PXD060149-1

PXD060149 is an original dataset announced via ProteomeXchange.

Title	Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon
Description	Degradation of complex dietary fibers 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 structure-function relationship and the interplay among its components, we applied an holistic multilayered approach and found that amylosome combinatorics, resistant starch degradation and enzymatic synergy are regulated at two levels: structural constraints enforcing enzyme proximity and expression-driven shifts in enzyme proportions. Cryo-electron tomography revealed that the amylosome comprises a constitutive extracellular layer extending toward the RS. However, proteomics demonstrated its remodeling across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses revealed complementarity and synergistic RS degradation by these enzymes, which allow R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism
HostingRepository	PRIDE
AnnounceDate	2025-11-02
AnnouncementXML	Submission_2025-11-02_12:05:05.904.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anke Trautwein-Schult
SpeciesList	scientific name: Ruminococcus bromii L2-63; NCBI TaxID: NEWT:657321;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-24 05:32:27	ID requested
⏵ 1	2025-11-02 12:05:06	announced

10.1038/S41467-025-65800-1;

submitter keyword: cryo-ET, cell-associated proteome,structure, cohesin, dockerin

Professor Dr.Dörte
contact affiliation	Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Anke Trautwein-Schult
contact affiliation	University of Greifswald
contact email	anke.trautwein-schult@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/11/PXD060149

PRIDE project URI

• PRIDE
  1. PXD060149
     1. Label: PRIDE project
     2. Name: Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon