Summary of Study ST002128

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001349. The data can be accessed directly via it's Project DOI: 10.21228/M8BM53 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST002128
Study Title	Discovery and characterization of virulence associated functional metabolites in Escherichia coli based on functional metabolomics strategy(siderophores metabolomics-1)
Study Summary	Bacterial metabolites are substrates of virulence factors of uropathogenic Escherichia coli (UPEC), but the mechanism underlying the role of functional metabolites in bacterial virulence from the perspective of small molecular metabolism is unclear. In the present study, we used a strategy of functional metabolomics integrated with bacterial genetics in attempt to decipher the mechanism of virulence formation in Escherichia coli (E. coli) from the viewpoint of small molecule metabolism. We identified the virulence-associated metabolome via analysis of the primary metabolome of the pathogenic UTI89 strain and the non-pathogenic MG1655 strain. Then, the iron-mediated virulence associated metabolome was identified by an iron fishing strategy. Also, the mechanism of siderophores in regulating pathogenicity in different environments was explored by investigating the effect of iron on siderophore biosynthesis. Finally, by knocking out genes related to siderophore biosynthesis, siderophore transport and iron utilization, siderophores dependent iron-regulating virulence associated metabolome, including 18 functional metabolites, was identified and verified to be involved in the regulation of bacterial virulence. Based on this we found that these functional metabolites regulated the virulence of E. coli by targeting multiple metabolic pathways in an iron-siderophores dependent manner. Moreover, a quantitative proteomics approach was implemented to further elucidate the mechanism of functional metabolites and functional proteins in modulating bacterial virulence. And our findings demonstrated that functional proteins regulated the virulence of E. coli by mediating iron binding, iron-siderophore transmembrane transport, and the biosynthesis and expression of functional metabolites. Interestingly, we found that functional metabolites enhance the virulence of E. coli by specifically modulating the key metabolic pathways involved in purine metabolism, proline metabolism, arginine metabolism and pyrimidine metabolism. Taken together, our study identified for the first time 18 functional metabolites regulating the of E. coli virulence, greatly enriching our understanding of the mechanism of functional metabolites that regulate the E. coli virulence by targeting primary metabolism, which will largely contribute to the development of new strategies to target virulence-based diagnosis and therapy of infections caused by different pathogens.
Institute	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Last Name	Lu
First Name	Haitao
Address	800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Email	haitao.lu@sjtu.edu.cn
Phone	15221478139
Submit Date	2022-03-23
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2022-04-27
Release Version	1

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Project:

Project ID:	PR001349
Project DOI:	doi: 10.21228/M8BM53
Project Title:	Discovery and characterization of virulence associated functional metabolites in Escherichia coli based on functional metabolomics strategy
Project Type:	Untargeted MS quantitative analysis
Project Summary:	Discovery and characterization of virulence associated functional metabolites in Escherichia coli based on functional metabolomics strategy
Institute:	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Department:	Shanghai Center for Systems Biomedicine
Laboratory:	Lu Group
Last Name:	Lu
First Name:	Haitao
Address:	800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Email:	longlonghu126@sjtu.edu.cn
Phone:	15221478139

Subject:

Subject ID:	SU002213
Subject Type:	Bacteria
Subject Species:	Escherichia coli
Taxonomy ID:	562

Factors:

Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA204416	fur-0-2S	No iron supplementation
SA204417	fur-0-1S	No iron supplementation
SA204418	fur-0-4S	No iron supplementation
SA204419	fur-0-3S	No iron supplementation
SA204420	fur-0-6S	No iron supplementation
SA204421	fur-0-5S	No iron supplementation
SA204422	fyuA-0-3S	standard growth conditions
SA204423	fyuA-0-4S	standard growth conditions
SA204424	fyuA-0-6S	standard growth conditions
SA204425	fyuA-0-2S	standard growth conditions
SA204426	fyuA-0-5S	standard growth conditions
SA204427	fyuA-0-1S	standard growth conditions
SA204428	ybtP-0-5S	standard growth conditions
SA204429	ybtP-0-6S	standard growth conditions
SA204430	ybtP-0-4S	standard growth conditions
SA204431	ybtP-0-3S	standard growth conditions
SA204432	ybtP-0-2S	standard growth conditions
SA204433	ybtQ-0-1S	standard growth conditions
SA204434	ybtQ-0-2S	standard growth conditions
SA204435	ybtQ-0-6S	standard growth conditions
SA204436	ybtQ-0-5S	standard growth conditions
SA204437	ybtQ-0-4S	standard growth conditions
SA204438	ybtQ-0-3S	standard growth conditions
SA204439	ybtP-0-1S	standard growth conditions

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO002206
Collection Summary:	After 18h of culture, the sample supernatant was isolated.Then, 2μL 0.1M ferric chloride was mixed with 2 mL of cell supernatant. After incubating at room temperature for 15 minutes, the precipitate was removed by centrifugation at 20000 × g for 15 min at 4 °C. The supernatant was added to an SPE plate (Waters, Oasis HLB) and washed with 0.5 mL 5% methanol, and then eluted with 0.5 mL 100% methanol to obtain the siderophores.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR002225
Treatment Summary:	M63 medium (1.36% monopotassium phosphate, 0.2% ammonium sulfate, 0.024% magnesium sulfate, 0.001% calcium chloride, and 0.0015% nicotinic acid) was used to form siderophores. The E. coli strain was incubated in LB-agar plate for 12 hours, one colony was isolated to LB broth for further 4 hours incubation, then diluted the solution into M63 medium at a ratio of 1:100 and the cultures were incubated for another18 h at 37°C, 200rpm to culture E. coli.

Treatment ID:

TR002225

Treatment Summary:

M63 medium (1.36% monopotassium phosphate, 0.2% ammonium sulfate, 0.024% magnesium sulfate, 0.001% calcium chloride, and 0.0015% nicotinic acid) was used to form siderophores. The E. coli strain was incubated in LB-agar plate for 12 hours, one colony was isolated to LB broth for further 4 hours incubation, then diluted the solution into M63 medium at a ratio of 1:100 and the cultures were incubated for another18 h at 37°C, 200rpm to culture E. coli.

Sample Preparation:

Sampleprep ID:	SP002219
Sampleprep Summary:	Siderophores were extracted as previously described. Briefly, 12μL 0.1M ferric chloride was mixed with 2 mL of cell supernatant. After incubating at room temperature for 15 minutes, the precipitate was removed by centrifugation at 20000 × g for 15 min at 4 °C. The supernatant was added to an SPE plate (Waters, Oasis HLB) and washed with 0.5 mL 5% methanol, and then eluted with 0.5 mL 100% methanol to obtain the siderophores. LC/MS analysis was performed using 5μL aliquots.

Sampleprep ID:

SP002219

Sampleprep Summary:

Siderophores were extracted as previously described. Briefly, 12μL 0.1M ferric chloride was mixed with 2 mL of cell supernatant. After incubating at room temperature for 15 minutes, the precipitate was removed by centrifugation at 20000 × g for 15 min at 4 °C. The supernatant was added to an SPE plate (Waters, Oasis HLB) and washed with 0.5 mL 5% methanol, and then eluted with 0.5 mL 100% methanol to obtain the siderophores. LC/MS analysis was performed using 5μL aliquots.

Combined analysis:

Analysis ID	AN003481
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent 1290 Infinity
Column	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Agilent 6560 Ion Mobility
Ion Mode	POSITIVE
Units	peak area

Chromatography:

Chromatography ID:	CH002570
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003242
Analysis ID:	AN003481
Instrument Name:	Agilent 6560 Ion Mobility
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QTOF)
Ion Mode:	POSITIVE