Table III

Relative concentration and oligomeric state of selected proteins detected in the stromal proteome using CN-PAGE

References are listed in which such oligomeric state was determined in the published literature from A. thaliana, other plant species, or bacteria. Note that in the absence of published data on Arabidopsis proteins this is information for homologues in closely related or more distant species. Additional parameters include the calculated mass of the monomeric protein and the native mass and relative concentration as determined by CN-PAGE in this study. Functional assignment according to MapMan (29) is also listed. FA, fatty acid; CHO, carbohydrates; x, not relevant; HMW, high molecular weight; APS, ATP sulfurylase; misc., miscellaneous; org., organic; cyt, cytosolic; TCA, tricarboxylic acid cycle.

AccessionaLaboratory annotationbOligomeric statecOligomeric state referencedOrganismeMolecular massRelative normalized concentration (×100)iMapMan Binj
PrecursorfProcessedgNativeh
kDa
At5g46290.1 Ketoacyl-ACP synthase I (Lipid Gene Database; Beisson)Dimer124 E. coli 50641290.0011.1.03 lipid metabolism.FA synthesis and FA elongation.ketoacyl-ACP synthase
At1g29900.1 Carbamoylphosphate synthetaseHeterodimer63, 125A. aeolicus, E. coli1301231740.1913.1.2.3 amino acid metabolism.synthesis.glutamate family.arginine; 23.1.1 nucleotide metabolism.synthesis.pyrimidine
At3g27740.1 Carbamoyl phosphate synthetase small subunitHeterodimer63, 125A. aeolicus, E. coli471011631.2413.1.2.3 amino acid metabolism.synthesis.glutamate family.arginine; 23.1.1 nucleotide metabolism.synthesis.pyrimidine
At3g22890.1 ATP sulfurylase (ATPS1)Tetramer62Spinach51521480.0914.01 sulfur assimilation.APS
At2g02500.1 4-Diphosphocytidyl-2C-methyl-d-erythritol synthase (ISPD), mevalonate-independentLikely a dimerThis study A. thaliana 34690.0516.1 secondary metabolism.isoprenoids
At3g45140.1 Lipoxygenase AtLOX2, plastidMonomerThis study A. thaliana 102341207.5317.7.1 hormone metabolism.jasmonate.synthesis-degradation
At2g44050.1 DMRL synthase (COS1) (vitamin B2 synthesis)Homohexacontamer (60-mer) (icosaeder of 12 pentamers)68–70E. coliand Bacillus, spinach24177383.5918 cofactor and vitamin metabolism
At1g03475.1 Coproporphyrinogen III oxidaseHomodimer71 A. thaliana 4135822.8019 tetrapyrrole synthesis
At1g48520.1 Glu-tRNA(Gln) amidotransferase subunit B (GATB or GLU-ADT subunit B)Homodimer72 C. reinhardtii 611990.0319 tetrapyrrole synthesis
At1g69740.1 Porphobilinogen synthase-1 (δ-aminolevulinic acid dehydratase-1) (ALAD-1)Homo-octamer24Pea47413430.1619 tetrapyrrole synthesis
At2g40490.1 Uroporphyrinogen decarboxylase (UPD)Homodimer126Tobacco44401260.3019 tetrapyrrole synthesis
At3g25660.1 Glutamyl-tRNA amidotransferase subunit AHomodimer72, 127C. reinhardtii, wheat57431910.0519 tetrapyrrole synthesis
At5g24300.1 Starch synthaseHomo- and heterodimer54, 55Potato, maize72741570.622.1.2.02 major CHO metabolism.synthesis.starch.starch synthase
At4g09020.1 Glycoside hydrolase family 13, similar to isoamylaseHomotetra- to homohexamer128Rice866796, 78, 840.042.1.2.04 major CHO metabolism.synthesis.starch.debranching
At3g29320.1 Starch phosphorylase-1Homo- and heterodimer54, 55Potato, maize109962340.682.2.2.02 major CHO metabolism.degradation.starch.starch phosphorylase
At1g03680.1 Thioredoxin m1 (Trxm1)Interacts with different targets129 A. thaliana 201496, 89, 480.1021.1 redox.thioredoxin
At1g50320.1 Thioredoxin X (TrxX)Interacts with different targets130 A. thaliana 20131540.0421.1 redox.thioredoxin
At3g02730.1 Thioredoxin F1 (TrxF1)Interacts with different targets129 A. thaliana 1913155, 212, 170, 1830.0121.1 redox.thioredoxin
At2g20270.1 Glutaredoxin protein familyUnknownNonex1913340.2721.4 redox.glutaredoxins
At3g11630.1 2-Cys peroxiredoxin A (PrxA)Monomer, dimer, or decamer77, 78Pea, barley2921360, 219, 119, 110, 5829.5921.5 redox.periredoxins
kDa
At3g52960.1 Peroxiredoxin II E (PrxE)Probably dimerThis study A. thaliana 2520840.2421.5 redox.periredoxins
At1g74260.1 Phosphoribosylformyl-glycinamidine synthaseUnknownNonex152142, 39, 114, 930.0423.1.2 nucleotide metabolism.synthesis.purine
At2g35040.1 Phosphoribosylamino-imidazolecarboxamide formyltransferaseUnknownNonex6560222, 213, 38, 1870.0923.1.2 nucleotide metabolism.synthesis.purine
At5g48960.1 Similar to 5′-nucleotidaseUnknownNonex7367166, 650.0123.2 nucleotide metabolism.degradation
At5g63310.1 NDPK2, stromalHexamer81Spinach26191331.0223.4 nucleotide metabolism.phosphotransfer and pyrophosphatases
At1g35420.1 Dienelactone hydrolase familyMonomer96Pseudomonas sp. B133430280.2226.1 misc.misc2
At3g03710.1 3′–5′ exoribonucleaseHomotrimer?89, 90Spinach100944100.5527.1 RNA.processing
At5g26742.1 DEAD box RNA helicase (RH3), mRNA etiolated seedlingUnknownNonex81459800.0327.1 RNA.processing
At1g77060.1 Isocitrate lyase and CoA biosynthesis domainUnknownNonex3733119, 1470.0127.3.99 RNA.regulation of transcription.unclassified
At3g63140.1 Ribosome-associated protein (RAP41)Interacts with 70 S ribosome84 C. reinhardtii 4478107, 126, 946, 2240.5827.4 RNA.RNA binding
At1g75350.1 50 S ribosomal protein L31 chloroplastHetero-59-mer20Spinach16132120.0129.2.1 protein.synthesis.chloroplast-plastid ribosomal protein
At5g13650.1 Elongation factor protein; typA/bipA likeUnknownNonex74299800.3229.2.4 protein.synthesis.elongation
At1g65260.1 Vipp1, mutant HCF155, PspA-likeHomohexacontamer (60-mer)?131 A. thaliana 36309320.6829.3 protein.targeting
At2g20890.1 THF1, thylakoid formation 1UnknownNonex34272700.0029.3 protein.targeting
At5g55220.1 Trigger factorDimer95 E. coli 6260146, 1630.0729.3 protein.targeting
At5g65620.1 Zinc oligopeptidase A (M3 family)UnknownNonex89801070.0729.5.07 protein.degradation.metalloprotease
At1g36390.1 GrpE-2Dimer/tetramer and in complex with HSP7093 C. reinhardtii 3124154, 1971.9529.6 protein.folding
At2g28000.1 CPN60-α-1Heterotetradecamer and HMW complex with CPN21 when ADP or ATP added132 Narcissus pseudonarcissus 62578032.8829.6 protein.folding
At2g44650.1 CPN10-1Heptamer and multiple forms133 A. thaliana 15111701.5029.6 protein.folding
At3g13470.1; At1g55490.1; At5g56500.1CPN60-β-1,2,3Heterotetradecamer and HMW complex with CPN21 when ADP or ATP added132 N. pseudonarcissus 63468072.2429.6 protein.folding
At3g62030.1 Peptidylprolyl isomerase ROC4UnknownNonex283610772.7829.6 protein.folding
At4g24280.1 cpHSP70-1 (DnaK homologue)Heterotrimer93 C. reinhardtii 77681237.2629.6 protein.folding
At5g17710.1 GrpE-1Dimer/tetramer and in complex with HSP7093 C. reinhardtii 3521154, 2021.2729.6 protein.folding
At5g20720.1 CPN21 (also CPN20)Multiple form and complexed with CPN60133, 134A. thaliana, spinach276617127.3029.6 protein.folding
At5g49910.1 cpHSP70-2 (DnaK homologue)Heterotrimer93 C. reinhardtii 77992150.3229.6 protein.folding
At5g50920.1 ClpC1Dimer16 A. thaliana 103591992.5029.6 protein.folding
At5g66530.1 Aldose 1-epimeraseDimer56 Aspergillus niger 3430610.313.5 minor CHO metabolism.others
kDa
At1g11430.1 DAG protein-RelatedUnknownNonex26209290.0633.99 development.unspecified
At1g21440.1 Carboxyvinyl-carboxyphosphonate phosphorylmutaseUnknownNonex36321190.0035.1 not assigned.no ontology
At1g09340.1 Ribosome-associated protein (RAP38)Hetero-59-mer84 C. reinhardtii 43602, 151, 946, 604, 224, 107, 126, 890, 450, 319, 195, 2300.6935.2 not assigned.unknown
At3g47520.1 Malate dehydrogenase (NAD), plastidicDimer57Sorghum4217154, 3231.318.2.09 TCA/org. transformation.other organic acid transformations.cyt MDH
At5g58330.1 Malate dehydrogenase (NADP)Dimer57Sorghum484395, 1093.528.2.09 TCA/org. transformation.other organic acid transformations.cyt MDH
  • a Accession number from TAIR. Note that only gene model (typically .1) is indicated. However, in most cases the mass spectrometry data also matched the other gene models; such details can be found in PPDB.

  • b Internal annotation in PPDB.

  • c Oliomeric state as reported in the literature.

  • d Oliomeric state in A. thalianaor other species.

  • e Organism used in the cited reference(s).

  • f Calculated molecular mass of the precursor proteins as reported in PPDB.

  • g Calculated molecular mass of the processed proteins as reported in PPDB.

  • h Experimental native mass as determined from the CN-PAGE gels. If proteins were identified in more than one spot (e.g. due to aggregation, smearing, or truly different oligomeric states), these additional native masses are also listed.

  • i Relative concentration (multiplied by 100) in the stroma as determined by normalize spot volume divided by experimental mass. If more than one protein was identified in a spot, the spot volume was divided by the number of its protein components.

  • j Functional assignment according to the MapMan Bin classification (29) and reported in PPDB.