Time‐series integrated “omic” analyses to elucidate short‐term stress‐induced responses in plant liquid cultures

Abstract

The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures. The latter were selected as the model system for this type of analysis, because they provide a well-controlled growth environment, ensuring that the observed plant response is due only to the applied perturbation. An enhanced gas chromatography–mass spectrometry (GC– MS) metabolomic data correction strategy and a new algorithm for the significance analysis of time-series “omic” data are used to extract information about the plant's transcriptional and metabolic response to the applied stress from the acquired datasets; in this article, it is the first time that these are applied for the analysis of a large biological dataset from a complex eukaryotic system. The case-study involved Arabidopsis thaliana liquid cultures subjected for 30 h to elevated (1%) CO2 stress. The advantages and validity of the methodological framework are discussed in the context of the known A. thaliana or plant, in general, physiology under the particular stress. Of note, the ability of the methodology to capture dynamic aspects of the observed molecular response allowed for 9 and 24 h of treatment to be indicated as corresponding to shifts in both the transcriptional and metabolic activity; analysis of the pathways through which these activity changes are manifested provides insight to regulatory processes.

Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases

“…Rapid (,1 h) transient changes in organic acid contents in Arabidopsis seedlings in response to CO 2 levels have also been reported, further showing that such dynamic responses in the metabolome are possible (Dutta et al, 2009). Recent metabolic studies have suggested a role for dicarboxylates in rapid respiratory responses to Pi starvation, and DICs are indeed induced within 1 h of transfer of plants to Pi depleted medium (Lin et al, 2011;Alexova et al, 2015).…”

Dielectric barrier discharge plasma used as a means for the remediation of soils contaminated by non-aqueous phase liquids

“…Dichloromethane (DCM, Sigma Aldrich) was used as extraction solvent, whereas the methods used for the extraction and chemical analysis of residual NAPL in soil by GC-FID and ATR-FTIR have been described in detail elsewhere [34]. For the high-throughput organic molecule profiling of the extracts by GC-MS, 1 lL of soil extract dissolved in dichloromethane was injected into a Saturn 2000 gas chromatograph-(ion trap) mass spectrometer (formerly Varian Inc, currently Bruker/ Agilent) and measured following the same method used for the polar metabolite profiling described elsewhere at 1:40 split ratio [36][37][38]. The derivatization of 100 lL soil extract dissolved in dichloromethane after its drying in a vacuum centrifuge was carried out in two steps, with 50 lL of 20 mg/mL methoxyamine hydrochloride in pyridine and 100 lL of N-methyl-trimethylsilyltrifluoroacetamide (MSTFA), as described in [36].…”

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants

“…The gas chromatography-mass spectrometry metabolic profile acquisition of the control and ABA-treated leaves was carried out after appropriate adaptation of previously published protocol (Dutta et al, 2009;Kanani et al, 2010). The metabolic profile of each physiological state/time point was estimated from the mean profile of two separate leaves harvested at the particular state, and the profile of each leaf was measured at least three times.…”