Table 3.
Classification of biological processes for drought-induced differential accumulated proteins in basal root-tip (RT1) tissues a
| Biological Process | Protein Accessions b | Description | Fold Change (Drought Treated/Control) c | ||
|---|---|---|---|---|---|
| SDT d | D1W e | D3W f | |||
| Phytohormones | Pavir.Ia03517.1 | PYR1-like 6 | 2.17 | ||
| Pavir.Ib01400.1 | 2.23 | ||||
| Pavir.J39695.1 | 2.06 | ||||
| Pavir.Gb00126.1 | IQ-domain 32 | 0.33 | |||
| Pavir.Ia01238.1 | ABI3-interacting protein 3 (negative regulator of ABA signaling, PP2C) | 0.51 | |||
| Pavir.Ca02694.1 | ABI3 (AP2/B3-like) TF | 0.46 | |||
| Pavir.Ia02723.1 | Nodulin-related protein 1 (a negative regulator of the ABA signaling/synthesis) | 3.04 | 3.14 | 1.70 | |
| Pavir.Ca02736.1 | IAA-induced protein 16 | 0.38 | |||
| Pavir.J10323.1; Pavir.Ea01573.1 | ACC oxidase 1 | 0.38 | 0.38–0.39 | ||
| Pavir.J06494.1 | Gibberellin-regulated family protein | 4.15 | 4.81 | ||
| Root organogenesis (meristem cell division) | Pavir.Bb01893.1 | Annexin 5 (apoptosis) | 3.11 | 2.7 | |
| Pavir.Db00940.1 Pavir.Aa00752.1 | microtubule-associated proteins | 0.36–0.37 | |||
| Pavir.Ib03538.1 | Tetratricopeptide repeat (TPR)-like superfamily protein (anphase-promoting complex (APC) subunits cdc16, cdc23 and cdc27) | 0.34 | 0.50 | ||
| Pavir.J21702.1 | 0.32 | ||||
| Pavir.Ib03761.1 | 0.44 | ||||
| Pavir.J29419.1 | Centrin2 (Required for centriole duplication and correct spindle formation) | 0.49 | |||
| Pavir.J28355.1 | Methionine sulfoxide reductase (a central regulator of cell proliferation and differentiation) | 0.35 | |||
| Pavir.Aa01553.1 | NAP1-related protein 2 (Acts as histone H2A/H2B chaperone in nucleosome assembly, playing a critical role for the correct expression of genes involved in root proliferation and patterning) | 0.23 | 0.43 | 0.48 | |
| Pavir.J19751.1 | Dormancy-associated protein (ethylene induced-negative regulator of Cell division from TF ERF114); | 2.82 | 4.43 | ||
| Pavir.Ib03775.1 | 2.88 | ||||
| Pavir.Ga01149.1 | Aquaporin for sustaining root meristem cell division) | 2.95 | |||
| Pavir.Gb00671.1 | 20.43 | ||||
| Cell wall proteins | 21 proteins in SDT; 24 proteins in D1W; 22 proteins in D3W | Beta-1,3-glucanase; Beta-hexosaminidase; chitinase; d-arabinono-1,4-lactone oxidase; Expansin; Laccase; Hydroxyproline-rich glycoprotein | 2.68–10.34 | 20.40–6.80 | 1.98–3.91 |
| Organogenesis and differentiation | Pavir.Ba01536.1 | Root hair specific 19 | 0.37 | ||
| Pavir.J03344.1 | Root hair initiation protein root hairless 1 (RHL1) | 0.49 | 0.49 | ||
| Pavir.Eb02336.1 | Dirigent-like protein (Castrip) | ||||
| Pavir.Ha00936.1 | 4.76 | 0.47 | |||
| Pavir.Aa03031.1; Pavir.J12222.1 | TPX2 (wvd2) protein (The wvd2 gain-of-function mutant has impaired cell expansion and root waving, and changed root skewing) | 0.36–0.38 | |||
| Pavir.Ba01202.1 | Transducin family protein / WD-40 repeat family protein (LATERAL ROOT STIMULATOR 1) | 0.36 | |||
| Pavir.Bb02689.1 Pavir.Ca00095.1 Pavir.Ha01893.1 Pavir.Ia01197.1 | 0.36–0.50 | ||||
| Water stress proteins (Dehydrins, LEA, Osmotins) | Pavir.Cb00662.1 | Dehydrin | 6.39 | 4.82 | 4.68 |
| Pavir.J13075.1 | 20.51 | ||||
| Pavir.Ea02542.1 | 5.86 | ||||
| Pavir.Aa00887.1 | 0.47 | ||||
| Pavir.J04551.1 | 0.46 | ||||
| Pavir.J13075.1 | 7.88 | ||||
| Pavir.Aa02737.1 | LEA | 6.14 | 4.86 | 3.09 | |
| Pavir.Bb02409.1 | 3.71 | 3.95 | 2.95 | ||
| Pavir.Ca01780.1 | 12.15 | 5.36 | 4.90 | ||
| Pavir.Eb02512.1 | 3.23 | 3.02 | 3.19 | ||
| Pavir.Ga00596.1 | 6.30 | 5.85 | 6.82 | ||
| Pavir.Gb00543.1 | 10.76 | 7.06 | 7.80 | ||
| Pavir.Ia03678.1 | 6.29 | 4.13 | 3.46 | ||
| Pavir.J00158.1 | 21.57 | 14.23 | 6.24 | ||
| Pavir.J28600.1 | 8.29 | 9.69 | 6.55 | ||
| Pavir.J24821.1 | 7.43 | 2.43 | |||
| Three proteins | 2.63–4.27 | 2.42–4.92 | |||
| Pavir.Db00310.1 | 0.42 | ||||
| Pavir.Bb00799.1 | Osmotin34 | 6.15 | |||
| Pavir.Bb03197.1 | 6.63 | 7.83 | 6.08 | ||
| Pavir.Ea03024.1 | 6.25 | ||||
| Pavir.Eb03806.1 | 5.55 | 6.43 | 5.32 | ||
| Pavir.J40731.1 | Galactinol synthase 1 (biosynthesis of raffinose osmoprotectants) | 3.77 | |||
| Oxidative stress | Pavir.Aa01787.1; Pavir.Aa03533.1; Pavir.Ab00019.1; Pavir.Ia03296.1 | Disulfide isomerases | 0.45–0.48 | ||
| Pavir.Fb02222.1 | 2.39 | 3.098 | |||
| Pavir.Ca00381.1 | Alkenal reductase | 3.02 | 2.56 | ||
| Pavir.Ea00295.1 | 2-oxoglutarate (2OG) and Fe(II)-DAPendent oxygenase superfamily protein | 4.11 | 3.99 | 3.16 | |
| Pavir.Ea01261.1 | Peroxidase | 3.01 | 3.20 | 3.98 | |
| Pavir.Eb03999.1 | 3.27 | 2.29 | 2.37 | ||
| Pavir.Ia02811.1 | 4.41 | 2.97 | 2.83 | ||
| Pavir.J14586.1 | 2.65 | 2.94 | 2.20 | ||
| Pavir.J15786.1 | 5.24 | 3.53 | 3.55 | ||
| Pavir.J14586.1 | Calatase 1 | 2.65 | 2.94 | 2.20 | |
| Detoxification | 31 proteins | Glutathione S-transferase; Glutaredoxin; Glutathione S-transferase; Formate dehydrogenase; metallothionein 2A; Heavy metal transport/detoxification superfamily protein; Glyoxalases | 2.63–16.26 | 2.23–4.19 | 1.98–6.55 |
| Transcriptional Regulation (TFs) | Pavir.Ia00088.1; Pavir.Ba01216.1; Pavir.Ba01215.1 | Ribonucleases (post-transcriptional regulation) | 2.34–7.66 | ||
| Pavir.Fb01805.1; Pavir.Gb01520.1; Pavir.Hb00704.1; Pavir.Fa00854.1 | General regulatory factor (TF (fatty acid synthase genes) | 0.29–0.50 | |||
| Pavir.Ab02229.1; Pavir.Gb01377.1; Pavir.Bb02517.1 | Basic helix-loop-helix (bHLH) DNA-binding superfamily protein | 0.17–0.37 | |||
| Pavir.Ib01088.1 | Homeodomain-like superfamily protein | 3.05 | |||
| Pavir.Da01122.1 | 0.44 | ||||
| Pavir.Eb00895.1 | NmrA-like negative transcriptional regulator family protein | 2.92 | |||
| Pavir.Db01330.1 | PHD finger protein-related | 0.37 | |||
| Pavir.Ib01055.1 | RAD-like 1 | 0.25 | |||
| Pavir.J31192.1 | RAD-like 1 | 0.24 | |||
| Pavir.Fb01946.1 | Squamosa promoter binding protein-like 9 | 0.31 | |||
| Pavir.Ib04454.1 | Winged-helix DNA-binding transcription factor family protein | 0.29 | |||
| Pavir.J31192.1 | 0.42 | ||||
| Pavir.Bb02517.1 | Basic helix-loop-helix (bHLH) DNA-binding superfamily protein | 0.43 | |||
| Pavir.J25625.1 | Basic-leucine zipper (bZIP) transcription factor family protein | 0.40 | |||
| Pavir.Eb00253.1 | CCCH-type zinc finger family protein | 0.43 | |||
| Pavir.J10403.1 | Zinc finger (C3HC4-type RING finger) family protein | 0.27 | 0.49 | ||
| Pavir.Cb00329.1 | Zinc finger (C3HC4-type RING finger) family protein | 0.43 | |||
| Pavir.Ab00438.1 | Zinc finger C-x8-C-x5-C-x3-H type family protein | 0.46 | |||
| Pavir.Da01847.1 | Growth-regulating factor 5 (Transcription activator that plays a role in the regulation of cell expansion) | 0.31 | |||
| Pavir.Fb01387.1 | Multiprotein bridging factor 1A (Transcriptional coactivator) | 2.83 | 2.54 | ||
| Pavir.Ea03968.1 | Nuclear factor Y, subunit B5 (TF) | 0.45 | |||
| Pavir.Ia04404.1 | Transcription activator-related | 9.73 | 8.95 | ||
| Pavir.Cb02016.1 | Transcription elongation factor (TFIIS) family protein | 0.44 | |||
| Pavir.Ea00508.1 | 0.48 | ||||
| Pavir.Ia02581.1 | Transcription factor TFIIE, alpha subunit | 0.50 | |||
| Pavir.J35507.1 | Splicing factor-related | 0.35 | |||
| Protein translation | 2 proteins in SDT, 7 in D1W, 8 in D3W | Ribosomal subunits | 0.37–0.38 | 0.28–0.43 | 0.35–0.50 |
| Pavir.J20711.1; Pavir.Gb01843.1 | 2.34–2.79 | ||||
| Pavir.J16816.1; Pavir.Ga01591.1 | Eukaryotic translation initiation factors | 0.35–0.38 | |||
| Pavir.J32559.1 | Nuclear transport factor 2 (NTF2) family protein with RNA binding (RRM-RBD-RNP motifs) domain | 0.42 | 0.41 | ||
| 14 proteins | Ekaryotic release factor 1-3, eukaryotic translation initiation factors; Translation elongation factor EF1B; Translation initiation factor IF2/IF5; GTP binding Elongation factor Tu family protein; Essential protein Yae1 | 0.40–0.50 | |||
| Amino acids | Pavir.Fa00915.1 | Glutamate decarboxylase (GABA) | 4.80 | 3.69 | |
| Pavir.Cb00192.1 | 3-methylcrotonyl-CoA carboxylase 1 (MCCA) (leucine catabolism) | 2.67 | |||
| Pavir.Da02439.1 | Homogentisate 1,2-dioxygenase (break down tyrosine and phenylalanine | 3.03 | 2.84 | ||
| Pavir.Db00968.1 | Dihydrodipicolinate synthase 1(lysine biosynthesis | 2.62 | |||
| Pavir.Eb03924.1 | Pyrroline-5-carboxylate (P5C) reductase (arginine and proline metabolism) | 0.51 | |||
| Carbohydrates Sucrose/Starch | Pavir.Ab00047.1 | Sucrose invertase | 0.34 | ||
| Pavir.J01866.1; Pavir.Ia03415.1 | Sucrose synthase | 3.37 | 2.51–3.66 | 2.42–2.58 | |
| Pavir.J01199.1 | Starch branching enzyme 2.2 | 3.56 | |||
| Pavir.Ba00222.1 | Melibiase family protein | 6.02 | 4.41 | 2.93 | |
| Glycolysis | Pavir.Cb01993.1 | Fructose-bisphosphate aldolase 2 | 2.86 | ||
| Pavir.J07576.1 | Phosphoglycerate kinase | 2.71 | 2.74 | 2.00 | |
| Pavir.J15479.1 | Phosphofructokinase 2 | 3.67 | |||
| Pavir.J13866.1 | Phosphoglycerate kinase | 2.31 | |||
| Pavir.Ib01540.1 | Phosphoglycerate mutase | 5.40 | |||
| Pavir.Ga01407.1 | phosphofructokinase 2 | 2.57 | |||
| Pentose shunt | Pavir.Gb02335.1 | Transketolase | 2.78 | ||
| Pavir.Db00351.1 | Aldolase-type TIM barrel family protein | 2.23 | |||
| TCA | Pavir.Bb02852.1 | Aconitase 3 | 4.72 | ||
| Pavir.J02207.1; Pavir.J15849.1 | Pyruvate orthophosphate dikinase | 0.15–0.23 | |||
| Pavir.Gb01988.1 Pavir.J33969.1 | Phosphoenolpyruvate carboxylase | 0.43–0.41 | |||
a Proteins with a fold change value (from drought-treated to non-treated control groups) greater than two standard deviations at adjusted p < 0.05 and identified with a minimum of two unique peptides. b Protein accession in switchgrass annotated database Pvirgatum_v1. 1. c Protein fold change from drought treated to non-drought treated groups. d Proteins from the severe drought-treated experiment. e Proteins from the 1-day re-watering experiment. f Proteins from the 3-day re-watering experiment.