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EASTBIO: Discovering patterns in the genome of RNA viruses that drive evolution and regulate replication

   College of Medicine and Veterinary Medicine

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  Dr E Gaunt, Dr F Grey  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

All genomes are composed of four bases, A, C, G and T (or U, in RNA genomes and mRNAs). If these were encoded randomly, every genome would comprise ~25% of each base; but this is not the case. Similarly, there are 16 possible combinations of nucleotide pairs, or dinucleotides. With random representation, each dinucleotide would occur 1/16 or 6.25% of the time, but in the genomes of all organisms, from bacteria to humans, TpA dinucleotides (‘p’ represents the phosphate bridge in the DNA backbone) are under-represented. The reason(s) are unknown, but intriguingly, RNA viruses mimic their hosts by suppressing UpA in their genomes [1].

When a virus infects a cell, this triggers an antiviral response resulting in hundreds of genes being upregulated. One such gene encodes the Ribonuclease L (RNaseL) enzyme. In 1981 it was reported that mRNA is cleaved at UpA motifs by RNaseL [2], potentially explaining why UpAs are suppressed in the genomes of viruses and their hosts. However, when UpAs are added into virus genomes, virus growth is impaired, but depletion of RNaseL does not remove the impairment (unpublished data from our lab), suggesting that other factors may be involved.

RNAseL is a known to have antiviral activity, and its activation drastically alters cellular gene translation, leading to the synthesis of novel proteins [3]. We hypothesise that RNaseL activation may also change the profile of viral proteins produced during infection.

In this project you will characterise how UpA dinucleotides influence virus replication, and determine whether RNAseL alters viral protein production during virus infection. Specifically you will:

1.     Design and synthesise mutants of influenza A virus with increased UpA content, and characterise the impact of UpA introduction on virus replication. You will test whether RNaseL depletion restores virus fitness.

2.     If RNaseL restricts virus replication, you will characterise the mechanism. If RNaseL is not restrictive, you will use a small screen based approach to identify cellular factor(s) that are important for cellular UpA recognition.

3.     Generate knockout RNAseL cells and infect them with influenza A virus, then perform mass spectrometry to determine whether RNAseL impacts the profile of viral peptides produced during infection.

You will learn laboratory skills including how to perform virus infections, molecular biology techniques including CRISPR, mass spectrometry, and in silico methods for virus genome recoding.

If you are interested in this project please contact [Email Address Removed].

Application Process:

EASTBIO Application and Reference Forms can be downloaded via  http://www.eastscotbiodtp.ac.uk/how-apply-0

 Please send your completed EASTBIO Application Form along with a copy of your academic transcripts to [Email Address Removed]

You should also ensure that two references have been sent to [Email Address Removed] by the deadline using the EASTBIO Reference Form. 

Please refer to Get a studentship to fund your doctorate – UKRI and Annex B of the UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf for full eligibility criteria.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (DTP) View Website http://www.eastscotbiodtp.ac.uk/how-apply-0
This opportunity is open to UK and international students and provides funding covering stipend and UK level tuition fees. The University of Edinburgh covers the difference between home and international fees meaning that the EASTBIO DTP offers fully-funded studentships to all appointees. There is a cap on the number of international students the DTP recruits. It is therefore important for us to know from the outset which fees status category applicants will fall under when applying to our university.

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