Summary of Study ST002131

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	ST002131
Study Title	Discovery and characterization of virulence associated functional metabolites in Escherichia coli based on functional metabolomics strategy（pellets metabolomics-2）
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	2022-03-25
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2022-04-20
Release Version	1

Select appropriate tab below to view additional metadata details:

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:	SU002216
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
SA204512	fur-0-2P	No iron supplementation
SA204513	fur-0-1P	No iron supplementation
SA204514	fur-0-4P	No iron supplementation
SA204515	fur-0-3P	No iron supplementation
SA204516	fur-0-6P	No iron supplementation
SA204517	fur-0-5P	No iron supplementation
SA204518	fyuA-0-3P	standard growth conditions
SA204519	fyuA-0-4P	standard growth conditions
SA204520	fyuA-0-6P	standard growth conditions
SA204521	fyuA-0-2P	standard growth conditions
SA204522	fyuA-0-5P	standard growth conditions
SA204523	fyuA-0-1P	standard growth conditions
SA204524	ybtP-0-5P	standard growth conditions
SA204525	ybtP-0-6P	standard growth conditions
SA204526	ybtP-0-4P	standard growth conditions
SA204527	ybtP-0-3P	standard growth conditions
SA204528	ybtP-0-2P	standard growth conditions
SA204529	ybtQ-0-1P	standard growth conditions
SA204530	ybtQ-0-2P	standard growth conditions
SA204531	ybtQ-0-6P	standard growth conditions
SA204532	ybtQ-0-5P	standard growth conditions
SA204533	ybtQ-0-4P	standard growth conditions
SA204534	ybtQ-0-3P	standard growth conditions
SA204535	ybtP-0-1P	standard growth conditions

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO002209
Collection Summary:	After 18h of culture, the sample pellet was isolated. The bacterial pellets harvested from 50 mL of broth culture were mixed with 1.2 mL 80% ice-cold methanol (added to internal standard 0.001mg/ml 4-chloro-DL-phenylalanine), then vortexed for 30 s, and placed on dry ice for 30 min. The samples were centrifuged at 18000 × g for 15 min at 4 °C. The frozen samples were ground with beads and the homogenates were centrifuged at 18000 × g for 15 min at 4 °C. The supernatant was mixed with 800μL ice-cold acetonitrile, and then left to stand for 20 minutes in an ice bath. After centrifugation at 18000 × g 4℃ for 15 min, the supernatant was removed and filtered through 0.22μm membrane.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR002228
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 UTI89 mutants. 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:

TR002228

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 UTI89 mutants. 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:	SP002222
Sampleprep Summary:	The bacterial pellets harvested from 50 mL of broth culture were mixed with 1.2 mL 80% ice-cold methanol (added to internal standard 0.001mg/ml 4-chloro-DLphenylalanine), then vortexed for 30 s, and placed on dry ice for 30 min. The samples were centrifuged at 18000 × g for 15 min at 4 °C. The frozen samples were ground with beads and the homogenates were centrifuged at 18000 × g for 15 min at 4 °C. The supernatant was mixed with 800μL ice-cold acetonitrile, and then left to stand for 20 minutes in an ice bath. After centrifugation at 18000 × g 4℃ for 15 min, the supernatant was removed and filtered through 0.22μm membrane. For LC/MS based metabolomics analysis, the dried samples were dissolved in 200μL water and 5μL aliquots were analyzed.

Sampleprep ID:

SP002222

Sampleprep Summary:

The bacterial pellets harvested from 50 mL of broth culture were mixed with 1.2 mL 80% ice-cold methanol (added to internal standard 0.001mg/ml 4-chloro-DLphenylalanine), then vortexed for 30 s, and placed on dry ice for 30 min. The samples were centrifuged at 18000 × g for 15 min at 4 °C. The frozen samples were ground with beads and the homogenates were centrifuged at 18000 × g for 15 min at 4 °C. The supernatant was mixed with 800μL ice-cold acetonitrile, and then left to stand for 20 minutes in an ice bath. After centrifugation at 18000 × g 4℃ for 15 min, the supernatant was removed and filtered through 0.22μm membrane. For LC/MS based metabolomics analysis, the dried samples were dissolved in 200μL water and 5μL aliquots were analyzed.

Combined analysis:

Analysis ID	AN003485	AN003486
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity	Agilent 1290 Infinity
Column	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	Agilent 6495 QQQ	Agilent 6495 QQQ
Ion Mode	POSITIVE	NEGATIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH002573
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:	MS003246
Analysis ID:	AN003485
Instrument Name:	Agilent 6495 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QQQ)
Ion Mode:	POSITIVE

MS ID:	MS003247
Analysis ID:	AN003486
Instrument Name:	Agilent 6495 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QQQ)
Ion Mode:	NEGATIVE