Summary of Study ST001752

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 PR001123. The data can be accessed directly via it's Project DOI: 10.21228/M8JD7N This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST001752
Study TitleDual RNA regulator VcdRP in V. cholerae modulates central metabolism
Study SummaryBacterial small RNAs (sRNAs) are well-known to modulate gene expression by base-pairing with trans-coded transcripts and are typically considered to be non-coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual-function regulators. We discovered a dual-function regulator from Vibrio cholerae, called VcdRP, harboring a 29 amino acid protein (VcdP), as well as a base-pairing sequence. In this study, we measured the metabolite abundance of glycolytic and citric acid cycle intermediates using LC-MS.
Institute
Helmholtz Centre for Environmental Research
DepartmentMolecular Systems Biology
LaboratoryFunctional Metabolomics
Last NameEngelmann
First NameBeatrice
AddressPermoserstraße 15, Leipzig, Saxony, 03418, Germany
Emailbeatrice.engelmann@ufz.de
Phone00493412351099
Submit Date2021-04-14
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-05-01
Release Version1
Beatrice Engelmann Beatrice Engelmann
https://dx.doi.org/10.21228/M8JD7N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001123
Project DOI:doi: 10.21228/M8JD7N
Project Title:Dual RNA regulator VcdRP in V.cholera modulates central metabolism
Project Summary:Bacterial small RNAs (sRNAs) are well-known to modulate gene expression by base-pairing with trans-coded transcripts and are typically considered to be non-coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual-function regulators. We discovered a dual-function regulator from Vibrio cholerae, called VcdRP, harboring a 29 amino acid protein (VcdP), as well as a base-pairing sequence. In this study, we measured the metabolite abundance of glycolytic and citric acid cycle intermediates using LC-MS.
Institute:Helmholtz Centre for Environmental Research
Department:Molecular Systems Biology
Laboratory:Functional Metabolomics
Last Name:Engelmann
First Name:Beatrice
Address:Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email:beatrice.engelmann@ufz.de
Phone:00493412351099

Subject:

Subject ID:SU001829
Subject Type:Bacteria
Subject Species:Vibrio cholerae
Taxonomy ID:666
Genotype Strain:V. cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961- access:2018.06.26)

Factors:

Subject type: Bacteria; Subject species: Vibrio cholerae (Factor headings shown in green)

mb_sample_id local_sample_id Condition Strain
SA16392135POD0.5 delta_GltA_pCtrl
SA16392223POD0.5 delta_GltA_pCtrl
SA16392329POD0.5 delta_GltA_pCtrl
SA16392424POD0.5 delta_GltA_pVcdP
SA16392530POD0.5 delta_GltA_pVcdP
SA16392636POD0.5 delta_GltA_pVcdP
SA16392726POD0.5 delta_VcdR_pCtrl
SA16392832POD0.5 delta_VcdR_pCtrl
SA16392920POD0.5 delta_VcdR_pCtrl
SA16393027POD0.5 delta_VcdR_pVcdP
SA16393133POD0.5 delta_VcdR_pVcdP
SA16393221POD0.5 delta_VcdR_pVcdP
SA16393322POD0.5 delta_VcdR_pVcdR
SA16393434POD0.5 delta_VcdR_pVcdR
SA16393528POD0.5 delta_VcdR_pVcdR
SA16391831POD0.5 WT_pCtrl
SA16391925POD0.5 WT_pCtrl
SA16392019POD0.5 WT_pCtrl
SA16393911POvernight delta_GltA_pCtrl
SA1639405POvernight delta_GltA_pCtrl
SA16394117POvernight delta_GltA_pCtrl
SA1639426POvernight delta_GltA_pVcdP
SA16394312POvernight delta_GltA_pVcdP
SA16394418POvernight delta_GltA_pVcdP
SA1639458POvernight delta_VcdR_pCtrl
SA1639462POvernight delta_VcdR_pCtrl
SA16394714POvernight delta_VcdR_pCtrl
SA16394815POvernight delta_VcdR_pVcdP
SA1639499POvernight delta_VcdR_pVcdP
SA1639503POvernight delta_VcdR_pVcdP
SA16395110POvernight delta_VcdR_pVcdR
SA16395216POvernight delta_VcdR_pVcdR
SA1639534POvernight delta_VcdR_pVcdR
SA1639367POvernight WT_pCtrl
SA16393713POvernight WT_pCtrl
SA1639381POvernight WT_pCtrl
Showing results 1 to 36 of 36

Collection:

Collection ID:CO001822
Collection Summary:V. cholerae wild-type, ΔvcdRP and ΔgltA each harboring an empty control plasmid (pCtrl) and ΔvcdRP with pVcdRP expression plasmids (pVcdRP and pVcdP) as well as ΔgltA harboring pVcdP were grown in LB medium to exponential and stationary phase, and were subsequently quenched in ice-cold methanol. The quenched samples were centrifuged at 3000 x g for 10 min at -9°C. 1ml aliquot of supernatant was stored for leakage analysis, while the rest of the pellets were flash frozen in liquid nitrogen.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001842
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP001835
Sampleprep Summary:The frozen cell pellets were thawed on ice and resuspended in 500 µl methanol. After three freeze (liquid nitrogen) and thaw cycles, the sample was centrifuged (16000 x g, -4 °C and 5 min). The supernatant was transferred into a new tube and stored on ice. The extraction step was repeated and the supernatants were combined prior to evaporation. The samples were stored at -80°C until further analysis.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002855
Analysis type MS
Chromatography type Ion pair
Chromatography system Agilent 1290 Infinity II
Column Waters XSelect HSS T3 XP (150 x 2.1mm,2.5um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 6500+ QTrap
Ion Mode NEGATIVE
Units relative abundance

Chromatography:

Chromatography ID:CH002114
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters XSelect HSS T3 XP (150 x 2.1mm,2.5um)
Column Temperature:40
Solvent A:5% methanol/2% isopropanol/93% water; 10 mM acetic acid; 10 mM tributylamine, pH 7.1
Solvent B:100% isopropanol
Chromatography Type:Ion pair

MS:

MS ID:MS002648
Analysis ID:AN002855
Instrument Name:ABI Sciex 6500+ QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS acquisition as well as data processing software was Analyst vs 1.7.0
Ion Mode:NEGATIVE
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