Understanding the molecular mechanisms that drive global CO2 fixation to improve photosynthesis

Lead Research Organisation: University of York
Department Name: Biology

Abstract

Photosynthetic algae fix approximately 50% of global CO2, yet our understanding of the molecular mechanisms driving this process are limited. Deep knowledge of algal CO2 fixation at the genetic level has great potential for enhancing photosynthesis to improve biological carbon capture to drive a future carbon neutral economy and to enhance crop yields to ensure food security. This multidisciplinary project will use cutting edge methods in microscopy, robotics and synthetic biology to give rapid advances in our understanding of CO2 fixation in algae and supply the knowledge and tools for future engineering efforts to increase crop yields and biological based carbon capture systems.

Nearly all algae have evolved a photosynthetic turbocharger called a CO2 concentrating mechanism (CCM) that increases the efficiency of the primary carbon fixing enzyme, Rubisco, by increasing levels of its substrate CO2 in its proximity. The engineering of a CCM into crop plants that have failed to evolve CCMs, such as rice and wheat, is predicted to increase yields by up to 60%. The data generated in this project will give us an unprecedented insight into CO2 fixation in prokaryotic and eukaryotic algae. The data will subsequently guide the assembly of the first test tube CO2 concentrating system that will act as a platform for testing different components (i.e. proteins) and optimising component combinations to enable the engineering of CCMs into plants.

To attain our goal, we will systematically identify the CCM components and regulatory mechanisms of two evolutionary distinct algae that are fundamental for global CO2 fixation, eukaryotic diatoms and prokaryotic cyanobacteria. We will use this data to identify the underlying principles for efficient CO2 fixation and provide the knowledge and molecular toolkit to engineer a synthetic CCM. To achieve this the project has three core objectives:

1) Generate the first complete cell protein map for a photosynthetic organism to give novel insights into cyanobacterial CO2 fixation.

2) Identify the core components of the poorly understood diatom CCM using high-throughput gene editing and protein localisation methods.

3) Build a synthetic CO2 fixation system to guide the engineering of enhanced photosynthesis in plants.

Together, I anticipate the data will pave the way for future engineering efforts of CCMs to enhance photosynthesis.

Planned Impact

Who will benefit from this research? In the short- to medium- term, the research will benefit academics and researchers across nearly all areas of algal research within the UK and internationally. The techniques, data and strains developed will be of particular interest to biologists working in all aspects of cyanobacterial and diatom biology. It will be of interest to biotechnologists and synthetic biologists working on algal strain engineering to enhance biomass and high-value products. This group will include UK based companies in this field such as Algenuity. The work will be of particular interest to researchers working on enhancing food security through photosynthesis engineering, this includes the international C4-Rice project and RIPE consortia. Medium- to long-term, agricultural biotechnology companies such as Syngenta and Bayer Crop Science, and charitable foundations such as the Bill and Melinda Gates Foundation may directly benefit from this research by building on it to generate photosynthesis based crop improvements. In addition, Government and Multinational Agencies can use results to strategize future funding in areas of high potential impact (e.g. GCRF). During the research, the PDRAs and undergraduates working on the project will benefit considerably from training. The general public will also benefit from planned outreach activities.

How will they benefit from the research? Academics and researchers will receive comprehensive new information about the CCM of diatoms and cyanobacteria and the components needed for a functional CCM. The field will have access to newly developed protocols, strains and plasmids once published. The algal industrial biotechnology industry will have data and methods to accelerate strain engineering and to enhance photosynthetic performance. The agro-industry and charitable organisations will have access to data to guide photosynthesis engineering and enable rapid testing of CCM designs. The PDRAs will receive a wide range of training in molecular biology, synthetic biology, biophysics, microfluidics and automated data analysis. They will develop a broad range of professional skills, with opportunities to attend training courses and interact closely with world leaders across multiple fields. Our research findings relate to issues of public interest including climate change, carbon cycling, sustainable crop production and global food security. The research also has a broad educational value, at both schools and universities.

How will we ensure they benefit from the research? I will ensure results are published as soon as feasible in high-impact open access journals. We will present research results at international meetings and invited seminars and promote new findings ahead of publications using the lab website (www.mackinderlab.com) and social media (i.e. Twitter). We will submit strains, plasmids, data and code to relevant depositories. When we are in a position to exploit our findings I will make informal contacts with biotechnologists once IP is protected. I will ensure that PDRAs are made aware of relevant training schemes and conferences and have regular progress reviews and career development plans. We will ensure that non-academic audiences have access to our findings through the University of York Outreach via the University website and press releases, through social media, talks by the fellow at local events including the Pints of Science public debate and interactions with secondary school students through the Future First network. I will seek opportunities to inform the work of charitable bodies by existing contacts, and I will involve undergraduate students by providing laboratory summer secondments.
 
Description - We have developed novel methods for tagging and localising proteins in diatoms and cyanobacteria, both fundamental organisms for global CO2 cycling. We have manuscripts on bioRxiv for both developed methods (https://doi.org/10.1101/2022.09.30.510313 and https://doi.org/10.1101/2024.02.28.582475). By applying these methods we are rapidly learning about the key proteins involved in CO2 uptake and fixation across diverse organisms. This data is starting to feed into plant engineering efforts with a goal to improve photosynthesis and yields. One example is that in diatoms we have found that instead of starch encapsulation of the Rubisco containing pyrenoid, the pyrenoid has a protein shell (https://doi.org/10.1101/2023.10.26.564148). We are currently investigating the assembly and function of this structure and testing its suitability for plant engineering to improve synthetic pyrenoid activity.

- Using preliminary data generated from this grant we have been successful in establishing and securing funding for two large consortium projects: An EPSRC Physics of Life project involves soft matter physicists, biophysicists, biochemists and cell biologists to investigate the underlying physics of CO2-fixing pyrenoids. The second consortium is through sLoLa funding based across York, Nottingham, Cambridge and Newcastle. This project looks at membrane repair mechanisms across diverse organisms.

- An exciting new area that the Future Leaders Fellowship has enabled is the exploration of how pyrenoids are assembled across diverse organisms. A recent key finding shows that they have convergently evolved and that some pyrenoid assembly proteins may be compatible with crop Rubisco's. This will considerably accelerate plant engineering efforts to engineer pyrenoids to improve yields. Related to this we have recently secure funding from the Carbon Technology Research Foundation to look at bio-based CO2 removal systems.
Exploitation Route Developed methodology and strains can be used to advance our understanding across multiple biological processes i.e. silification in diatoms or biotechnology approaches in cyanobacteria. Discovered components can be used for future plant engineering to improve photosynthesis for yield enhancement and CDR. Data can feed into global carbon models.
Sectors Agriculture

Food and Drink

Education

Manufacturing

including Industrial Biotechology

URL http://www.mackinderlab.weebly.com
 
Description This award has led to the formation of a consortium at York that recently was awarded a Physics of Life Grant to study phase separated CO2-fixing pyrenoids. This project aims to uncover the underlying physics of pyrenoids and is a new research area bringing together soft-matter physicists, biophysicists, biochemists and algal biologists. The award has led to the involvement in a successful sLoLa looking at membrane damage and protection across the tree of life. The tools and organisms directly supported by this award enabled this integration into the sLoLa consortium. The development of new research tools in diatoms and using proteoliposomes has led to several early stage collaborations with international research groups. It has also resulted in seminar and conference speaker invites at World leading research institutions and field leading conferences (i.e. University of Oxford, Weizmann Institute (Israel), Molecular Life of Diatoms conference). Recent data has shed light on how algae have efficient CO2 fixation capabilities and identified promising new approaches to engineer enhanced CO2 fixation in plants. We anticipate that this will accelerate on going engineering efforts through Gates Foundation and potentially UKRI funding.
First Year Of Impact 2021
Sector Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology
Impact Types Societal

 
Description UKRI CO2 Removal Hub - Green House Gas Removal Pathfinders Call 1 panel member
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description UKRI Engineering Biology Breakthrough Award panel member
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description UKRI Engineering Biology Mission Award Panel
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description 2022BBSRC-NSF/BIO: A synthetic pyrenoid to guide the engineering of enhanced crops
Amount £1,000,000 (GBP)
Funding ID BB/Y000323/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2023 
End 12/2026
 
Description Combining Algal and Plant Photosynthesis (CAPP)
Amount $2,318,123 (USD)
Funding ID INV-054558 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 01/2024 
End 01/2026
 
Description Cryo-electron tomography of CO2-fixing pyrenoids to guide synthetic assembly
Amount £25,061 (GBP)
Funding ID BB/X004953/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2022 
End 10/2023
 
Description The York Physics of Pyrenoids Project (YP3): Nanostructured Biological LLPS:Next-Level-Complexity Physics of CO2-fixing Organelles
Amount £2,488,444 (GBP)
Funding ID EP/W024063/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 03/2025
 
Description Understanding an ancient universal membrane effector system
Amount £4,431,990 (GBP)
Funding ID BB/X003035/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2022 
End 08/2027
 
Title CRISPR/Cas9 guided GFP knock-in diatoms 
Description The method enables the precise scarless GFP knock-in into the nuclear genome of the diatom Thalassiosira pseudonana to create GFP fusion proteins for localisation. To our knowledge this is the first endogenous tagging method developed for eukaryotic algae. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? No  
Impact Large interest at the premier diatom conference (Molecular Life of Diatoms) resulting in a poster prize award and invited short talk for technician Irina Grouneva. 
 
Title Scarless endogenous fluorescent protein tagging in cyanobacteria 
Description We have developed a scalable scarless fluorescent protein tagging method for the cyanobacterium Synechococcus elongatus PCC7942. This is now being used to fluorescently tag the complete proteome. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? No  
Impact We have established collaborations with Jeffrey Cameron (University of Colorado, Boulder) for high-content imaging and with Guang Yang (UKRI-FLF at Imperial College London) for machine-learning image analysis. 
 
Title TurboID proximity labelling in Chlamydomonas 
Description Establishment of proximity labelling in the chloroplasts of Chlamydomonas reinhardtii 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? Yes  
Impact Still early days as method has only just been published. 
 
Title CyanoTag 
Description Fluorescently tagged protein library in a model cyanobacteria 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact Several requests for lines and plasmids 
URL https://morf-db.org/projects/York-Mackinder-Lab/MORF000032
 
Description Cryo electron tomography with Ben Engel, Basel 
Organisation University of Basel
Department Biozentrum Basel
Country Switzerland 
Sector Academic/University 
PI Contribution We will be providing biological samples for imaging.
Collaborator Contribution They will be providing imaging expertise and facilities. A PhD student, Sabina Musial, has spent ~10 weeks based in the Engel lab learning cryoET data acquisition and analysis.
Impact Further funding. Collaborating on a range of projects. Publications are in the pipeline.
Start Year 2022
 
Description York Physics of Pyrenoids Project 
Organisation University of York
Department Department of Physics
Country United Kingdom 
Sector Academic/University 
PI Contribution The research is based on preliminary data generated by my lab across multiple UKRI supported projects. We provide the biological expertise within the consortium.
Collaborator Contribution They provide theoretical modelling, biophysics and biochemistry expertise to enable a multidisciplinary approach to understand pyrenoid evolution, structure and function.
Impact This is multi-disciplinary including biology, biophysics and soft matter physics.
Start Year 2020
 
Description sLoLa: Understanding an ancient universal membrane effector system 
Organisation Newcastle University
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in genetic engineering of diverse photosynthetic microbes
Collaborator Contribution Diverse expertise with a range of methods and study systems.
Impact Still early days.
Start Year 2022
 
Description sLoLa: Understanding an ancient universal membrane effector system 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in genetic engineering of diverse photosynthetic microbes
Collaborator Contribution Diverse expertise with a range of methods and study systems.
Impact Still early days.
Start Year 2022
 
Description sLoLa: Understanding an ancient universal membrane effector system 
Organisation University of York
Department Department of Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in genetic engineering of diverse photosynthetic microbes
Collaborator Contribution Diverse expertise with a range of methods and study systems.
Impact Still early days.
Start Year 2022
 
Description Invited Seminar (Biozentrum, Basel University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar to research groups.
Year(s) Of Engagement Activity 2023
 
Description Invited Seminar (Gregor Mendel Institute, Vienna) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research seminar to faculty and students
Year(s) Of Engagement Activity 2023
 
Description Invited Seminar (Michigan State University, USA) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research seminar with faculty and students.
Year(s) Of Engagement Activity 2023
 
Description Invited Seminar (Newcastle University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Invited seminar to researchers as part of the North East UK SynBioNet series
Year(s) Of Engagement Activity 2023
 
Description Invited Seminar (University of Cambridge) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research seminar with faculty and students
Year(s) Of Engagement Activity 2024
 
Description Invited Talk (Oxford University) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Gave a research presentation to the Oxford Plant Biology department. ~70 people attended. Exposed me to research at Oxford and potential future collaboration opportunities.
Year(s) Of Engagement Activity 2021
 
Description Invited Talk (Weizmann University, Israel) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar. Exploring two early stage collaborations with groups at the Weizmann Institute.
Year(s) Of Engagement Activity 2023
 
Description Regular guest scientist in secondary school outreach group (Charlotte Walker) 
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 Guest scientist at "I'm a scientist get me out of here" during the 2020 lockdowns. Online classroom discussion with various school groups.
Year(s) Of Engagement Activity 2020
URL https://imascientist.org.uk/
 
Description SEB Leaders of the Future Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited speaker as part of the Society for Experimental Biology Leaders of the Future centenary celebrations. The seminar was online and recorded. ~50 people attended the seminar and the video received >50 views over the following two weeks.
Year(s) Of Engagement Activity 2023
URL https://www.sebiology.org/events/ems-event-calendar/leaders-of-the-future-with-prof-luke-mackinder.h...
 
Description Science communication article on algal CO2 concentrating mechanisms and potential engineering into higher plants (Charlotte Walker) 
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 Popular science article published in the Marine Biologist magazine on algal CO2 concentrating mechanisms and their potential for engineering into higher plants. Also created illustrative content to accompany article.
Year(s) Of Engagement Activity 2020
URL https://www.mba.ac.uk/marine-biologist