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Table 3 Clustering of de novo synthesized proteins with identified functional assignment

From: The link between transcript regulation and de novo protein synthesis in the retrograde high light acclimation response of Arabidopsis thaliana

Cluster Response pattern Transcripts/genes Functional role
1 LH & NH low DHAR Antioxidant defence
GAPDH B subunit Photosynthesis
PSII subunit O-2 Photosynthesis
PSII subunit P-1 Photosynthesis
Ribose 5-P isomerase A Photosynthesis
RPL12, ribosomal protein Protein synthesis
SOD, Cu/Zn Antioxidant defence
Thioredoxin m2 Redox regulation
2 LH & NH high Carbonic anhydrase 2 Photosynthesis
Chaperonin 60 beta Protein folding
FBP aldolase1 Photosynthesis
FBP aldolase 2 Photosynthesis
HCF 136 Photosynthesis
HSP 70-1, cp Stress response
Lactate/malate DH Respiration
O-Acetyl serine thiol lyase B Sulfur metabolism
3 NH high, LH low 3-Ketoacyl CoA thiolase 3 Fatty acid metabolism
GAP C2 subunit Photosynthesis
Glutamine synthetase 2 Nitrogen metabolism
Phosphoglycerate kinase 1 Photosynthesis
Phosphoribulo kinase Photosynthesis
Rubisco activase Photosynthesis
Plastid-lipid-associated protein 1 Stress response
RubisCO SU 1A Photosynthesis
SBPase Photosynthesis
SAM synthetase 1 Sulfur metabolism
4 N, NH-high; L, LH-low ATP synthase beta Photosynthesis
ATP synthase delta Photosynthesis
APX 1 Antioxidant defence
APx, stromal, cp Antioxidant defence
Carbonic anhydrase 1 Photosynthesis
Cyclophilin Cyp 20-3 Redox regulation
Malate DH cyt Redox regulation
PSII OEC Photosynthesis
No peculiar group pattern   2-Cys Peroxiredoxin Antioxidant defence
Germin 3 oxalate oxidase Stress defence
GST F8 Stress defence
GST F9 Stress defence
HSP 70-2, cp Stress defence
Malate DH, cp Redox regulation
Mn SOD Antioxidant defence
Phosphoglycerate mutase Glycolysis
Plastocyanin (DRT 112) Photosynthesis
Ribosomal protein S1 Protein synthesis
RubisCo large subunit Photosynthesis
Ribulose-5-P epimerase Photosynthesis
Thioredoxin m1 Redox regulation
Triosephosphate isomerase Photosynthesis
  1. The proteins were clustered using the Delta 2D-software package and assigned to four major types of regulation (Clusters 1 to 4) as outlined.