More immune receptor papers galore: It’s raining cryo-EM structures!
We ended 2023 with this recap “Papers galore: A year-end update on immune receptor networks,” but 2024 was equally busy. Our lab along with collaborators published several papers on various aspects of the biology of the NRC network, a major network of these NLR immune receptors. These include cryo-EM structures of NRC helper NLR proteins in both their resting and activated hexameric states.
Selvaraj, M., Toghani, A., Pai, H., Sugihara, Y., Kourelis, J., Yuen, E.L.H., Ibrahim, T., Zhao, H., Xie, R., Maqbool, A., De la Concepcion, J.C., Banfield, M.J., Derevnina, L., Petre, B., Lawson, D.M., Bozkurt, T.O., Wu, C.-H. Kamoun, S., and Contreras, M.P. 2024. Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. PLOS Biology, 22:e3002868.
Madhuprakash, J., Toghani, A., Contreras, M.P., Posbeyikian, A., Richardson, J., Kourelis, J., Bozkurt, T.O., Webster, M.W., and Kamoun, S.2024. A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity. Science Advances, 10:eadr2594.
AlphaFold bonanza: accelerating the pace of disease resistance research
AlphaFold 3 was only released in May 2024, yet it has already revolutionized our approach to structural modeling, significantly impacting several of our recent papers. Remarkably, AlphaFold 3 outperforms its predecessors in predicting the structure of CC-NLR oligomers, particularly in producing high-confidence models of NRC helpers and the notoriously challenging CC-NLR amino-terminal α1 helices. These regions have typically been difficult to resolve using experimental methods.
With AlphaFold 3, we’ve been able to model receptor complexes that had previously eluded resolution, even with cutting-edge cryo-EM techniques. This has saved us months — if not years — of experimental work, propelling our projects forward at a pace we could not have imagined. The potential of this tool to accelerate disease resistance research and guide receptor bioengineering is truly transformative.
Madhuprakash, J., Toghani, A., Contreras, M.P., Posbeyikian, A., Richardson, J., Kourelis, J., Bozkurt, T.O., Webster, M.W., and Kamoun, S.2024. A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity. Science Advances, 10:eadr2594.
Ibrahim, T., Yuen, E.L.H., Wang, H.Y., King, F.J., Toghani, A., Kourelis, J., Vuolo, C., Adamkova, V., Castel, B., Jones, J.D.G., Wu, C.-H., Kamoun, S. and Bozkurt, T.O. 2024. A helper NLR targets organellar membranes to trigger immunity. bioRxiv, doi: https://doi.org/10.1101/2024.09.19.613839.
Toghani, A., Frijters, R., Bozkurt, T.O., Terauchi, R., Kamoun, S. and Sugihara, Y. 2024. Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors? bioRxiv, doi: https://doi.org/10.1101/2024.11.24.625045.
Inter-species transfer of disease resistance: a little help from a helper
Tranfer of disease resistance genes across species doen’t always work limiting the deployment of useful resistance traits in agriculture. We demonstrated that the disease resistance protein Rx and its matching helper NRC2, constitute a minimal unit capable of being transferred across distantly related plant species. This transferability extends from solanaceous plants (lamiids) to the Campanulid species lettuce (Lactuca sativa). That’s about 100 million-years of evolution. This finding holds substantial implications for bioengineering disease resistance, as it raises the potential for transferring an even wider set of disease resistance genes across different crop species as further illustrated by a recent study by Du et al.
Contreras, M.P., Pai, H., Thompson, R., Marchal, C., Claeys, J., Adachi, H., and Kamoun, S. 2023. The nucleotide binding domain of NRC-dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling. New Phytologist, https://doi.org/10.1111/nph.19818.
Distrutto! Destroyed! Vandals attack disease-resistant rice in Italy
We’re thrilled that our long-term collaboration with researchers from the University of Milan led to Italy’s first field trial of gene-edited crops. Unfortunately, the trial was vandalized. As our colleagues wrote: “As public scientists, we express dismay and sadness at having suffered unjustified destruction, a result of obscurantism and anti-scientific knee-jerk reactions.”
Here is the link to the English and Italian versions of a blog post on the topic, featuring Giuseppe Verdi’s opera “Rigoletto”.
Horizontal mini-chromosome transfers drove fungal genome evolution
We published a study showing how multiple horizontal mini-chromosome transfers drive genome evolution in clonal lineages of the blast fungus. This is a fearsome plant pathogen that threaten two of the world’s most important food crops: rice and wheat. The study focused on populations of rice blast fungus in Italy’s Po Valley.
This summer, we visited again Po Valley to follow the evolution of the blast fungus across the many grass species it infects. Stay tuned and follow Thorsten Langner’s lab at the Max Planck in Tuebingen for more on the topic.
Barragan, A.C., Latorre, S.M., Malmgren, A., Harant, A., Win, J., Sugihara, Y., Burbano, H.A., Kamoun, S., and Langner, T. 2024. Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages. Molecular Biology and Evolution, 41:msae164.
2024: A year in blogs
This year, the KamounLab medium blog featured its usual eclectic mix of science, career advice, and musings on anything that sparked inspiration. I introduced a new travelogue category, inspired by trips to Antigua and Tenerife (here and here). A visit to a museum in Paris led me to reflect on the intersection of art and science, noting how both natural history illustrators and structural biologists rely on symmetry and wondering about the risk of inappropriately imposing symmetry on biological data.
Two inspiring conferences motivated me to share highlights of what I learned in Asilomar and Janelia, while current affairs cast a darker shadow, prompting more somber reflections. Posts offering career tips for PhD students, insights into the importance of stepping out of your comfort zone, and thoughts on hiring the best people attracted attention. However, the most popular posts by far delved into the topic of toxic academic environments, striking a chord with many readers (here and here).
GetGenome comes of age
GetGenome, our nonprofit spinout dedicated to addressing inequality in access to genome sequencing, truly came of age in 2024. Under James Canham’s leadership, the initiative has continued to expand its network and solidify its reputation. Having already made a tangible impact on over 100 early-career researchers, GetGenome is demonstrating the power of equitable access to genomic resources to drive discovery and innovation.
Find out more in this post: GetGenome Story Inspires.
Canham, J., Win, J., GetGenome Network, and Kamoun, S. 2024. GetGenome: Overcoming inequalities in access to genomics technology. PLOS Biology, 22:e3002804.
Preprint Review: Addressing inequality in the evaluation of science
We are passionate advocates for open science and firmly believe that scientific research should be “free to publish, free to read.” For us, this commitment to open science starts with preprinting — a practice we’ve embraced for years by preprinting every paper we write. Even our posters are shared openly on platforms like Zenodo.
The next frontier in the preprint movement is the rise of preprint review. Members of our lab have taken a leading role in community-driven efforts to bring expert review and curation to preprints, paving the way for a more inclusive, transparent, and efficient model of research communication. This approach promises to reshape how science is evaluated and shared, fostering a more equitable future.
Curious about preprint review? Consider starting a Preprint Club and check out this news item on The Sainsbury Laboratory website and the Avissar-Whiting et al. article.
Avissar-Whiting, M., Belliard, F., Bertozzi, S.M., Brand, A., Brown, K., Clement-Stoneham, G., Dawson, S., Dey, G., Ecer, D., Edmunds, S.C., Farley, A., Fischer, T.D., Franko, M., Fraser, J.S., Funk, K., Ganier, C., Harrison, M., Hatch, A., Hazlett, H., Hindle, S., Hook, D.W., Hurst, P., Kamoun, S., Kiley, R., Lacy, M.M., LaFlamme, M., Lawrence, R., Lemberger, T., Leptin, M., Lumb, E., MacCallum, C.J., Marcum, C.S., Marinello, G., Mendonca, A., Monaco, S., Neves, K., Pattinson, D., Polka, J.K., Puebla, I., Rittman, M., Royle, S.J., Saderi, D., Sever, R., Shearer, K., Spiro, J.E., Stern, B., Taraborelli, D., Vale, R., Vasquez, C.G., Waltman, L,, Watt, F.M., Weinberg, Z.Y., and Williams, M. 2024. Recommendations for accelerating open preprint peer review to improve the culture of science. PLOS Biology, 22:e3002502.
Acknowledgements
I dedicate this post to all team members and collaborators for their incredible work throughout the year. This article was written with assistance from ChatGPT.
This article is available on a CC-BY license via Zenodo.
Cite as: Kamoun, S. (2024) 2024 the year in review. Zenodo. https://doi.org/10.5281/zenodo.14541603
