title: Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.
abstract: Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.
authors.affiliation: Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Mayers
authors.affiliation: Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Clara
authors.initials: C
authors.lastname: Moon
authors.affiliation: Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Stupp
authors.affiliation: Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Andrew I
authors.initials: AI
authors.lastname: Su
authors.affiliation: Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Dennis W
authors.identifier: 0000-0001-9879-8353
authors.initials: DW
authors.lastname: Wolan
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D002853:Chromatography, Liquid; D004195:Disease Models, Animal; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D017353:Gene Deletion; D015870:Gene Expression; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics / Q000382:microbiology* / Q000473:pathology; D007422:Intestines / Q000382:microbiology / Q000473:pathology; D007553:Isotope Labeling; D054892:Metagenome; D051379:Mice; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D018398:Homeodomain Proteins; D020543:Proteome; C064658:RAG-1 protein
keywords: ComPIL; GO term enrichment; MudPIT; SILAM; activity-based probes; metaproteomics; microbiome; quantitative proteomics