Download Supplementary

Supplementary Information
Figure S1. IPA representation of mitochondrial pathways. The complete list of identified proteins was submitted to IPA. Almost all the mitochondrial functional proteins
were mapped (shown in grey).
Int. J. Mol. Sci. 2015, 16, S1–S7; doi:10.3390/ijms161125973
www.mdpi.com/journal/ijms
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S1. Differentially expressed proteins involved in cell death and mitochondrial quality control in response to stress.
Accession Number
Gene Name
Mitochondria-mediated cell death:
G3V741
Slc25a3
Q9WVJ6
Tgm2
Q9Z2L0
Vdac1
P81155
Vdac2
Q9R1Z0
Vdac3
Mitochondria quality control:
G3V913
Hspb1
P63018
Hspa8
P97541
Hspb6
Protein Name
Function, Process
IR-LT3S (FC)
IR-NT3 (FC)
Phosphate carrier protein
Protein Tgm2
Voltage-dependent anion-selective channel protein 1
Voltage-dependent anion-selective channel protein 2
Voltage-dependent anion-selective channel protein 3
Mitochondria permeability transitinon (cell death)
Clearance of damaged mitochondria
Apoptosis, necrosis
Apoptosis, necrosis
Apoptosis, necrosis
NS
7.0
3.4
3.4
3.5
−2.2 *
39 *
NS *
1.80
2.05
Heat shock 27 kDa protein 1
Heat shock cognate 71 kDa
Heat shock protein β-6
Chaperone, negative regulation of oxidative stress
Chaperone-mediated protein folding
Chaperone, protein homodimerization
Chaperone, maturation, structural maintenance and proper
regulation of target proteins
Mitochondrial protein import and macromolecular assembly
Proteins translocation from the inner membrane into the
mitochondrial matrix
Chaperone-like activity, preventing aggregation of various proteins
under stress conditions
Chaperone-like protein essential for mitochondrial complex assemby
Chaperone-like. Proper conformation and functioning
of protein complexes in the respiratory chain
Assembly of mitochondrial respiratory complex COX23
Cytochrome C Oxidase Assembly Homolog
Mitochondrial protein biosynthesis
Cofactor biosynthesis
Chaperone-like, protein folding and guiding
through the mitochondrial intermembrane space
Repair of damaged DNA
Cellular response to DNA damage stimulus
Serine protease inhibitor, responce to oxidative stress and wounding
Translation or stability of mitochondrially encoded cytochrome c
oxidase subunits
Abolishes mitochondrial damage and BNIP3-mediated apoptosis
42
NS
NS
67 *
20 *
3.1 *
7.5
24 *
4.4
4.1
4.9
7.3
14
27 *
4.2
5.3
5.6
6.2
7.3
1.4 *
5.1
2.4
3.7 *
8.0 *
NS
1.3 *
8.7
7.3
3.7
28 *
15 *
14 *
2.9
4.4
13
15
P34058
Hsp90ab1
Heat shock protein HSP 90-β
P63039
Hspd1
Heat shock protein 60 kDa
P97576
Grpel1
GrpE protein homolog 1
P23928
Cryab
α-crystallin B chain
Q5XIM0
Bcs1l
BCS1-like (Yeast)
Q5BJQ0
Adck3
Chaperone activity of bc1 complex-like
D4AC73
Chchd7
Protein Chchd7
P85834
Q68FT1
Tufm
Coq9
P62076
Timm13
P62909
G3V8V6
P31044
Rps3
Macrod1
Pebp1
Elongation factor Tu
Ubiquinone biosynthesis protein
Mitochondrial import inner membrane
translocase subunit Tim13
40S ribosomal protein S3
O-acetyl-ADP-ribose deacetylase MACROD1
Phosphatidylethanolamine-binding protein 1
F1LM33
Lrpprc
Leucine-rich PPR
P13437
Acaa2
3-ketoacyl-CoA thiolase
S2
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S1. Cont.
Accession Number
Antioxidant defence:
G3V7J0
F1LN88
P35704
Q9R063
P07632
P07895
Gene Name
Protein Name
Function, Process
IR-LT3S (FC)
IR-NT3 (FC)
Aldh6a1
Aldh2
Prdx2
Prdx5
Sod1
Sod2
Aldehyde dehydrogenase family 6, isoform CRA
Aldehyde dehydrogenase
Peroxiredoxin-2
Peroxiredoxin-5
Superoxide dismutase [Cu-Zn]
Superoxide dismutase [Mn]
Aldehyde clearance, prevents aldehyde mediated oxidative stress
Aldehyde clearance, prevents aldehyde mediated oxidative stress
Antioxidant
Antioxidant
Antioxidant
Antioxidant
4.2
NS
NS
NS
NS
NS
10 *
9.6 *
19 *
39 *
8.8 *
12 *
Comparison among groups was performed as described in statistical analysis. FC = fold change with respect to sham group; NS = not significantly different from sham
group; * p vs. IR-LT3S < 0.017.
Table S2. Differentially expressed proteins involved in electron transport and oxidative phosphorilation.
Accession Number
P11608
P15999
G3V6D3
P31399
G3V7Y3
P29419
F7FFJ9
Q06647
P21571
Q68FY0
P32551
Q5M9I5
Q7TQ16
P20788
Q8SEZ5
P10888
P11240
Gene Name
Mt-atp8
Atp5a1
Atp5b
Atp5h
Atp5d
Atp5i
Atp5c1
Atp5o
Atp5j
Uqcrc1
Uqcrc2
Uqcrh
Uqcrq
Uqcrfs1
Mt-co2
Cox4i1
Cox5a
Protein Name
ATP synthase protein 8
ATP synthase subunit α
ATP synthase subunit β
ATP synthase subunit d
ATP synthase subunit δ
ATP synthase subunit e
ATP synthase subunit γ
ATP synthase subunit O
ATP synthase-coupling factor 6
Cytochrome b-c1 complex subunit 1
Cytochrome b-c1 complex subunit 2
Cytochrome b-c1 complex subunit 6
Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit Rieske
Cytochrome c oxidase subunit 2
Cytochrome c oxidase subunit 4 isoform 1
Cytochrome c oxidase subunit 5A
S3
Function, Process
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
ATP synthesis complex V
Electron transport complex III
Electron transport complex III
Electron transport complex III
Electron transport complex III
Electron transport complex III
Electron transport complex IV
Electron transport complex IV
Electron transport complex IV
IR-LT3S (FC)
−55
−4.5
−3.0
−10
−6.4
−9.2
−1.92
−3.6
−4.4
−3.1
−2.0
1.30
−4.3
−5.6
NS
−1.7
NS
IR-NT3 (FC)
−40
−5.2
−2.7
−15
−7.7
−13
−2.5
−3.3
−16
−4.7 *
−2.4
−15 *
−3.9
−6.0
−3.6 *
−6.2 *
−3.4 *
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S2. Cont.
Accession Number
D3ZD09
P11951
P35171
D3ZYX8
D3ZFQ8
Q66HF3
Q5RK08
F1LXA0
B2RYS8
D4A565
D3ZZ21
D3ZLT1
B2RYW3
D3ZG43
Q5RJN0
B0BNE6
Q5XIH3
Q561S0
D3ZS58
Q63362
Q5BK63
Q5PQZ9
P19234
Q641Y2
Q5XIF3
Q66HF1
Q8SEZ0
A9UMV9
D4A5L9
D4A4P3
F1LPG5
Gene Name
Cox6b1
Cox6c2
Cox7a2
Cox7a2l
Cyc1
Etfdh
Gbas
Ndufa12
Ndufb8
Ndufb5
Ndufb6
Ndufb7
Ndufb9
Ndufs3
Ndufs7
Ndufs8
Ndufv1
Ndufa10
Ndufa2
Ndufa5
Ndufa9
Ndufc2
Ndufv2
Ndufs2
Ndufs4
Ndufs1
Mt-nd5
Ndufa7
LOC679794
Ndufa3
Ndufa4
Protein Name
Cytochrome c oxidase subunit 6B1
Cytochrome c oxidase subunit 6C-2
Cytochrome c oxidase subunit 7A2
Cytochrome c oxidase subunit VIIa polypeptide 2 like
Cytochrome c-1 (Predicted), isoform CRA_b
Electron transfer flavoprotein-ubiquinone oxidoreductase
Glioblastoma amplified sequence
NADH dehydrogenase (Ubiquinone) 1 α subcomplex, 12
NADH dehydrogenase (Ubiquinone) 1 β subcomplex 8
NADH dehydrogenase (Ubiquinone) 1 β subcomplex, 5
NADH dehydrogenase (Ubiquinone) 1 β subcomplex, 6
NADH dehydrogenase (Ubiquinone) 1 β subcomplex, 7
NADH dehydrogenase (Ubiquinone) 1 β subcomplex, 9
NADH dehydrogenase (Ubiquinone) Fe-S protein 3
NADH dehydrogenase (Ubiquinone) Fe-S protein 7
NADH dehydrogenase (Ubiquinone) Fe-S protein 8
NADH dehydrogenase (Ubiquinone) flavoprotein 1
NADH dehydrogenase (Ubiquinone) 1 α subcomplex subunit 10
NADH dehydrogenase (Ubiquinone) 1 α subcomplex subunit 2
NADH dehydrogenase (Ubiquinone) 1 α subcomplex subunit 5
NADH dehydrogenase (Ubiquinone) 1 α subcomplex subunit 9
NADH dehydrogenase (Ubiquinone) 1 subunit C2
NADH dehydrogenase (Ubiquinone) flavoprotein 2
NADH dehydrogenase (Ubiquinone) iron-sulfur protein 2
NADH dehydrogenase (Ubiquinone) iron-sulfur protein 4
NADH-ubiquinone oxidoreductase 75 kDa subunit
NADH-ubiquinone oxidoreductase chain 5
Ndufa7 protein
Protein LOC679794
Protein LOC100361144
Protein LOC688963
Function, Process
Electron transport complex IV
Electron transport complex IV
Electron transport complex IV
Electron transport complex IV
Electron carrier protein
Electron carrier protein
Oxidative phosphorylation
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron transport complex I
Electron carrier protein
Electron carrier protein
Electron carrier protein
IR-LT3S (FC)
−3.6
−3.3
−4.0
−27
NS
NS
9.00
−2.4
1.24
NS
NS
−1.71
NS
1.73
2.07
4.0
1.43
−3.1
1.37
2.7
2.8
−25
NS
1.97
3.30
1.44
−3.0
−7.9
−11
2.14
−2.4
IR-NT3 (FC)
−5.6
−8.8 *
−4.4
−12.5
−3.8 *
−2.3 *
6.5 *
−2.7
−5.4 *
−2.1 *
−4.7 *
−1.29
−6.2 *
−2.2
NS *
NS *
−2.2 *
−1.8 *
−4.2 *
−2.7 *
NS *
−29
−3.1 *
−1.4 *
NS *
−3.1
−5.4
−5.2
NS *
−6.2 *
−2.4
Comparison among groups was performed as described in statistical analysis. FC = fold change with respect to sham group; NS = not significantly different from sham
group; * p vs. IR-LT3S < 0.017.
S4
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S3. Differentially expressed proteins involved in pyruvate metabolism and tricarboxylic acid cycle.
Accession
Number
P00507
P38718
D4A5G8
P49432
F1MA54
Q64536
Q8VHF5
Q9ER34
F1LNF7
Q68FX0
P56574
Q5XIJ3
Q5XI78
G3V6P2
Q6P6R2
F1LM47
P13086
Q641Z9
Q6PCT8
Q920L2
P21913
Q5M964
P04636
Gene
Name
Got2
Mpc2
Pdha1l1
Pdhb
Pdk1
Pdk2
Cs
Aco2
Idh3a
Idh3B
Idh2
Idh3g
Ogdh
Dlst
Dld
Sucla2
Suclg1
Sdhc
Sdhd
Sdha
Sdhb
Fh
Mdh2
Protein Name
Function, Process
Aspartate aminotransferase
Mitochondrial pyruvate carrier 2
Protein Pdha1/1
Pyruvate dehydrogenase E1 component subunit β
Pyruvate dehydrogenase (acetyl-transferring) kinase isozyme 1
Pyruvate dehydrogenase (acetyl-transferring) kinase isozyme 2
Citrate synthase
Aconitate hydratase
Isocitrate dehydrogenase (NAD) subunit α
Isocitrate dehydrogenase (NAD) subunit β
Isocitrate dehydrogenase (NADP)
Isocitrate dehydrogenase 3 (NAD), γ
2-oxoglutarate dehydrogenase
Dihydrolipoamide S-succinyltransferase
Dihydrolipoyl dehydrogenase
Protein Sucla2
Succinyl-CoA synthetase (ADP/GDP-forming) subunit α
Succinate dehydrogenase complex, subunit c, integral membrane
Succinate dehydrogenase (ubiquinone) cytochrome b small subunit
Succinate dehydrogenase (ubiquinone) flavoprotein subunit
Succinate dehydrogenase (ubiquinone) iron-sulfur subunit
Fumarate hydratase 1
Malate dehydrogenase
Pre TCA, anaplerotic reaction
Mitochondrial pyruvate transport (pre TCA)
Conversion of pyruvate to acetyl-CoA (pre TCA)
Conversion of pyruvate to acetyl-CoA (pre TCA)
Conversion of pyruvate to acetyl-CoA (pre TCA)
Conversion of pyruvate to acetyl-CoA (pre TCA)
TCA
TCA
TCA
TCA
TCA
TCA
TCA
TCA, (E2 component of 2-oxo-glutarate complex)
TCA, (E3 component of 2-oxo-glutarate complex)
TCA (succinyl-CoA synthetase)
TCA
TCA (succinate dehydrogenase activity)
TCA
TCA
TCA
TCA
TCA
IR-LT3S
(FC)
NS
16
2.8
1.7
11
6.7
NS
2.0
4.2
5.1
5.8
10
N.S
NS
−1.8
12
3.1
1.6
3.0
1.4
1.4
NS
−7.7
IR-NT3
(FC)
10 *
25
5.0 *
3.6
15 *
13 *
7.2 *
4.9 *
4.5
7.0
10 *
15
4.0 *
2.3 *
4.7 *
18 *
5.3 *
1.7
3.3
−1.4 *
NS *
3.4 *
NS *
TCA = tricarboxylic acid cycle. Comparison among groups was performed as described in statistical analysis. FC = fold change with respect to sham group; NS = not
significantly different from sham group; * p vs. IR-LT3S < 0.017.
S5
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S4. Differentially expressed proteins involved in fatty acid transport, biosynthesis and oxidation.
Accession
Number
G3V734
Gene
Name
Decr1
Protein Name
Function, Process
IR-LT3S
(FC)
2.6
IR-NT3
(FC)
13 *
2,4-dienoyl CoA reductase 1
D3ZA93
Acot13
Protein Acot13
G3V796
Q6IMX3
D3ZF13
Q499N5
Q6IMX8
Q5M9H2
Q63704
P18886
Q62651
Acadm
Acads
Ndufab1
Acsf2
Acot2
Acadvl
Cpt1b
Cpt2
Ech1
Q68G41
Eci1
P13803
Q68FU3
Q5XIC0
P14604
P07483
Q9WVK7
P15650
P14882
Q68FZ8
M0R7V3
Etfa
Etfb
Eci2
Echs1
Fabp3
Hadh
Acadl
Pcca
Pccb
Apoo
Acetyl-Coenzyme A dehydrogenase, medium chain
Acetyl-Coenzyme A dehydrogenase, short chain
Acyl carrier protein
Acyl-CoA synthetase family member 2
Acyl-CoA thioesterase 2
Acyl-Coenzyme A dehydrogenase, very long chain
Carnitine O-palmitoyltransferase 1
Carnitine O-palmitoyltransferase 2
Δ(3,5)-Δ(2,4)-dienoyl-CoA isomerase
Dodecenoyl-Coenzyme A δ isomerase
(3,2 trans-enoyl-Coenzyme A isomerase)
Electron transfer flavoprotein subunit α
Electron transfer flavoprotein subunit β
Enoyl-CoA δ isomerase 2
Enoyl-CoA hydratase
Fatty acid-binding protein
Hydroxyacyl-coenzyme A dehydrogenase
Long-chain specific acyl-CoA dehydrogenase
Propionyl-CoA carboxylase α chain
Propionyl coenzyme A carboxylase, β polypeptide
Protein Apoo
Auxiliary enzyme of β oxidation
Regulate intracellular levels of acyl-CoAs,
free fatty acids and CoASH
Fatty acid β oxidation
Fatty acid β oxidation
Fatty acid biosynthesis
Fatty acid metabolism
Increases the utilization of fatty acid substrate
Fatty acid β oxidation
Fatty acid β oxidation
Fatty acid β oxidation
Lipid metabolism, fatty acid β oxidation
6.1
10 *
3.5
4.8
1.4
7.3
NS
4.0
2.9
3.0
NS
5.9 *
6.1 *
−3.4 *
15 *
7.1 *
2.4
1.6 *
3.0
6.2 *
Fatty acid β oxidation
NS
2.1 *
Lipid metabolism
Lipid metabolism
Fatty acid β oxidation
Fatty acid β oxidation
Long chain fatty acid transport, fatty acid β oxidation
Lipid metabolism; fatty acid β-oxidation
Fatty acid β oxidation
Lipid metabolism
Lipid metabolism
Lipid transport
4.04
2.30
3.7
NS
NS
NS
2.2
5.2
2.8
−1.4
3.76
2.72
6.0
6.4 *
49 *
22 *
5.0 *
5.2
4.5
−3.1
Comparison among groups was performed as described in statistical analysis. FC = fold change with respect to sham group; NS = not significantly different from sham
group; * p vs. IR-LT3S < 0.017.
S6
Int. J. Mol. Sci. 2015, 16, S1–S7
Table S5. Differentially expressed proteins involved in various metabolic process and energy homeostasis.
Accession
Gene Name
Protein Name
Number
Carbohydrate, amino acid and keton body metabolism:
P42123
Ldhb
L-lactate dehydrogenase B chain
M0R4B8
N/A
Pyruvate kinase
P16617
Pgk1
Phosphoglycerate kinase 1
G3V6Y6
Pygb
Glycogen phosphorylase
B2GV15
Dbt
Dihydrolipoamide branched chain transacylase E2
B1WBN3
Bckdha
2-oxoisovalerate dehydrogenase subunit α
P29266
Hibadh
3-hydroxyisobutyrate dehydrogenase
P12007
Ivd
Isovaleryl-CoA dehydrogenase
Q5XIT9
Mccc2
Methylcrotonoyl-CoA carboxylase β chain
F1LP30
Mccc1
Methylcrotonoyl-CoA carboxylase subunit α
F1LQZ0
Tmem65
Protein Tmem65
B2GV06
Oxct1
Succinyl-CoA:3-ketoacid coenzyme A transferase 1
P17764
Acat1
Acetyl-CoA acetyltransferase
Energy homeostasis:
Q9WUS0
Ak4
Adenylate kinase 4
M0RC66
Ak1
Adenylate kinase isoenzyme 1 (Fragment)
P09605
Ckmt2
Creatine kinase S-type
Function, Pathway
IR-LT3S
(FC)
IR-NT3
(FC)
Glycolysis, lactate clearance
Glycolysis
Glycolysis
Carbohydrate metabolism
Amino acid catabolic process
Amino acid catabolic process
Amino acid degradation
Amino acid degradation
Amino acid degradation
Amino acid degradation
Amino acid catabolic process
Keton body catabolism
Ketone body metabolism, lipid metabolism
NS
2.4
3.8
12
6.7
5.8
3.2
3.0
3.4
9.7
3.2
NS
−1.9
35 *
30 *
22 *
40 *
5.5
5.6
6.3 *
7.3 *
4.5
7.9
2.1
4.9 *
1.6 *
Homeostasis of cellular nucleotides, cellular energy homeostasis
Homeostasis of cellular nucleotides, cellular energy homeostasis
Energy transduction in tissues with large, fluctuating energy
1.9
27
−6.1
2.3
50
−2.7 *
Comparison among groups was performed as described in statistical analysis. FC = fold change with respect to sham group; NS = not significantly different from sham
group; * p vs. IR-LT3S < 0.017.
S7