Dataset Information

A Proteomic View of Escherichia coli Metabolic Features

ABSTRACT: Escherichia coli is an important human pathogen, among others a cause of severe diarrhea diseases and urinary tract infections. The ability to distinguish different pathogenic E. coli subspecies is crucial for correct treatment of the infection. Characterization and quantification of clinical isolates proteomes can provide details of the organisms’ metabolism and specific virulence factors. We performed a systematic quantitative proteomic analysis on a representative selection of 16 pathogenic and 2 commensal E. coli strains, together with 5 pathogenic Shigella strains. The analysis yielded a dataset of more than 4 thousand proteins, with an average of 2 thousand proteins per strain and 980 proteins common to all strains. Statistical comparison of label-free quantitative levels of 750 proteins, which were quantified in all strains, revealed that levels of a majority of the shared proteins vary substantially among specific strains. Theses quantitative protein profiles clearly distinguished E. coli strains from Shigella and largely separated commensal E. coli strains from intestinal and extraintestinal E. coli isolates.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

DISEASE(S): Bacterial Infectious Disease

SUBMITTER: Veronika Kucharova

LAB HEAD: Harald G. Wiker

PROVIDER: PXD005760 | Pride | 2020-10-19

REPOSITORIES: Pride

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Publications

Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label-Free Quantitative Proteomics.

Pettersen Veronika Kuchařová VK Steinsland Hans H Wiker Harald G HG

Proteomics 20201026 2

Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra-species variation at the proteome level is currently unknown. The proteomes of 16 pathogenic E. coli, 2 non-pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages are investigated. By applying label-free quantitative proteomics on trypsin-digested cell ex ...[more]

PMID: 33025732

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Project description:Extraintestinal pathogenic Escherichia coli (ExPEC) have a capacity to cause serious infections of blood, the central nervous system and particularly the urinary tract. Relatively little is known about how ExPEC adapt their cell-wide protein expression to environments with different carbon sources and other required nutrients. We used label-free quantitative (LFQ) proteomic analysis to determine proteomes of five ExPEC strains purified from clinical blood cultures, and compared them with proteomes of reference uropathogenic E. coli strain 536 derived from blood culture and two chemically different solid media. We identified 2,883 proteins in total, and for 90% of the detected proteins described their relative quantitative levels based on LFQ intensity scores. Comparison of anaerobic and aerobic blood cultures revealed significant differences in the levels of 32 proteins out of 1854 shared proteins. A majority of these proteins was associated with acquisition and utilization of metal ions, which are critical either for anaerobic (nickel) or aerobic (iron) respiration. ANOVA analysis of the relative quantitative levels of 1758 proteins shared between the strains identified 47 differentially expressed proteins, including proteins involved in vitamin B6 metabolism, cell motility and virulence. Comparison of strain 536 proteomes derived from blood cultures and solid media showed substantial variation in the relative quantitative levels of 200 proteins, which represented 11% of the common proteins between the conditions. Blood culture condition was characteristic by upregulation of anaerobic fermentative metabolism, cell motility and iron utilization. In a response to the growth on solid media increased levels of proteins functional in aerobic respiration, catabolism of various biochemicals obtained from the media and protection against environmental stresses. The study presents the largest coverage of ExPEC/UPEC proteome to date,with a detail account of ExPEC metabolism under three chemically different environments.

Project description:Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (“pan-genome”) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Keywords: Comparative genomic hybridizations

Project description:Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (âpan-genomeâ) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Factorial design: Each of four test samples (G 1/2, G3/10, G 4/9, G5) are co-hybridized with two control strain samples (K-12 MG1655 and O157:H7 EDL933). Additional replicate co-hybridizations are included of the two control strain samples (O157:H7 EDL933 vs. K-12 MG1655).

Dataset Information

A Proteomic View of Escherichia coli Metabolic Features

Publications

Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label-Free Quantitative Proteomics.

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