Recommendations for Reporting Metabolite Data

Fernie, Alisdair R.; Aharoni, Asaph; Willmitzer, Lothar; Stitt, Mark; Tohge, Takayuki; Kopka, Joachim; Carroll, Adam J.; Saito, Kazuki; Fraser, Paul D.; Deluca, Vincenzo

doi:10.1105/tpc.111.086272

Cited by 287 publications

(230 citation statements)

References 53 publications

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“…Metabolite identification and annotation were performed using metabolite databases [34] and literature survey of H. rhodopensis [35] and Gesneriaceae species [36]. Peak annotation of detected compounds is shown in Supplemental Table 5 with information on ''Recommendations for Reporting Metabolite Data'' described in [37]. The VANTED software was used to generate a metabolic map from the relative metabolic levels [38].…”

Section: Metabolome Analysismentioning

confidence: 99%

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Gechev¹,

Benina²,

Obata

et al. 2012

Cell. Mol. Life Sci.

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167

262

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Section: Metabolome Analysismentioning

confidence: 99%

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Gechev¹,

Benina²,

Obata

et al. 2012

Cell. Mol. Life Sci.

Self Cite

167

262

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“…Peak areas of the mass (m/z) fragments were normalized to the internal standard (ribitol) and fresh weight of the samples. Identification and annotation of detected peaks are shown in Supplemental Table S2 following recent recommendations for reporting metabolite data (Fernie et al, 2011).…”

Section: Metabolite Profiling By Gas Chromatography/time Of Flight-mamentioning

confidence: 99%

Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway

et al. 2016

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Cytosolic monothiol glutaredoxins (GRXs) are required in iron-sulfur (Fe-S) cluster delivery and iron sensing in yeast and mammals. In plants, it is unclear whether they have similar functions. Arabidopsis (Arabidopsis thaliana) has a sole class II cytosolic monothiol GRX encoded by GRXS17. Here, we used tandem affinity purification to establish that Arabidopsis GRXS17 associates with most known cytosolic Fe-S assembly (CIA) components. Similar to mutant plants with defective CIA components, grxs17 loss-of-function mutants showed some degree of hypersensitivity to DNA damage and elevated expression of DNA damage marker genes. We also found that several putative Fe-S client proteins directly bind to GRXS17, such as XANTHINE DEHYDROGENASE1 (XDH1), involved in the purine salvage pathway, and CYTOSOLIC THIOURIDYLASE SUBUNIT1 and CYTOSOLIC THIOURIDYLASE SUBUNIT2, both essential for the 2-thiolation step of 5-methoxycarbonylmethyl-2-thiouridine (mcm 5 s 2 U) modification of tRNAs. Correspondingly, profiling of the grxs17-1 mutant pointed to a perturbed flux through the purine degradation pathway and revealed that it phenocopied mutants in the elongator subunit ELO3, essential for the mcm 5 tRNA modification step, although we did not find XDH1 activity or tRNA thiolation to be markedly reduced in the grxs17-1 mutant. Taken together, our data suggest that plant cytosolic monothiol GRXs associate with the CIA complex, as in other eukaryotes, and contribute to, but are not essential for, the correct functioning of client Fe-S proteins in unchallenged conditions.

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“…At each time point, leaf material was harvested, immediately frozen in liquid nitrogen, and stored at 280°C as recommended by Fernie et al (2011). For metabolite analysis, we used 50 mg of fully expanded rosette leaves from at least five biological replicates (growth stage 5.1 according to Boyes et al [2001]).…”

Section: Metabolite Analysismentioning

confidence: 99%

Serine Acts as a Metabolic Signal for the Transcriptional Control of Photorespiration-Related Genes in Arabidopsis

et al. 2013

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Photosynthetic carbon assimilation including photorespiration is dynamically regulated during the day/night cycle. This includes transcriptional regulation, such as the light induction of corresponding genes, but little is known about the contribution of photorespiratory metabolites to the regulation of gene expression. Here, we examined diurnal changes in the levels of photorespiratory metabolites, of enzymes of the photorespiratory carbon cycle, and of corresponding transcripts in wild-type plants of Arabidopsis (Arabidopsis thaliana) and in a mutant with altered photorespiratory flux due to the absence of the peroxisomal enzyme Hydroxypyruvate Reductase1 (HPR1). Metabolomics of the wild type showed that the relative amounts of most metabolites involved in photorespiration increased after the onset of light, exhibited maxima at the end of the day, and decreased during the night. In accordance with those findings, both the amounts of messenger RNAs encoding photorespiratory enzymes and the respective protein contents showed a comparable accumulation pattern. Deletion of HPR1 did not significantly alter most of the metabolite patterns relative to wild-type plants; only serine accumulated to a constitutively elevated amount in this mutant. In contrast, the hpr1 mutation resulted in considerable deregulation of the transcription of photorespiration-related genes. This transcriptional deregulation could also be induced by the external application of L-serine but not glycine to the Arabidopsis wild type, suggesting that serine acts as a metabolic signal for the transcriptional regulation of photorespiration, particularly in the glycine-to-serine interconversion reactions.

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Recommendations for Reporting Metabolite Data

Cited by 287 publications

References 53 publications

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway

Serine Acts as a Metabolic Signal for the Transcriptional Control of Photorespiration-Related Genes in Arabidopsis

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