Summary of Study ST003064
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 PR001910. The data can be accessed directly via it's Project DOI: 10.21228/M8TT6W 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 | ST003064 |
| Study Title | Metabolic responses of Amaranthus caudatus roots and leaves to zinc stress |
| Study Type | GCMS-based untargeted and targeted analysis |
| Study Summary | During the last decades pollution with heavy metals became an important stress factor. Plants are characterized by significant biochemical plasticity and can adjust their metabolism to ensure survival under changing environmental conditions. In the most straightforward way these metabolic shifts can be addressed by the untargeted mass spectrometry-based metabolomics approach. However, so far this methodology was only minimally employed in studies of Zn-induced metabolic shifts in plants. Moreover, the genus Amaranthus is still not addressed in this respect. Therefore, here we propose, to the best of our knowledge, the first gas chromatography-mass spectrometry (GC-MS)-based metabolomics study of Zn2+-induced stress responses in Amaranthus caudatus plants. The GC-MS-based study was performed with root and leaf aqueous methanolic extracts after their lyophylization and sequential derivatization with methoxylamine hydrochloride and N-trimethylsilyl-N-methyl trifluoroacetamide. Thereby, 419 derivatives were detected, of which 144 could be putatively annotated. The metabolic shifts in seven-week old A.caudatus plants in response to a seven-day treatment with 300 µmol/L ZnSO4·7H2O in nutrient solution were organ-specific and more pronounced in roots. The most of the responsive metabolites were up-regulated and dominated with sugars and sugar acids. These effects could be attributed to the involvement of these metabolites in osmoregulation, ROS scavenging and complexation of Zn2+ ions. Galactose was the most Zn2+-responsive root sugar that indicated its possible role in the binding of Zn2+ ions to the root cell walls. A 59-fold up-regulation of gluconic acid in roots clearly indicated its involvement in chelation of Zn2+. A high Zn2+–induced up-regulation of salicylic acid in roots and shoots suggested a key role of this hormone in the activation of Zn2+ stress tolerance mechanisms. Thus, our study provides the first insight in the general trends in Zn-induced biochemical rearrangements and main adaptive metabolic shifts in A. caudatus plants. |
| Institute | K.A. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia |
| Laboratory | Laboratory of Analytical Biochemistry and Biotechnology |
| Last Name | Frolov |
| First Name | Andrej |
| Address | Botanicheskaya st. 35., Moskow, 127276, Russian Federation |
| frolov@ifr.moscow | |
| Phone | +79046097095 |
| Submit Date | 2024-01-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2024-04-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001910 |
| Project DOI: | doi: 10.21228/M8TT6W |
| Project Title: | Metabolic responses of Amaranthus caudatus roots and leaves to zinc stress |
| Project Type: | GCMS-based untargeted and targeted analysis |
| Project Summary: | During the last decades pollution with heavy metals became an important stress factor. Plants are characterized by significant biochemical plasticity and can adjust their metabolism to ensure survival under changing environmental conditions. In the most straightforward way these metabolic shifts can be addressed by the untargeted mass spectrometry-based metabolomics approach. However, so far this methodology was only minimally employed in studies of Zn-induced metabolic shifts in plants. Moreover, the genus Amaranthus is still not addressed in this respect. Therefore, here we propose, to the best of our knowledge, the first gas chromatography-mass spectrometry (GC-MS)-based metabolomics study of Zn2+-induced stress responses in Amaranthus caudatus plants. The GC-MS-based study was performed with root and leaf aqueous methanolic extracts after their lyophylization and sequential derivatization with methoxylamine hydrochloride and N-trimethylsilyl-N-methyl trifluoroacetamide. Thereby, 419 derivatives were detected, of which 144 could be putatively annotated. The metabolic shifts in seven-week old A.caudatus plants in response to a seven-day treatment with 300 µmol/L ZnSO4·7H2O in nutrient solution were organ-specific and more pronounced in roots. The most of the responsive metabolites were up-regulated and dominated with sugars and sugar acids. These effects could be attributed to the involvement of these metabolites in osmoregulation, ROS scavenging and complexation of Zn2+ ions. Galactose was the most Zn2+-responsive root sugar that indicated its possible role in the binding of Zn2+ ions to the root cell walls. A 59-fold up-regulation of gluconic acid in roots clearly indicated its involvement in chelation of Zn2+. A high Zn2+–induced up-regulation of salicylic acid in roots and shoots suggested a key role of this hormone in the activation of Zn2+ stress tolerance mechanisms. Thus, our study provides the first insight in the general trends in Zn-induced biochemical rearrangements and main adaptive metabolic shifts in A. caudatus plants. |
| Institute: | K.A. Timiryazev Institute of Plant Physiology RAS |
| Laboratory: | Laboratory of Analytical Biochemistry and Biotechnology |
| Last Name: | Frolov |
| First Name: | Andrej |
| Address: | Botanicheskaya st. 35., Moskow, 127276, Russian Federation |
| Email: | frolov@ifr.moscow |
| Phone: | +79046097095 |
| Funding Source: | Russian Scientific Foundation (grant # 21-74-30003), Ministry of Science and Higher Education of the Russian Federation (theme # 122042700043-9) |
Subject:
| Subject ID: | SU003179 |
| Subject Type: | Plant |
| Subject Species: | Amaranthus caudatus L. |
| Taxonomy ID: | 3567 |
| Gender: | Not applicable |
Factors:
Subject type: Plant; Subject species: Amaranthus caudatus L. (Factor headings shown in green)
| mb_sample_id | local_sample_id | Plant_organs | Treatment |
|---|---|---|---|
| SA331973 | LM_cont_2 | Mature_leaves | Control |
| SA331974 | LM_cont_1 | Mature_leaves | Control |
| SA331975 | LM_cont_3 | Mature_leaves | Control |
| SA331976 | LM_Zn_3 | Mature_leaves | Zn |
| SA331977 | LM_Zn_2 | Mature_leaves | Zn |
| SA331978 | LM_Zn_1 | Mature_leaves | Zn |
| SA331979 | R_cont_3 | Roots | Control |
| SA331980 | R_cont_2 | Roots | Control |
| SA331981 | R_cont_1 | Roots | Control |
| SA331982 | R_Zn_2 | Roots | Zn |
| SA331983 | R_Zn_1 | Roots | Zn |
| SA331984 | R_Zn_3 | Roots | Zn |
| SA331985 | LY_cont_2 | Young_leaves | Control |
| SA331986 | LY_cont_3 | Young_leaves | Control |
| SA331987 | LY_cont_1 | Young_leaves | Control |
| SA331988 | LY_Zn_2 | Young_leaves | Zn |
| SA331989 | LY_Zn_3 | Young_leaves | Zn |
| SA331990 | LY_Zn_1 | Young_leaves | Zn |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO003172 |
| Collection Summary: | Amaranthus caudatus L., variety Karwa dauta plants were used in the study. After two weeks culturing in the hydroponic system (nutrient solution (in mmol/L) was as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005), the vessels with six-week-old plants (experimental group) were subjected to Zn2+ stress for one week which was accomplished by supplementation of 300 µmol/L ZnSO4·7H2O in the nutrient solution. Control plants remained untreated. Roots, young and mature leaves of seven-week-old Zn-treated and control plants were collected separately. Approximately 10 and 20 mg of ground dry leaf and root material, respectively, were extracted with 1 mL methanol. After vortexing (3000 g, 30 s) and centrifugation (12000 g, 4 °C, 10 min) of the suspensions, the resulted supernatants were collected. The plant material residues were additionally supplemented with 0.1 mL of deionized water. After a following vortex and centrifugation cycle, the obtained supernatants were combined with the first portions. The total extract volume was 1090 μL. Aliquots (30 μL) of the resulted aq. methanolic extracts were freeze-dried under reduced pressure with Labconco CentriVap centrifugal concentrator. The residues were sequentially derivatized with methoxyamine hydrochloride in pyridine, and N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) according to the established procedure (Leonova et al., 2020, http://dx.doi.org/10.3390/ijms21020567) |
| Sample Type: | Plant leaves and roots |
Treatment:
| Treatment ID: | TR003188 |
| Treatment Summary: | Amaranthus caudatus L., variety Karwa dauta plants were used in the study. After two weeks culturing in the hydroponic system (nutrient solution (in mmol/L) was as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005), the vessels with six-week-old plants (experimental group) were subjected to Zn2+ stress for one week which was accomplished by supplementation of 300 µmol/L ZnSO4·7H2O in the nutrient solution. Control plants remained untreated. Roots, young and mature leaves of seven-week-old Zn-treated and control plants were collected separately. |
| Treatment Protocol Comments: | 6 sample groups: LY_cont - young leaves of control plants; LY_Zn - young leaves of Zn-treated plants; LM_cont - mature leaves of control plants; LM_Zn - mature leaves of Zn-treated plants; R_cont - roots of control plants; R_Zn - roots of Zn-treated plants. |
| Treatment: | Heavy metal stress |
| Treatment Compound: | ZnSO4·7H2O |
| Treatment Route: | supplementation in the nutrient solution |
| Treatment Dose: | 300 µmol/L |
| Treatment Doseduration: | 1 week |
| Plant Plot Design: | total 27 plants in nine vessels |
| Plant Light Period: | 16 : 8 day/night regimen |
| Plant Humidity: | 70-75% relative humidity |
| Plant Temp: | day/night temperatures of 24/18° C |
| Plant Watering Regime: | plant were culturing in the hydroponic system |
| Plant Nutritional Regime: | nutrient solution in mmol/L as follows: Ca(NO3)2·4H2O - 3.81; KNO3 - 6.44; MgSO4·7H2O - 0.81; KH2PO4 - 1.83; NH4NO3 - 0.87; Fe-EDTA - 0.09; H3BO3 - 0.047; MnSO4·5H2O - 0.007; ZnSO4·7H2O - 0.0007; CuSO4·5H2O - 0.0008; (NH4)2MoO4 - 0.0005 |
| Plant Growth Stage: | vegetative stage |
Sample Preparation:
| Sampleprep ID: | SP003185 |
| Sampleprep Summary: | Approximately 10 and 20 mg of ground dry leaf and root material, respectively, were extracted with 1 mL methanol. After vortexing (3000 g, 30 s) and centrifugation (12000 g, 4 °C, 10 min) of the suspensions, the resulted supernatants were collected. The plant material residues were additionally supplemented with 0.1 mL of deionized water. After a following vortex and centrifugation cycle, the obtained supernatants were combined with the first portions. The total extract volume was 1090 μL. Aliquots (30 μL) of the resulted aq. methanolic extracts were freeze-dried under reduced pressure with Labconco CentriVap centrifugal concentrator. The residues were sequentially derivatized with methoxyamine hydrochloride in pyridine, and N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) according to the established procedure (Leonova et al., 2020, http://dx.doi.org/10.3390/ijms21020567). |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN005019 | AN005020 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | GC | GC |
| Chromatography system | Shimadzu GC-2010 | Shimadzu GC-2010 |
| Column | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) |
| MS Type | EI | EI |
| MS instrument type | Single quadrupole | Single quadrupole |
| MS instrument name | Shimadzu QP2010 Plus | Shimadzu QP2010 Plus |
| Ion Mode | POSITIVE | POSITIVE |
| Units | peak areas | μmol/g DW |
Chromatography:
| Chromatography ID: | CH003792 |
| Chromatography Summary: | The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201 operating under the instrumental settings summarized in PR_2.pdf |
| Instrument Name: | Shimadzu GC-2010 |
| Column Name: | Phenomenex ZB-5MS (30 m × 0.25 mm, 0.25 μm) |
| Column Temperature: | 1 min at 40°C, ramp 15°C/min to 70°C, 1 min at 70°C, ramp 6°C/min to 320°C, 12 min at 320°C |
| Flow Gradient: | - |
| Flow Rate: | 1 mL/min |
| Injection Temperature: | 250 |
| Sample Injection: | 1μm |
| Solvent A: | - |
| Solvent B: | - |
| Analytical Time: | 5.5-55 min |
| Chromatography Type: | GC |
| Solvent C: | - |
MS:
| MS ID: | MS004758 |
| Analysis ID: | AN005019 |
| Instrument Name: | Shimadzu QP2010 Plus |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | Targeted GC-MS analysis The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201. The GC-MS instrumental settings are summarized in PR_2.pdf. The quality of the acquired chromatograms was assessed by verification of the baseline regularity, background MS noise, the symmetry, width and height of chromatographic peaks. To obtain qualitative information about the Zn-related dynamics of individual metabolites, the chromatograms were processed by AMDIS software (www.amdis.net/) to accomplish deconvolution of mass spectra, peak picking, calculation of Kovach retention indices (RI) and annotation of analytes. The analytes annotated in the experimental samples were quantified by integration of the corresponding extracted ion chromatograms (XIC, m/z ± 0.5 Da) for representative intense signals at specific retention times. This analyte quantification procedure was accomplished with XcaliburTM (version 2.0.7), LCquanTM (version 2.5.6, TermoFisher Scientific Inc., Bremen, Germany) and MSDial (http://prime.psc.riken.jp/compms/msdial/main.html) softwares which perform alignment of chromatograms by retention times of analytes and the integration of analyte peak areas. Metabolite identification and targeted absolute quantitative analysis relied on external standardization with 29 authentic standards (oxalic acid, malonic acid, succinic acid, tartaric acid, malic acid, aconitic acid, citric acid, fumaric acid, benzoic acid, ascorbic acid, erythronic acid, glycerol, arabinose, glucose, galactose, myo-inositol, sucrose, urea, Ala, Trp, Ile, Leu, Asn, Asp, Glu, Pro, Val, Ser, Thr) prepared as a total mix serially diluted in the range from 0.2 pmol/μL to 200 pmol/μL. Among these, only 21 compounds were confirmed in leaves and roots of control and Zn2+-treated A. caudatus plants (Result table). |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 240 |
| Ionization: | EI |
| Ionization Energy: | 70eV |
| MS ID: | MS004759 |
| Analysis ID: | AN005020 |
| Instrument Name: | Shimadzu QP2010 Plus |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | Untargeted GC-MS analysis The samples (1μL) were injected with CTC GC PAL Liquid Injector (Shimadzu Deutschland GmbH, Duisburg, Germany) into GC2010 gas chromatograph coupled online to a quadrupole mass selective detector Shimadzu GCMS QP201 operating under the settings summarized in PR_2.pdf. The quality of the acquired chromatograms was assessed by verification of the baseline regularity, background MS noise, the symmetry, width and height of chromatographic peaks. The chromatograms were processed by AMDIS software (www.amdis.net/) to accomplish deconvolution of mass spectra, peak picking, calculation of Kovach retention indices (RI) and annotation of analytes. The further analysis relied on the untargeted approach, i.e. unbiased TIC-based identification of all signals with the signal to noise ratio (S/N) ≥ 3 and relative quantification via direct comparison of individual analyte abundances, derived as integral areas of corresponding peaks in extracted ion chromatograms built for characteristic signals (XIC, m/z ± 0.5 Da) in EI mass spectra. For this, the trimethylsilyl (TMS) and methyl oxime (MEOX)-TMS derivatives underlying all detected individual chromatographic peaks were annotated by retention indexes (calculated by retention time of C8–C20 alkanes, and EI-MS data - the results of spectral similarity search against available EI-MS spectral libraries such as NIST (https://webbook.nist.gov/chemistry/), GMD (http://gmd.mpimp-golm.mpg.de/), HMDB (https://hmdb.ca/), RIKEN Center for Sustainable Resource Science (http://prime.psc.riken.jp/Metabolomics Software/MS-DIAL/) and in-house spectral library. The quantitation results (i.e. integrated peak areas detected in each sample) were organized into a digital matrix, normalized to the dry weights of the samples, filtered to exclude the features not detected in ≥ 20% of the samples, and processed by statistical methods using the Metaboanalyst 5.0 (https://www.metaboanalyst.ca/). |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 240 |
| Ionization: | EI |
| Ionization Energy: | 70eV |
