{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001752","ANALYSIS_ID":"AN002855","VERSION":"1","CREATED_ON":"April 23, 2021, 5:56 pm"},

"PROJECT":{"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","FIRST_NAME":"Beatrice","ADDRESS":"Permoserstraße 15, Leipzipg, Saxony, 03418, Germany","EMAIL":"beatrice.engelmann@ufz.de","PHONE":"00493412351099","PROJECT_TITLE":"Dual RNA regulator VcdRP in V.cholera modulates central metabolism","LAST_NAME":"Engelmann"},

"STUDY":{"STUDY_TITLE":"Dual RNA regulator VcdRP in V. cholerae modulates central metabolism","STUDY_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 - UFZ","DEPARTMENT":"Molecular Systems Biology","LABORATORY":"Functional Metabolomics","LAST_NAME":"Engelmann","FIRST_NAME":"Beatrice","ADDRESS":"Permoserstraße 15, Leipzig, Saxony, 03418, Germany","EMAIL":"beatrice.engelmann@ufz.de","PHONE":"00493412351099"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Vibrio Cholerae","GENOTYPE_STRAIN":"V. cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961- access:2018.06.26)"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1P",
"Factors":{"Condition":"Overnight","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"2P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"3P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"4P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"5P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"6P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"7P",
"Factors":{"Condition":"Overnight","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"8P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"9P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"10P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"11P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"12P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"13P",
"Factors":{"Condition":"Overnight","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"14P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"15P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"16P",
"Factors":{"Condition":"Overnight","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"17P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"18P",
"Factors":{"Condition":"Overnight","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"19P",
"Factors":{"Condition":"OD0.5","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"20P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"21P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"22P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"23P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"24P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"25P",
"Factors":{"Condition":"OD0.5","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"26P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"27P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"28P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"29P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"30P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"31P",
"Factors":{"Condition":"OD0.5","Strain":"WT_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"32P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"33P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"34P",
"Factors":{"Condition":"OD0.5","Strain":"delta_VcdR_pVcdR"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"35P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pCtrl"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
},
{
"Subject ID":"-",
"Sample ID":"36P",
"Factors":{"Condition":"OD0.5","Strain":"delta_GltA_pVcdP"},
"Additional sample data":{"RAW_FILE_NAME":"VibrioCholerae_CentralCarbon.wiff"}
}
],
"COLLECTION":{"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_SUMMARY":"No treatment"},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Ion pair chromatography","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters XSelect HSS T3 XP (2.1 x 1500mm, 2.5 µm)","COLUMN_TEMPERATURE":"40","SOLVENT_A":"10 mM tributylamine, 10 mM acetic acid, 5% methanol and 2% 2-propanol (pH 7.1) in water","SOLVENT_B":"100% 2-propanol"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"AB Sciex 6500+ QTRAP","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"MS acquisition as well as data processing software was Analyst vs 1.7.0"},

"MS_METABOLITE_DATA":{
"Units":"relative abundance",

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"Metabolites":[{"Metabolite":"acetyl coenzyme A","KEGG":"C00024"},{"Metabolite":"pyruvic acid","KEGG":"C00022 "},{"Metabolite":"citric acid","KEGG":"C00158"},{"Metabolite":"succinic acid","KEGG":"C00042"},{"Metabolite":"glutamic acid","KEGG":"C00025"},{"Metabolite":"cis-aconitic acid","KEGG":"C00417"},{"Metabolite":"glucose 6-phosphate","KEGG":"C00668"},{"Metabolite":"fructose 6-phosphate","KEGG":"C05345"},{"Metabolite":"phosphoenolpyruvic acid","KEGG":"C00074 "},{"Metabolite":"lactic acid","KEGG":"C00186 "},{"Metabolite":"aspartic acid","KEGG":"C00049"},{"Metabolite":"asparagine","KEGG":"C00152"},{"Metabolite":"malic acid","KEGG":"C00149"},{"Metabolite":"glutamine","KEGG":"C00064"},{"Metabolite":"alanine","KEGG":"C00041"},{"Metabolite":"fructose 1,6-bisphosphate","KEGG":"C05378"},{"Metabolite":"glucose","KEGG":"C00267"},{"Metabolite":"alpha ketoglutaric acid","KEGG":"C00026"}]
}

}