Figure S1. Principal component analysis of metabolite profiles of Arabidopsis seedlings grown under different conditions. Sample distribution across 1st and 2nd principal components (A) and 1st and 3rd principal components (B) is presented. Variance explained by each component is indicated on the plot in percentages.

Figure S2. Changes in N-compounds content of in vitro-grown Arabidopsis seedlings samples in response to different media and GABA treatment. Relative content (Y axis) is given according to normalization by fresh weight and ribitol. Data are mean (n=4) ± SD.

Figure S3. Changes in C-compounds content of in vitro-grown Arabidopsis seedlings samples in response to different media and GABA treatment. Relative content (Y axis) is given according to normalization by fresh weight and ribitol. Data are mean (n=4) ± SD.

Table S1. Eigenvectors values (in descending order) of metabolites were calculated by PCA algorithm for 1st and 3rd components.  

Metabolite 1st PC Metabolite 3rd PC Glutamine 3.2 Alanine 4.9 Ornithine 2.4 Glycerol 2.9 Arginine 2.0 GABA 2.5 Asparagine 1.9 Tyrosine 2.4 Glycine 1.5 Proline 1.4 Kestose 1.4 Maltose 1.3 Raffinose 1.4 Phenylalanine 1.1 Succinate 1.1 Glutamine 1.1 Citrate 1.1 beta-Alanine 1.1 Lactate 1.0 Ornithine 1.1

Table S2A. Results of Student's t-test performed with tMEV software. The differences in a relative content of each metabolite were compared and checked for significance between FN media and low C and, separately, between FN media and low N. Values of metabolites shown in the table are significantly different at P=0.05.

FN vs C(-) t value FN vs N(-) t value Alanine 20.6 Alanine 41.6 beta-Alanine 4.3 beta-Alanine 5.8 Arginine 2.8 Arginine 53.1 Aspartate 3.4 Asparagine 35.3 Lysine 4.0 Aspartate 9.3 Serine 7.8 Glutamate 18.3 Methionine 5.0 Glutamine 62.8 Ornithine 12.2 Glycine 25.4 Proline 4.3 Lysine 4.1 Tyrosine 8.5 Serine 7.3 Phenilalanine 4.8 Threonine 4.8 GABA 11.9 Methionine 5.0 Spermine 4.1 Ornithine 23.2 Malate 16.2 Proline 6.8 Fumarate 9.6 Tyrosine 6.1 Citrate 28.5 Phenilalanine 4.8 Glycerate 14.0 GABA 10.8 Succinate 39.1 Malate 4.6 Lactate 16.3 Glycerate 18.1 Shikimate 9.4 Succinate 4.3 Sucrose 4.7 Vitamin C 4.7 Maltose 16.8 Nicotinate 3.8 Raffinose 18.0 Sucrose 3.7 Melibiose 6.8 Raffinose 2.9 Fructose 14.7 Rhamnose 10.5 Turanose 4.0 Turanose 2.9 Palatinose 6.8 Kestose 2.7 Kestose 18.6 Xylose 7.0 Glucose 19.2 Glycerol 12.6 Glucose-6-phosphate 10.1 Hexacosanoic acid 5.5 Xylose 2.7

Glycerol 12.0

Table S2B. Results of one-way ANOVA performed with tMEV software. GABA concentration was used as a condition for analysis. Values of metabolites shown in the table are significantly different at P=0.05 with Bonferroni correction.

FN medium F value C (-) medium F value N (-) medium F value Alanine 25.2 Alanine 56.1 Alanine 40.3 Arginine 98.3 Arginine 17.8 Arginine 31.1 Asparagine 65.4 Asparagine 74.7 Sucrose 16.8 Glutamine 86.0 Glutamine 36.8 Rhamnose 20.7 Maltose 34.5 Ornithine 32.8 Fructose 21.6

Proline 22.1

Tyrosine 21.1

Phenylalanine 24.7

GABA 28.5

Malate 62.0

Citrate 48.0

Maltose 39.7

Glycerol 825.0

Inositol 28.0

Table S3. Functional annotation and enrichment analysis according to DAVID on-line tool and database of genes up- and down-regulated under low C supplemented with 1 mM GABA compared to those under low C only.

Up-regulation

Cluster # (enrichment score) Biological process Genes p value

I (3.01)

response to abiotic stimulus 11 0.000013 response to light stimulus 6 0.001 response to radiation 6 0.0012 response to temperature stimulus 5 0.0029 response to heat 3 0.02

II (2.02)

response to inorganic substance 7 0.00024 response to hydrogen peroxide 3 0.017 response to reactive oxygen species 3 0.024 response to oxidative stress 3 0.086

Down-regulation

I (4.16)

cellular glucan metabolic process 6 0.000008 glucan metabolic process 6 0.000022 cellular polysaccharide metabolism 6 0.000024 polysaccharide metabolic process 6 0.00013 cell wall organization 6 0.00038

II (2.61)

external encapsulating structure 6 0.00049 methane metabolism 5 0.00044 cellular response to hydrogen peroxide 4 0.00094 hydrogen peroxide catabolic process 4 0.00094 hydrogen peroxide metabolic process 4 0.001 phenylpropanoid biosynthesis 5 0.0012 cellular response to reactive oxygen 4 0.0013 cellular response to oxidative stress 4 0.0013 oxygen metabolic process 4 0.0019 response to hydrogen peroxide 4 0.0024 cellular response to stress 6 0.0026 response to reactive oxygen species 4 0.0039 response to oxidative stress 5 0.004 phenylalanine metabolism 4 0.0059 biosynthesis of phenylpropanoids 5 0.026 response to inorganic substance 5 0.033

Table S4. Functional annotation according to DAVID on-line tool and database of genes up- and down-regulated under low C supplemented with 1 mM GABA compared to those under low C only.

Up-regulation

ID Gene Name 264436_at AT1G10370 263260_at AT1G10570 260668_at AT1G19530 255883_at AT1G20270 263216_s_at AT1G30720 261615_at AT1G33050 263150_at AT1G54050 265536_at AT2G15880 267024_s_at AT2G29870 266965_at AT2G39510 267383_at AT2G44360 258879_at AT3G03270 257844_at AT3G28480 245226_at AT3G29970 252746_at AT3G43190 252364_at AT3G48450 254232_at AT4G23600 251026_at AT5G02200 250680_at AT5G06570 250464_at AT5G10040 247851_at AT5G58070 260869_at Acyl-[acyl-carrier protein]-desaturase 264953_at Alcohol dehydrogenase class-P 245951_at Aspartate aminotransferase 256243_at Basic endochitinase B 250781_at Dehydration-responsive element-binding protein 2A 245173_at Ethylene-responsive transcription factor ERF071 261266_at Expansin-A10 255625_at G-box-binding factor 2 253887_at Oligopeptide transporter 6 255111_at Peroxidase 38 261191_at Probable granule-bound starch synthase 1, chloroplastic 253616_at Putative EG45-like domain containing protein 1 255806_at Putative fructokinase-5 253264_at Serine/threonine-protein kinase SRK2E 246481_s_at Stress-induced protein KIN1 245998_at Sucrose synthase 1

Down-regulation

253999_at 1-aminocyclopropane-1-carboxylate synthase 7 255284_at 5'-adenylylsulfate reductase 1, chloroplastic 254343_at 5'-adenylylsulfate reductase 3, chloroplastic 260914_at AT1G02640 260915_at AT1G02660 260969_at AT1G12240 259388_at AT1G13420 256352_at AT1G54970 265588_at AT2G19970 258181_at AT3G21670 251298_at AT3G62040 255516_at AT4G02270 254954_at AT4G10910 245346_at AT4G17090 254574_at AT4G19430 254326_at AT4G22610 253814_at AT4G28290 253697_at AT4G29700 253305_at AT4G33666 253353_at AT4G33730 253073_at AT4G37410

246959_at AT5G24690 246652_at AT5G35190 248657_at AT5G48570 261562_at Actin-depolymerizing factor 10 255632_at Actin-depolymerizing factor 8 262883_at Ammonium transporter 1 member 2 248725_at BAHD acyltransferase At5g47980 250207_at Chalcone synthase 248727_at Cytochrome P450 705A5 249203_at Cytochrome P450 71A16 253534_at Cytochrome P450 83B1 250304_at Elongation factor 1-beta 1 260856_at Ethylene-responsive transcription factor ERF012 263376_at Fasciclin-like arabinogalactan protein 6 248118_at GDSL esterase/lipase At5g55050 252238_at Peroxidase 35 249934_at Peroxidase 60 246991_at Peroxidase 73 261157_at Peroxidase 8 252679_at Probable CCR4-associated factor 1 homolog 9 255524_at Probable pectinesterase/pectinesterase inhibitor 41 250801_at Probable pectinesterase/pectinesterase inhibitor 46 247871_at xyloglucan endotransglucosylase/hydrolase protein 12 252607_at xyloglucan endotransglucosylase/hydrolase protein 31 263207_at xyloglucan endotransglucosylase/hydrolase protein 33 260429_at Protein TIFY 11B 247914_at xyloglucan endotransglucosylase/hydrolase protein 13 260126_at Serine-hydroxymethyltransferase 252827_at Tryptophan-N-hydroxylase 1 254044_at Xyloglucan endotransglucosylase/hydrolase protein 14