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Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome

Sasha L. Evans, Monsour M. J. Al-Hazeem, Daniel Mann, Nicolas Smetacek, Andrew J. Beavil, Yaqi Sun, Taiyu Chen, Gregory F. Dykes, Lu-Ning Liu, Julien R. C. Bergeron
doi: https://doi.org/10.1101/2022.02.18.481072
Sasha L. Evans
1Randall Centre for cell and molecular biophysics, King’s College London, UK
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Monsour M. J. Al-Hazeem
2Institute of systems, molecular and integrative biology, University of Liverpool, UK
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Daniel Mann
3Ernst-Ruska centre 3, Forschungszentrum Jülich, Jülich, Germany
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Nicolas Smetacek
4Department of molecular biology and biotechnology, The University of Sheffield, UK
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Andrew J. Beavil
1Randall Centre for cell and molecular biophysics, King’s College London, UK
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Yaqi Sun
2Institute of systems, molecular and integrative biology, University of Liverpool, UK
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Taiyu Chen
2Institute of systems, molecular and integrative biology, University of Liverpool, UK
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Gregory F. Dykes
2Institute of systems, molecular and integrative biology, University of Liverpool, UK
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Lu-Ning Liu
2Institute of systems, molecular and integrative biology, University of Liverpool, UK
5College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, China
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  • For correspondence: luning.liu@liverpool.ac.uk Julien.bergeron@kcl.ac.uk
Julien R. C. Bergeron
1Randall Centre for cell and molecular biophysics, King’s College London, UK
4Department of molecular biology and biotechnology, The University of Sheffield, UK
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  • For correspondence: luning.liu@liverpool.ac.uk Julien.bergeron@kcl.ac.uk
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Abstract

Carboxysomes are proteaceous bacterial microcompartments (BMCs) that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating carbonic anhydrase and ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which catalyses the dehydration of bicarbonate into CO2, the first step of the Calvin–Benson–Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural characterization of native carboxysomes, including the shell and the internal organization, is currently limited to low-resolution tomography studies. Notably, the degree of heterogeneity of the shell, and the internal arrangement of enzymes, remain poorly understood. Here, we report the structural characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryo-EM. We determine the structure of RuBisCO enzyme at 2.9 Å resolution. In addition, we obtain low-resolution maps of the icosahedral protein shell and the concentric interior organisation. In combination with artificial intelligence (AI)-driven modelling approaches, we exploited these maps to propose a complete atomic model of an intact carboxysome. This study provides insight into carboxysome structure and protein-protein interactions involved in carboxysome assembly. Advanced knowledge about carboxysome architecture and structural plasticity is critical for not only a better understanding of biological carbon fixation mechanism but also repurposing carboxysomes in synthetic biology for biotechnological applications.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted February 18, 2022.
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Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome
Sasha L. Evans, Monsour M. J. Al-Hazeem, Daniel Mann, Nicolas Smetacek, Andrew J. Beavil, Yaqi Sun, Taiyu Chen, Gregory F. Dykes, Lu-Ning Liu, Julien R. C. Bergeron
bioRxiv 2022.02.18.481072; doi: https://doi.org/10.1101/2022.02.18.481072
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Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome
Sasha L. Evans, Monsour M. J. Al-Hazeem, Daniel Mann, Nicolas Smetacek, Andrew J. Beavil, Yaqi Sun, Taiyu Chen, Gregory F. Dykes, Lu-Ning Liu, Julien R. C. Bergeron
bioRxiv 2022.02.18.481072; doi: https://doi.org/10.1101/2022.02.18.481072

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