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Table 1 Mitochondrial proteins affected by rotenone treatment

From: Identification of novel proteins affected by rotenone in mitochondria of dopaminergic cells

Increased ≥ two-fold after rotenone treatment
protein Description ASAPRatio* Ref(s) for relevance to neurodegenerative disease
IPI00319790 Dnaj (Hsp40) homolog, subfamily C, member 7 0  
IPI00331385 Mdj11   
IPI00371053 Similar to dnaj (Hsp40) homolog, subfamily C, member 7   
IPI00128647 Crumbs-like protein 1 precursor 0  
IPI00204778 (IPI00129395) Large neutral amino acids transporter small, subunit 1 0  
IPI00331577 Solute carrier family 7 (Cationic amino acid transporter y+ system) member 5   
IPI00223004 Peroxisomal CA-dependent solute carrier homolog 0  
IPI00208799 Solute carrier organic anion transporter family member 1A5 0  
IPI00130878 Voltage-dependent T-type calcium channel alpha-1H subunit 0  
IPI00388311 Ensembl_locations(Chr-bp):10-14622136   
IPI00189595 Voltage-dependent T-type calcium channel alpha-1H subunit   
IPI00213584 Alanine – glyoxylate aminotransferase 2 mitochondrial precursor 0  
IPI00365283 Similar to capping protein beta subunit, isoform 2 0  
IPI00406800 Splice isoform 1 of P47757 F-actin capping protein beta subunit   
IPI00113992 GDP-mannose pyrophosphorylase B homolog 0  
IPI00153603 28S ribosomal protein s18c, mitochondrial precursor 0  
IPI00372556 Similar to NG26 0  
IPI00130339 Protein BAT5   
IPI00123138 Leucyl-trna synthetase 0  
IPI00116966 Asparagine synthetase 0  
IPI00406634 Ensembl_locations(Chr-bp):8-124923273 0 [48]
IPI00170128 (IPI00327108) Paraplegin   
IPI00134390 Microsomal dipeptidase precursor 0  
IPI00200392 SMHS2 0  
IPI00177183 RIKEN cDNA 4833427E09 gene   
IPI00116913 Laminin alpha-5 chain precursor 0  
IPI00331507
(IPI00325517)
Cullin homolog 5 0  
IPI00135708 Dual specificity mitogen-activated protein kinase kinase 2 0 [49]
IPI00407256 Mitogen activated protein kinase kinase 2   
IPI00231331 Dual specificity mitogen-activated protein kinase kinase 2   
IPI00118384 14-3-3 protein epsilon 0  
(IPI00325135)    
IPI00309516 Hedgehog-interacting protein 0  
IPI00318010 Polycystic kidney disease 1-like 2 0  
IPI00368473 Nuclear mitotic apparatus protein 1 0  
IPI00371741 Similar to zinc finger protein TZF-L 0  
IPI00408182 Tmc3 protein 0  
IPI00222063 Weakly similar to hypothetical 71.7 kda protein 0  
IPI00222264 HRIHFB2003 protein homolog 0  
IPI00366079 Similar to expressed sequence AL022641 0.02  
IPI00163011 Thioredoxin domain containing protein 5 precursor   
IPI00396730 Growth differentiation factor 10 0.1 ± 0.02  
IPI00165799 UBX domain-containing protein 2 0.12 ± 0.1  
IPI00371952 Similar to RIKEN cDNA 1300013G12   
IPI00129470 Ran gtpase-activating protein 1 0.13 ± 0.03  
IPI00319167 Hydrocephalus inducing 0.13 ± 0.05  
IPI00310128 Tissue inhibitor of metalloproteinase 2 0.15 ± 0.02  
IPI00132801 Glucagon-like peptide 1 receptor precursor 0.22 ± 0.05  
IPI00311576 Testis expressed gene 10 0.24 ± 0.08  
IPI00400137 RIKEN cDNA 1200011N24 0.27 ± 0.05  
IPI00403336 MKIAA0567 protein   
IPI00117657 Dynamin-like 120 kda protein, mitochondrial precursor   
IPI00341975 RIKEN cDNA 6430598A04 gene 0.27 ± 0.09  
IPI00317309 Annexin A5 0.27 ± 0.12 [50]
IPI00231954 6-phosphofructokinase, type C 0.31 ± 0.06  
IPI00113824 Basement membrane-specific heparan sulfate proteoglycan core protein precursor 0.33 ± 0.09  
IPI00132276 (IPI00210971) Vesicle-associated membrane protein 3 0.34 ± 0.07  
IPI00210089 Voltage-gated sodium channel 0.35 ± 0.06 [51]
IPI00110560 Talin 1 0.36 ± 0.06  
IPI00362014 similar to talin   
IPI00191107 Similar to mitochondrial ribosomal protein S21 0.37 ± 0.16  
IPI00391281 Ensembl_locations(Chr-bp):2-190609002   
IPI00127069 Sideroflexin 2 0.38 ± 0.05 [52]
IPI00400079 Splice isoform 1 of Q9JLT4 Thioredoxin reductase 2, mitochondrial precursor 0.4 ± 0.19  
IPI00124699 Thioredoxin reductase 2   
IPI00403407 Adult male stomach cDNA, RIKEN full-length enriched library, clone:2210009O12 product:thioredoxin reductase 2, full insert sequence   
IPI00350590 Splice isoform 4 of Q9JLT4 Thioredoxin reductase 2, mitochondrial precursor   
IPI00207072 NADH-ubiquinone oxidoreductase 13 kda-A subunit, mitochondrial precursor 0.41 ± 0.13  
IPI00330862 Villin 2 0.42 ± 0.07  
IPI00111460 Williams-Beuren syndrome chromosome region 16 protein homolog 0.46 ± 0.12  
IPI00189798 Similar to Williams-Beuren syndrome chromosome region 16 homolog   
IPI00112935 Serine hydroxymethyltransferase 0.47 ± 0.06 [53]
IPI00131577 Heme oxygenase 1 0.47 ± 0.12 [54]
IPI00177038 Actin-like protein 2 0.47 ± 0.17  
IPI00400012 Similar to Actin-like protein 2 (Actin-related protein 2)   
IPI00362072 Similar to actin-related protein 2   
IPI00364385 Similar to RIKEN cDNA 5730406I15 0.5 ± 0.19  
IPI00228236 Microsomal signal peptidase 25 kda subunit   
Decreased ≥ two-fold after rotenone treatment
IPI00212082 Ensembl_locations(Chr-bp):1-153887103 2.03 ± 0.62  
IPI00368435 Similar to Ten-m4   
IPI00157497 Ten-m4   
IPI00351867 Odd Oz\ten-m homolog 4   
IPI00210503 Long-chain-fatty-acid – coa ligase 4 2.04 ± 0.44  
IPI00403180
(IPI00378474)
Similar to mitochondrial isoleucine trna synthetase 2.06 ± 0.22  
IPI00408243 Similar to single-stranded DNA binding protein 2.07 ± 0.19  
IPI00124980 Prolactin regulatory element-binding protein 2.09 ± 0.48  
IPI00229040 Retinol dehydrogenase 13 2.15 ± 2.41  
IPI00198369 Sorting nexin 1 2.21 ± 0.6  
IPI00125441 Sorting nexin 1   
IPI00124120 Sacsin 2.26 ± 0.38  
IPI00373012 Similar to sacsin   
IPI00364603 Similar to RNA-binding protein EWS 2.33 ± 0.31  
IPI00191745 Similar to coproporphyrinogen oxidase 2.38 ± 0.41  
IPI00192034
(IPI00114375)
Dihydropyrimidinase related protein-2 2.46 ± 0.44  
IPI00285485 Protein kinase C-binding protein NELL2 precursor 2.57 ± 0.61  
IPI00136067 Jagged 2 precursor 2.73 ± 0.46  
IPI00365920 Jagged 2   
IPI00311509 Aladin 2.9 ± 0.64  
IPI00205182 Interleukin-6 receptor alpha chain precursor 3.03 ± 0.48  
IPI00206288 interleukin 6 receptor   
IPI00344360 Transcription termination factor, mitochondrial 4 ± 1.42 [55]
IPI00370029 Similar to NG28 4.43 ± 0.97  
IPI00378753 Similar to aminopeptidase N 4.68 ± 0.99  
IPI00405386 T-complex protein 10a 5.36 ± 0.87  
IPI00230453 Similar to VIP36-like protein precursor (Lectin, mannose-binding 2-like) 5.45 ± 0.6  
IPI00357887 Similar to lectin, mannose-binding 2-like   
IPI00123314 Sonic hedgehog protein precursor 5.47 ± 0.98 [56]
IPI00196054
(IPI00125256)
C-C chemokine receptor type 2 6.4 ± 1.67  
IPI00353420 Cytoskeletal protein 7.56 ± 1.41  
IPI00388450 Protein tyrosine phosphatase, receptor type, U 8 ± 1.03  
IPI00338565 Mutant fibrillin-1 8.39 ± 2.97  
IPI00122438 Fibrillin 1 precursor   
IPI00229434 Apoptosis stimulating of p53 protein 2 38.26 ± 2.99  
IPI00269076 Adenylate kinase 2 999  
IPI00214038
(IPI00118120)
Myosin Va 999  
IPI00393437 Ensembl_locations(Chr-bp):8-80002855   
IPI00405881 Ensembl_locations(Chr-bp):9-77611564   
IPI00331016 Similar to SEC24 related gene family, member B 999  
IPI00372727 Similar to Protein transport protein Sec24B (SEC24-related protein B)   
IPI00309437 ALDR protein 999  
IPI00387535 Fatty acid coenzyme A ligase, long chain 3 999  
IPI00169772 Long-chain-fatty-acid – coA ligase 3   
IPI00330207 Splicing factor 3B subunit 1 999 [57]
IPI00366952 Splicing factor 3b, subunit 1, 155kd   
IPI00118235 Mitochondrial 60S ribosomal protein L3 999  
IPI00115094 [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor 999  
IPI00409229 Ensembl_locations(Chr-bp):7-120047962   
IPI00204344 [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor   
IPI00324180 Breast cancer type 2 susceptibility protein homolog 999  
IPI00366614 Breast cancer susceptibility protein BRCA2   
IPI00118021 Gtrgeo22 999  
IPI00313998 Sulfide:quinone oxidoreductase, mitochondrial precursor 999  
IPI00357889 Similar to 28S ribosomal protein S9, mitochondrial precursor (MRP-S9) 999  
IPI00132700 39S ribosomal protein L35, mitochondrial precursor 999  
IPI00189766 Membrane associated progesterone receptor component 1 999  
IPI00208648 Disks large-associated protein 2 999  
IPI00117912 Semaphorin 5B precursor 999  
IPI00400269 Hypothetical protein   
IPI00365296 Similar to sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B   
IPI00403907 Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain   
IPI00127131 Osa1 nuclear protein 999  
IPI00113214 Ubiquitin carboxyl-terminal hydrolase 5 999 [58]
IPI00118333 RW1 protein 999  
IPI00362105 Similar to proteasome 26S ATPase subunit 6 999  
IPI00125971 26S protease regulatory subunit S10B   
IPI00231757 Proteasome (prosome, macropain) subunit, alpha type 2 999 [59]
IPI00404117 Proteasome subunit alpha type 2   
IPI00318970 Proteasome (Prosome, macropain) subunit, alpha type 2   
IPI00337930 RIKEN cDNA 4930432B04 999  
IPI00203604 Brain protein 44-like protein 999  
IPI00402961 Ensembl_locations(Chr-bp):12-106426680   
IPI00124292 Brain protein 44-like protein   
IPI00406403 Ensembl_locations(Chr-bp):Un_random_NT_060620-5611 999  
IPI00381837 similar to putative pheromone receptor   
IPI00372549 Similar to MHC class I cell surface glycoprotein 999  
IPI00367751 Similar to pecanex 1 999  
IPI00365997 Similar to PHD finger protein 2 999  
IPI00114424 RIKEN cDNA D930036F22 gene 999  
IPI00326141 Augmenter of liver regeneration 999  
IPI00191045 Similar to zinc finger protein 296 999  
IPI00210183 Nuclear receptor binding factor-1 999  
  1. IPI: International protein index. ASAP Ratio: Automated Statistical Analysis of Protein abundance ratio. The results are expressed as 12C (DMSO)/13C (Rotenone). *: Ratio was expressed as 0 and 999 when only the 13C- and 12C-labeled peptides were found, respectively, in the sample. Proteins sharing the same peptides but with different protein identification numbers are listed in one cell.