Summary of Study ST003251
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 PR002018. The data can be accessed directly via it's Project DOI: 10.21228/M8RV57 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 | ST003251 |
| 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 |
| jpsaenz81@gmail.com | |
| Phone | (+49) 351 463 43066 |
| Submit Date | 2024-05-30 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002018 |
| Project DOI: | doi: 10.21228/M8RV57 |
| 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 |
Subject:
| Subject ID: | SU003370 |
| Subject Type: | Bacteria |
| Subject Species: | Mycoplasma mycoides, Minimal cell JCVI-syn3B |
Factors:
Subject type: Bacteria; Subject species: Mycoplasma mycoides, Minimal cell JCVI-syn3B (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Temperature | Time (hrs) |
|---|---|---|---|---|
| SA353531 | S3_30_0h | Minimal cell JCVI-Syn3B | 25 | 0 |
| SA353532 | S3_30_1h | Minimal cell JCVI-Syn3B | 25 | 1 |
| SA353533 | S3_30_2h | Minimal cell JCVI-Syn3B | 25 | 2 |
| SA353534 | S3_30_24h | Minimal cell JCVI-Syn3B | 25 | 24 |
| SA353535 | S3_30_4h | Minimal cell JCVI-Syn3B | 25 | 4 |
| SA353536 | S3_30_8h | Minimal cell JCVI-Syn3B | 25 | 8 |
| SA353537 | S3_30 (adapted) | Minimal cell JCVI-Syn3B | 30 | - |
| SA353538 | S3_33.5 (adapted) | Minimal cell JCVI-Syn3B | 33.5 | - |
| SA353539 | S3_37 (adapted) | Minimal cell JCVI-Syn3B | 37 | - |
| SA353540 | S3_37 start (Temporal) | Minimal cell JCVI-Syn3B | 37 | -0.25 |
| SA353541 | S3_37_0h | Minimal cell JCVI-Syn3B | 37 | 24.25 |
| SA353542 | S3_37_1h | Minimal cell JCVI-Syn3B | 37 | 25.25 |
| SA353543 | S3_37_2h | Minimal cell JCVI-Syn3B | 37 | 26.25 |
| SA353544 | S3_37_4h | Minimal cell JCVI-Syn3B | 37 | 28.25 |
| SA353545 | S3_37_8h | Minimal cell JCVI-Syn3B | 37 | 32.25 |
| SA353546 | S3_37_24h | Minimal cell JCVI-Syn3B | 37 | 48.25 |
| SA353513 | MM_25 (adapted) | M. mycoides | 25 | - |
| SA353514 | MM_25_0h | M. mycoides | 25 | 0 |
| SA353515 | MM_25_1h | M. mycoides | 25 | 1 |
| SA353516 | MM_25_2h | M. mycoides | 25 | 2 |
| SA353517 | MM_25_24h | M. mycoides | 25 | 24 |
| SA353518 | MM_25_4h | M. mycoides | 25 | 4 |
| SA353519 | MM_25_8h | M. mycoides | 25 | 8 |
| SA353520 | MM_27 (adapted) | M. mycoides | 27 | - |
| SA353521 | MM_30 (adapted) | M. mycoides | 30 | - |
| SA353522 | MM_33.5 (adapted) | M. mycoides | 33.5 | - |
| SA353523 | MM_37 (adapted) | M. mycoides | 37 | - |
| SA353524 | MM_37 start (Temporal) | M. mycoides | 37 | -0.25 |
| SA353525 | MM_37_0h | M. mycoides | 37 | 24.25 |
| SA353526 | MM_37_1h | M. mycoides | 37 | 25.25 |
| SA353527 | MM_37_2h | M. mycoides | 37 | 26.25 |
| SA353528 | MM_37_4h | M. mycoides | 37 | 28.25 |
| SA353529 | MM_37_8h | M. mycoides | 37 | 32.25 |
| SA353530 | MM_37_24h | M. mycoides | 37 | 48.25 |
| Showing results 1 to 34 of 34 |
Collection:
| Collection ID: | CO003363 |
| 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 ID: | TR003379 |
| 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 |
Sample Preparation:
| Sampleprep ID: | SP003377 |
| 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) |
Combined analysis:
| Analysis ID | AN005325 | AN005326 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | None (Direct infusion) | None (Direct infusion) |
| Chromatography system | none | none |
| Column | none | none |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | mol percent | mol percent |
Chromatography:
| Chromatography ID: | CH004028 |
| Instrument Name: | none |
| Column Name: | none |
| Column Temperature: | None |
| Flow Gradient: | None |
| Flow Rate: | None |
| Solvent A: | None |
| Solvent B: | None |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS005055 |
| Analysis ID: | AN005325 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| 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. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005056 |
| Analysis ID: | AN005326 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| 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 PC, PC O-, as acetate adducts; and CL, PA, PE, PE O-, PG, PI and PS as deprotonated anions. MS only is used to monitor LPA, LPE, LPE O-, LPI and LPS as deprotonated anions; Cer, HexCer, SM, LPC and LPC O- as acetate adducts. |
| Ion Mode: | NEGATIVE |
