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

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UpAs are added into virus genomes, virus growth is impaired, but depletion of RNaseL does not remove the impairment (unpublished data from our lab), suggesting that other factors may be involved.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.

[1] Gaunt and Digard, 2022. Compositional biases in RNA viruses: Causes, consequences and applications. WIREs RNA, e1679.
[2] Wreschner et al., 1981. Interferon action - sequence specificity of the ppp(A2'p)nA-dependent ribonuclease. Nature, 289: 414-7.
[3] Karasik et al., 2021. Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences. Nucleic Acids Research, 49 (11): 6007-26.