| Project ID | IMP_100029 |
| Title | Proteomics to Unveil Orchestration of Photorespiration and Central Carbon Pathway in Microchloropsis gaditana NIES 2587 |
| Uploaded by | Pannaga Pavan |
| Research Area | Biological Sciences |
| Funding Source | Department of Biotechnology (DBT) |
| Contributors | Pannaga Pavan Jutur |
| Description | 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. |
| Study ID | IMS_100023 |
| Title | Integration of Metabolomics and Proteomics to Unveil Orchestration of Photorespiration and Central Carbon Pathway in Microchloropsis gaditana NIES 2587 |
| Uploaded by | Pannaga Pavan |
| Study Type | Mass Spectrometry (MS) |
| Data Type | Untargeted |
| Release Date | March 21, 2025 |
| IEC/IBSC No. | |
| Publication | |
| 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. |
| # | Sample ID | Sample Name | Organism | Source | Sample Type | Experimental Condition | Gender | Age | Replicates | Storage | Files/Sample |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IMSM_101080 | HC_12hr_1 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 2 | IMSM_101081 | HC_12hr_2 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 3 | IMSM_101082 | HC_12hr_3 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 4 | IMSM_101083 | HC_24hr_1 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 5 | IMSM_101084 | HC_24hr_2 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 6 | IMSM_101085 | HC_24hr_3 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 7 | IMSM_101086 | HC_6hr_1 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 8 | IMSM_101087 | HC_6hr_2 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 9 | IMSM_101088 | HC_6hr_3 | Microchloropsis | Algae | Algae | high CO2 (30,000 ppm) | NA | NA | NA | NA | |
| 10 | IMSM_101089 | VLC_12hr_1 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 11 | IMSM_101090 | VLC_12hr_2 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 12 | IMSM_101091 | VLC_12hr_3 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 13 | IMSM_101092 | VLC_24hr_1 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 14 | IMSM_101093 | VLC_24hr_2 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 15 | IMSM_101094 | VLC_24hr_3 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 16 | IMSM_101095 | VLC_6hr_1 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 17 | IMSM_101096 | VLC_6hr_2 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA | |
| 18 | IMSM_101097 | VLC_6hr_3 | Microchloropsis | Algae | Algae | very-low CO2 (300 ppm) | NA | NA | NA | NA |
| # | MS Exp ID | Sample Name / ID | MS Type | Instrument Name | Instrument Type | Ionization Method | Ion Mode | Software Used |
|---|---|---|---|---|---|---|---|---|
| 1 | IME_100554 | HC_12hr_1 / IMSM_101080 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 2 | IME_100555 | HC_12hr_2 / IMSM_101081 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 3 | IME_100556 | HC_12hr_3 / IMSM_101082 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 4 | IME_100557 | HC_24hr_1 / IMSM_101083 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 5 | IME_100558 | HC_24hr_2 / IMSM_101084 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 6 | IME_100559 | HC_24hr_3 / IMSM_101085 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 7 | IME_100560 | HC_6hr_1 / IMSM_101086 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 8 | IME_100561 | HC_6hr_2 / IMSM_101087 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 9 | IME_100562 | HC_6hr_3 / IMSM_101088 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 10 | IME_100563 | VLC_12hr_1 / IMSM_101089 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 11 | IME_100564 | VLC_12hr_2 / IMSM_101090 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 12 | IME_100565 | VLC_12hr_3 / IMSM_101091 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 13 | IME_100566 | VLC_24hr_1 / IMSM_101092 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 14 | IME_100567 | VLC_24hr_2 / IMSM_101093 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 15 | IME_100568 | VLC_24hr_3 / IMSM_101094 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 16 | IME_100569 | VLC_6hr_1 / IMSM_101095 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 17 | IME_100570 | VLC_6hr_2 / IMSM_101096 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| 18 | IME_100571 | VLC_6hr_3 / IMSM_101097 | GCMS (Gas Chromatography -Mass Spectrometry) | Agilent 7890A | Triple quadrupole | Electron Ionization - EI | Positive | NA |
| # | First Name | Last Name | Organization | Designation | |
|---|---|---|---|---|---|
| 1 | Pannaga Pavan | Jutur | jppavan@icgeb.res.in | International Centre for Genetic Engineering and Biotechnology, New Delhi | principal_investigator |
| # | FTP Run ID | MS Exp ID | MS Data File |
|---|---|---|---|
| 1 | IMR_101153 | IME_100554 | HC_12hr_1.mzdata.xml |
| 2 | IMR_101154 | IME_100555 | HC_12hr_2.mzdata.xml |
| 3 | IMR_101155 | IME_100556 | HC_12hr_3.mzdata.xml |
| 4 | IMR_101156 | IME_100557 | HC_24hr_1.mzdata.xml |
| 5 | IMR_101157 | IME_100558 | HC_24hr_2.mzdata.xml |
| 6 | IMR_101158 | IME_100559 | HC_24hr_3.mzdata.xml |
| 7 | IMR_101159 | IME_100560 | HC_6hr_1.mzdata.xml |
| 8 | IMR_101160 | IME_100561 | HC_6hr_2.mzdata.xml |
| 9 | IMR_101161 | IME_100562 | HC_6hr_3.mzdata.xml |
| 10 | IMR_101162 | IME_100563 | VLC_12hr_1.mzdata.xml |
| 11 | IMR_101163 | IME_100564 | VLC_12hr_2.mzdata.xml |
| 12 | IMR_101164 | IME_100565 | VLC_12hr_3.mzdata.xml |
| 13 | IMR_101165 | IME_100566 | VLC_24hr_1.mzdata.xml |
| 14 | IMR_101166 | IME_100567 | VLC_24hr_2.mzdata.xml |
| 15 | IMR_101167 | IME_100568 | VLC_24hr_3.mzdata.xml |
| 16 | IMR_101168 | IME_100569 | VLC_6hr_1.mzdata.xml |
| 17 | IMR_101169 | IME_100570 | VLC_6hr_2.mzdata.xml |
| 18 | IMR_101170 | IME_100571 | VLC_6hr_3.mzdata.xml |