Figures (4)  Tables (2)
    • Figure 1. 

      Number of differentially accumulated proteins among different samples.

    • Figure 2. 

      Hierachical clustering of proteins showing different abundance profiles across different samples. The data were transferred using log2.

    • Figure 3. 

      Correlation analysis of transcript (log2 FPKM value) and protein (log2 iTRAQ value) among different samples. (a) CA vs NA; (b) CA vs DA; (c) DA vs NA.

    • Figure 4. 

      Analysis of transcript levels of the selected proteins among NA, CA and DA stages by qRT-PCR. Those genes which showed similar patterns are marked using black boxes. All data are the mean ± SD (n = 3).

    • GO termNA vs CACA vs DADA vs NA
      Cellular componentExtracellular regionCell wallExtracellular region
      Plastid stromaPlastid partCell wall
      Cytoplasmic vesiclePlastid stromaPlastid envelope
      VesicleThylakoid light-harvesting complexExternal encapsulating structure
      Chloroplast thylakoid membraneOrganelle envelope
      Light-harvesting complexEnvelope
      Plastid thylakoid membraneMicrobody
      Chromosome
      Membrane part
      Molecular functionAmmonia ligase activityAdenylyltransferase activityBinding
      Acid-ammonia (or amide) ligase activityRacemase and epimerase activityProtein kinase activity
      Oxidoreductase activity, acting on the
      CH-NH2 group of donors, disulfide as
      acceptor
      O-acyltransferase activityAmmonia ligase activity
      Ligase activity, forming carbon-nitrogen
      bonds
      Racemase and epimerase activity, acting
      on carbohydrates and derivatives
      Acid-ammonia (or amide) ligase activity
      Binding
      Biological processRibosome biogenesisElectron transport chainElectron transport chain
      Glutamine metabolic processOxidation reductionOxidation reduction
      Cellular carbohydrate metabolic processNucleoside phosphate metabolic processPhotosynthetic electron transport chain
      Reproductive developmental processWater-soluble vitamin metabolic processNucleotide metabolic process
      Reproductive processNucleobase, nucleoside and nucleotide metabolic processGeneration of precursor metabolites and energy
      Glycine metabolic processPhotosynthetic electron transport chainRibosome biogenesis
      Cellular amino acid metabolic processNucleotide metabolic processNucleoside phosphate metabolic process
      Cellular amine metabolic processSeed germinationGlutamine metabolic process
      Sulfur amino acid metabolic processMucilage metabolic processNucleobase, nucleoside and nucleotide metabolic process
      Reproductive structure developmentGlucan metabolic processNegative regulation of molecular function
      Carbohydrate metabolic processVitamin metabolic processProtein complex assembly
      ReproductionNADP metabolic processOxidoreduction coenzyme metabolic process
      Amine metabolic processNADPH regenerationTissue development
      Respiratory electron transport chainNicotinamide metabolic processPyridine nucleotide metabolic process
      Flower developmentAlkaloid metabolic processCellular macromolecular complex assembly
      Organic acid catabolic processNucleobase, nucleoside, nucleotide and nucleic acid metabolic processCellular protein complex assembly
      Carboxylic acid catabolic processCellular glucan metabolic processNicotinamide nucleotide metabolic process
      Response to chemical stimulusPhotosynthesis, light reactionProtein complex biogenesis
      Response to inorganic substancePurine nucleotide metabolic processCellular component biogenesis
      Energy derivation by oxidation of organic compoundsOxidoreduction coenzyme metabolic
      process
      Cellular component organization
      Organic acid metabolic processPyridine nucleotide metabolic processSulfur metabolic process
      Carboxylic acid metabolic processNicotinamide nucleotide metabolic processPrimary metabolic process
      Cellular ketone metabolic processCellular polysaccharide metabolic processPhotosynthesis
      Oxoacid metabolic processGlycogen metabolic processPurine nucleotide metabolic process
      Sulfur amino acid biosynthetic processEnergy reserve metabolic processFatty acid metabolic process
      Serine family amino acid metabolic processPhotosynthesisPhotosynthesis, light reaction
      Generation of precursor metabolites and energyPlastid membrane organization
      Stomatal movement
      Membrane organization

      Table 1. 

      Gene Ontology (GO) enrichment analysis of differentially accumulated protein species among the comparisons between sample NA, CA and DA ( p -value < 0.05).

    • NumberPathwayCountPathway ID
      Total
      (1,015)
      CA vs NA
      (319)
      CA vs DA
      (196)
      DA vs NA
      (362)
      1Metabolic pathways45814991168ko01100
      2Biosynthesis of secondary metabolites247753374ko01110
      3Microbial metabolism in diverse environments190703273ko01120
      4Ribosome83241727ko03010
      5Carbon fixation in photosynthetic organisms71331331ko00710
      6Glycolysis / Gluconeogenesis6522525ko00010
      7Methane metabolism5317821ko00680
      8Starch and sucrose metabolism52191024ko00500
      9Protein processing in endoplasmic reticulum49171115ko04141
      10Lysosome49111016ko04142
      11Pyruvate metabolism4818720ko00620
      12Amino sugar and nucleotide sugar metabolism4311814ko00520
      13Photosynthesis43131317ko00195
      14Glutathione metabolism367714ko00480
      15Phenylpropanoid biosynthesis3411713ko00940
      16Alanine, aspartate and glutamate metabolism3112711ko00250
      17Citrate cycle (TCA cycle)3110310ko00020
      18Plant-pathogen interaction3012715ko04626
      19Pentose phosphate pathway3013612ko00030
      20Glycine, serine and threonine metabolism2913613ko00260
      21Antigen processing and presentation291058ko04612
      22Oxidative phosphorylation2811812ko00190
      23Glyoxylate and dicarboxylate metabolism2612511ko00630
      24Purine metabolism25747ko00230
      25Huntington's disease25945ko05016
      26Phenylalanine metabolism2510810ko00360
      27Fructose and mannose metabolism25887ko00051
      28Peroxisome23749ko04146
      29Galactose metabolism22458ko00052
      30Arginine and proline metabolism22735ko00330
      31Phagosome213511ko04145
      32Nitrogen metabolism21131013ko00910
      33Cysteine and methionine metabolism19716ko00270
      34Spliceosome19636ko03040
      35Other glycan degradation19637ko00511
      36Alzheimer's disease18838ko05010
      37Valine, leucine and isoleucine degradation17417ko00280
      38Parkinson's disease16533ko05012
      39Butanoate metabolism16525ko00650
      40Ascorbate and aldarate metabolism16734ko00053
      41RNA degradation16526ko03018
      42Pentose and glucuronate interconversions15747ko00040
      43Glycerolipid metabolism15637ko00561
      44Endocytosis13543ko04144
      45Toxoplasmosis13533ko05145
      46Propanoate metabolism13523ko00640
      47Phenylalanine, tyrosine and tryptophan biosynthesis13332ko00400
      48Aminoacyl-tRNA biosynthesis13414ko00970
      49Cyanoamino acid metabolism13826ko00460
      50Renin-angiotensin system13356ko04614
      51Aminobenzoate degradation12446ko00627
      52Inositol phosphate metabolism12424ko00562
      53RNA transport12727ko03013
      54Valine, leucine and isoleucine biosynthesis12312ko00290
      55Selenoamino acid metabolism11334ko00450
      56Tyrosine metabolism11634ko00350
      57Tropane, piperidine and pyridine alkaloid biosynthesis11351ko00960
      58Proteasome1122ko03050
      59Reductive carboxylate cycle (CO2 fixation)1113ko00720
      60Tryptophan metabolism10315ko00380
      61Two-component system10658ko02020
      62MAPK signaling pathway10432ko04010
      63Fatty acid metabolism1046ko00071
      64Porphyrin and chlorophyll metabolism922ko00860
      65beta-Alanine metabolism9312ko00410
      66Glycosphingolipid biosynthesis - globo series9515ko00603
      67alpha-Linolenic acid metabolism9114ko00592
      68Terpenoid backbone biosynthesis9112ko00900
      69Prion diseases9723ko05020
      70Type I diabetes mellitus932ko04940
      71Pyrimidine metabolism911ko00240
      72One carbon pool by folate9534ko00670
      73Flavonoid biosynthesis8412ko00941
      74Chagas disease834ko05142
      75Lysine biosynthesis8112ko00300
      76Insulin signaling pathway8212ko04910
      77Chloroalkane and chloroalkene degradation8212ko00625
      78Carotenoid biosynthesis8213ko00906
      79Pathogenic Escherichia coli infection8146ko05130
      80Proximal tubule bicarbonate reclamation8122ko04964
      81Glycosphingolipid biosynthesis - ganglio series7223ko00604
      82PPAR signaling pathway723ko03320
      83Limonene and pinene degradation733ko00903
      84Glycosaminoglycan degradation7223ko00531
      85Metabolism of xenobiotics by cytochrome P4507343ko00980
      86Sphingolipid metabolism7334ko00600
      87Glycerophospholipid metabolism7313ko00564
      88Vibrio cholerae infection724ko05110
      89Drug metabolism - cytochrome P4507343ko00982
      90Lysine degradation733ko00310
      91Amyotrophic lateral sclerosis (ALS)7424ko05014
      92Calcium signaling pathway611ko04020
      93NOD-like receptor signaling pathway6323ko04621
      94Protein digestion and absorption642ko04974
      95Isoquinoline alkaloid biosynthesis6321ko00950
      96Pathways in cancer6323ko05200
      97Prostate cancer6323ko05215
      98Neurotrophin signaling pathway624ko04722
      99Folate biosynthesis6133ko00790
      100Ubiquinone and other terpenoid-quinone biosynthesis623ko00130
      101Protein export522ko03060
      102Photosynthesis - antenna proteins5222ko00196
      103Histidine metabolism522ko00340
      104Riboflavin metabolism5422ko00740
      105Sulfur metabolism5121ko00920
      106Streptomycin biosynthesis52ko00521
      107Benzoate degradation523ko00362
      108Bisphenol degradation5111ko00363
      109MAPK signaling pathway - yeast5122ko04011
      110Arachidonic acid metabolism5111ko00590
      111Progesterone-mediated oocyte maturation5312ko04914
      112Type II diabetes mellitus511ko04930
      113Biosynthesis of ansamycins5424ko01051
      114Chlorocyclohexane and chlorobenzene degradation522ko00361
      115Novobiocin biosynthesis5211ko00401
      116Fatty acid biosynthesis412ko00061
      117Polycyclic aromatic hydrocarbon degradation4311ko00624
      118Linoleic acid metabolism41ko00591
      119Systemic lupus erythematosus412ko05322
      120Bacterial invasion of epithelial cells421ko05100
      121Regulation of actin cytoskeleton4223ko04810
      122Biosynthesis of unsaturated fatty acids42ko01040
      123Geraniol degradation412ko00281
      124Focal adhesion4121ko04510
      125Collecting duct acid secretion43ko04966
      126Pantothenate and CoA biosynthesis41ko00770
      127Epithelial cell signaling in Helicobacter pylori infection43ko05120
      128Oocyte meiosis413ko04114
      129Cell cycle412ko04110
      130Fluorobenzoate degradation31ko00364
      131Gap junction323ko04540
      132Toll-like receptor signaling pathway311ko04620
      133N-Glycan biosynthesis31ko00510
      134Taurine and hypotaurine metabolism3111ko00430
      135Amoebiasis31ko05146
      136mRNA surveillance pathway322ko03015
      137Caprolactam degradation3111ko00930
      138Carbohydrate digestion and absorption322ko04973
      139Ether lipid metabolism3111ko00565
      140Toluene degradation31ko00623
      141Shigellosis3122ko05131
      142Tight junction321ko04530
      143Phototransduction - fly322ko04745
      144Vitamin B6 metabolism311ko00750
      145Drug metabolism - other enzymes2ko00983
      146Leukocyte transendothelial migration221ko04670
      147Leishmaniasis211ko05140
      148D-Glutamine and D-glutamate metabolism2ko00471
      149Phosphatidylinositol signaling system21ko04070
      150Cell cycle - Caulobacter2111ko04112
      151Naphthalene degradation211ko00626
      152Bacterial secretion system21ko03070
      153Ethylbenzene degradation21ko00642
      154C5-Branched dibasic acid metabolism2ko00660
      155Base excision repair211ko03410
      156Fc gamma R-mediated phagocytosis2212ko04666
      157Viral myocarditis221ko05416
      158GnRH signaling pathway2112ko04912
      159Flavone and flavonol biosynthesis222ko00944
      160Arrhythmogenic right ventricular cardiomyopathy (ARVC)221ko05412
      161Dilated cardiomyopathy221ko05414
      162Apoptosis211ko04210
      163ECM-receptor interaction21ko04512
      164Hypertrophic cardiomyopathy (HCM)221ko05410
      165DDT degradation221ko00351
      166Ubiquitin mediated proteolysis211ko04120
      167Adherens junction221ko04520
      168Melanogenesis11ko04916
      169Vascular smooth muscle contraction11ko04270
      170Basal transcription factors111ko03022
      171Lipopolysaccharide biosynthesis1ko00540
      172Nucleotide excision repair1ko03420
      173Stilbenoid, diarylheptanoid and gingerol biosynthesis111ko00945
      174Steroid biosynthesis1ko00100
      175RIG-I-like receptor signaling pathway1ko04622
      176Cardiac muscle contraction111ko04260
      177Phototransduction11ko04744
      178Sulfur relay system111ko04122
      179Gastric acid secretion11ko04971
      180Retinol metabolism111ko00830
      181Circadian rhythm - plant1ko04712
      182Mismatch repair1ko03430
      183Salivary secretion11ko04970
      184Benzoxazinoid biosynthesis1ko00402
      185Fatty acid elongation in mitochondria1ko00062
      186Notch signaling pathway1111ko04330
      187Thiamine metabolism111ko00730
      188DNA replication1ko03030
      189Indole alkaloid biosynthesis1ko00901
      190Synthesis and degradation of ketone bodies111ko00072
      191Long-term potentiation11ko04720
      192Diterpenoid biosynthesis1ko00904
      193SNARE interactions in vesicular transport1ko04130
      194Glioma11ko05214
      195Olfactory transduction11ko04740

      Table 2. 

      Pathway analysis of total proteins and enriched proteins in the comparisons among different samples.