Dissecting the functional link between immune signaling and defense-related autophagy
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
By 2050, global food production needs to increase by 70% to feed the rapidly growing human population. Filamentous plant pathogens including oomycetes and fungi cause the most destructive crop diseases and pose a major threat to our food security. The late blight, caused by the Irish famine pathogen Phytophthora infestans, is a deadly disease of potato and tomato. Outbreaks caused by late blight, as well as the control measures undertaken to manage the disease, lead to more than £6 billion in annual losses globally. The management of the disease relies on costly agrochemicals some of which are under rigorous regulations due to environmental and health concerns. Reduced fungicide sensitivity in newly emerging strains worsen the situation. A sustainable alternative is to genetically improve resistance, a specific and targeted approach which requires a deeper understanding of plant immunity.
Although plants have the genetic toolkit to fight diseases, the capacity of pathogens to adapt and evade plant immunity has constrained traditional resistance breeding. Plants defend against parasites through specialized immune sensors. Surface immune sensors, recognize molecules released by the parasites that are distinct from anything found in the plant. Activation of these surface receptors triggers immunity - known as pattern triggered immunity, or PTI. This kickstarts intricate signalling cascades that translate external immune stimuli into defense responses. The role of PTI in providing resistance to plant pathogens is well-established. However, the molecular mechanisms leading to enhanced resistance following PTI activation are not fully understood. Nevertheless, successful transfer of surface immune sensors from model plant species to crops has sparked renewed interest in understanding the innerworkings of PTI.
Like other filamentous plant pathogens, the late blight pathogen invades host cells through finger-like extensions called haustoria, through which it secretes immunity-breaking factors to gain control of the invaded cells. Invaded plant cells often respond by concentrating their immune responses at the pathogen extensions to prevent further infection. Although PTI is implicated in the production of defense-compounds that are deployed towards the pathogen haustoria, the extent to which PTI regulates targeted cellular transport routes to the pathogen interface is not known.
All plants and animals undergo a process of self-recycling called autophagy - this ensures that cellular components are degraded when necessary, while preserving the building-blocks, that can be reused in other cellular processes. Recently, ourselves and others discovered that autophagy is activated to contribute to defense against Phytophthora infestans, bacteria and viruses. We later discovered that defense-related autophagy machinery is diverted to pathogen interface to contribute to targeted immune responses. This pointed to more complex functions for autophagy than the widely known recycling roles. However, how defense-related autophagy pathways are activated and regulated at the molecular level, as well as the extent to which it is altered by PTI is unknown.
In this proposal, we aim to characterize the molecular mechanisms that govern defense-related autophagy. We have generated substantial preliminary data that a regulator of defense-related autophagy machinery interacts with the PTI signaling components. Hence, we will specifically focus on investigating the molecular interplay between PTI and defense-related autophagy pathways to elucidate the molecular events leading to enhanced disease resistance. By decrypting these mechanisms, we will generate fundamental knowledge that will be helpful to remodel plant immune system towards improved pathogen resistance. This work will have far-reaching implications, as the defense-related autophagy machinery provides resistance to a diversity of important pathogens.
Although plants have the genetic toolkit to fight diseases, the capacity of pathogens to adapt and evade plant immunity has constrained traditional resistance breeding. Plants defend against parasites through specialized immune sensors. Surface immune sensors, recognize molecules released by the parasites that are distinct from anything found in the plant. Activation of these surface receptors triggers immunity - known as pattern triggered immunity, or PTI. This kickstarts intricate signalling cascades that translate external immune stimuli into defense responses. The role of PTI in providing resistance to plant pathogens is well-established. However, the molecular mechanisms leading to enhanced resistance following PTI activation are not fully understood. Nevertheless, successful transfer of surface immune sensors from model plant species to crops has sparked renewed interest in understanding the innerworkings of PTI.
Like other filamentous plant pathogens, the late blight pathogen invades host cells through finger-like extensions called haustoria, through which it secretes immunity-breaking factors to gain control of the invaded cells. Invaded plant cells often respond by concentrating their immune responses at the pathogen extensions to prevent further infection. Although PTI is implicated in the production of defense-compounds that are deployed towards the pathogen haustoria, the extent to which PTI regulates targeted cellular transport routes to the pathogen interface is not known.
All plants and animals undergo a process of self-recycling called autophagy - this ensures that cellular components are degraded when necessary, while preserving the building-blocks, that can be reused in other cellular processes. Recently, ourselves and others discovered that autophagy is activated to contribute to defense against Phytophthora infestans, bacteria and viruses. We later discovered that defense-related autophagy machinery is diverted to pathogen interface to contribute to targeted immune responses. This pointed to more complex functions for autophagy than the widely known recycling roles. However, how defense-related autophagy pathways are activated and regulated at the molecular level, as well as the extent to which it is altered by PTI is unknown.
In this proposal, we aim to characterize the molecular mechanisms that govern defense-related autophagy. We have generated substantial preliminary data that a regulator of defense-related autophagy machinery interacts with the PTI signaling components. Hence, we will specifically focus on investigating the molecular interplay between PTI and defense-related autophagy pathways to elucidate the molecular events leading to enhanced disease resistance. By decrypting these mechanisms, we will generate fundamental knowledge that will be helpful to remodel plant immune system towards improved pathogen resistance. This work will have far-reaching implications, as the defense-related autophagy machinery provides resistance to a diversity of important pathogens.
Technical Summary
The Irish famine pathogen Phytophthora infestans penetrates host cells and forms haustoria that enable translocation of effector proteins. Invaded plant cell counters with a spatially confined cell-autonomous defense response known as focal immunity, a poorly understood process implicated in the concentration of immune responses around pathogen contact sites. We recently discovered that a selective form of autophagy, mediated by the autophagy cargo receptor Joka2, targets haustorium interface to contribute to plant focal immunity. This pointed to more complex functions for autophagy than the widely known degradative roles. Remarkably, Joka2 is also implicated in plant defence against bacteria and viruses. How Joka2 contributes to immunity, and the molecular mechanisms underlying defense-related selective autophagy are poorly understood. Specifically, how Joka2 is activated by the plant immune system is unknown. In this project, our goal is to characterize the molecular mechanisms underpinning Joka2-mediated immunity. We have generated unpublished data showing Joka2 interacts with MAPKs, the signaling components of the PAMP triggered immunity (PTI). Our central hypothesis is that Joka2 links PTI and autophagy pathways to boost basal plant resistance. Our working model is that Joka2 associates with MAPKs at the haustorium interface to modulate immunity by enhancing PTI outputs and/or to modulate defense-related autophagy. Consistent with this view, a mammalian orthologue of Joka2 is known to function as a signalling scaffold to regulate diverse cellular processes. By deciphering the molecular code underpinning the complexity of the Joka2 mediated autophagy, including its interactions with PTI signaling, we will gain insights into the detailed mechanisms of basal plant resistance at the genetic, biochemical and cell biological levels. The knowledge gained will enable remodelling of the defense-related autophagy machinery to counteract manipulation by pathogens.
Planned Impact
The project will provide insight into a recently discovered defense-related autophagy pathway in agronomically important solanaceous plants. This involves a selective autophagy cargo receptor, which interacts with the signaling components of the PAMP triggered immunity (PTI). The project will dissect the mechanisms by which defense-related autophagy is functionally linked to PTI. Thus, the project bridges two processes previously only considered in isolation. By crossing the boundaries of defence related processes, the work pushes the field by moving away from a reductionist view on immunity, and towards a holistic view of plant immune responses and cellular processes. Defense-related autophagy is implicated in resistance against important plant pathogens such as oomycetes, bacteria and viruses. Thus, this work will have a broader impact not only because it will build on the emerging paradigm of defense-related autophagy, but also is applicable to multiple pathosystems.
The knowledge produced will contribute to the scientific leadership of the UK in plant pathology and biotechnology, and will broadly impact BBSRCs strategic priority area of food security.
Proposed research will benefit following non-academic units;
i. Ag-Biotechnology industry
The Ag-Biotechnology industry will gain new insights into the functioning of basal plant resistance mediated by autophagy and PTI. The knowledge gained on the mechanistic interplay between PTI signalling and autophagy machinery, which is actively targeted by pathogens, will lead to discovery of novel strategies and target genes for engineering disease resistance. In particular, remodelling of defense-related autophagy to avoid pathogen manipulation should prove a useful method for improving pathogen resistance.
In plants, selective autophagy also plays critical roles in stress tolerance and development. Therefore, the project will generate conceptual knowledge in selective autophagy that will underpin future efforts of generating stress tolerant plants which can better cope with environmental fluctuations.
The plant-based expression systems have been successfully used for biopharming of clinically and industrially valuable recombinant proteins including the Ebola virus vaccine. However, factors affecting protein degradation negatively impact large-scale biopharming. Because autophagy is a major cellular degradation pathway, knowledge gained on this will have a huge impact in biopharming practices.
ii. Breeders
The proposed work will provide new perspectives for exploiting crucial components of basal plant immunity in plant breeding. Breeders will gain new knowledge on key players of immunity and genes involved in autophagy mediated stress tolerance. This should help plant breeding practices by ensuring that essential components of immunity are maintained in the newly generated lines.
iii. The public
Our ultimate aim is to help produce cheaper and healthier food. We expect that our efforts to understand basic principles of plant immunity will lead to improved food productivity by preventing crop losses and reducing the usage of costly and environmentally hazardous agrochemicals.
iv. The environment
The environment will benefit from reduced usage of agrochemicals. Efforts to improve genetic resistance as an alternative to chemical control of plant diseases will have a positive influence on the environment, considering the health concerns due to excessive usage agrochemicals.
vi. Undergraduate and postgraduate students
Students enrolled in Imperial College Biological Sciences will benefit from having access to the proposed cutting-edge program. I have already prepared a practical course for the 3rd year students involving plant immune activation. Additionally, motivated students will have the chance to participate in the proposed research program through summer placements and final year projects.
The knowledge produced will contribute to the scientific leadership of the UK in plant pathology and biotechnology, and will broadly impact BBSRCs strategic priority area of food security.
Proposed research will benefit following non-academic units;
i. Ag-Biotechnology industry
The Ag-Biotechnology industry will gain new insights into the functioning of basal plant resistance mediated by autophagy and PTI. The knowledge gained on the mechanistic interplay between PTI signalling and autophagy machinery, which is actively targeted by pathogens, will lead to discovery of novel strategies and target genes for engineering disease resistance. In particular, remodelling of defense-related autophagy to avoid pathogen manipulation should prove a useful method for improving pathogen resistance.
In plants, selective autophagy also plays critical roles in stress tolerance and development. Therefore, the project will generate conceptual knowledge in selective autophagy that will underpin future efforts of generating stress tolerant plants which can better cope with environmental fluctuations.
The plant-based expression systems have been successfully used for biopharming of clinically and industrially valuable recombinant proteins including the Ebola virus vaccine. However, factors affecting protein degradation negatively impact large-scale biopharming. Because autophagy is a major cellular degradation pathway, knowledge gained on this will have a huge impact in biopharming practices.
ii. Breeders
The proposed work will provide new perspectives for exploiting crucial components of basal plant immunity in plant breeding. Breeders will gain new knowledge on key players of immunity and genes involved in autophagy mediated stress tolerance. This should help plant breeding practices by ensuring that essential components of immunity are maintained in the newly generated lines.
iii. The public
Our ultimate aim is to help produce cheaper and healthier food. We expect that our efforts to understand basic principles of plant immunity will lead to improved food productivity by preventing crop losses and reducing the usage of costly and environmentally hazardous agrochemicals.
iv. The environment
The environment will benefit from reduced usage of agrochemicals. Efforts to improve genetic resistance as an alternative to chemical control of plant diseases will have a positive influence on the environment, considering the health concerns due to excessive usage agrochemicals.
vi. Undergraduate and postgraduate students
Students enrolled in Imperial College Biological Sciences will benefit from having access to the proposed cutting-edge program. I have already prepared a practical course for the 3rd year students involving plant immune activation. Additionally, motivated students will have the chance to participate in the proposed research program through summer placements and final year projects.
People |
ORCID iD |
Tolga Bozkurt (Principal Investigator) |
Publications


Leong JX
(2022)
A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component.
in The EMBO journal

Yuen ELH
(2024)
A pathogen effector co-opts a host RabGAP protein to remodel pathogen interface and subvert defense-related secretion.
in Science advances

Yuen ELH
(2024)
A RabGAP negatively regulates plant autophagy and immune trafficking.
in Current biology : CB

Selvaraj M
(2024)
Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome
in PLOS Biology




Ibrahim T
(2023)
AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs.
in PLoS biology
Description | This research project aims to investigate the role of autophagy (a catabolic cellular process) in plant immunity. We discovered a key component of autophagy interacts with other proteins involved in plant immune signalling, undertaking a non-degradative role in plant immunity by enhancing defense-related cell death. Overall, these findings shed new light on the mechanisms of plant immunity and may have important implications for future crop protection strategies. This award also helped us develop an artificial intelligence (AI) guided approach to discover key autophagy regulators. We used a machine learning-based protein folding prediction system called AlphaFold2-multimer, developed by DeepMind, to accurately predict protein complexes that control the degradation of certain cellular molecules through autophagy. Through this AI-guided strategy, we were able to locate the critical regulatory interface of a central modulator of autophagy in both plants and humans. These findings have important implications for understanding the underlying mechanisms of autophagy and could potentially lead to new therapies for diseases associated with autophagy dysfunction. |
Exploitation Route | Overall, our findings of the defense-related roles of autophagy shed new light on the mechanisms of plant immunity and may have important implications for future crop protection strategies. The AI-guided approach we developed has important implications for understanding the underlying mechanisms of autophagy and could potentially lead to new therapies for diseases associated with autophagy dysfunction. |
Sectors | Agriculture Food and Drink Education Healthcare |
Title | AI-guided approach to discover new autophagy modulators |
Description | We report an artificial intelligence (AI) guided pipeline to discover key regulators of the cellular process of autophagy. We show that AlphaFold2-multimer, a machine learning-based protein folding prediction system developed by DeepMind, accurately predicts protein complexes that control which and when certain cellular molecules are degraded by autophagy. Using this AI-guided strategy, we located the critical regulatory interface of a central modulator of autophagy in both plants and humans. |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Autophagy is a process by which cells break down and recycle damaged or unnecessary cellular components as well as infectious agents. Autophagy cargo receptors and adaptors play a crucial role in this process by recognizing and binding to specific cellular components or pathogen molecules to be targeted for degradation. Understanding the function of these receptors and adaptors can provide insight into how cells maintain their health and respond to stress and infections. The AI-guided approach we report has the potential to significantly advance the field of autophagy by speeding up the discovery of new autophagy modulators. Since autophagy is involved in various physiological and pathological processes, such as development, aging, and diseases like cancer and neurodegeneration, eliminating infectious agents, discovering new autophagy modulators could potentially lead to new therapeutic strategies for these conditions. |
Description | Structural and functional insights into defense-related autophagy machinery in plants |
Organisation | The Sainsbury Laboratory |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Providing research and generating knowledge in the field of plant immunity with a focus on defense-related autophagy |
Collaborator Contribution | Providing expertise and research skills in Structural Biology and Biochemistry (post-translational protein modifications. |
Impact | This is a multi-multi-diciplinary collaboration involving biochemistry, strucrtural biology and plant cell biology and immunity. We have generated knowledge in better understanding of the autophagy machinery in plant immunity. |
Start Year | 2020 |
Description | 36th New Phytologist meeting (Munich) on cell biology at the plant-microbe interface |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The Activity was to disseminate our findings on reprogramming of host cell processes by plant pathogens |
Year(s) Of Engagement Activity | 2015 |
Description | 3rd Autophagy UK Network Meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | I gave a talk to disseminate our findings funded by BSBRC. |
Year(s) Of Engagement Activity | 2017 |
URL | http://autophagy.uk/2017-london-meeting-2/ |
Description | 4th Annual and Final Conference of the Sustain COST Action |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | To disseminate findings of our ongoing BBSRC funded research |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.cost-sustain.org/Events-and-meetings/4th-Annual-and-Final-Conference-of-the-Sustain-COST... |
Description | B-DEBATE |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | This was an international meeting on plant stress entitled, "When Development meets Stress" which took place in CRAG, Barcelona, Spain. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.bdebate.org/en/forum/when-development-meets-stress-understanding-developmental-reprogram... |
Description | BSPP presidential meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | This was a conference organised by the British Society of Plant Pathology on Imaging plant-microbe interactions. |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.bspp.org.uk/meetings/bspppres2018.php |
Description | Biology Seminar at GMI - Gregor Mendel Institute (GMI) of Molecular Plant Biology, Austria, Vienna |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | I have shared our BBSRC funded reseach outcomes with an audience of postgraduate students and group leaders working in one of the world leading institutes (GMI vienna). My talk covered topics on how pathogens manipulate plant cellular processes for their own benefit. The activity was useful for establishing future collaborations and stimulating scientific interest. |
Year(s) Of Engagement Activity | 2017 |
URL | http://seminars.viennabiocenter.org/seminars.php?display=seminar/2836&kal_monat=20 |
Description | COST Action Plant Autophagy meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Dissemination of our BBSRC funded research on modulation of plant autophagy by the oomycete pathogens. |
Year(s) Of Engagement Activity | 2017 |
URL | http://cost-transautophagy.eu/wp-content/uploads/2016/11/Report-WG3-Meeting-Madrid-March2017Pilar_Ca... |
Description | Göttingen Botanical Seminar Series, Department of Plant Cell Biology, Georg-August-University Goettingen (Germany), Dec 9th. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | more than 50 postgraduate/undergraduate students and academics joined the seminar, which sparked questions and insights, enhancing interest in molecular plant pathology |
Year(s) Of Engagement Activity | 2021 |
Description | Imperial Fringe: Food for tomorrow |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | The Imperial Fringe is a series of free evening public events that explore the livelier side of science. They provide a unique opportunity to share the wonder and importance of our research with the public, the College and the wider College community. It also provides an opportunity to create links with new research groups, collaborate with other institutes, and try out new ways to present research to new and diverse audiences Around 5-700 people attend each Fringe event, made up of families and general members of the public as well as staff, students, alumni and neighbours, including local schools and workers. We as a grop introduced our research on how to improve crop resistance against pathogens |
Year(s) Of Engagement Activity | 2016 |
URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_26-2-2016-10-16-55 |
Description | International Conference on Plant Proteostasis |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | More than 100 people attended on this conference on Plant Proteostasis. This was an international forum for the scientific community working on the various pathways contributing to cellular proteostasis and is part of an ongoing effort to reinforce the development of the community in this important and relatively young scientific area. I could not attend the meeting due to visa issues my phD student Alex Leary presented our BBSRC funded work to a wide community of researchers that attended the meeting |
Year(s) Of Engagement Activity | 2019 |
URL | http://plantproteostasis2019.com |
Description | Key note speaker for the DLUT (Dalian University of Technology, China) online seminar series on Molecular Plant Microbe Interactions (MPMI), 5th July 2021. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | more than 100 postgraduate/undergraduate students and academics joined the seminar, which sparked questions and insights, enhancing interest in immune receptor trafficking and its implications in plat disease resistance |
Year(s) Of Engagement Activity | 2021 |
Description | London Evolutionary Research Network (LERN), UCL and Linnean Society The Future of Plant science |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Arround 100 people joined this presentation/debate on The Future of Plant science. I had the opportunity to publicise our BSBRC funded research |
Year(s) Of Engagement Activity | 2019 |
Description | Oomycete Molecular Genetics Network Annual Meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The purpose for attending this meeting was to disseminate our findings from our ongoing BBSRC grant |
Year(s) Of Engagement Activity | 2022 |
URL | https://omgn.org/about/ |
Description | The International Society for Molecular Plant-Microbe Interactions (IS-MPMI) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The purpose was to disseminate the findings of our ongoing BBSRC grant |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.ismpmi.org/Congress/2016/Pages/default.aspx |
Description | The Sainsbury Laboratory Seminar Series, Norwich, UK, 21st June, 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | more than 50 postgraduate/undergraduate students and academics joined the seminar, which sparked questions and insights, enhancing interest in plant immune receptor trafficking |
Year(s) Of Engagement Activity | 2021 |
Description | XVIII International Symposium on MPMI |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | International Congress on Molecular Plant-Microbe Interactions (MPMI), the major conference on plant microbe interactions that hosts >1,400 researchers. I have chaired a session and have disseminated the outcomes of our BSBRC funded research |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.ismpmi.org/Congress/2019/Pages/default.aspx |