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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.