SE163:/S1/M1/D1

Sample Set Information

ID	TSE1325
Title	Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis.
Description	Glucosinolates (GSLs) are a group of plant secondary metabolites that have repellent activity against herbivore insects and pathogens, and anti-carcinogenic activity in humans. They are produced in plants of the Brassicaceae and other related families. Biosynthesis of GSLs from precursor amino acids takes place in two subcellular compartments; amino acid biosynthesis and side chain elongation occur mainly in the chloroplast, whereas the following core structure synthesis takes place in the cytosol. Although the genes encoding biosynthetic enzymes of GSLs are well known in Arabidopsis thaliana, the transporter genes responsible for translocation of biosynthetic intermediates between the chloroplast and cytosol are as yet unidentified. In this study, we identified the bile acid:sodium symporter family protein 5 (BASS5) gene in Arabidopsis as a candidate transporter gene involved in methionine-derived GSL (Met-GSL) biosynthesis by means of transcriptome co-expression analysis. Knocking out BASS5 resulted in a decrease of Met-GSLs and concomitant increase of methionine. A transient assay using fluorescence fusion proteins indicated a chloroplastic localization of BASS5. These results supported the idea that BASS5 plays a role in translocation across the chloroplast membranes of the biosynthetic intermediates of Met-GSLs.
Authors	Sawada Y, Toyooka K, Kuwahara A, Sakata A, Nagano M, Saito K, Hirai MY.
Reference	Plant Cell Physiol. 2009 Sep;50(9):1579-86. doi: 10.1093/pcp/pcp110. Epub 2009 Jul 24.
Comment

PubMed

Sample Information

ID	S1
Title	Arabidopsis thaliana
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation	Plant growth conditions Wild-type A. thaliana (accession Colombia-0) and T-DNA insertion lines were grown in a pre-fabricated room-type chamber at 22°C and a 16 h photoperiod on agar-solidified 1/2 MS (Murashige–Skoog) medium containing 1% sucrose for transcriptome and metabolome analyses.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M1
Title	LC-MS
Method Details ID	MS1
Sample Amount	1 μL
Comment

Analytical Method Details Information

ID	MS1
Title	LC-MS (for widely targeted metabolomics)
Instrument	UPLC-TQD system (Waters)
Instrument Type
Ionization	ESI
Ion Mode	positive and negative
Description	Approximately 50–100 mg of the leaves of wild-type and T-DNA insertion lines (bass5-1 and bass5-2) 3 weeks after germination were used for metabolic profiling with ultra performance liquid chromatography (UPLC)-ZQ (Waters) (for GSL and amino acid analyses) and UPLC-TQD (Waters) (for widely targeted metabolomics) as previously described (Sawada et al. 2009a, Sawada et al. 2009b). Met-GSL and tryptophan-derived indole-GSL are the two major GSL classes of Arabidopsis. The sum of the contents of Met-GSL molecular species (methylthioalkyl and methylsulfinylalkyl GSLs with C4–C8 chains) was indicated as Met-GSL content in Fig. 3C. Similarly, the sum of the contents of indole-GSL molecular species (indol-3-ylmethyl, 1-methoxyindol-3- ylmethyl and 4-methoxyindol-3-ylmethyl GSLs) was indicated as indole-GSL content. Analytical conditions for UPLC-TQD are released in the data repository and distribution site DROP Met at our website PRIMe (http://prime.psc.riken.jp/) (Akiyama et al. 2008).
Comment_of_details

PubMed

Data Analysis Information

ID	D1
Title	Data Processing
Data Analysis Details ID	DS1
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS1
Title	Data processing
Description	The metabolites whose accumulation levels changed remarkably (fold change >2 or <0.5, Q-value by the Welch’s t-test <0.1) were identified (Table 1). Q-values were calculated with the ‘qvalue’ package (Storey and Tibshirani 2003) in R (www.r-project.org).
Comment_of_details