Functional investigations of the influenza virus proteome.

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Viruses are often portrayed as extremely simple infectious agents, but in most cases our efforts to control them have only limited success. This can be clearly seen for influenza viruses, which despite decades of intensive research still cause severe and widespread clinical and veterinary disease, and remain capable of causing devastating pandemics. Viruses are small enough that their replication has to be understood at the level of molecular biology. At this scale, functions are typically carried out through the interactions of proteins. Yet, despite influenza viruses having a limited number of protein-encoding genes (their entire genome could be written out on a couple of sheets of paper) our understanding of how proteins mediate influenza infections is very far from complete. This proposal aims to deepen our understanding of the functions that proteins - those encoded by influenza viruses, and those which viruses co-opt from their hosts - play in an infection.There are three main reasons why, despite much effort, we do not fully understand the various ways in which proteins mediate viral infections. The first is the remarkable efficiency of viruses in encoding many proteins in a small genome, and in putting those proteins to many different uses. The second is that the function of many proteins can be regulated by chemical modifications ('post-translational modifications') which can act as switches and cause profound changes in their stability, activity or localisation within the cell. The third problem is that we are mistaken when we think of viruses as simple. A viral infection makes use of the thousands of proteins already encoded by an infected cell, with the proteins the virus actually encodes entering this complex environment and steering it towards the production of new virus particles.I study proteins in viral infections by combining mass spectrometry, a method which can identify and characterise proteins even when in complex mixtures, with molecular biological and virological methods, which can be used to test hypotheses about the function of proteins in infections. During this fellowship I will use this combined approach to search for previously uncharacterised viral proteins and determine new roles for known proteins. I will identify the sites of chemical modification and mutation in viral proteins and determine their effects on function. The information gained through mass spectrometry will allow me to make meaningful molecular biological investigations of complex systems, from the roles of host proteins in forming virus particles to determining the waves of regulatory chemical modifications which sweep through a cell as it enters an infected state.This work is of fundamental interest, particularly as understanding the intimate association of viruses with their hosts frequently informs the molecular biology of our own cells. Beyond this, the study addresses issues of practical importance. Although I am proposing a programme of basic research, understanding the basic biology of an infection is vital if we are to control it. A detailed understanding of the precise composition of influenza virus particles will be of value to the manufacturers of influenza vaccines, and a better understanding of the regulatory chemical changes in infections will help in the development of antivirals. Antivirals inhibiting such changes have been shown to limit influenza virus replication but their mode of action is unclear, and we need to know which changes the virus relies on in order to improve the action of these drugs.