Dataset Information

Proteome profiling of cultivated Echerichia coli isolates from Crohn's disease patients

ABSTRACT: One of the dysbioses often observed in CD patients is an increased abundance of Escherichia coli (10-100 fold compared to healthy individuals) [Gevers et al., 2014]. E. coli isolates collected from CD and healthy patients were cultivated on LB medium at aerobic conditions up to medium log phase and their total proteomes were analysed by shotgun proteomics by HPLC-MS/MS. Refs. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. 2014. Cell Host Microbe 15: 382–92.

INSTRUMENT(S): maXis

ORGANISM(S): Escherichia Coli

DISEASE(S): Crohn's Disease

SUBMITTER: Daria Rakitina

LAB HEAD: Gleb Yurievich Fisunov

PROVIDER: PXD010920 | Pride | 2019-08-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Ecoli-16032016-kerat.fasta	Fasta
	Escherichia_coli_LF82_uid161965-1.fasta	Fasta
	Fileslist.txt	Txt
	Nissle1917_goodProt_kerat.fasta	Fasta
	cen1-1-10-10_RA1_01_1729-1603.csv	Csv

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Proteomic dataset: Profiling of cultivated Echerichia coli isolates from Crohn's disease patients and healthy individuals.

Rakitina Daria D Baikova Julia J Pobeguts Olga O Bukato Olga O Butenko Ivan I Garanina Irina I Levites Mark M Manolov Alexander A Kanygina Alexandra A Kostryukova Elena E Semashko Tatiana T Karpova Irina I Babenko Vladislav V Scherbakov Petr P Khalif Igor I Shapina Marina M Parfenov Asfold A Ruchkina Irina I Knyazev Oleg O Fadeeva Nina N Subbotin Alexandr A Chamkin Sergey S Pyrkh Alexandr A Ivantsova Marina M Govorun Vadim V

Data in brief 20190307

One of the dysbioses often observed in Crohn's disease (CD) patients is an increased abundance of Escherichia coli (10-100 fold compared to healthy individuals) (Gevers et al., 2014). The data reported is a large-scale proteome profile for E. coli isolates collected from CD patients and healthy individuals. 43 isolates were achieved from 30 CD patients (17 male, 12 female, median age 30) and 19 isolates from 7 healthy individuals (7 male, median age 19). Isolates were cultivated on ...[more]

PMID: 31372401

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Project description:Crohn’s disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. Its pathogenesis mechanisms remain obscure. One of the factors of CD pathogenesis is reduced diversity of gut microbiota which is accompanied by the characteristic increase of representation of Escherichia coli strains, several of which are able to penetrate the mucin layer, adhere to the epithelial cells, cross the epithelial barrier, and colonize macrophages. During the internalization, these E. coli strains can modulate macrophages’ defensive functions in a way that allows them to survive in a presence of such negative factors as low pH, oxidative stress, proteolytic enzymes and antimicrobial solutions. These strains were collectively assigned to the adhesive–invasive group of E. coli (AIEC). Earlier we sequenced 28 E. coli isolates from 10 patients with CD [Rakitina DV et al. Genome analysis of E. coli isolated from Crohn disease patients. BMC Genomics. 2017, 18(1):544. doi: 10.1186/s12864-017-3917-x] It has been demonstrated that the majority of enteropathogens feature specific metabolic pathways allowing them to use alternative carbon sources which leads to survivability and enhaced competitiveness in the host organism. Previously, we demonstrated that virulent properties of CD isolates are dependent on the carbon source: prolonged growth on propionate containing medium stimulates virulent properties while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655 [Pobeguts OV et al. Propionate Induces Virulent Properties of Crohn’s Disease-Associated Escherichia coli. Frontiers in Microbiology. 2020, 11:1460. doi: 10.3389/fmicb.2020.01460]. Thus, cultivation of E. coli on different growth mediums: M9 supplied with propionate and glucose made it possible to distinguish two states of each CD isolate: active (aAIEC) and inactive (iAIEC). In order to identify the major changes that occur upon change of carbon source, we carried out LC–MS-based proteomic analysis of aAIEC and iAIEC states of three CD isolates of E. coli ZvL2 (RCE07), BruB2 (RCE03) and К5 (RCE06) grown on glucose and propionate.

Dataset Information

Proteome profiling of cultivated Echerichia coli isolates from Crohn's disease patients

Dataset's files

Publications

Proteomic dataset: Profiling of cultivated <i>Echerichia coli</i> isolates from Crohn's disease patients and healthy individuals.

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