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TitleSpatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 10763, Year 2025
Publish dateNov 26, 2025
AuthorsBenedikt 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 / Itzhak Mizrahi /
PubMed AbstractDegradation 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 ...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.
External linksNat Commun / PubMed:41298524 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution2.8 - 14.0 Å
Structure data

53097

9qf3

EMDB-53097, PDB-9qf3:
Structure of the GH13 domain of Ruminococcus bromii Amy4
Method: EM (single particle) / Resolution: 2.8 Å

53101

9qf8

EMDB-53101, PDB-9qf8:
Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy10
Method: EM (single particle) / Resolution: 3.1 Å

53102

9qf9

EMDB-53102, PDB-9qf9:
Structure of the GH13 domain of Ruminococcus bromii Amy16
Method: EM (single particle) / Resolution: 4.6 Å

53103

9qfa

EMDB-53103, PDB-9qfa:
Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy12
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-53104: Ruminococcus bromii ribosome
Method: EM (subtomogram averaging) / Resolution: 14.0 Å

Source
  • ruminococcus bromii l2-63 (bacteria)
KeywordsHYDROLASE / GH13 / Ruminococcus bromii / Amy4 / Amy10 / MucBP / Amy16 / Amy12

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