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.

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Study IDST001965
Study TitleIntegration of Metabolomics and Proteomics to Unveil Orchestration of Photorespiration and Central Carbon Pathway in Microchloropsis gaditana NIES 2587
Study TypeTime Course VLC HC Metabolome
Study SummaryPhotosynthetic 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
DepartmentIntegrative Biotechnology
LaboratoryOmics of Algae
Last NameJutur
First NamePavan
AddressOmics of Algae Lab, 2nd Floor, New Building, ICGEB, Aruna Asaf Ali Marg, New Delhi
Emailjppavan@gmail.com
Phone01126741358
Submit Date2021-08-30
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-08-31
Release Version1
Pavan Jutur Pavan Jutur
https://dx.doi.org/10.21228/M80T39
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA184876HC_12hr_2HC
SA184877HC_12hr_1HC
SA184878HC_6hr_3HC
SA184879HC_12hr_3HC
SA184880HC_24hr_1HC
SA184881HC_24hr_3HC
SA184882HC_24hr_2HC
SA184883HC_6hr_2HC
SA184884HC_6hr_1HC
SA184885VLC_12hr_1VLC
SA184886VLC_6hr_3VLC
SA184887VLC_6hr_2VLC
SA184888VLC_12hr_2VLC
SA184889VLC_12hr_3VLC
SA184890VLC_24hr_3VLC
SA184891VLC_24hr_2VLC
SA184892VLC_24hr_1VLC
SA184893VLC_6hr_1VLC
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 EI
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:EI
MS Comments:Mass Hunter
Ion Mode:POSITIVE
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