Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon

Benedikt H. Wimmer, Sarah Moraïs, Itai Amit, Omar Tovar-Herrera, Meltem Tatli, Anke Trautwein-Schult, Barbara Pfister, Ran Zalk, Paloma Tödtli, Sebastian Simoni, Matteo Lisibach, Liron Levin, Dörte Becher, Edward A. Bayer, Ohad Medalia () and Itzhak Mizrahi ()
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Benedikt H. Wimmer: University of Zurich, Department of Biochemistry
Sarah Moraïs: Ben-Gurion-University of the Negev, Department of Life Sciences
Itai Amit: Ben-Gurion-University of the Negev, Department of Life Sciences
Omar Tovar-Herrera: Ben-Gurion-University of the Negev, Department of Life Sciences
Meltem Tatli: University of Zurich, Department of Biochemistry
Anke Trautwein-Schult: University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics
Barbara Pfister: ETH Zurich, Institute of Molecular Plant Biology
Ran Zalk: Ben-Gurion University of the Negev, Ilse Katz Institute for Nanoscale Science and Technology
Paloma Tödtli: University of Zurich, Department of Biochemistry
Sebastian Simoni: University of Zurich, Department of Biochemistry
Matteo Lisibach: University of Zurich, Department of Biochemistry
Liron Levin: Ben-Gurion University of the Negev, Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology
Dörte Becher: University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics
Edward A. Bayer: Ben-Gurion-University of the Negev, Department of Life Sciences
Ohad Medalia: University of Zurich, Department of Biochemistry
Itzhak Mizrahi: Ben-Gurion-University of the Negev, Department of Life Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its architecture, function, and the interplay among its components, we applied a holistic multilayered approach: Cryo-electron tomography reveals that the amylosome comprises a constitutive extracellular layer extending toward the RS substrate. Proteomics demonstrates remodeling of its contents across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses reveal complementarity and synergistic RS degradation by these enzymes. We demonstrate that amylosome composition and RS degradation are regulated at two levels: structural constraints and expression-driven shifts in enzyme proportions enforce enzyme proximity, which allows R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism.

Date: 2025
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DOI: 10.1038/s41467-025-65800-1

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