{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003251","ANALYSIS_ID":"AN005325","PROJECT_ID":"PR002018","VERSION":"1","CREATED_ON":"June 11, 2024, 9:26 am"},

"PROJECT":{"PROJECT_TITLE":"Temperature change elicits lipidome adaptation in the simple organisms Mycoplasma mycoides and JCVI-syn3B","PROJECT_TYPE":"Publication","PROJECT_SUMMARY":"Cell membranes mediate interactions between life and its environment, with lipids determining their properties. Understanding how cells adjust their lipidomes to tune membrane properties is crucial yet poorly defined due to the complexity of most organisms. We used quantitative shotgun lipidomics to study temperature adaptation in the simple organism Mycoplasma mycoides and the minimal cell, JCVI-syn3B. We show that lipid abundances follow a universal logarithmic distribution across eukaryotes and bacteria, with comparable degrees of lipid remodeling for adaptation regardless of lipidomic or organismal complexity. Lipid features analysis demonstrates head group-specific acyl chain remodeling as characteristic of lipidome adaptation; its deficiency in Syn3B is associated with impaired homeoviscous adaptation. Temporal analysis reveals a two-stage cold adaptation process: swift cholesterol and cardiolipin shifts followed by gradual acyl chain modifications. This work provides an in-depth analysis of lipidome adaptation in minimal cells, laying a foundation to probe the design principles of living membranes.","INSTITUTE":"TU Dresden","LAST_NAME":"Saenz","FIRST_NAME":"James","ADDRESS":"Tatzberg 41, Dresden, Saxony, 01307, Germany","EMAIL":"jpsaenz81@gmail.com","PHONE":"(+49) 351 463 43066"},

"STUDY":{"STUDY_TITLE":"Temperature change elicits lipidome adaptation in the simple organisms Mycoplasma mycoides and JCVI-syn3B","STUDY_SUMMARY":"Cell membranes mediate interactions between life and its environment, with lipids determining their properties. Understanding how cells adjust their lipidomes to tune membrane properties is crucial yet poorly defined due to the complexity of most organisms. We used quantitative shotgun lipidomics to study temperature adaptation in the simple organism Mycoplasma mycoides and the minimal cell, JCVI-syn3B. We show that lipid abundances follow a universal logarithmic distribution across eukaryotes and bacteria, with comparable degrees of lipid remodeling for adaptation regardless of lipidomic or organismal complexity. Lipid features analysis demonstrates head group-specific acyl chain remodeling as characteristic of lipidome adaptation; its deficiency in Syn3B is associated with impaired homeoviscous adaptation. Temporal analysis reveals a two-stage cold adaptation process: swift cholesterol and cardiolipin shifts followed by gradual acyl chain modifications. This work provides an in-depth analysis of lipidome adaptation in minimal cells, laying a foundation to probe the design principles of living membranes.","INSTITUTE":"TU Dresden","LAST_NAME":"Saenz","FIRST_NAME":"James","ADDRESS":"Tatzberg 41, Dresden, Saxony, 01307, Germany","EMAIL":"jpsaenz81@gmail.com","PHONE":"(+49) 351 463 43066"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Mycoplasma mycoides and JCVI-syn3B"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"MM_37 (adapted)",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_33.5 (adapted)",
"Factors":{"Sample source":"M. mycoides","Temperature":"33.5","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_30 (adapted)",
"Factors":{"Sample source":"M. mycoides","Temperature":"30","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_27 (adapted)",
"Factors":{"Sample source":"M. mycoides","Temperature":"27","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25 (adapted)",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37 (adapted)",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_33.5 (adapted)",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"33.5","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30 (adapted)",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"30","Time, hrs":"-"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37 start (Temporal)",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"-0.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_0h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"0"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_1h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"1"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_2h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"2"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_4h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"4"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_8h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"8"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_25_24h",
"Factors":{"Sample source":"M. mycoides","Temperature":"25","Time, hrs":"24"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_0h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"24.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_1h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"25.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_2h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"26.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_4h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"28.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_8h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"32.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"MM_37_24h",
"Factors":{"Sample source":"M. mycoides","Temperature":"37","Time, hrs":"48.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37 start (Temporal)",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"-0.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_0h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"0"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_1h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"1"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_2h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"2"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_4h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"4"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_8h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"8"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_30_24h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"25","Time, hrs":"24"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_0h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"24.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_1h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"25.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_2h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"26.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_4h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"28.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_8h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"32.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
},
{
"Subject ID":"-",
"Sample ID":"S3_37_24h",
"Factors":{"Sample source":"JCVI-Syn3B","Temperature":"37","Time, hrs":"48.25"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"240528_TempAdapt_Manuscript_Data.xlsx"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Lipidomics data of M. mycoides and JCVI-syn3B membranes,extracted at different temperatures and time points, represented as molp for each of the samples. Quantification in mol % sample. mol% data were calculated, using pmols of lipid intensities (calculated from intensities of each lipid, measured m/z from the mass spectrometry), standardised to total lipid amount.","COLLECTION_PROTOCOL_FILENAME":"240528_TempAdapt_Manuscript_Data.xlsx","SAMPLE_TYPE":"Mycoplasma"},

"TREATMENT":{"TREATMENT_SUMMARY":"M. mycodies and JCVI-syn3B cells were grown at different temperatures in 25°C-37°C range and their membranes were extracted at adapted state or at different time points for lipidomic data analysis"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Bacterial samples are harvested at designated time points from the continuous cell culture in the bioreactor system and washed twice at their growth temperature in mycoplasma wash buffer (200 mM NaCl, 25 mM HEPES, 1% glucose, pH 7.0) to remove traces of the growth medium (21000g, 2 min centrifuging steps). Washed cell pellet is resuspended in 150 uL PBS and flash-frozen in liquid nitrogen. Lipids are extracted using a two-step chloroform/methanol procedure (Bligh-Dyer lipid extraction protocol)"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"None (Direct infusion)","INSTRUMENT_NAME":"none","COLUMN_NAME":"none","SOLVENT_A":"None","SOLVENT_B":"None","FLOW_GRADIENT":"None","FLOW_RATE":"None","COLUMN_TEMPERATURE":"None"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Lipotype","SOFTWARE_VERSION":"LipidXplorer"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Samples are analyzed by direct infusion on a QExactive mass spectrometer (Thermo Scientific) equipped with a TriVersa NanoMate ion source (Advion Biosciences). Samples are analyzed in both positive and negative ion modes with a resolution of Rm/z=200=280000 for MS (species structural resolution) and Rm/z=200=17500 for MSMS (subspecies structural resolution) experiments, in a single acquisition. MSMS is triggered by an inclusion list encompassing corresponding MS mass ranges scanned in 1 Da increments. Both MS and MSMS data are combined to monitor CE, DAG and TAG ions as ammonium adducts; cholesterol as ammonium adduct of an acetylated derivative."},

"MS_METABOLITE_DATA":{
"Units":"mol percent",

"Data":[{"Metabolite":"Cer 32:1;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"","MM_30 (adapted)":"","MM_27 (adapted)":"","MM_25 (adapted)":"","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"","MM_25_0h":"0.006848628","MM_25_1h":"0.010842985","MM_25_2h":"0.007322052","MM_25_4h":"0.006814013","MM_25_8h":"0.007922292","MM_25_24h":"0.008899399","MM_37_0h":"0.007297737","MM_37_1h":"0.006453973","MM_37_2h":"0.004567553","MM_37_4h":"0.005379951","MM_37_8h":"0.005245275","MM_37_24h":"0.006064272","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 34:0;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"","MM_30 (adapted)":"","MM_27 (adapted)":"","MM_25 (adapted)":"","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"","MM_25_0h":"","MM_25_1h":"","MM_25_2h":"","MM_25_4h":"0.001432708","MM_25_8h":"0.001568808","MM_25_24h":"0.001542164","MM_37_0h":"0.00139848","MM_37_1h":"0.001297873","MM_37_2h":"","MM_37_4h":"","MM_37_8h":"","MM_37_24h":"","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 34:1;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"","MM_30 (adapted)":"","MM_27 (adapted)":"","MM_25 (adapted)":"","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"0.040280896","MM_25_0h":"0.028781682","MM_25_1h":"0.035527632","MM_25_2h":"0.03056643","MM_25_4h":"0.027653035","MM_25_8h":"0.030174307","MM_25_24h":"0.03061597","MM_37_0h":"0.025334881","MM_37_1h":"0.026986059","MM_37_2h":"","MM_37_4h":"","MM_37_8h":"","MM_37_24h":"0.027168814","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 34:2;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"0.002817315","MM_30 (adapted)":"0.00207058","MM_27 (adapted)":"0.003171759","MM_25 (adapted)":"0.003261281","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"0.018302307","MM_25_0h":"0.011874529","MM_25_1h":"0.015095054","MM_25_2h":"0.016169669","MM_25_4h":"0.015155474","MM_25_8h":"0.015622555","MM_25_24h":"0.014736695","MM_37_0h":"0.012105427","MM_37_1h":"0.008162388","MM_37_2h":"0.006623718","MM_37_4h":"0.008322967","MM_37_8h":"0.007938274","MM_37_24h":"0.009382069","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 36:1;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"","MM_30 (adapted)":"","MM_27 (adapted)":"","MM_25 (adapted)":"","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"0.00860522","MM_25_0h":"0.006794348","MM_25_1h":"0.007463485","MM_25_2h":"0.006524559","MM_25_4h":"0.004985615","MM_25_8h":"0.006097922","MM_25_24h":"0.005539456","MM_37_0h":"0.005747775","MM_37_1h":"0.006050571","MM_37_2h":"0.00422328","MM_37_4h":"0.003943685","MM_37_8h":"","MM_37_24h":"0.005187258","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 36:2;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"0.001725351","MM_30 (adapted)":"0.001164135","MM_27 (adapted)":"0.00174497","MM_25 (adapted)":"0.001821876","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start (Temporal)":"0.004994895","MM_25_0h":"0.002884587","MM_25_1h":"0.005216615","MM_25_2h":"0.004190669","MM_25_4h":"0.003643155","MM_25_8h":"0.003332066","MM_25_24h":"0.003234872","MM_37_0h":"0.003097468","MM_37_1h":"0.003257661","MM_37_2h":"0.001864115","MM_37_4h":"0.001774492","MM_37_8h":"0.001743966","MM_37_24h":"0.00246647","S3_37 start (Temporal)":"","S3_30_0h":"","S3_30_1h":"","S3_30_2h":"","S3_30_4h":"","S3_30_8h":"","S3_30_24h":"","S3_37_0h":"","S3_37_1h":"","S3_37_2h":"","S3_37_4h":"","S3_37_8h":"","S3_37_24h":""},{"Metabolite":"Cer 38:1;2","MM_37 (adapted)":"","MM_33.5 (adapted)":"","MM_30 (adapted)":"","MM_27 (adapted)":"","MM_25 (adapted)":"","S3_37 (adapted)":"","S3_33.5 (adapted)":"","S3_30 (adapted)":"","MM_37 start 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}