Table II. Summary of significantly affected proteins in the developing seedlings of clpr2-1 as compared with wt seedlings and response of stromal chloroplast proteins in fully developed clpr2-1 and wt leaves.
Bio1, biological replicate 1; Bio2, biological replicate 2; LHC, light-harvesting complex.
| Accessionsa | Protein (group) name | Curated locationb | Protein functionc | ΣAdjusted SPCd | Seedling stages 1.07 and 1.14 |
Chloroplast stroma (mature leaves) |
|||
|---|---|---|---|---|---|---|---|---|---|
| clpr2-1/wt seedling 1.07-Bio1e | clpr2-1/wt seedling 1.07-Bio2f | clpr2-1/wt seedling 1.14g | clpr2-1/wt stroma countsh | clpr2-1/wt stroma ICATi | |||||
| AT2G07698.1 | ATP synthase α, β | M | Mitochondrial electron transport | 229 | 1.0 | 2.4 | 4.0 | ||
| ATMG01190.1 | |||||||||
| AT5G49910.1 | cpHSP70-2 | S | Protein folding | 499 | 3.3 | 2.9 | 3.2 | 4.9 | 2.20 (0.09) |
| AT2G28000.1 | CPN60-α1 | S | Protein folding | 1733 | 2.4 | 1.9 | 2.3 | 1.6 | 1.78 (0.41) |
| AT3G13470.1 | |||||||||
| AT5G56500.2 | CPN60-β1,2,3 | S | Protein folding | 1429 | 2.3 | 1.7 | 2.7 | 4.08 (2.30) | |
| AT1G55490.1 | |||||||||
| AT3G62030.1 | Peptidyl-prolyl isomerase ROC4 | S | Protein folding | 1073 | 2.0 | 1.4 | 2.8 | 1.1 | 0.56 (ND) |
| AT5G15450.1 | ClpB3 | S | Protein folding | 116 | 4.5 | 2.5 | 9.6 | 10.0 | 4.20 (ND) |
| AT2G04030.1 | cpHSP90 | S | Protein folding | 730 | 2.8 | 1.8 | 2.4 | 1.4 | 2.63 (0.61) |
| AT4G24280.1 | cpHSP70-1 | S | Protein folding | 532 | 3.3 | 2.0 | 1.4 | 2.1 | 2.41 (0.03) |
| AT3G19170.1 | PreP1,2 | S | Protein degradation | 422 | 4.0 | 3.3 | 4.7 | 1.00 (0.01) | |
| AT1G49630.1 | |||||||||
| AT3G48870.1 | ClpC1,2 | S | Protein degradation | 1236 | 1.8 | 1.5 | 1.7 | 2.03 (0.58) | |
| AT5G50920.1 | |||||||||
| AT1G06950.1 | Tic110 | IE | Protein sorting | 373 | 4.6 | 2.6 | 3.6 | ||
| AT5G13650.1 | Elongation factor TU, TypA/BipA | S | Protein synthesis | 222 | 8.9 | 4.0 | 2.7 | 2.4 | 4.73 (ND) |
| AT4G20360.1 | Elongation factor TU (EF-TU-1) | S | Protein synthesis | 2055 | 1.7 | 1.6 | 1.4 | 1.8 | 2.43 (0.15) |
| AT5G26742.1 | DEAD box RNA helicase (RH3) | S | RNA metabolism | 386 | 13.5 | 5.4 | 6.6 | 2.6 | |
| AT4G04020.1 | Fibrillin (FIB1a) | PG | Plastoglobules | 280 | 3.4 | 6.1 | 3.2 | 4.1 | |
| AT4G22240.1 | Fibrillin (FIB1b) | PG | Plastoglobules | 193 | 1.8 | 4.2 | 8.6 | ||
| AT1G10760.1 | Water dikinase (Sex1) | S | Starch degradation | 141 | 7.0 | 4.8 | 1.2 | 1.35 (0.06) | |
| AT5G13630.1 | Mg2+-protoporphyrin IX chelatase H (GUN5) | IE | Tetrapyrrole synthesis | 273 | 19.0 | 5.1 | 10.1 | 1.5 | |
| AT4G18480.1 | Mg2+-protoporphyrin IX chelatase I-1 (CHLI-1) | S | Tetrapyrrole synthesis | 184 | 4.93 | 2.68 | 1.26 | 2.01 (0.10) | |
| AT5G54770.1 | THI1 | S + M | Thiamine metabolism | 678 | 6.8 | 3.8 | 5.5 | 1.5 | |
| AT3G14210.1 | GDSL-like lipase/acylhydrolase | ND | Secondary metabolism | 811 | 2.0 | 1.9 | 1.0 | ||
| AT5G60600.1 | HDS | TS | Non-mevalonate pathway | 261 | 10.1 | 3.0 | 14.6 | 1.1 | 2.13 (0.03) |
| AT1G74470.1 | GGR | TS | Non-mevalonate pathway | 352 | 2.8 | 2.0 | 0.8 | ||
| AT5G04140.2 | Ferredoxin-dependent glutamate synthase/glu1/Fd-GOGAT 1 | S | Nitrogen metabolism | 1112 | 2.1 | 1.7 | 1.3 | 1.2 | 1.56 (0.06) |
| AT5G52920.1 | Pyruvate kinase-2 | S | Glycolysis | 104 | 3.9 | 2.7 | 10.1 | ||
| AT3G26650.1 | Glyceraldehyde-3-phosphate dehydrogenase A1 (GAPA-1) | S | Calvin cycle | 1842 | 0.7 | 0.9 | 1.0 | 0.7 | 1.01 (0.10) |
| AT5G38420.1 | Rubisco small subunit 2,3b (RBCS-2,3b) | S | Calvin cycle | 523 | 0.5 | 0.5 | 1.4 | ||
| AT5G38410.1 | |||||||||
| ATCG00490.1 | Rubisco large subunit (RBCL) | S | Calvin cycle | 13210 | 0.9 | 0.8 | 0.9 | 0.9 | 1.03 (0.24) |
| ATCG00120.1 | CF1a, atpA | TS | ATP synthase | 2629 | 0.8 | 0.8 | 0.8 | ||
| ATCG00480.1 | CF1b, atpB | TS | ATP synthase | 4608 | 0.9 | 0.7 | 1.0 | ||
| AT1G31330.1 | psaF, subunit III | TI | Photosystem I | 644 | 0.3 | 0.6 | 0.7 | ||
| AT1G61520.1 | LHCI-3, LHCI-680A CAB4 | TI | Photosystem I | 1040 | 0.7 | 0.8 | 0.8 | ||
| AT4G05180.1 | PsbQ OEC16-like Tat lTP | TL | Photosystem II | 518 | 0.2 | 0.5 | 0.3 | ||
| ATCG00680.1 | PsbB CP47 | TI | Photosystem II | 1553 | 0.6 | 1.0 | 0.6 | ||
| ATCG00280.1 | PsbC CP43 | TI | Photosystem II | 827 | 0.5 | 0.9 | 0.5 | ||
| ATCG00270.1 | PsbD D2 | TI | Photosystem II | 801 | 0.6 | 0.9 | 0.5 | ||
| AT3G50820.1 | PsbO OEC33-like | TL | Photosystem II | 353 | 0.4 | 0.6 | 0.4 | ||
| AT1G06680.1 | PsbP-1 OEC23 Tat lTP | TL | Photosystem II | 941 | 0.4 | 0.7 | 0.9 | ||
| AT1G44575.1 | PsbS | TI | Photosystem II | 674 | 0.5 | 0.6 | 1.1 | ||
| AT5G66570.1 | PsbO OEC33 | TL | Photosystem II | 394 | 0.5 | 0.5 | 0.6 | ||
| AT4G10340.1 | LHCII-5, CP26 | TI | Photosystem II | 1524 | 0.7 | 0.9 | 0.7 | ||
| AT2G05100.1 | |||||||||
| AT3G27690.1 | LHCII-2.1,2,3 | TI | Photosystem II | 329 | 0.7 | 0.9 | 0.5 | ||
| AT2G05070.1 | |||||||||
| AT5G54270.1 | LHCII-3 | TI | Photosystem II | 843 | 0.4 | 0.9 | 0.5 | ||
| AT2G21330.1 | Fructose-bisphosphate aldolase-1 (SFBA-1) | S + PG | Calvin cycle | 460 | 1.6 | 1.2 | 1.6 | 1.1 | 0.93 (0.10) |
| AT5G61410.1 | Ribulose-5-phosphate-3-epimerase (RPE) | S | Calvin cycle | 480 | 2.9 | 1.4 | 1.3 | 1.0 | 0.75 (ND) |
| AT5G38430.1 | Rubisco small subunit 1b (RBCS-1b) | S | Calvin cycle | 801 | 0.8 | 0.9 | 0.7 | 1.0 | 0.99 (0.09) |
| AT3G60750.1 | Transketolase-1 (TKL-1) | S | Calvin cycle | 1499 | 2.1 | 1.5 | 1.0 | 0.9 | 0.97 (0.04) |
| AT5G35630.1 | Glutamate-ammonia ligase (GS2), chloroplast | S | Nitrogen metabolism | 1012 | 0.9 | 1.0 | 0.5 | 0.6 | 0.67 (0.03) |
| AT1G63770.2 | Glycyl aminopeptidase (M1) | S | Protein degradation | 60 | 1.3 | 5.7 | 1.5 | 1.03 (ND) | |
| AT4G29060.1 | PSRP-7 | S | Protein synthesis | 371 | 2.4 | 2.3 | 2.1 | 1.3 | 3.28 (0.31) |
| AT1G62750.1 | Elongation factor TU-G (EF-G) (sco1) | S | Protein synthesis | 780 | 3.1 | 1.6 | 1.7 | 1.8 | 2.13 (0.12) |
| AT2G38270.1 | Glutaredoxin | S | Redox regulation | 44 | 2.0 | 6.6 | 0.7 | 1.1 (ND) | |
| AT1G69830.1 | α-Amylase, AtAMY3 | S | Starch degradation | 55 | 10.1 | 2.0 | 0.7 | 1.33 (ND) | |
a Accession numbers. Protein names of accession numbers in italics show significance change in only one of the biological seedling replicates but were quantified in the stroma of mature leaves by both ICAT and spectral counting.
b Curated locations are from the PPDB. M, mitochondria; S, stroma; IE, inner envelope; ND, not determined; TS, thylakoid peripherally associated stromal side; TI, thylakoid integral membrane; TL, thylakoid lumenal side.
c Functional classification is based on the MapMan bin system.
d Total matched MS/MS spectra (spectral counts) adjusted for shared spectral counts across the three biological replicates of the seedling analysis.
e clpr2-1/wt ratio for replicate 1 of seedling analysis, stage 1.07. Ratios in bold passed the significance test (>95% confidence).
f clpr2-1/wt ratio for replicate 2 of seedling analysis, stage 1.07. Ratios in bold passed the significance test (>95% confidence).
g clpr2-1/wt ratio for replicate 3 of seedling analysis, stage 1.14. Ratios in bold passed the significance test (>95% confidence).
h clpr2-1/wt ratio determined by the spectral counting technique for the stromal proteome analysis of chloroplasts isolated from fully developed plants.
i clpr2-1/wt ratio determined by the ICAT technique for the stromal proteome analysis of chloroplasts isolated from fully developed plants. The standard deviation is indicated in parentheses. ND, not determined.