Modified method for determination of sulfur metabolites in plant tissues by stable isotope dilution-based liquid chromatography–electrospray ionization–tandem mass spectrometry

Chang, Yu‐Ling; Hsieh, Chin‐Lin; Huang, Yao‐Moan; Chiou, Wen‐Liang; Kuo, Yueh‐Hsiung; Tseng, Mei‐Hui

doi:10.1016/j.ab.2013.07.026

Cited by 10 publications

(4 citation statements)

References 67 publications

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“…Since we have repeatedly encountered inconsistent results with these techniques we turned to the use of an internal standard (IS). Although single nucleoside species have been used as general IS for all modifications in a given sample ( 19 , 25 ), we maintain that accurate response factors can only derive from isotopomers for each specific modification ( 26 ), obtained by stable isotope labeling (SIL) ( 27 – 29 ). The Carell laboratory has recently published impressive quantification results ( 30 , 31 ) based on a series of isotope-labeled internal standards obtained by means of synthetic organic chemistry.…”

Section: Introductionmentioning

confidence: 99%

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

Kellner

Ochel

Thüring

et al. 2014

Nucleic Acids Research

120

105

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In the resurging field of RNA modifications, quantification is a bottleneck blocking many exciting avenues. With currently over 150 known nucleoside alterations, detection and quantification methods must encompass multiple modifications for a comprehensive profile. LC–MS/MS approaches offer a perspective for comprehensive parallel quantification of all the various modifications found in total RNA of a given organism. By feeding 13C-glucose as sole carbon source, we have generated a stable isotope-labeled internal standard (SIL-IS) for bacterial RNA, which facilitates relative comparison of all modifications. While conventional SIL-IS approaches require the chemical synthesis of single modifications in weighable quantities, this SIL-IS consists of a nucleoside mixture covering all detectable RNA modifications of Escherichia coli, yet in small and initially unknown quantities. For absolute in addition to relative quantification, those quantities were determined by a combination of external calibration and sample spiking of the biosynthetic SIL-IS. For each nucleoside, we thus obtained a very robust relative response factor, which permits direct conversion of the MS signal to absolute amounts of substance. The application of the validated SIL-IS allowed highly precise quantification with standard deviations <2% during a 12-week period, and a linear dynamic range that was extended by two orders of magnitude.

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Section: Introductionmentioning

confidence: 99%

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

Kellner

Ochel

Thüring

et al. 2014

Nucleic Acids Research

120

105

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“…Perchloric acid was used to protect metabolites from enzymatic degradation [ 41 ], and to avoid sulfur metabolites oxidation and degradation [ 14 , 42 , 43 ] under basic and neutral condition. Formic acid was used for enhancing electrospray ionization.…”

Section: Methodsmentioning

confidence: 99%

Simultaneous untargeted and targeted metabolomics profiling of underivatized primary metabolites in sulfur-deficient barley by ultra-high performance liquid chromatography-quadrupole/time-of-flight mass spectrometry

Ghosson

Schwarzenberg²,

Jamois³

et al. 2018

Plant Methods

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BackgroundMetabolomics based on mass spectrometry analysis are increasingly applied in diverse scientific domains, notably agronomy and plant biology, in order to understand plants’ behaviors under different stress conditions. In fact, these stress conditions are able to disrupt many biosynthetic pathways that include mainly primary metabolites. Profiling and quantifying primary metabolites remain a challenging task because they are poorly retained in reverse phase columns, due to their high polarity and acid–base properties. The aim of this work is to develop a simultaneous untargeted/targeted profiling of amino acids, organic acids, sulfur metabolites, and other several metabolites. This method will be applied on sulfur depleted barley, in order to study this type of stress, which is difficult to detect at early stage. Also, this method aims to explore the impact of this stress on barley’s metabolome.ResultsUltra-high performance liquid chromatography–high resolution mass spectrometry-based method was successfully applied to real samples allowing to discriminate, detect, and quantify primary metabolites in short-runs without any additional sampling step such as derivatization or ion pairing. The retention of polar metabolites was successfully achieved using modified C18 columns with high reproducibility (relative standard deviation below 10%). The quantification method showed a high sensitivity and robustness. Furthermore, high resolution mass spectrometry detection provided reliable quantification based on exact mass, eliminating potential interferences, and allowing the simultaneous untargeted metabolomics analysis. The untargeted data analysis was conducted using Progenesis QI software, performing alignment, peak picking, normalization and multivariate analysis. The simultaneous analysis provided cumulative information allowing to discriminate between two plant batches. Thus, discriminant biomarkers were identified and validated. Simultaneously, quantification confirmed coherently the relative abundance of these biomarkers.ConclusionsA fast and innovated simultaneous untargeted/targeted method has successfully been developed and applied to sulfur deficiency on barley. This work opens interesting perspectives in both fundamental and applied research. Biomarker discovery give precious indication to understand plant behavior during a nutritional deficiency. Thus, direct or indirect measurement of these compounds allows a real time fertilization management and encounter the challenges of sustainable agriculture.Electronic supplementary materialThe online version of this article (10.1186/s13007-018-0329-0) contains supplementary material, which is available to authorized users.

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“…For determination of the sulfur metabolites, plant tissue was freeze-dried at À60 C for 48-72 h. Freeze-dried plant tissues were ground to powder with liquid nitrogen in a mortar with pestle. The sulfur metabolites were extracted as described in (Chang et al 2013). For isotope dilution mass spectrometry analysis, the 34 S-labeled Arabidopsis thaliana tissue were extracted and added to the calibration standards, QC samples, and plant samples in a fixed ratio (Chang et al 2013).…”

Section: -S -S/+s -S/cysmentioning

confidence: 99%

“…The sulfur metabolites were extracted as described in (Chang et al 2013). For isotope dilution mass spectrometry analysis, the 34 S-labeled Arabidopsis thaliana tissue were extracted and added to the calibration standards, QC samples, and plant samples in a fixed ratio (Chang et al 2013). Chromatographic separations of sulfur metabolites were performed on a Thermo Accela LC system using a Thermo Scientific Hypersil Gold aQ C18 (1.9 μm, 2.1 mm Â 10 cm).…”

Section: -S -S/+s -S/cysmentioning

confidence: 99%

The Sulfur Pathway and Diagnosis of Sulfate Depletion in Grapevine

Tavares

Amâncio

2017

Proceedings of the International Plant Sulfur Workshop

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Sulfur is an essential nutrient to all plant species. Plants assimilate sulfur in a well-described pathway, which has been taken up by roots. Regulatory mechanism has been the subject of many research papers. However, recent studies highlighted differences between crop plants and the model plant Arabidopsis thaliana. Our work focuses on the identification of genes involved in the sulfur metabolism in the Vitis vinifera genome, and their response to sulfur deficiency and other abiotic stress endured by grapevine in the field, namely water stress. Here, we describe the identification and brief characterization of the first assimilation enzymes involved in the sulfur pathway, the enzyme responsible for sulfur activation, ATP sulfurylase (ATPS), and the two enzymes that reduce sulfate to sulfide, Adenosine 5 0-phosphosulate reductase (APR) and Sulfite reductase (SiR). A reduction was observed in the number of ATPS and APR isoforms identified in V. vinifera genome when compared to A. thaliana or Glycine max genomes. Two ATPS isoforms were present in the Vitis genome, of which only ATPS1 transcript was detected in the tested tissues, and one APR isoform, suggesting an absence of redundancy in the role of both enzymes. ATPS1, APR and SiR transcript level was up-regulated in response to 2 days exposure to sulfur deficiency in V. vinifera cell cultures, which was completely reversed by the addition of GSH to the culture medium. Apparently, oxidative stress triggered GSH has a pivotal role in the regulation of ATPS1, APR and SiR transcription level, since their up-regulation was observed in mRNA from field grapevine berries under water stress, which is known to induce oxidative stress. Grapevine (Vitis vinifera L.) is one of the most important crops worldwide for winemaking and also for table grapes. Grapevines can be successfully grown in a range of different climates and management conditions. Global climate changes are associated with water deficit and high evapotranspiration rates that can affect berry development, yield, and wine quality (Hannah et al. 2013).

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Modified method for determination of sulfur metabolites in plant tissues by stable isotope dilution-based liquid chromatography–electrospray ionization–tandem mass spectrometry

Cited by 10 publications

References 67 publications

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

Simultaneous untargeted and targeted metabolomics profiling of underivatized primary metabolites in sulfur-deficient barley by ultra-high performance liquid chromatography-quadrupole/time-of-flight mass spectrometry

The Sulfur Pathway and Diagnosis of Sulfate Depletion in Grapevine

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