Structural studies of human viruses and host interactions

Lead Research Organisation: MRC Virology Unit

Abstract

Virus particles are dynamic structures that replicate inside the cells of their host. We wish to understand their structure and how they interact with the cell. This can provide insights into many aspects of virus biology and may suggest strategies for treatment. The viruses being studied include measles virus, viruses that cause respiratory illnesses (influenza virus and respiratory syncytial virus), viruses that cause liver disease (Hepatitis B and C viruses) and viruses related to those that cause winter vomiting disease (Caliciviruses and Norovirus). We are determining the three-dimensional structures of the viruses at different stages during their replication and as they interact with host molecules to determine how their form relates to their function. We are also interested in the use of viruses to prevent disease through development of novel vaccines.

Technical Summary

Knowledge of the structure of viruses and how they interact with the host cell is essential for understanding the processes involved in infection. Virion morphogenesis is a central feature of the life cycle of any virus, and a clear understanding of this process can provide insights into many aspects of virus biology and may suggest possible strategies for therapeutic intervention. We use both cryogenic electron microscopy and tomography to visualise virus particles at various stages during their replication. Five virus families that cause disease in humans are currently under study; caliciviruses and hepaciviruses (positive strand RNA viruses), orthomyxoviruses and paramyxoviruses (negative strand RNA viruses) and hepadnaviruses (double-stranded DNA viruses).
Paramyxoviruses (measles and respiratory syncytial virus) have characteristic, helical ribonucleoprotein (RNP) cores that act as the templates for genome replication and expression. We are interested in investigating these structures as they undergo their different biological processes: mRNA and genomic RNA synthesis and packaging during virion morphogenesis. Virus assembly in Orthomyxoviruses (Influenza viruses) and Paramyxoviruses leads to both filamentous and spherical forms of enveloped virions. Cryotomography approaches are being used to analyse asymmetric entities such as these, as well as virus-infected cells. In particular we are interested in applying 3D imaging to the study of more biologically relevant cell systems that mimic the host tissue in which infection takes place.
Caliciviruses, hepaciviruses and hepadnaviruses all have icosahedral particles, which in hepaci and hepadnaviruses are surrounded by a lipid envelope. Icosahedral reconstruction is being used to investigate the structure of hepadnavirus capsids that have been modified to display foreign epitopes for use both as a vaccine candidate and also to solve the structure of the inserted polypeptides. We are studying virus entry and tropism in calicivirus and hepaciviruses by investigating the interaction between particles and specific host molecules: cellular receptors, neutralising antibodies. Knowledge of these interactions can inform vaccine design and development of antiviral therapies.

Publications

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Bakker, S.E. (2013) Pretty Nasty, symmetry in virus architecture. in The Biochemist

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Bhella D (2015) The role of cellular adhesion molecules in virus attachment and entry. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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McElwee M (2018) Structure of the herpes simplex virus portal-vertex. in PLoS biology

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Neuman BW (2011) A structural analysis of M protein in coronavirus assembly and morphology. in Journal of structural biology

 
Title Continuum - Movie for display in a planetarium 
Description Following an artist in residence scheme, Newcastle artist Paul Grimmer created a movie inspired by viral symmetry for display in a digital planetarium 
Type Of Art Film/Video/Animation 
Year Produced 2009 
Impact Screened at British Association of Planetaria conference, launched at the Centre for Life. http://www.paulgrimmer.co.uk/2010/05/continuum-press-release.html 
URL http://youtu.be/Z2J6ZwTkAas
 
Title Molecular Machines 
Description Molecular Machines was a touring exhibition of artworks based on images from virology research 
Type Of Art Artwork 
Year Produced 2007 
Impact Considerable news reporting in print and broadcast media. 
URL http://www.molecularmachines.org.uk
 
Title Movie - Engineering adenoviruses for gene therapy 
Description A short CGI animation of adenovirus interaction with coagulation factor X 
Type Of Art Film/Video/Animation 
Year Produced 2012 
Impact 13,000 views on YouTube 
URL http://youtu.be/ONPShTMR6To
 
Description RCUK CATALYSTS panel membership
Geographic Reach National 
Policy Influence Type Participation in advisory committee
 
Description BBSRC WestBio DTG
Amount £101,704 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2013 
End 09/2017
 
Description Cryo-Electron Microscopy Equipment Grants
Amount £4,400,000 (GBP)
Funding ID MC_PC_17135 
Organisation LifeArc 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2017 
End 07/2022
 
Description R01
Amount $190,789 (USD)
Funding ID 1R01AI113321 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 07/2014 
End 07/2018
 
Description Response Mode
Amount £751,764 (GBP)
Funding ID MR/M000451/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 11/2014 
End 11/2017
 
Description Calicivirus attachment and entry 
Organisation Cornell University
Department Baker Institute for Animal Health
Country United States 
Sector Academic/University 
PI Contribution We solved the structure of Calicivirus bound to it's receptor and identified structural changes that occur - possibly a first step towards uncoating
Collaborator Contribution Provided purified virus and protein
Impact Papers in Journal of Virology Pubmed 18550656, 21865392, 27902397
Start Year 2007
 
Description Calicivirus attachment and entry 
Organisation European Molecular Biology Laboratory
Department European Molecular Biology Laboratory Heidelberg
Country Germany 
Sector Public 
PI Contribution We solved the structure of Calicivirus bound to it's receptor and identified structural changes that occur - possibly a first step towards uncoating
Collaborator Contribution Provided purified virus and protein
Impact Papers in Journal of Virology Pubmed 18550656, 21865392, 27902397
Start Year 2007
 
Description Calicivirus attachment and entry 
Organisation University of Cambridge
Department Virology
Country United Kingdom 
Sector Academic/University 
PI Contribution We solved the structure of Calicivirus bound to it's receptor and identified structural changes that occur - possibly a first step towards uncoating
Collaborator Contribution Provided purified virus and protein
Impact Papers in Journal of Virology Pubmed 18550656, 21865392, 27902397
Start Year 2007
 
Description Focussed Ion Beam Milling of Virus infected cells 
Organisation University of Glasgow
Department Physics and Astronomy Department
Country United Kingdom 
Sector Academic/University 
PI Contribution Conceived and performed experiments to explore the use of FIB-SEM to image the virus infected cell, secured funding to add cryo-capability to instrument, collaborated on design of bespoke components to allow transfer of frozen hydrated cells into the FIB-SEM microscope.
Collaborator Contribution Worked to help us develop this technology using their microscope, providing access to the instrument.
Impact Preliminary data collected. Work is multidisciplinary - with Physics dept, Grant funding secured (MR/M000451/1)
Start Year 2012
 
Description Structural studies of Adenovirus Factor X interaction 
Organisation University of Glasgow
Department BHF Glasgow Cardiovascular Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We solved the structure of Adenovirus bound to Factor X, an interaction which directs the virus to the liver. Based on our low-resolution EM structure we constructed an atomic resolution model which guided mutagenesis studies to ablate binding.
Collaborator Contribution Several papers in high impact journals
Impact Papers in Cell, Blood and Molecular therapy Pubmed 19603000, 19429866, 18267072
 
Description Structure of Paramyxovirus Nucleocapsids 
Organisation Pasteur Institute, Paris
Department Department of Virology
Country France 
Sector Multiple 
PI Contribution Provided low-resolution structural data to facilitate solution of X-ray structure of Respiratory Syncytial Virus. Solved structure of helical assembly to allow modelling of authentic nucleocapsid structure.
Collaborator Contribution Publication of high impact papers
Impact Paper in Science (Pubmed 19965480) Paper in Journal of General Virology (Pubmed 23677789)
Start Year 2006
 
Description Structure of RSV RNA dependent RNA polymerase 
Organisation Boston University
Country United States 
Sector Academic/University 
PI Contribution Structural analysis of Respiratory Syncytial Virus RdRp complexes
Collaborator Contribution Providing protein preparations and expertise
Impact Secured grant funding (MR/M000451/1)
Start Year 2012
 
Description Structure of Respiratory Syncytial Virus 
Organisation Medical Research Council (MRC)
Department MRC Laboratory of Molecular Biology (LMB)
Country United Kingdom 
Sector Public 
PI Contribution Designed experiments, collected and processed preliminary data.
Collaborator Contribution Use of LMB cryomicroscope to collect higher quality EM data on RSV. Training in helical reconstruction provided by Dr Jude Short of LMB to support our project.
Impact Data collection ongoing Secured grant funding (MR/M000451/1
Start Year 2013
 
Description Article in SGM magazine microbiology today 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact I wrote an article describing outreach activities conducted by the CVR in partnership with Glasgow Science Centre.

This year I was nominated for the Peter Wildy prize for microbiology communication by the SGM virus group. I think this article prompted that nomination.
Year(s) Of Engagement Activity 2012
 
Description Article in The Biochemist 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact We wrote an article on virus structure and symmetry for a special edition of 'The Biochemist'. The magazine of the biochemical society.

Read by members of the society
Year(s) Of Engagement Activity 2013
 
Description Glasgow Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact ~40 students attended a workshop where they investigated a fictional virus outbreak by molecular biology and diagnostic methods

The workshop received excellent evaluation feedback from participants
Year(s) Of Engagement Activity 2011,2012,2013,2014
 
Description Meet the expert 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact We regularly conduct drop in meet the expert activities at Glasgow Science Centre, involving a range of activities: Build a virus - young children make models of viruses, Strawberry DNA children and adults extract DNA from fruit, Diagnosing viral diarrhoea - children and adults perform a mocked up latex agglutination test, Virus culture - children and adults look at (formaldehyde fixed) viral cultures.
In November 2014, I will be running a microscopy themed school activity in partnership with the Scottish Microscopy Group.

These activities achieve a high degree engagement depth with detailed one-to-one discussions.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
 
Description PCR Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact We provide a schools workshop on molecular biology, as part of this day workshop I give a careers talk with examples from my own research. 100 school students each year plus teachers. In 2012 the workshop expanded from 4 to 6 days reaching another ~48 students. In 2016 the workshop was revised as the subject matter moved in to the Higher Biology Curriculum. This workshop was delivered at Glasgow science centre previously, it is now delivered in the teaching laboratories of the University of Glasgow.
We have excellent documented feedback on this project and in the process of applying for funding to roll out the workshop on a national level. We are in dialog with the University of Glasgow to deliver the workshop to a larger audience through use of the University teaching labs in 2016. This is largely owing to the 'curriculum for excellence' initiative which has moved teaching of PCR from advanced higher biology to higher biology which is taken by a greater number of students each year.

Teaching resources adopted by Learning Teaching Scotland to teach higher biology.
Article in Nexxus magazine. Workshop previously praised in HMIE report.
Evaluation student feedback is very positive each year.
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010