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EASTBIO Engineering the genome of bacteriophage T5


   School of Biology

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  Dr S MacNeill  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Bacteriophage T5 is a model E. coli-infecting lytic phage with a 121 kb linear double-stranded DNA genome that is arranged into pre-early, early and late transcription units, encoding in total around 160 proteins and 20-25 tRNAs. The genomes of over 100 T5-like bacteriophages have now been sequenced - these display a high level of genetic synteny, highlighting the importance of this conserved genetic organisation for successful phage infection.

Within the last year, we have developed efficient methods for editing the T5 genome. This has allowed us to delete non-essential genes from the genome, and to insert non-T5 genes into the genome, but at all times respecting the pre-existing genetic organisation. In this PhD project, we propose to exploit the editing methodology to ask wider questions about the genetic structure of T5, in order to gain an understanding of the importance of genetic organisation in the T5 life cycle.

We aim to address four questions:

1.      To what extent is transcription unit orientation crucial for T5 infection? To address this, the student will attempt to flip the orientation of selected early transcription units and determine the consequences.

1.      To what extent is gene order within transcription units important for T5 infection? The student will re-engineer selected early transcription units to alter gene order and examine the impact on lytic infection.

2.      How important is the temporal order of expression during the infection cycle and what are the consequences of disrupting this? To address this, the student will engineer late genes (or promoters) into early transcription units and early genes (or promoters) into late transcription units.

3.      How tolerant is the genome of insertions? We have already generated engineered phage with increased genome lengths, but the length increases are marginal (1-2%) when compared to the wild-type genome. The student will determine the limits of T5 genome size by attempting to engineer phage with ever-longer genomes by inserting foreign sequences at non-essential regions. Defining the limits of length increase will be important to establish the suitability of the T5 genome as a vehicle for delivering non-T5 functionalities into cells.

Taken together, the results of this work will provide novel insights in the importance of genetic organisation in the T5-like phages that will almost certainly be generalisable to other phage families. The PhD will offer the student an excellent opportunity to use state-of-the-art bacteriophage genome engineering methods in a project at the interface of molecular microbiology and engineering biology.

HOW TO APPLY

Application instructions can be found on the EASTBIO website- http://www.eastscotbiodtp.ac.uk/how-apply-0

1)     Download and complete the Equality, Diversity and Inclusion survey.

2)     Download and complete the EASTBIO Application Form.

3)     Submit an application to St Andrews University through the Online Application Portal

Your online application must include the following documents:

-         Completed EASTBIO application form

-         2 References (to be completed on the EASTBIO Reference Form, also found on the EASTBIO website)

-         Academic Qualifications

-         English Language Qualification (if applicable)

Unfortunately due to workload constraints, we cannot consider incomplete applications. Please make sure your application is complete by Monday 5th December 2022.

CONTACT

Queries on the project can be directed to the project supervisor.

Queries on the application process can be directed to Jess Fitzgerald at [Email Address Removed]

UKRI eligibility guidance: Terms and Conditions: View Website International/EU: View Website


Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership.
This opportunity is open to UK and International students and provides funding to cover stipend at UKRI standard rate and UK level tuition fees. The University of St Andrews will cover the Home-International fee difference.

References



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