Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis.

Autor:	Thuy-Boun PS; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Wang AY; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Crissien-Martinez A; Scripps Green Hospital Division of Gastroenterology, La Jolla, California, USA., Xu JH; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Chatterjee S; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA., Stupp GS; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA., Su AI; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA., Coyle WJ; Scripps Green Hospital Division of Gastroenterology, La Jolla, California, USA., Wolan DW; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. Electronic address: wolan@scripps.edu.
Jazyk:	angličtina
Zdroj:	Molecular & cellular proteomics : MCP [Mol Cell Proteomics] 2022 Mar; Vol. 21 (3), pp. 100197. Date of Electronic Publication: 2022 Jan 13.
DOI:	10.1016/j.mcpro.2022.100197
Abstrakt:	The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified ("dark peptidome") by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC. Competing Interests: Conflict of interest The authors declare no competing interests. (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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