage co-evolution. We already have a bacterial host that evolves high levels of CRISPR immunity in response to some, but not all phages. We will use this experimental system to first examine if levels of evolved CRISPR immunity increase when bacteria are equipped with different types of RM systems, to reveal putative synergistic RM-CRISPR interactions. We will then compare the genetic changes that accompany the evolution of CRISPR immunity in the presence and absence of RM, in order to reconstruct the mechanistic basis underlying the synergistic RM-CRISPR interactions. This will be complemented with in vitro biochemical studies that examine how purified RM components digest DNA molecules. Finally, we will investigate how an integrated RM-CRISPR immune response impacts bacteria-phage co-evolution, specifically the ability of phage to overcome immunity, compared to bacteria carrying a single immune mechanism and examine trade-offs associated with encoding multiple immune mechanisms.
The student will receive training in experimental evolution, biochemistry, molecular microbiology and genetics. This interdisciplinary project integrates expertise on CRISPR-Cas (Westra, Exeter), RM (Sczcelkun, Bristol) and bacteria-phage co-evolution (Buckling, Exeter).
The student will receive training in experimental evolution, biochemistry, molecular microbiology and genetics. This interdisciplinary project integrates expertise on CRISPR-Cas (Westra, Exeter), RM (Sczcelkun, Bristol) and bacteria-phage co-evolution (Buckling, Exeter).
Organisations
Publications
Common J
(2019)
CRISPR evolution and bacteriophage persistence in the context of population bottlenecks
in RNA Biology
Common J
(2019)
CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M009122/1 | 30/09/2015 | 31/03/2024 | |||
1771625 | Studentship | BB/M009122/1 | 30/09/2016 | 29/09/2020 | Jack Common |
Description | Featured on the alumni section of the University of Oxford Department of Zoology website |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Schools |
Results and Impact | The Department of Zoology outreach team asked for recently-graduated alumni to answer a few questions about their experience of Biology at Oxford, as well as their current activities. I used this opportunity to share my experience of going to Oxford from a state-school, first-generation background, and the importance of and enthusiasm for my research. This is featured on their website, which is used as part of their outreach to applicants and current undergraduates thinking about their next steps. |
Year(s) Of Engagement Activity | 2018 |
URL | https://biology.web.ox.ac.uk/people/jack-common |
Description | Speaking to GCSE & 6th form students about higher education and research |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | I have given several presentations to GCSE and A-level students from schools in the Falmouth area and Cornwall more generally. I spoke about my career path from state school, through undergraduate study, and onto postgraduate level. I also talk about my research in a way that is accessible to people of this educational level, as well as answering questions and speaking to small groups of students about science, research, and university applications, to name a few. |
Year(s) Of Engagement Activity | 2017,2018 |
Description | Spoke at a "Keg of Knowledge" event at local pub |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Gave a short presentation on my research to members of the public at Beerwolf Books, a pub in Falmouth, followed by questions and informal discussion |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.facebook.com/events/2503912082971873/ |
Description | Spoke to first-year undergraduate students about my research |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | Delivered a short research seminar about my research, linking it with the course material covered by the 1st year curriculum |
Year(s) Of Engagement Activity | 2019 |