Table 2.
Functional classification of proteins showing differential abundance in roots of nitrate- and ammonium-cultured A. thaliana plants.
| Protein Description | TAIR ID | Uniprot ID | p-Value | Fold Change NO3−/NH4+ |
|---|---|---|---|---|
| Organic acid transformation | ||||
| Dihydrolipoyllysine-residue acetyltransferase component 5 of pyruvate dehydrogenase complex | AT1G34430 | Q9C8P0 | 0.010 | 5.27 |
| Dihydrolipoyl dehydrogenase 1 | AT1G48030 | Q9M5K3 | 0.019 | 0.30 |
| ATP-citrate synthase alpha chain protein 3 | AT1G09430 | O80526 | 0.001 | 0.11 |
| Photorespiration | ||||
| Serine hydroxymethyltransferase 3, chloroplastic | AT4G32520 | Q94JQ3 | 0.011 | 0.19 |
| Carbohydrate metabolism | ||||
| ADP-glucose pyrophosphorylase family protein | AT1G74910 | F4HXD1 | 0.008 | 0.13 |
| Glycolysis | ||||
| Pyruvate kinase | AT5G56350 | Q9FM97 | 0.009 | 0.21 |
| Gluconeogenese/Glyoxylate cycle | ||||
| Phosphoenolpyruvate carboxykinase (ATP) | AT4G37870 | Q9T074 | 0.010 | 0.14 |
| Mitochondrial electron transport | ||||
| Gamma carbonic anhydrase-like 1 | AT5G63510 | F4KAG8 | 0.003 | 0.17 |
| Amino acid metabolism | ||||
| Glutamate decarboxylase 2 | AT1G65960 | Q42472 | 0.027 | 0.24 |
| Aspartate semialdehyde dehydrogenase | AT1G14810 | Q8VYI4 | 0.040 | 5.29 |
| Methylmalonate-semialdehyde dehydrogenase (acylating) | AT2G14170 | A8MQR6 | 0.048 | 4.36 |
| Secondary metabolism | ||||
| 3-isopropylmalate dehydratase large subunit 1 | AT4G13430 | Q94AR8 | 0.003 | 5.48 |
| Methylthioalkylmalate synthase 3 | AT5G23020 | Q9FN52 | 0.003 | 3.25 |
| Acetyl-CoA acetyltransferase | AT5G48230 | Q854Y1-2 | 0.049 | 0.30 |
| Betaine aldehyde dehydrogenase 1 | AT1G74920 | F4HXD2 | 0.037 | 0.26 |
| Chalcone synthase | AT5G13930 | P13114 | 0.039 | 0.26 |
| Hormone metabolism | ||||
| Delta(24)-sterol reductase | AT3G19820 | Q39085 | 0.037 | 0.31 |
| Co-factor and vitamin metabolism | ||||
| Nicotinate-nucleotide pyrophosphorylase (carboxylating) | AT2G01350 | F41NA0 | 0.015 | 0.10 |
| Cell wall synthesis | ||||
| UDP-glucuronic acid decarboxylase 3 | AT5G59290 | F4KHU8 | 0.029 | 2.93 |
| Tetrapyrrole synthesis | ||||
| Protoporphyrinogen oxidase 2 | AT5G14220 | Q8S9J1-2 | 0.003 | 0.19 |
| Abiotic stress | ||||
| Endoplasmin homolog | AT4G24190 | F4JQ55 | 0.031 | 3.16 |
| DnaJ protein ERDJ38 | AT3G62600 | Q9LZK5 | 0.002 | 6.67 |
| Probable methyltransferase PMt24 | AT1G29470 | Q6NPR7 | 0.004 | 5.51 |
| Germin-like protein subfamily T member 1 | AT1G18970 | P92995 | 0.031 | 3.55 |
| Redox response | ||||
| Protein disulfide isomerase-like 1-2 | AT1G21750 | F4HZN9 | 0.036 | 4.41 |
| Protein disulfide-isomerase | AT1G77510 | Q9SRG3 | 0.002 | 8.12 |
| Protein disulfide isomerase-like 1-6 | AT3G16110 | Q66GQ3 | 0.025 | 0.21 |
| Thioredoxin reductase 2 | AT2G17420 | Q39242 | 0.013 | 0.28 |
| Nucleotide metabolism | ||||
| Nudix hydrolase 3 | AT1G79690 | Q8L831 | 0.018 | 0.26 |
| RNA processing | ||||
| Polyadenylate-binding protein 2 | AT4G34110 | P42731 | 0.048 | 0.39 |
| Polyadenylate-binding protein 4 | AT2G23350 | O22173 | 0.006 | 0.18 |
| Reactive intermediate deaminase A | AT3G20390 | Q94JQ4 | 0.002 | 11.07 |
| Protein synthesis | ||||
| 30S ribosomal protein S3 | ATCG00800 | P56798 | 0.043 | 2.82 |
| 40S ribosomal protein S3-3 | AT5G35530 | Q9FJA6 | 0.004 | 7.52 |
| Elongation factor Tu (mitochondrial) | AT4G02930 | Q9ZT91 | 0.034 | 3.43 |
| Elongation factor Tu (chloroplastic) | AT4G20360 | P17745 | 0.026 | 5.32 |
| Protein degradation | ||||
| 26S proteasome non-ATPase regulatory subunit 14 homolog | AT5G23540 | Q9LT08 | 0.012 | 0.27 |
| Proteasome subunit beta type-4 | AT1G56450 | Q7DLR9 | 0.035 | 0.27 |
| Protein targeting | ||||
| Nuclear pore complex protein NUP155 | AT1G14850 | F4HXV6 | 0.033 | 2.99 |
| ADP-ribosylation factor 2-A | AT3G62290 | Q9M1P5 | 0.031 | 4.87 |
| Signaling | ||||
| Rho GDP-dissociation inhibitor 1 | AT3G07880 | Q9SFC6 | 0.021 | 5.59 |
| Dynamin-related protein 1A | AT5G42080 | P42697 | 0.003 | 5.79 |
| GTP-binding nuclear protein Ran-1 | AT5G20010 | P41916 | 0.020 | 4.92 |
| 14-3-3-like protein GF14 chi | AT4G09000 | P42643 | 0.032 | 0.22 |
| Cell vesicle transport | ||||
| Tubulin beta 6-chain (Cell organization) | AT5G12250 | P29514 | 0.020 | 0.28 |
| AP-4 complex subunit epsilon | AT1G31730 | Q8L7A9 | 0.030 | 3.63 |
| Coatomer subunit beta-1 | AT4G31480 | Q95V21 | 0.007 | 8.98 |
| Golgin candidate 5 | AT1G79830 | F4HQB9 | 0.015 | 5.49 |
| COG complex component-related protein | AT5G51430 | Q9FGN0 | 0.023 | 6.23 |
| Transport | ||||
| V-type proton ATPase subunit E3 | AT1G64200 | P0CAN7 | 0.044 | 2.89 |
| ATPase 2, plasma membrane-type | AT4G30190 | P19456 | 0.046 | 3.26 |
| Mitochondrial dicarboxylate/tricarboxylate transporter DTC | AT5G19760 | Q9C5M0 | 0.010 | 3.54 |
| ABC transporter A family member 2 | AT3G47730 | Q84K47 | 0.010 | 3.82 |
| ABC transporter F family member 1 | AT5G60790 | Q9FJH5 | 0.009 | 0.15 |
| Miscellaneous | ||||
| AT3g23600/MDB19_9 | ATG23600 | Q9LUG8 | 0.012 | 4.83 |
| Dolichyl-diphosphooligosaccharide-protein glycosyltransferase 48 kDa subunit | AT5G66680 | Q944K2 | 0.009 | 0.17 |
| Methylesterase 3 | AT2G23610 | O80477 | 0.0369 | 2.93 |
| Glutathione S-transferase L3 | AT5G02790 | Q9LZO6 | 0.0218 | 3.61 |
| Peroxidase 34 | AT3G49120 | Q9SMU8 | 0.0070 | 0.16 |
| Peroxidase 30 | AT3G21770 | Q9LSY7 | 0.0165 | 4.46 |
| AT4g13180/F17N18-70 | AT4G13180 | Q9SVQ9 | 0.0322 | 0.22 |
| Not assigned ontology | ||||
| NADH dehydrogenase (ubiquinone) iron-sulfur protein 2 | ATMG00510 | P93306 | 0.0167 | 1.78 |
| tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit | AT1G03110 | Q93WD7 | 0.0376 | 0.31 |
| Pheromone receptor, putative (AR401) | AT1G66680 | Q9C9M1 | 0.0143 | 4.38 |
| WD40 domain-containing protein | AT5G24710 | F4K1H8 | 0.0265 | 0.29 |
| Protein EMBRYO DEFECTIVE 2734 | AT5G19820 | Q93V68 | 0.0208 | 0.20 |
| Calcium-dependent lipid-binding family protein | AT1G48090 | F4HWS2 | 0.0156 | 0.29 |
| Metal-dependent protein hydrolase | AT5G41970 | F4K000 | 0.0349 | 3.09 |