Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Ron Kelley, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, Grigory Tagiltsev, Alicia K. Michael, Sofie van Dorst, Florent Waltz, Caitlyn L. McCafferty, Lorenz Lamm, Simon Zufferey, Philippe Van der Stappen, Hugo van den Hoek, Wojciech Wietrzynski, Pavol Harar, William Wan, John A.G. Briggs, Jürgen M. Plitzko, Benjamin D. Engel, Abhay Kotecha
Abstract
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.