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Table 1 Overview of protein and transcript that are significantly differentially expressed in the targeted OnPLS model

From: OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

JGI V2.2 ID

MapMan name

MapMan symbol

AS-SOD9

AS-SOD24

   

P

/

T

P

/

T

POPTR_0002s14740

Amino acid metabo.

3-phosphoshikimate 1-carboxyvinyltransferase

↑

/

↑

↑

/

↑

POPTR_0013s05850

 

ATCIMS (cobalamin-independent methionine synthase)

↑

/

―

↓

/

―

POPTR_0010s16420

Cell wall

RGP3 (reversibly glycosylated polypeptide 3)

↓

/

↓

↓

/

↑

POPTR_0017s13350

 

RGP2 (reversibly glycosylated polypeptide 2)

↓

/

↓

↓

/

↓

POPTR_0017s12760

 

UDP-glucose 6-dehydrogenase

↑

/

―

↓

/

―

POPTR_0009s13270

Cell.cycle

Peptidyl-prolyl cis-trans isomerase/cyclophilin (CYP2)/rotamase

↓

/

―

↓

/

―

POPTR_0003s21080

Cell.organisation

TUA5 (tubulin alpha-5)

↓

/

―

↓

/

―

POPTR_0002s09610

 

ANNAT1 (annexin arabidopsis 1)

↓

/

―

↓

/

―

POPTR_0001s31700

 

ACT7 (actin 7)

↓

/

―

↓

/

―

POPTR_0001s04180

 

TUA5 (tubulin alpha-5)

↓

/

―

↓

/

―

POPTR_0001s29670

 

TUA6 (tubulin alpha-6 chiain)

↓

/

―

↓

/

―

POPTR_0002s11250

 

TUA6 (tubulin alpha-6 chiain)

↓

/

―

↓

/

―

POPTR_0006s15090

DNA.synthesis

3, NFA3

↑

/

↓

↓

/

↓

POPTR_0009s03310

 

H2B/HTB2 (histone h2b)

↓

/

―

↓

/

―

POPTR_0016s12760

Fermentation

Pyruvate decarboxylase

↓

/

↑

↓

/

↑

POPTR_0001s38560

Gluconeogenesis

Malate dehydrogenase (NAD), mitochondrial

↑

/

―

↓

/

―

POPTR_0006s17940

Glycolysis

Fructose-bisphosphate aldolase

↑

/

↑

↓

/

↑

POPTR_0015s14380

 

LOS2 (low expression of osmotically responsive genes 1)

↑

/

―

↓

/

―

POPTR_0010s06560

 

GAPDH.3 (glyceraldehyde-3-phosphate dehydrogenase (GAPDH))

↓

/

―

↓

/

―

POPTR_0012s09570

 

GAPDH 1.1

↓

/

―

↓

/

―

POPTR_0006s11400

 

2,3-biphosphoglycerate-independent phosphoglycerate mutase

↑

/

―

↓

/

―

POPTR_0002s23510

Hormone metabolism

ATB2

↓

/

↑

↓

/

↑

POPTR_0001s05100

Lipid metabolism.

MOD1 (mosaic death 1)

↓

/

―

↓

/

―

POPTR_0007s01850

Major CHO metabolism

pfkB-type carbohydrate kinase family protein

↑

/

↑

↑

/

↑

POPTR_0002s14730

 

Transketolase

↑

/

―

↑

/

―

POPTR_0001s05690

 

AAC2 (ADP/ATP carrier 2)

↑

/

―

↓

/

―

POPTR_0002s25950

Misc.

Acid phosphatase class B family protein

↓

/

―

↓

/

―

POPTR_0006s18240

 

GDSL-motif lipase/hydrolase family protein

↑

/

―

↓

/

―

POPTR_0010s15250

 

Tropinone reductase, putative/tropine dehydrogenase

↓

/

↓

↓

/

↑

POPTR_0007s07960

N-metabolism

ATGSR1 (Arabidopsis thaliana glutamine synthase clone R1)

↑

/

―

↓

/

―

POPTR_0013s05480

 

GDH1 (glutamate dehydrogenase 1)

↓

/

―

↓

/

―

POPTR_0001s10670

Nucleotide metabolism

NDPK1 (nucleoside diphosphate kinase 1)

↑

/

―

↓

/

―

POPTR_0001s32490

Protein.aa activation

Methionine--tRNA ligase, putative/methionyl-tRNA synthetase

↑

/

―

↓

/

―

POPTR_0006s24090

Protein.degradation

APM1 (aminopeptidase M1)

↓

/

―

↓

/

―

POPTR_0016s12720

 

ATG2 (G2p-related protein)

↓

/

―

↓

/

―

POPTR_0005s02520

 

RPT5A (regulatory particle triple-A 5A)

↓

/

―

↓

/

―

POPTR_0018s14290

 

PBA1 (20S proteasome beta subunit A 1)

↑

/

↑

↑

/

↑

POPTR_0009s15910

Protein.folding

Chaperonin

↓

/

―

↓

/

―

POPTR_0001s35790

Protein.folding

Chaperonin

↓

/

―

↓

/

―

POPTR_0001s14040

 

HSP60 (Heat shock protein 60)

↓

/

―

↓

/

―

POPTR_0008s04230

Protein.synthesis

Elongation factor 1-alpha/EF-1-alpha

↑

/

↑

↓

/

↑

POPTR_0001s23190

 

Elongation factor 1-beta/EF-1-beta

↑

/

―

↓

/

―

POPTR_0012s09840

 

Elongation factor 1-beta, putative/EF-1-beta

↓

/

↓

↓

/

↓

POPTR_0002s05220

  

↑

/

―

↓

/

―

POPTR_0009s12150

 

40S ribosomal protein S25 (RPS25B)

↑

/

―

↑

/

―

POPTR_0016s05530

 

40S ribosomal protein S2 (RPS2C)

↓

/

―

↓

/

―

POPTR_0008s04400

 

40S ribosomal protein S23 (RPS23B)

↓

/

―

↓

/

―

POPTR_0006s21210

 

ATRPS5B (ribosomal protein 5B)

↓

/

―

↓

/

―

POPTR_0004s09830

 

40S ribosomal protein S25 (RPS25B)

↑

/

↑

↑

/

↑

POPTR_0001s26950

 

40S ribosomal protein S8 (RPS8B)

↑

/

―

↓

/

―

POPTR_0002s24410

 

60S ribosomal protein L13A (RPL13aC)

↓

/

―

↓

/

―

POPTR_0002s14250

 

60S ribosomal protein L15 (RPL15A)

↓

/

―

↓

/

―

POPTR_0012s03450

 

60S ribosomal protein L19 (RPL19B)

↓

/

―

↓

/

―

POPTR_0004s07620

 

60S ribosomal protein L19 (RPL19B)

↓

/

―

↓

/

―

POPTR_0001s35630

 

60S ribosomal protein L27 (RPL27C)

↓

/

―

↓

/

―

POPTR_0008s05970

 

60S ribosomal protein L35a (RPL35aC)

↓

/

―

↓

/

―

POPTR_0018s13700

 

60S ribosomal protein L7 (RPL7C)

↓

/

―

↓

/

―

POPTR_0002s18010

 

60s acidic ribosomal protein P1

↓

/

↑

↓

/

↑

POPTR_0013s01220

Protein.targeting

AT-IMP (Arabidopsis thaliana importin alpha)

↓

/

―

↓

/

―

POPTR_0002s19210

 

ATARFA1E (ADP-ribosylation factor A1E)

↓

/

↑

↓

/

↑

POPTR_0008s12550

PS.lightreaction.

ATP synthase beta chain 2, mitochondrial

↓

/

↓

↓

/

↑

POPTR_0006s11570

Redox.

ATMDAR1 (monodehydroascorbate reductase 1)

↑

/

―

↓

/

―

POPTR_0006s13440

 

APX2 (ascorbate peroxidase 2)

↓

/

―

↓

/

―

POPTR_0001s44990

 

TPX1 (thioredoxin-dependent peroxidase 1)

↑

/

―

↑

/

―

POPTR_0003s11350

 

ATHIP1 ( HSP70-interacting protein 1)

↓

/

―

↓

/

―

POPTR_0005s25420

 

ATTRX1 (Arabidopsis thaliana thioredoxin H-type 1)

↑

/

↑

↑

/

↑

POPTR_0002s19940

 

ATPDIL2-1/MEE30/UNE5 (PDI-like 2–1)

↑

/

―

↑

/

―

POPTR_0014s15820

 

ATPDIL2-2 (PDI-like 2–2)

↑

/

―

↓

/

―

POPTR_0018s03000

RNA

Chloroplast nucleoid DNA-binding protein

↓

/

―

↓

/

―

POPTR_0004s16260

 

ATGRP7 (cold, circadian rhythm, and rna binding 2)

↑

/

↑

↑

/

↑

POPTR_0002s03580

Secondary metabolism

Isoflavone reductase

↓

/

―

↓

/

―

POPTR_0002s10000

Signaling

GRF2 (general regulatory factor 2)

↓

/

―

↓

/

―

POPTR_0004s17840

Stress.abiotic.cold

ATGRP2B (glycine-rich protein 2B)

↑

/

↓

↓

/

↓

POPTR_0001s18040

 

HSP91 (heat shock protein 91)

↓

/

―

↓

/

―

POPTR_0009s08320

 

mtHSC70-2 (heat shock protein 70)

↑

/

―

↑

/

―

POPTR_0004s04450

 

Pollen Ole e 1 allergen and extensin family protein

↓

/

―

↓

/

―

POPTR_0008s16670

TCA

Malate dehydrogenase, cytosolic

↓

/

―

↓

/

―

POPTR_0004s07320

TCA

Isocitrate dehydrogenase

↑

/

―

↓

/

―

POPTR_0013s11070

Transport.misc

SEC14 cytosolic factor family protein

↓

/

↓

↓

/

↓

POPTR_0001s36710

Not assigned

2-oxoacid dehydrogenase family protein

↑

/

↑

↓

/

↑

POPTR_0010s16050

 

Stable protein 1-related

↓

/

↑

↓

/

↑

POPTR_0602s00200

 

VEP1 (vein patterning 1)

↓

/

―

↓

/

―

POPTR_0017s10720

 

Unknown protein

↓

/

―

↓

/

―

POPTR_0017s13710

 

Unknown protein

↑

/

―

↑

/

―

POPTR_0005s26930

 

Unknown protein

↑

/

―

↑

/

―

  1. Columns indicate Populus trichocarpa gene ID; Mapman name with similar classes grouped in rows; Mapman symbol; and AS-SOD9, AS-SOD24 protein (P) and transcript (T) expression levels, respectively. Symbols indicate: ↑, upregulated (relative to WT); ↓, downregulated; - not significantly differentiated expression. Data shown in Additional file 2: Table S2.2, Additional file 2: Table S1.2.