Summary of Study ST001965
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 PR001251. The data can be accessed directly via it's Project DOI: 10.21228/M80T39 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 | ST001965 |
| Study Title | Integration of Metabolomics and Proteomics to Unveil Orchestration of Photorespiration and Central Carbon Pathway in Microchloropsis gaditana NIES 2587 |
| Study Type | Time Course VLC HC Metabolome |
| Study Summary | Photosynthetic organisms have evolved and adapted strategies to overcome the limiting concentrations of CO2. In this regard, the CO2-concentrating mechanism (CCM) developed by microalgae implies an efficient machinery to acquire CO2 in limiting environment. Inorganic carbon transporters channelize CO2 towards Rubisco, however, there are significant differences in the CCM of some species and it is obscurely understood. In the present study, we performed qualitative metabolomics and proteomics on Microchloropsis gaditana, under the influence of very-low CO2 (VLC; 300 ppm, or 0.03%) and high CO2 (HC; 30,000 ppm, or 3% v/v) at the time intervals of 0, 6, 12 and 24 hrs. Our results demonstrate that HC supplementation channelizes the carbon flux towards enhancing the biomass yield, increasing up to 1.7-fold. Cyclic electron flow driven (CEF) by PSI confers energy to the cells in the case of VLC in the initial acclimatization stage. Our qualitative metabolomic analyses has identified nearly 35 essential metabolites among which significant fold-change was observed as a photorespiratory by-product, glycolate, in VLC resulting in delayed growth and lower biomass. Whole cell proteomics study was performed in M. gaditana in both VLC and HC conditions and a total of 998 proteins were identified. Cells in VLC, undergoes dynamic changes to activate biophysical CCM with the help of bicarbonate transporters. In conclusion, comprehensive changes occur inside the cell that consequently mediate the assimilation and regulation of carbon metabolic loadout such that it favours fatty acid biosynthesis in HC. In conclusion, our emphasis is to delineate carbon assimilation in M. gaditana with the help of advanced multi-omics tools and provide translational approach for the enhanced production of biofuels and biorenewables. |
| Institute | International Centre for Genetic Engineering and Biotechnology |
| Department | Integrative Biotechnology |
| Laboratory | Omics of Algae |
| Last Name | Jutur |
| First Name | Pavan |
| Address | Omics of Algae Lab, 2nd Floor, New Building, ICGEB, Aruna Asaf Ali Marg, New Delhi |
| jppavan@gmail.com | |
| Phone | 01126741358 |
| Submit Date | 2021-08-30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-08-31 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001251 |
| Project DOI: | doi: 10.21228/M80T39 |
| Project Title: | Proteomics to Unveil Orchestration of Photorespiration and Central Carbon Pathway in Microchloropsis gaditana NIES 2587 |
| Project Type: | Time Course VLC HC Metabolome |
| Project Summary: | Photosynthetic organisms have evolved and adapted strategies to overcome the limiting concentrations of CO2. In this regard, the CO2-concentrating mechanism (CCM) developed by microalgae implies an efficient machinery to acquire CO2 in limiting environment. Inorganic carbon transporters channelize CO2 towards Rubisco, however, there are significant differences in the CCM of some species and it is obscurely understood. In the present study, we performed qualitative metabolomics and proteomics on Microchloropsis gaditana, under the influence of very-low CO2 (VLC; 300 ppm, or 0.03%) and high CO2 (HC; 30,000 ppm, or 3% v/v) at the time intervals of 0, 6, 12 and 24 hrs. Our results demonstrate that HC supplementation channelizes the carbon flux towards enhancing the biomass yield, increasing up to 1.7-fold. Cyclic electron flow driven (CEF) by PSI confers energy to the cells in the case of VLC in the initial acclimatization stage. Our qualitative metabolomic analyses has identified nearly 35 essential metabolites among which significant fold-change was observed as a photorespiratory by-product, glycolate, in VLC resulting in delayed growth and lower biomass. Whole cell proteomics study was performed in M. gaditana in both VLC and HC conditions and a total of 998 proteins were identified. Cells in VLC, undergoes dynamic changes to activate biophysical CCM with the help of bicarbonate transporters. In conclusion, comprehensive changes occur inside the cell that consequently mediate the assimilation and regulation of carbon metabolic loadout such that it favours fatty acid biosynthesis in HC. In conclusion, our emphasis is to delineate carbon assimilation in M. gaditana with the help of advanced multi-omics tools and provide translational approach for the enhanced production of biofuels and biorenewables. |
| Institute: | International Centre for Genetic Engineering and Biotechnology |
| Department: | Integrative Biotechnology |
| Laboratory: | Omics of Algae |
| Last Name: | Jutur |
| First Name: | Pannaga Pavan |
| Address: | Omics of Algae Group, ICGEB campus, Aruna Asaf Ali Marg, New Delhi, Delhi, 110070, India |
| Email: | jppavan@icgeb.res.in |
| Phone: | 26781358 |
Subject:
| Subject ID: | SU002045 |
| Subject Type: | Other organism |
| Subject Species: | Microchloropsis |
Factors:
Subject type: Other organism; Subject species: Microchloropsis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA184876 | HC_12hr_2 | HC |
| SA184877 | HC_12hr_1 | HC |
| SA184878 | HC_6hr_3 | HC |
| SA184879 | HC_12hr_3 | HC |
| SA184880 | HC_24hr_1 | HC |
| SA184881 | HC_24hr_3 | HC |
| SA184882 | HC_24hr_2 | HC |
| SA184883 | HC_6hr_2 | HC |
| SA184884 | HC_6hr_1 | HC |
| SA184885 | VLC_12hr_1 | VLC |
| SA184886 | VLC_6hr_3 | VLC |
| SA184887 | VLC_6hr_2 | VLC |
| SA184888 | VLC_12hr_2 | VLC |
| SA184889 | VLC_12hr_3 | VLC |
| SA184890 | VLC_24hr_3 | VLC |
| SA184891 | VLC_24hr_2 | VLC |
| SA184892 | VLC_24hr_1 | VLC |
| SA184893 | VLC_6hr_1 | VLC |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002038 |
| Collection Summary: | Marine microalgae Microchloropsis gaditana NIES 2587 is procured from Microbial Culture Collection, National Institute for Environmental Studies (NIES), Tsukuba, Japan. The strain was grown in minimal medium F/2 (Guillard and Ryther, 1962) under a light regime of 16:8 h and an illumination of 150 µmol m−2 s−1 photosynthetically active radiation (PAR) in a multi-cultivator MC 1000-OD (Photon Systems Instruments, Czech Republic) with a flow rate of 800 mL min-1 with continuous bubbling of air at 24 °C. |
| Sample Type: | Algae |
Treatment:
| Treatment ID: | TR002057 |
| Treatment Summary: | Microchloropsis gaditana cells were grown in a Multicultivator in the presence of very-low CO2 (300 ppm) and high CO2 (30,000 ppm) for 24 hours with an illumination intensity of 150 uE. |
| Treatment Compound: | CO2 |
Sample Preparation:
| Sampleprep ID: | SP002051 |
| Sampleprep Summary: | Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis. |
| Processing Storage Conditions: | Described in summary |
| Extraction Method: | Sonication |
| Sample Derivatization: | MSTFA |
| Sample Spiking: | Ribitol (Internal Standard) |
Combined analysis:
| Analysis ID | AN003203 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Agilent HP5-MS (30m x 0.25mm, 0.25 um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 7890A |
| Ion Mode | POSITIVE |
| Units | Area |
Chromatography:
| Chromatography ID: | CH002368 |
| Chromatography Summary: | GC-triple quadrupole analysis was performed on an HP-5 gas chromatograph with standard liners containing glass wool in split mode (1:5) at 250°C injector temperature. The GC was operated at constant flow of 1 ml/min helium on a 30-m, 0.25-mm i.d., 0.25-μm HP-5 column, a start temperature of 60°C, 3 min isothermal, temperature ramping by 5°C/min to 180°C, 3 min isothermal and finally temperature ramping of 10°C/min to 310°C. |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent HP5-MS (30m x 0.25mm, 0.25 um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002981 |
| Analysis ID: | AN003203 |
| Instrument Name: | Agilent 7890A |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Mass Hunter |
| Ion Mode: | POSITIVE |
