Table II

The most abundant proteins in the chloroplast stroma and their functional classification, relative protein mass, and relative concentrations

The 23 most abundant proteins in terms of “relative protein mass” and in terms of relative concentration with their assigned functional categories and predicted protein location are listed. These 23 proteins represent about 85% of the stromal protein mass. All protein spots on the CN-PAGE gels of stroma were quantified based on spot “volume,” and volumes were normalized to the total spot volume. Proteins in the spots were identified by mass spectrometry. Normalized spot volumes were converted in a measure of approximate relative concentration by division of volume by the calculated mass (for details see “Experimental Procedures”). PS, photosynthesis; PP, pentose phosphate; TCA, tricarboxylic acid cycle; org., organic; GAP, glyceraldehyde 3-phosphate dehydrogenase; Rib5P, ribulose-5-phosphate.

AccessionNameMapMan BinRankaVolumebRelative concentrationc
AtCg00490 RBCL1.3.01 PS.Calvin cycle.Rubisco large subunit1 (1)46.020.852
At1g67090.1 RBCS-4 and other paralogues 1–3d1.3.02 PS.Calvin cycle.small subunit2 (2)12.150.810
At5g35630.1 Glutamate-ammonia ligase (GS2), chloroplast12.2.02 nitrogen metabolism.ammonia metabolism.glutamine synthase3 (3)7.010.152
At3g60750.1 Transketolase (TKL)1.3.07 PS.Calvin cycle.transketolase; 7.2 OPPP.non-reductive PP4 (6)3.370.042
At3g12780.1 Phosphoglycerate kinase-1 (PGK-1)1.3.03 PS.Calvin cycle.phosphoglycerate kinase; 4.10 glycolysis.phosphoglycerate kinase5 (9)1.690.036
At3g62030.1 Peptidylprolyl isomerase ROC429.6 protein.folding6 (4)1.670.073
At2g21330.1 SFBA-11.3.06 PS.Calvin cycle.aldolase; 4.07 glycolysis.aldolase7 (8)1.640.040
At1g56190.1 Phosphoglycerate kinase-1 (PGK-2)1.3.03 PS.Calvin cycle.phosphoglycerate kinase8 (11)1.390.029
At2g21170.1 TPI-1 (plastid)1.3 PS.Calvin cycle9 (5)1.290.044
At3g01500.1 CA18.3 TCA/org. transformation.carbonic anhydrases10 (7)1.050.041
At3g45140.1 Lipoxygenase AtLOX2, plastid17.7.1 hormone metabolism.jasmonate.synthesis-degradation11 (22)0.750.008
At5g20720.1 CPN2129.6 protein.folding12 (13)0.650.027
At3g26650.1 Glyceraldehyde-3-phosphate dehydrogenase A-2 (GAPA-2)1.3.04 PS.Calvin cycle.GAP13 (15)0.650.017
At3g11630.1 2-Cys peroxiredoxin A21.5 redox.periredoxins14 (10)0.620.030
At1g12900.1 Glyceraldehyde-3-phosphate dehydrogenase A-1 (GAPA-1)1.3.04 PS.Calvin cycle.GAP15 (16)0.620.016
At5g06290.1 2-Cys peroxiredoxin B21.5 redox.periredoxins16 (12)0.610.028
At3g04790.1 Ribose-5-phosphate isomerase (PRI)1.3.09 PS.Calvin cycle.Rib5P isomerase; 7.2 OPPP.non-reductive PP17 (14)0.580.021
At4g24280.1 cpHSP70–1 (DnaK homologue)e29.6 protein.folding18 (23)0.570.007
At1g42970.1 Glyceraldehyde-3-phosphate dehydrogenase B (GAPB)1.3.04 PS.Calvin cycle.GAP19 (19)0.560.013
At3g55800.1 Sedoheptulose-bisphosphatase (SBPase)1.3.08 PS.Calvin cycle.seduheptulose bisphosphatase20 (17)0.550.014
At2g39730.1 Rubisco activase (R activase)1.3.12 PS.Calvin cycle.Rubisco-interacting21 (20)0.520.011
At4g38970.1 SFBA-21.3.06 PS.Calvin cycle.aldolase; 4.07 glycolysis.aldolase22 (18)0.510.014
At4g20360.1 EF-Tu, chloroplast precursor29.2.4 protein.synthesis.elongation23 (21)0.500.010
  • a Rank determined by relative abundance measured in terms of relative spot volume; in parentheses, rank according to normalized concentration.

  • b Protein abundance as measured by spot volume with appropriate corrections.

  • c Relative concentration with appropriate corrections.

  • d In the case of RBCS with four genes (At5g38410, At5g38420, At5g38430, and At1g67090) and very high homology, mass spectrometry measurements typically could not distinguish between the different paralogues.

  • e cpHSP70-2 (At5g49910.1) appears to be expressed at slightly lower levels than cpHSP70-1 in the stroma.