The role of LC3 Interacting Regions in Viral Subversion of Autophagy
Lead Research Organisation:
University of Cambridge
Department Name: Pathology
Abstract
Flu can be a very unpleasant illness, but in severe cases it can be life-threatening. I have discovered a way in which the virus that causes flu interacts with one of the body's defence mechanisms called autophagy. Autophagy (literally self-eating) usually provides nutrients to cells when they are under conditions of starvation by recycling internal parts of the cell. This has been adapted for self-defence, so invading bacteria can be targeted to this recycling mechanism. Unfortunately most viruses seem not to be susceptible to this, and some viruses like flu even seem to benefit from autophagy.
The way we discovered that flu was interacting with autophagy was by looking in the virus for a particular binding region that we know usually interacts with an autophagy protein. We have found similar regions in other viruses, and it seems that both Herpes virus and the very dangerous Ebola virus may do the same thing. We therefore propose to try and unravel the details of how the flu virus subverts the autophagy defense mechanism, and also to discover if other viruses use a similar strategy. This could be helpful therefore for advancing our understanding of a lot of different viral diseases, and might lead to better vaccines or antiviral drugs in the future.
The way we discovered that flu was interacting with autophagy was by looking in the virus for a particular binding region that we know usually interacts with an autophagy protein. We have found similar regions in other viruses, and it seems that both Herpes virus and the very dangerous Ebola virus may do the same thing. We therefore propose to try and unravel the details of how the flu virus subverts the autophagy defense mechanism, and also to discover if other viruses use a similar strategy. This could be helpful therefore for advancing our understanding of a lot of different viral diseases, and might lead to better vaccines or antiviral drugs in the future.
Technical Summary
The molecular mechanisms by which viruses subverts autophagy remain largely unknown. I have discovered that binding of the C-terminus of the Matrix 2 (M2) to ATG8-like molecules occurs via LC3-Interacting Region (LIR), and have shown that this has a role to play in viral stability, filament formation and presumably therefore the critical step in the viral life-cycle of transmission between hosts. The M2 LIR also seems to mediate a process by which the plasma membrane becomes LC3 positive, a phenomenon which we describe for the first time. The utilization of a LIR to subvert autophagy by a virus may be a widespread viral strategy, as an accessory matrix protein of Ebola and a type II membrane protein of HSV also appear to contain a LIR motif. This project will explore these convergently evolved strategies in an effort to understand better the way in which these important human pathogens interact with the cell; exploiting technologies recently developed in the host institutions.
Planned Impact
The research planned is investigating the molecular mechanisms by which many viruses potentially subvert a host defence mechanism. This will be of direct benefit to immunologists, virologists and cell biologists. As well as developing new lines of research, there may be important discoveries that will guide therapy for multiple viruses, including discovering potential drug targets and aiding the design of vaccines. It is clearly significant that the principal viruses which will be investigated are important human pathogens. Influenza pandemics claim many lives, and the highly deadly nature of filoviruses such as ebola means their capacity to cause harm is immense. Therefore although the timescales on which the likely benefits will be obtained are relatively long (probably from 5 years to decades), they have the potential to be important for human health on a global scale.
In economic terms, the development of new technologies raises the possibility of patenting some aspects of this research. I have a personal track record of doing this where appropriate, and the institutions in which I plan to work are well set up to support such initiatives. This may have a positive economic impact for the UK. The acquisition of skills pertaining to new technologies developed overseas and brining that expertise back to the UK biomedical community also has the potential to stimulate future research and consequently economic growth.
In economic terms, the development of new technologies raises the possibility of patenting some aspects of this research. I have a personal track record of doing this where appropriate, and the institutions in which I plan to work are well set up to support such initiatives. This may have a positive economic impact for the UK. The acquisition of skills pertaining to new technologies developed overseas and brining that expertise back to the UK biomedical community also has the potential to stimulate future research and consequently economic growth.
Publications
Klionsky DJ
(2016)
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
in Autophagy
Ulferts R
(2021)
Subtractive CRISPR screen identifies the ATG16L1/vacuolar ATPase axis as required for non-canonical LC3 lipidation.
in Cell reports
Timimi L
(2022)
The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment.
in Autophagy
Fletcher K
(2018)
The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes.
in The EMBO journal
Description | Clinician Scientist Group Leader programme. |
Amount | £2,000,000 (GBP) |
Funding ID | Francis Crick Institute intramural funding, value of award is approximate. |
Organisation | Francis Crick Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2019 |
End | 01/2025 |
Description | Ita Askonas Bursary (awarded to Dr R Ulferts, Research Associate on my grant) |
Amount | £5,500 (GBP) |
Organisation | University of Cambridge |
Sector | Academic/University |
Country | United Kingdom |
Start | 11/2015 |
End | 04/2016 |
Description | Universal cells to overcome HLA barriers in regenerative medicine. |
Amount | £823,632 (GBP) |
Funding ID | MR/S02090X/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2019 |
End | 01/2022 |
Description | Machine learning in Autophagy |
Organisation | Microsoft Research |
Department | Microsoft Research Cambridge |
Country | United Kingdom |
Sector | Private |
PI Contribution | Ongoing collaboration with Matthew Johnson's team at Microsoft Research. Using machine learning to discriminate between different forms of 'Autophagy'. MPhil student co-supervised (University of Cambridge), PhD student due to start. |
Collaborator Contribution | Considerable expertise in convolutional neural networks. |
Impact | Multi-disciplinary, molecular cell biology/Machine learning. MPhil awarded to S Isaksson. |
Start Year | 2017 |
Description | Proteomic analysis of subversion of autophagy by influenza. |
Organisation | University of Cambridge |
Department | Cambridge Institute for Medical Research (CIMR) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have produced autophagy deficient cell lines from which wild-type or mutant influenza can be produced. In collaboration we are developing a new SILAC technique that can be applied to influenza. |
Collaborator Contribution | They are undertaking a proteomic analysis. |
Impact | Preliminary data supports the idea that neuraminidase inhibitors can aid the development of a proteomic technique suitable for analysing influenza's effects on the plasma membrane during budding. |
Start Year | 2016 |
Description | Cambridge in Europe Question Time event. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | My participation (alongside politicians such as Rt Hon Charles Clarke, Lord Balfe) is in order to explain my research, and how it benefits from our continued membership of the EU. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.cambridgeforeurope.co.uk/event/questiontime/ |
Description | Interviewed by Adrian Chiles on Radio 5 Live |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Interviewed by Adrian Chiles about my research (alongside colleagues from Virology) and the impact of influenza. |
Year(s) Of Engagement Activity | 2016 |
Description | Wrote article on CRISPR for London review of Books |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I wrote about the discovery of CRISPR and some of its technological uses for a high profile literary and political magazine. It generated a certain amount of interest on social media. I have been asked to write a popular science book and to contribute a chapter to a textbook (in the US). |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.lrb.co.uk/v40/n04/rupert-beale/diary |