SE138:/S1/M1

Sample Set Information

ID	TSE1239
Title	Effects of molybdenum deficiency and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolism in Arabidopsis thaliana.
Description	Molybdenum (Mo) is a micronutrient essential for plant growth, as several key enzymes of plant metabolic pathways contain Mo cofactor in their catalytic centres. Mo-containing oxidoreductases include nitrate reductase, sulphite oxidase, xanthine dehydrogenase, and aldehyde oxidase. These are involved in nitrate assimilation, sulphite detoxification, purine metabolism or the synthesis of abscisic acid, auxin and glucosinolates in plants. To understand the effects of Mo deficiency and a mutation in a molybdate transporter, MOT1, on nitrogen and sulphur metabolism in Arabidopsis thaliana, transcript and metabolite profiling of the mutant lacking MOT1 was conducted in the presence or absence of Mo. Transcriptome analysis revealed that Mo deficiency had impacts on genes involved in metabolisms, transport, stress responses, and signal transductions. The transcript level of a nitrate reductase NR1 was highly induced under Mo deficiency in mot1-1. The metabolite profiles were analysed further by using gas chromatography time-of-flight mass spectrometry, capillary electrophoresis time-of-flight mass spectrometry, and ultra high performance liquid chromatography. The levels of amino acids, sugars, organic acids, and purine metabolites were altered significantly in the Mo-deficient plants. These results are the first investigation of the global effect of Mo nutrition and MOT1 on plant gene expressions and metabolism.
Authors	Ide Y, Kusano M, Oikawa A, Fukushima A, Tomatsu H, Saito K, Hirai MY, Fujiwara T.
Reference	J Exp Bot. 2011 Feb;62(4):1483-97. doi: 10.1093/jxb/erq345. Epub 2010 Dec 3.
Comment

PubMed

Sample Information

ID	S1
Title	Arabidopsis thaliana seeds
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation	Arabidopsis thaliana wild-type, ecotype Col-0 (referred to hereafter as WT) and a T-DNA inserted mutant, mot1-1 (Tomatsu et al., 2007) were grown in Mo-deficient hydroponic solutions and the seeds from the Mo-deficient plants were used in this study. Seeds were surface-sterilized in 15% bleach for 10 min, washed five times with distilled water, and placed at 4 °C for 4 d. MGRL solutions (Fujiwara et al., 1992) were prepared without Mo (−Mo), and the Mo solution was added to 170 nM for the control (+Mo) media as described previously (Tomatsu et al., 2007). The media contain 7 mM nitrate and 1.5 mM sulphate. For the preparation of solid media, 1% sucrose and 1.2% gellan gum (Wako, Osaka, Japan) were added before autoclaving. Plants were grown for 18 d on the solid media at 22 °C under a 16/8 h light/dark cycle in the growth chambers (NK system LPH-220S, Nihon-ika Co., Ltd., Osaka, Japan) and harvested about 10 h after the beginning of the light period.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M1
Title	Targeted analysis of metabolites
Method Details ID	MS1
Sample Amount	2 μL
Comment

Analytical Method Details Information

ID	MS1
Title	Targeted analysis of metabolites
Instrument	CE:Agilent G1607A MS:Agilent G3250AA LC / MSD TOF,Agilent G1603A CE-TOF
Instrument Type
Ionization	ESI
Ion Mode
Description	For the measurement of the inorganic ion concentrations, whole shoots were harvested and frozen in liquid nitrogen before extraction. Frozen tissues (approximately 50 mg fresh weight) were homogenized in ten times volumes of 80% ethanol using the mixer mill MM300 (Retsch, Haan, Germany) and zirconia beads, and vacuum-evaporated at 38 °C to dryness. The dried samples were reconstituted in ten times volumes of milli-Q water (Millipore, Billerica, MA), vortexed for 10 min, and ultrafiltrated through a 0.22 μm pore filter (Millipore, Billerica, MA). The filtrates were diluted 10-fold in milli-Q water and the ion concentrations were determined using a Hewlett-Packard HP 3D capillary electrophoresis photodiode array detection system and an inorganic anion analysis kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's protocol. Four biological replicates for each treatment were used for analysis. For the measurement of the amino acid concentrations, whole shoots were dried in the same way as for the analysis of inorganic ions, then reconstituted in four times volumes of 10 mM HCl, vortexed for 10 min, and ultrafiltrated through a 0.22 μm pore filter (Millipore, Billerica, MA). The filtrates were immediately used for the reaction with an AccQ-Fluor reagent kit (Waters, Milford, MA). Ten μl of the filtrate was mixed with 10 μl of AccQ-Fluor borate buffer, and 5 μl of AccQ-Fluor reagent solution was added, then vortexed immediately for 10 s. The mixture was incubated at 55 °C for 10 min, and centrifuged at 14 000 g at 4 °C for 5 min. The supernatants were placed into glass vials and 2 μl of the sample was applied to the ACQUITY UPLC system (Waters, Milford, MA) and separated on ACQUITY UPLC BEH C18 column (φ 2.1×50 mm). Solvent A (0.2% acetic acid, 0.1% dibutylamine, pH 5.02 with NH4OH) and solvent B (55% acetonitrile) were used for elution at 0.5 ml min−1 at 40 °C and metabolites were detected by an ACQUITY UPLC tunable UV detector at 250 nm. The gradient program was as follows: 100–96.0% solvent A (0–0.1 min, curve 6), 96.0–92.5% solvent A (0.1–2.0 min, curve 6), 92.5–60.0% solvent A (2.0–7.5 min, curve 7), 60.0–40.0% solvent A (7.5–8.0 min, curve 6), 40.0% solvent A (8.0–9.5 min), 40.0–100% solvent A (9.5–9.6 min, curve 6), 100% solvent A (9.6–10 min). The remaining portion of solvent A was solvent B. For standards, the amino acid mixture standard solution, type H (Wako, Osaka, Japan) was diluted and the standard solution for Gln, Asn, Trp, O-acetylserine (OAS), and homoserine were prepared separately before use. The chromatography data were analysed using Empower software (Waters, Milford, MA). Eight biological replicates for each treatment were used for analysis. Metabolites were also analysed by capillary electrophoresis time-of-flight mass spectrometry (CE-TOF/MS) as described previously (Watanabe et al., 2008). In each analysis, 10 biological replicates were used.
Comment_of_details	Watanabe et al., 2008 Plant Physiol.Jan;146(1):310-20.

PubMed