Supplementary Table1 Biochemical Comparison of Commercial Se Yeast Preparations

Supplementary Table1 Biochemical comparison of commercial Se yeast preparations

Supplementary Table 1. Fold Changes are based on protein intensities as calculated using MaxQuant LFQ algorithm and only proteins with a significant change in abundance (p < 0.05; ≥ 2 fold change in abundance) are included. Positive numbers indicate increased abundance and negative figures indicated decreased abundance, relative to the levels in SELM-1. Qualitative differences are also included and indicated as unique to a specific product. Values in red represent proteins with a higher abundance in the Products 2, 3 or 4 relative to SELM-1 and green indicates a lower abundance of that protein relative to SELM-1 (quantitative or qualitative).

Fold Change Yeast Product 2 v. SELM-1 / Fold Change Yeast Product 3 v. SELM-1 / Fold Change Yeast Product 4 v. SELM-1 / Gene Name / Protein IDs / Peptides / Sequence coverage [%] / Mol. weight [kDa] / Protein Description /
2.5417 / ACB1 / YGR037C / 9 / 89.7 / 10.061 / Acyl-CoA-binding protein
Unique to Product 3 / ACC1 / YNR016C / 3 / 1.6 / 250.35 / Acetyl-CoA carboxylase
2.1162 / ACH1 / YBL015W / 12 / 30.4 / 58.711 / Protein with CoA transferase activity
Unique to SELM-1 / ACP1 / YKL192C / 2 / 20.8 / 13.943 / Mitochondrial matrix acyl carrier protein, involved in biosynthesis of octanoate
2.4062 / ACS1 / YAL054C / 19 / 24.4 / 79.14 / Acetyl-coA synthetase isoform
-2.1058 / ADE13 / YLR359W / 9 / 26.1 / 54.51 / Adenylosuccinate lyase, catalyzes two steps in the 'de novo' purine nucleotide biosynthetic pathway
Unique to Product 2 / ADE16 / YLR028C / 5 / 11.5 / 65.282 / Enzyme of 'de novo' purine biosynthesis, isozyme of Ade17p
2.1221 / ADE17 / YMR120C / 7 / 15.9 / 65.262 / Enzyme of 'de novo' purine biosynthesis, isozyme of Ade16p
Unique to SELM-1 / ADE2 / YOR128C / 3 / 5.6 / 62.339 / Phosphoribosylaminoimidazole carboxylase
-2.6954 / ADH1 / YOL086C / 20 / 61.8 / 36.849 / Alcohol dehydrogenase
4.8329 / ADH2 / YMR303C / 14 / 37.1 / 36.731 / Glucose-repressible alcohol dehydrogenase II
3.8602 / Unique to SELM-1 / ADH4 / YGL256W / 8 / 31.2 / 41.142 / Alcohol dehydrogenase isoenzyme type IV
5.4704 / ADH6 / YMR318C / 6 / 23.9 / 39.617 / NADPH-dependent medium chain alcohol dehydrogenase with broad substrate specificity
-2.4789 / ADO1 / YJR105W / 6 / 31.8 / 36.372 / Adenosine kinase, required for the utilization of S-adenosylmethionine (AdoMet)
5.2213 / ADY2 / YCR010C / 3 / 16.3 / 30.726 / Acetate transporter required for normal sporulation
-2.9690 / -3.7902 / -2.4416 / AHP1 / YLR109W / 12 / 89.2 / 19.114 / Thiol-specific peroxiredoxin
-3.7649 / -17.6713 / AIM2 / YAL049C / 8 / 39.8 / 27.089 / Cytoplasmic protein involved in mitochondrial function or organization
-2.4435 / AIM21 / YIR003W / 15 / 31.1 / 74.762 / Protein of unknown function involved in mitochondrial migration along actin filament
-2.3771 / AIM31 / YML030W / 5 / 21.4 / 18.477 / Putative protein of unknown function
3.9127 / AIM38 / YNR018W / 5 / 18.8 / 25.344 / Putative protein of unknown function
2.8055 / AIM41 / YOR215C / 9 / 41.1 / 21.229 / Putative protein of unknown function
2.0078 / ALD4 / YOR374W / 22 / 58.6 / 56.723 / Mitochondrial aldehyde dehydrogenase
6.4126 / AMS1 / YGL156W / 11 / 11.8 / 124.5 / Vacuolar alpha mannosidase, involved in free oligosaccharide (fOS) degradation
8.0620 / APE3 / YBR286W / 14 / 26.1 / 60.137 / Vacuolar aminopeptidase Y, processed to mature form by Prb1p
-2.0876 / ARA1 / YBR149W / 11 / 53.8 / 38.883 / NADP+ dependent arabinose dehydrogenase, involved in carbohydrate metabolism
-3.6997 / ARG1 / YOL058W / 7 / 21.7 / 46.927 / Arginosuccinate synthetase
Unique to SELM-1 / 2.2160 / ARG3 / YJL088W / 4 / 13.9 / 37.845 / Ornithine carbamoyltransferase (carbamoylphosphate:L-ornithine carbamoyltransferase)
-2.6808 / ARG4 / YHR018C / 7 / 20.1 / 51.989 / Argininosuccinate lyase, catalyzes the final step in the arginine biosynthesis pathway
-2.6781 / ARO2 / YGL148W / 8 / 22.1 / 40.838 / Bifunctional chorismate synthase and flavin reductase
-2.3718 / ARO8 / YGL202W / 12 / 32.4 / 56.177 / Aromatic aminotransferase I
2.1400 / -2.5784 / ATP14 / YLR295C / 5 / 62.1 / 14.128 / Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large
6.5428 / 2.3687 / ATP15 / YPL271W / 5 / 90.3 / 6.7425 / Epsilon subunit of the F1 sector of mitochondrial F1F0 ATP synthase
-2.1197 / ATP16 / YDL004W / 7 / 72.5 / 17.02 / Delta subunit of the central stalk of mitochondrial F1F0 ATP synthase
-2.3172 / ATP18 / YML081C-A / 3 / 25.4 / 6.6877 / Subunit of the mitochondrial F1F0 ATP synthase
Unique to Product 4 / ATP3 / YBR039W / 3 / 11.9 / 34.35 / Gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
3.4719 / ATP5 / YDR298C / 8 / 50.5 / 22.814 / Subunit 5 of the stator stalk of mitochondrial F1F0 ATP synthase
3.7586 / ATP7 / YKL016C / 11 / 54 / 19.809 / Subunit d of the stator stalk of mitochondrial F1F0 ATP synthase
-3.1927 / -2.5465 / BGL2 / YGR282C / 12 / 52.4 / 34.118 / Endo-beta-1,3-glucanase, major protein of the cell wall, involved in cell wall maintenance
Unique to Product 4 / BIO2 / YGR286C / 5 / 21.6 / 41.884 / Biotin synthase, catalyzes the conversion of dethiobiotin to biotin
Unique to SELM-1 / BMH1 / YER177W / 14 / 50.6 / 30.091 / 14-3-3 protein, major isoform
Unique to SELM-1 / 2.8198 / BUL1 / YMR275C / 3 / 2 / 109.17 / Ubiquitin-binding component of the Rsp5p E3-ubiquitin ligase complex
-2.8802 / -3.6399 / CAB3 / YKL088W / 5 / 9.1 / 65.237 / Subunit of a phosphopantothenoylcysteine decarboxylase (PPCDC)
Unique to SELM-1 / CAP1 / YKL007W / 2 / 6.7 / 30.699 / Alpha subunit of the capping protein (CP) heterodimer (Cap1p and Cap2p)
-3.5496 / CCS1 / YMR038C / 5 / 25.3 / 27.33 / Copper chaperone for superoxide dismutase Sod1p, involved in oxidative stress protection
-2.7744 / CCW14 / YLR390W-A / 2 / 17.6 / 23.268 / Covalently linked cell wall glycoprotein, present in the inner layer of the cell wall
Unique to Product 3 / CDS1 / YBR029C / 2 / 4.2 / 51.822 / Phosphatidate cytidylyltransferase (CDP-diglyceride synthetase)
-2.2374 / CHZ1 / YER030W / 5 / 43.8 / 17.462 / Histone chaperone for Htz1p/H2A-H2B dimer
Unique to Product 4 / CIT2 / YCR005C / 3 / 7.8 / 51.413 / Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate, peroxisomal isozyme involved in glyoxylate cycle
3.2375 / Unique to SELM-1 / CKS1 / YBR135W / 4 / 30.7 / 17.795 / Cyclin-dependent protein kinase regulatory subunit and adaptor
2.0814 / 2.3985 / CLC1 / YGR167W / 16 / 53.6 / 26.531 / Clathrin light chain
Unique to SELM-1 / CMC4 / YMR194C-B / 3 / 57.5 / 8.2024 / Protein that localizes to the mitochondrial intermembrane space via the Mia40p-Erv1p system
-3.7915 / CMD1 / YBR109C / 13 / 97.3 / 16.135 / Calmodulin
Unique to SELM-1 / -3.1845 / CNB1 / YKL190W / 6 / 56 / 19.639 / Calcineurin B
Unique to Product 2 / COQ5 / YML110C / 2 / 8.5 / 34.684 / 2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase, involved in ubiquinone (Coenzyme Q) biosynthesis
2.5521 / COR1 / YBL045C / 12 / 35.2 / 50.227 / Core subunit of the ubiquinol-cytochrome c reductase complex
2.2818 / -3.5356 / COX12 / YLR038C / 5 / 53 / 9.7878 / Subunit VIb of cytochrome c oxidase
-2.5626 / -4.3436 / COX13 / YGL191W / 4 / 29.5 / 15.021 / Subunit VIa of cytochrome c oxidase
2.2210 / COX23 / YHR116W / 5 / 38.4 / 17.318 / Mitochondrial intermembrane space protein that functions in mitochondrial copper homeostasis
-2.1744 / COX4 / YGL187C / 13 / 79.4 / 17.142 / Subunit IV of cytochrome c oxidase
-5.4010 / COX6 / YHR051W / 9 / 54.7 / 17.341 / Subunit VI of cytochrome c oxidase
2.2891 / CPR6 / YLR216C / 4 / 14.3 / 42.071 / Peptidyl-prolyl cis-trans isomerase (cyclophilin)
-3.8510 / 4.7191 / CPS1 / YJL172W / 3 / 6.9 / 64.596 / Vacuolar carboxypeptidase yscS
-2.1230 / CRH1 / YGR189C / 9 / 17 / 52.757 / Chitin transglycosylase
-2.3369 / CRP1 / YHR146W / 12 / 29.5 / 51.115 / Protein that binds to cruciform DNA structures
-2.6407 / 2.6810 / CTA1 / YDR256C / 5 / 13.2 / 58.555 / Catalase A, breaks down hydrogen peroxide in the peroxisomal matrix formed by acyl-CoA oxidase (Pox1p) during fatty acid beta-oxidation
-2.2302 / CTT1 / YGR088W / 9 / 21.9 / 64.583 / Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide
Unique to SELM-1 / CUE1 / YMR264W / 4 / 25.6 / 22.762 / Endoplasmic reticulum membrane protein that recruits the ubiquitin-conjugating enzyme Ubc7p
2.0335 / CYB2 / YML054C / 10 / 22.7 / 65.539 / Cytochrome b2 (L-lactate cytochrome-c oxidoreductase)
-5.3034 / CYC1 / YJR048W / 12 / 67 / 12.182 / Cytochrome c, isoform 1
2.3946 / 3.7046 / DAP1 / YPL170W / 4 / 44.1 / 16.757 / Heme-binding protein involved in regulation of cytochrome P450 protein Erg11p
-4.4841 / DDR48 / YMR173W / 16 / 65.3 / 46.233 / DNA damage-responsive protein, expression is increased in response to heat-shock stress or treatments that produce DNA lesions
-2.2201 / DED81 / YHR019C / 4 / 10.8 / 62.206 / Cytosolic asparaginyl-tRNA synthetase
2.4728 / DJP1 / YIR004W / 2 / 8.1 / 48.574 / Cytosolic J-domain-containing protein
5.4429 / DLD1 / YDL174C / 11 / 21.1 / 65.292 / D-lactate dehydrogenase, oxidizes D-lactate to pyruvate, transcription is heme-dependent, repressed by glucose, and derepressed in ethanol or lactate
Unique to Product 3 / DLD2 / YDL178W / 4 / 9.4 / 59.268 / D-lactate dehydrogenase, located in the mitochondrial matrix
Unique to Product 3 / DLD3 / YEL071W / 2 / 5.4 / 55.224 / D-lactate dehydrogenase
2.7937 / DOS2 / YDR068W / 2 / 8.4 / 35.964 / Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
-2.4334 / DUG1 / YFR044C / 6 / 15 / 52.871 / Cys-Gly metallo-di-peptidase
-3.6170 / EBP2 / YKL172W / 4 / 8.9 / 49.734 / Required for 25S rRNA maturation and 60S ribosomal subunit assembly
-90.8434 / -7.3471 / ECM15 / YBL001C / 4 / 73.1 / 11.518 / Non-essential protein of unknown function, may have a role in yeast cell-wall biogenesis
2.6263 / Unique to SELM-1 / ECM19 / YLR390W / 2 / 22.3 / 12.515 / Putative protein of unknown function
Unique to SELM-1 / 3.5162 / ECM4 / YKR076W / 8 / 31.9 / 43.273 / Omega class glutathione transferase
Unique to SELM-1 / Unique to SELM-1 / Unique to SELM-1 / EFR3 / YMR212C / 3 / 5 / 89.19 / Protein required for Stt4-containing phosphoinositide kinase patch assembly
4.2439 / EGD1 / YPL037C / 6 / 42.7 / 17.02 / Subunit beta1 of the nascent polypeptide-associated complex (NAC) involved in protein targeting, associated with cytoplasmic ribosomes
2.2927 / EGD2 / YHR193C / 7 / 47.7 / 18.709 / Alpha subunit of the heteromeric nascent polypeptide-associated complex (NAC)
4.7701 / EMI5 / YOL071W / 4 / 28.4 / 19.042 / Subunit of succinate dehydrogenase
-2.1225 / ENO1 / YGR254W / 31 / 81.2 / 46.816 / Enolase I
-2.1858 / ENO2 / YHR174W / 33 / 84.7 / 46.914 / Enolase II
-2.0313 / ENT2 / YLR206W / 3 / 10.6 / 71.806 / Epsin-like protein required for endocytosis and actin patch assembly and functionally redundant with Ent1p
3.3217 / ERG10 / YPL028W / 12 / 42.7 / 41.728 / Acetyl-CoA C-acetyltransferase (acetoacetyl-CoA thiolase)
Unique to SELM-1 / ESF1 / YDR365C / 2 / 3 / 72.409 / Nucleolar protein involved in pre-rRNA processing
2.3870 / ETR1 / YBR026C / 2 / 10 / 42.066 / 2-enoyl thioester reductase
-5.2863 / -3.8622 / EXG1 / YLR300W / 12 / 38.8 / 51.31 / Major exo-1,3-beta-glucanase of the cell wall
Unique to Product 2 / Unique to Product 3 / FAS1 / YKL182W / 6 / 3.9 / 228.69 / Beta subunit of fatty acid synthetase
4.0058 / FAS2 / YPL231W / 9 / 5.8 / 206.94 / Alpha subunit of fatty acid synthetase
Unique to Product 2 / Unique to Product 3 / FET5 / YFL041W / 2 / 5.6 / 70.879 / Multicopper oxidase, integral membrane protein with similarity to Fet3p
Unique to SELM-1 / FLC3 / YGL139W / 3 / 8.1 / 90.76 / Putative FAD transporter, similar to Flc1p and Flc2p
2.2265 / FMP21 / YBR269C / 8 / 54.3 / 15.504 / Putative protein of unknown function
Unique to Product 2 / Unique to Product 3 / Unique to Product 4 / FMP45 / YDL222C / 3 / 15.2 / 34.135 / Integral membrane protein localized to mitochondria (untagged protein)
Unique to Product 4 / FMP46 / YKR049C / 2 / 19.5 / 15.65 / Putative redox protein containing a thioredoxin fold
Unique to SELM-1 / FPR2 / YDR519W / 4 / 39.3 / 14.487 / Membrane-bound peptidyl-prolyl cis-trans isomerase (PPIase), binds to the drugs FK506 and rapamycin
-2.8206 / GAS3 / YMR215W / 5 / 16 / 56.793 / Low abundance, possibly inactive member of the GAS family of GPI-containing proteins
-5.4184 / GAS5 / YOL030W / 9 / 25 / 51.869 / 1,3-beta-glucanosyltransferase, has similarity to Gas1p
Unique to Product 2 / Unique to Product 3 / Unique to Product 4 / GCY1 / YOR120W / 6 / 20.8 / 35.079 / Putative NADP(+) coupled glycerol dehydrogenase
-16.4066 / GDH1 / YOR375C / 24 / 67.4 / 49.569 / NADP(+)-dependent glutamate dehydrogenase
12.6964 / GDH3 / YAL062W / 13 / 31.5 / 49.627 / NADP(+)-dependent glutamate dehydrogenase
Unique to SELM-1 / GFD1 / YMR255W / 2 / 12.8 / 21.571 / Coiled-coiled protein of unknown function, identified as a high-copy suppressor of a dbp5 mutation
-2.0275 / GIS2 / YNL255C / 8 / 60.1 / 17.103 / Translational activator for mRNAs with internal ribosome entry sites
Unique to Product 4 / GLC3 / YEL011W / 3 / 6.8 / 81.115 / Glycogen branching enzyme, involved in glycogen accumulation
2.1661 / 2.2113 / GLC8 / YMR311C / 12 / 58.5 / 26.649 / Regulatory subunit of protein phosphatase 1 (Glc7p)
2.5511 / GLN1 / YPR035W / 4 / 16.8 / 41.766 / Glutamine synthetase (GS)
-2.3076 / Unique to SELM-1 / GLO1 / YML004C / 5 / 19.3 / 37.208 / Monomeric glyoxalase I