Metabolomics and hormonomics to crack the code of filbert growth

Erland, Lauren A. E.; Turi, Christina E.; Saxena, Praveen K.; Murch, Susan J.

doi:10.1007/s11306-020-01684-0

Cited by 11 publications

(21 citation statements)

References 75 publications

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“…Significant features were putatively identified in Excel and matched by monoisotopic mass in FooDB (±0.02 Da) [ 46 ]. Those which did not yield a plausible match were transformed through the loss of one (−220.041882) or two (2 × −220.041882) TDZ molecules to identify potential conjugates.…”

Section: Methodsmentioning

confidence: 99%

“…The results from pairwise t-tests and volcano analysis along with pattern searching were input in Peaks to Pathways (ranked by p -value for volcano analysis, formatted as three column m.z, p -value, t.score for all other results), with mass accuracy (ppm) of 5, in positive mode and subjected to Mummichog ( p -value cut off set to top 10 percent of peaks) and gene set enrichment analysis (GSEA) pathway analysis, with mapping to known Arabidopsis thaliana KEGG metabolic pathways (v. October 2019), using standard settings for adducts and currency metabolites [ 46 ]. Data were compared to known carbon metabolism pathways (KEGG v 2019) by matching to monoisotopic mass (±0.02 Da).…”

Section: Methodsmentioning

confidence: 99%

“…A hormonomics analysis was also performed by mining the monoisotopic mass for phytohormones and their related metabolites within the dataset (±0.02 Da) [ 46 ]. The query metabolites are summarized in Supplementary Table S2 .…”

Section: Methodsmentioning

confidence: 99%

“…Significant features identified through MetaboAnalyst analysis and features predicted through biotransformations or logical algorithms were uploaded into FooDB (M + H, v1.0, foodb.ca, ±0.02) and ChemSpider (M ± 0.001 Da) for putative identification. All identifications are putative and are based on m / z [ 36 , 39 , 41 , 42 , 46 ]. In all cases where a feature was detected in multiple modes the relative peak intensities were summed prior to plotting.…”

Section: Methodsmentioning

confidence: 99%

“…Pairwise analysis between control and high TDZ and control and low TDZ were additionally performed in MetaboAnalyst by t-test, volcano analysis, significant analysis of microarray (SAM) analysis and empirical Bayes analysis of microarrays (EBAM) to identify possible important features in specific morphogenetic responses (organogenesis at low TDZ and embryogenesis at high TDZ) [43,44,46,47 [37,[47][48][49]. The monoisotopic mass for each biotransformation (±0.02 Da) was mined within our dataset in order to identify potential anabolic or metabolic products.…”

Section: Detection Of Significant Ions and Linear Trendsmentioning

confidence: 99%

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The Morphoregulatory Role of Thidiazuron: Metabolomics-Guided Hypothesis Generation for Mechanisms of Activity

et al. 2020

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Thidiazuron (TDZ) is a diphenylurea synthetic herbicide and plant growth regulator used to defoliate cotton crops and to induce regeneration of recalcitrant species in plant tissue culture. In vitro cultures of African violet thin petiole sections are an ideal model system for studies of TDZ-induced morphogenesis. TDZ induces de novo shoot organogenesis at low concentrations and somatic embryogenesis at higher concentrations of exposure. We used an untargeted metabolomics approach to identify metabolites in control and TDZ-treated tissues. Statistical analysis including metabolite clustering, pattern and pathway tools, logical algorithms, synthetic biotransformations and hormonomics identified TDZ-induced changes in metabolism. A total of 18,602 putative metabolites with extracted masses and predicted formulae were identified with 1412 features that were found only in TDZ-treated tissues and 312 that increased in response to TDZ. The monomer of TDZ was not detected intact in the tissues but putative oligomers were found in the database and we hypothesize that these may form by a Diels–Alder reaction. Accumulation oligomers in the tissue may act as a reservoir, slowly releasing the active TDZ monomer over time. Cleavage of the amide bridge released TDZ-metabolites into the tissues including organic nitrogen and sulfur containing compounds. Metabolomics data analysis generated six novel hypotheses that can be summarized as an overall increase in uptake of sugars from the culture media, increase in primary metabolism, redirection of terpene metabolism and mediation of stress metabolism via indoleamine and phenylpropanoid metabolism. Further research into the specific mechanisms hypothesized is likely to unravel the mode of action of TDZ and to provide new insights into the control of plant morphogenesis.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%