“Africa is ripe with possibilities and despite the challenges we face, I believe in the potential of Africans to change the world.”
Dr Jeremy Woodward, University of Cape Town
The problem
In recent years, cryo-EM has evolved into a crucial tool for medicine, biotechnology, and agriculture. The insights derived from these reconstructions inform the development of vaccines and medicines and allow scientists to reimagine naturally occurring biocatalysts so that they can be used to manufacture the materials we need in sustainable ways. They contribute to products that improve crop yields and lead to better animal health. This tool and the skills to use it are urgently needed by African scientists to address the continent’s challenges but there is only one facility in Africa with the capacity to perform cryo-EM experiments – the Electron Microscope Unit (EMU) at the University of Cape Town (UCT). What is required is a vibrant cryo-EM network across Southern Africa with the tools, infrastructure, and expertise to tackle the important scientific questions of relevance to Africa.
The Challenge
Imaging scientists at the EMU have spent the last twenty years developing the facility to perform cryo-EM experiments. This involved sustained support and collaboration from the international Structural Biology community in the form of student training, equipment donations, advice, and mentoring. None of the students at the facility had undergraduate backgrounds in Structural Biology, but they shared a passion for solving the problems around them using these exciting tools.
Africa is ripe with possibilities and despite the challenges we face, I believe in the potential of Africans to change the world. It is therefore essential to have an active research programme within imaging core facilities, especially in an African context where potential facility users might be interested in imaging but lack the necessary specialist skills. Academic groups embedded within these types of facilities create an environment that other research groups can benefit from.”
Dr Jeremy Woodward, University of Cape Town
Prior to 2018, much of the experimental effort was directed towards establishing protein expression and purification facilities, figuring out the microscopy, and laborious script-based image processing. Although several EM structures were published during this period1, none showed more than the general outline of the proteins they were interested in due to the limitations of the equipment. At the same time, a Nobel-prize-winning cryo-EM ‘resolution revolution’ was taking the world by storm. Without the necessary infrastructure and investment, African countries were left behind.
The solution
Ultimately, cryo-EM and synchrotron science bring biology into the realm of physics and chemistry where precise predictions can be made and tested. This allows the functional components of biological processes to be directly visualised in three dimensions at resolutions which make it possible to determine the positions of individual atoms.
The START project introduced groundbreaking opportunities for researchers in South Africa to access cryo-EM and synchrotron facilities. The three-year GCRF START grant (2018-2021), and subsequently START: Health & Bio Science, enabled access to funding, increased support, and close contact to the UK’s national synchrotron – Diamond Light Source (Diamond), especially the Electron Bio-Imaging Centre (eBIC) embedded at Diamond. eBIC houses five world class Titan Krios microscopes, a Talos Arctica, two Glacios, a Scios and an Aquilos cryo-FIB/SEM, and a Leica CryoCLEM.
Impact
As a result, researchers across Southern Africa have been exposed to cutting edge cryo-EM techniques, such as single particle analysis, electron tomography and electron diffraction, in combination with novel synchrotron approaches offered by Diamond. For many – such as Jeremy Woodward in the Electron Microscopy Unit at UCT – it was the first time in their careers that they had access to a world-class microscope.
START subsequently became the stepping stone for a successful South African eBIC BAG application by Jeremy (South African eBIC access: bi24039), which provides cutting-edge cryo-EM data to South African researchers. He has so far taken twelve projects, tackling, amongst others, problems like tuberculosis (TB) and emerging viruses, through the cryo-EM pipeline from sample optimisation to cutting-edge data collection, data processing and interpretation. These projects have yielded world class results putting Africa on the global cryo-EM map, with some exciting new results lined up for publication. Some of the highlights include:
- The first cryo-EM reconstruction from Africa that could be interpreted to atomic resolution published by Jeremy Woodward, START-funded Postdoctoral Research Fellow, Andani Mulelu, and Angela M. Kirykowicz2.
- The first complete structure of soluble angiotensin converting enzyme, an important blood pressure regulator, published by START-funded Postdoctoral Research Fellow, Lizelle Lubbe et al., in 20223 The structure shows the role of enzyme dynamics for substrate selection.
- The structure of a new HIV vaccine candidate consisting of mi3 by Malebo et al. a designed icosahedral protein complex, surrounded by HIV envelope proteins (unpublished).
- The structure of Mycobacterium tuberculosis encapsulin at 2.2 Å resolution by Woodward et al. (Fig.1). This bacterial nano-organelle houses enzymes involved in the oxidative stress response (emd-13420 PDBID: 7phm).
Mycobacterium tuberculosis (Mtb) uses a range of strategies to survive and replicate within human immune cells. One such defence is an Mtb enzyme called peroxidase, which is involved in defending the bacterium against oxidative stress. Jeremy Woodward et al, have demonstrated that Mtb packages peroxidase inside a nano-scale protein compartment and exports it from the cell. This compartment protects the enzyme, but presumably needs to allow access to the human defence molecules that we know are converted. Woodward et al., have reconstructed the compartment using data from the Electron Bio-Imaging Centre (eBIC) embedded at the UK’s national synchrotron – Diamond Light Source – at high resolution, which has allowed us to build an unambiguous atomic model; and we have observed that the wall of the compartment forms an impermeable barrier, broken by 12 small holes. Surprisingly, some of the molecules that are converted are too large to pass through the holes so another mechanism must be at play. Eliminating the nano-compartment from Mtb prevents it from establishing an infection, so we are interested in finding ways to block its function and develop new treatments for tuberculosis.
“Investing in cryo-EM benefits Africa by putting tools into people’s hands, which is a far more effective strategy than solely trying to identify and solve problems from the outside; and it benefits the rest of the world too. The recent pandemic was a stark reminder that the world is highly connected, no part of which can be neglected without it affecting everyone.”
Dr Jeremy Woodward, University of Cape Town
Capacity building
Becoming a START investigator had a transformative effect on Jeremy’s career, with START forming a crucial bridge between a soft-funded early career fellowship and a tenured academic post. The research also opened exciting opportunities for Andani Mulelu in innovative African drug discovery at H3D and subsequently at NANT SA.
START also had a transformative effect on Jeremy’s thinking, which led him to rally together investigators from around South Africa who might be interested in cryo-EM. This has transformed EMU at UCT as a centre for cryo-EM training. To date, Jeremy has trained researchers from South Africa, Zimbabwe, Malawi, Kenya, Swaziland, and one from France4, in addition to ten UCT students every year who take a practical Jeremy runs for postgraduate students.
“I was first exposed to Structural Biology eighteen years ago when I moved to Cape Town to join a Structural Biology MSc programme run by Trevor Sewell, the only such course in South Africa at the time. The programme consisted of an intense course in mathematics, physics, molecular biology, and biochemistry designed to make up for the shortcomings and gaps in our education up to that point. Famous international figures, such as Edward Egelman and Tom Blundell, and Nobel Prize winners Richard Henderson and Joachim Frank generously gave of their time to come to Cape Town and teach us, which made a lasting impression on all of us. Now we plan to build on this legacy and bring the cryo-EM revolution to the whole of Southern Africa. For this we need sustainable investment in infrastructure and talent.”
Dr Jeremy Woodward, University of Cape Town
START has been a springboard to Jeremy securing follow-on funding to expand his vision to spread cryo-EM knowledge throughout Southern Africa with his project: Cryo-EM for Southern Africa. This project is generously sponsored by the Chan Zuckerberg Initiative under their Expanding Global Access to Bio-imaging programme. The project consists of a series of one-on-one intensive training workshops in cryo-EM specimen preparation, imaging, data processing and interpretation. Participants receive funding to cover all their travel-related expenses and experimental costs and usually leave with publishable results. One of the unique aspects of this project is that researchers are trained on their own projects: acceptance is dependent on applicants demonstrating that they have suitable samples for cryo-EM.
References
1 EMD-1050, EMD-1204, EMD-1205, EMD-1313, EMD-1469, EMD-1870, EMD-3486, EMD3496, EMD3497, EMD3498, EMD3499, EMD3500, EMD3501, EMD3503, EMD3504, EMD3505
2 Mulelu, A.E., Kirykowicz, A.M. & Woodward, J.D. Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure. Commun Biol 2, 260 (2019). https://doi.org/10.1038/s42003-019-0505-4
3 Lubbe, L., Sewell, B.T., Woodward, J.D., Sturrock, E.D. (2022) Cryo‐EM reveals mechanisms of angiotensin I‐converting enzyme allostery and dimerization. EMBO J https://www.embopress.org/doi/10.15252/embj.2021110550. DOI: 10.15252/embj.2021110550
4 Researchers trained to date (March 2023): 15 South African researchers, 4 Zimbabwean, and one each from Malawi, Kenya, Swaziland, and France.