Emergence of fractal geometries in the evolution of a metabolic enzyme

Franziska L. Sendker, Yat Kei Lo, Thomas Heimerl, Stefan Bohn, Louise J. Persson, Christopher-Nils Mais, Wiktoria Sadowska, Nicole Paczia, Eva Nußbaum, María Carmen Sánchez Olmos, Karl Forchhammer, Daniel Schindler, Tobias J. Erb, Justin L. P. Benesch, Erik G. Marklund, Gert Bange, Jan M. Schuller () and Georg K. A. Hochberg ()
Additional contact information
Franziska L. Sendker: Max Planck Institute for Terrestrial Microbiology
Yat Kei Lo: Philipps–University Marburg
Thomas Heimerl: Philipps–University Marburg
Stefan Bohn: Helmholtz Munich
Louise J. Persson: Uppsala University
Christopher-Nils Mais: Philipps–University Marburg
Wiktoria Sadowska: University of Oxford
Nicole Paczia: Max Planck Institute for Terrestrial Microbiology
Eva Nußbaum: Tübingen University
María Carmen Sánchez Olmos: Max Planck Institute for Terrestrial Microbiology
Karl Forchhammer: Tübingen University
Daniel Schindler: Philipps–University Marburg
Tobias J. Erb: Philipps–University Marburg
Justin L. P. Benesch: University of Oxford
Erik G. Marklund: Uppsala University
Gert Bange: Philipps–University Marburg
Jan M. Schuller: Philipps–University Marburg
Georg K. A. Hochberg: Max Planck Institute for Terrestrial Microbiology

Nature, 2024, vol. 628, issue 8009, 894-900

Abstract: Abstract Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2–4; however, so far, molecular assembly into fractals is restricted to synthetic systems5–12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.

Date: 2024
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DOI: 10.1038/s41586-024-07287-2

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