Table I

Summary of significant protein expression changes in multiplex Xrn1Δ-Upf1Δ-WT comparative study

Protein nameCountaXrn1Δ ratiobXrn1Δ S.D.Upf1Δ ratiobUpf1Δ S.D.Xrn1Δ fold changecRepd,e
Xrn1Δ-up
    (P22943) 12-kDa heat shock protein (glucose and lipid-regulated protein)50.7920.0690.4530.0843.806Yes
    (P23776) Glucan 1,3-β-glucosidase I/II precursor (EC 3.2.1.58)40.7320.0210.5360.0662.738Yes
    (P03965) Carbamoyl-phosphate synthase, arginine-specific, large chain (EC 6.3.5.5)110.6820.0410.5460.0492.148Yes
    (P56628) 60S ribosomal protein L22-B20.6810.0780.5260.0442.138Yes
    (P06208) 2-isopropylmalate synthase (EC 2.3.3.13) (α-isopropylmalate synthase)150.680.0470.5460.0382.125Yes
    (P49334) Mitochondrial import receptor subunit TOM2220.6790.0370.5840.112.118Yes
    (P04806) Hexokinase A (EC 2.7.1.1) (Hexokinase PI)30.670.0750.4660.0532.031Yes
    (P00890) Citrate synthase, mitochondrial precursor (EC 2.3.3.1)20.660.0480.5280.0361.969Yes
    (P17709) Glucokinase (EC 2.7.1.2) (glucose kinase) (GLK)20.6560.0820.4940.0671.906Yes
    (P39726) Glycine cleavage system H protein, mitochondrial precursor20.6540.0990.5760.121.892Yes
    (Q00055) Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)20.6510.0180.4590.0531.868Yes
    (P46992) Hypothetical 43.0-kDa protein in CPS1-FPP1 intergenic region20.6490.0110.5370.00741.85
    (Q12019) Midasin (MIDAS-containing protein)20.6460.0440.5120.0521.826
    (P04076) Argininosuccinate lyase (EC 4.3.2.1) (arginosuccinase) (ASAL)40.6420.0540.5690.0611.797Yes
    (P00498) ATP phosphoribosyltransferase (EC 2.4.2.17)50.6280.0540.5370.0371.689Yes
    (Q08965) Ribosome biogenesis protein BMS120.6250.0160.5210.0141.665Yes
    (P40482) Protein transport protein Sec24 (abnormal nuclear morphology 1)20.6150.0750.5250.051.595Yes
    (P00812) Arginase (EC 3.5.3.1)30.6140.0190.5670.0321.59Yes
    (P06168) Ketol-acid reductoisomerase, mitochondrial precursor (EC 1.1.1.86)180.6130.0990.5250.0571.587Yes
    (Q04182) ATP-dependent permease PDR1520.5630.0450.5350.0161.293Yes
    (P33416) Heat shock protein 78, mitochondrial precursor20.6140.0150.5150.0441.581
    (P31539) Heat shock protein 104100.6120.0410.5340.031.579
    (P37291) Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (serine methylase)140.6120.0630.5150.041.578Yes
    (P22768) Argininosuccinate synthase (EC 6.3.4.5) (citrulline-aspartate ligase)30.6110.00530.5720.0151.574Yes
    (P07273) Transcription elongation factor S-II (DNA strand transfer protein α)30.610.0940.5310.0111.563Yes
    (P38777) Hypothetical 27.3-kDa protein in AAP1-SMF2 intergenic region40.6090.0690.5340.0271.561
    (P39522) Dihydroxy-acid dehydratase, mitochondrial precursor (EC 4.2.1.9) (DAD)100.6060.0610.5050.0371.54Yes
    (Q04869) Hypothetical 38.2-kDa protein in PRE5-FET4 intergenic region30.6060.0410.4930.0281.536Yes
    (P40215) Hypothetical 62.8-kDa protein in RPS16A-TIF34 intergenic region30.6050.0780.4570.0571.534Yes
    (P47119) HAM1 protein30.6030.0500.4880.0111.516Yes
    (P00937) Anthranilate synthase component II (EC 4.1.3.27)20.6020.0080.490.0081.515Yes
    (P53332) Hypothetical 34.3-kDa protein in TAF145-YOR1 intergenic region20.6020.00470.4750.0071.512
    (P42940) Probable electron transfer flavoprotein β-subunit (β-ETF)20.6010.0430.5530.0871.509Yes
    (P17505) Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)50.6000.030.4910.0351.504Yes
    (P00128) Ubiquinol-cytochrome C reductase complex 14-kDa protein (EC 1.10.2.2)40.600.0340.4760.0551.5Yes
    (P18239) ADP,ATP carrier protein 2 (ADP/ATP translocase 2)30.60.0490.4790.0541.5Yes
    (P06634) Probable ATP-dependent RNA helicase DED1250.5980.0520.4910.0371.49Yes
    (P32454) Aminopeptidase II (EC 3.4.11.-) (YscII)20.5980.0610.5320.0271.487Yes
    (P00427) Cytochrome c oxidase polypeptide VI, mitochondrial precursor (EC 1.9.3.1)20.5930.0210.4780.021.457Yes
    (Q04636) Hypothetical 63.0-kDa protein in DAK1-ORC1 intergenic region20.5910.0290.5630.0481.445Yes
    (P38715) Probable oxidoreductase GRE3 (EC 1.-.-.-)20.5910.0080.4750.0111.443Yes
    (P27616) Phosphoribosylamidoimidazole-succinocarboxamide synthase (EC 6.3.2.6)30.5870.0790.5170.0471.421
    (P04046) Amidophosphoribosyltransferase (EC 2.4.2.14)20.5860.0230.540.00971.418Yes
    (P23542) Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (transaminase A)50.5850.0440.5230.0211.407Yes
    (P33734) Imidazole glycerol phosphate synthase hisHF (IGP synthase)30.5840.0460.5330.0191.403Yes
    (P07256) Ubiquinol-cytochrome c reductase complex core protein I, mito precurs.)20.5820.0270.460.0361.393Yes
    (P10591) Heat shock protein SSA1 (heat shock protein YG100)60.5810.0750.540.0381.384Yes
    (P34227) Hypothetical 29.5-kDa protein in SEF1-KIP1 intergenic region20.580.0380.5240.0331.383Yes
Xrn1Δ-down
    (P40029) Peptide methionine sulfoxide reductase (EC 1.8.4.6)20.2990.02440.4540.00890.446Yes
    (P05747) 60S ribosomal protein L29 (YL43)110.3420.0360.4710.020.546Yes
    (P07215) Metallothionein precursor (Cu-MT) (copper chelatin)30.350.0560.5620.0240.565Yes
    (P14796) 60S ribosomal protein L40 (CEP52)40.3540.0460.4410.0220.576Yes
    (P05748) 60S ribosomal protein L15-A (YL10) (L13) (RP15R) (YP18)120.370.0560.470.0280.618Yes
    (P05755) 40S ribosomal protein S9-B (S13) (YS11) (RP21) (YP28)20.3730.0150.4630.00560.625
    (P02293) Histone H2B.120.3780.0290.4310.0440.64Yes
    (Q12213) 60S ribosomal protein L7-B (L6B) (YL8B)80.3820.0940.4570.0160.696Yes
    (P53297) PAB1-binding protein 160.3830.0920.4570.0250.653Yes
    (P87262) 60S ribosomal protein L34-A20.3850.0760.4890.0030.706Yes
    (P41057) 40S ribosomal protein S29-A (S36) (YS29)60.3880.070.470.0130.668Yes
    (P04650) 60S ribosomal protein L39 (L46) (YL40)20.3890.0190.4450.00170.67Yes
    (P14126) 60S ribosomal protein L3 (YL1) (RP1) (trichodermin resistance protein)250.3890.0690.4720.0310.671Yes
    (P10614) Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1)60.390.0660.4970.030.671Yes
    (P47100) Transposon Ty1 protein B160.3990.0770.5140.0230.672Yes
    (P26786) 40S ribosomal protein S7-A (RP30)20.3990.0130.4740.0090.672Yes
    (P05743) 60S ribosomal protein L26-A (YL33)50.3990.0600.440.0380.722Yes
    (P46784) 40S ribosomal protein S10-B60.3930.0810.4610.0250.731Yes
    (Q03834) MUTS protein homolog 620.39370.0750.5130.120.734Yes
    (P41805) 60S ribosomal protein L10 (L9)230.3940.0610.4630.0170.684Yes
    (P40150) Heat shock protein SSB220.3970.0150.4420.0110.693Yes
    (P54780) 60S ribosomal protein L15-B (YL10) (L13) (RP15R) (YP18)30.4030.0340.510.0230.764Yes
    (P47098) Transposon Ty1 protein B40.4030.0550.5270.0570.765Yes
    (Q01855) 40S ribosomal protein S15 (S21) (YS21) (RP52) (RIG protein)50.4040.0450.4740.0410.714Yes
    (Q02753) 60S ribosomal protein L21-A30.4050.0560.4710.0120.716Yes
    (P23301) Eukaryotic translation initiation factor 5A-2 (eIF-5A 2) (eIF-4D)50.4050.0780.4680.0240.718Yes
    (P29547) Elongation factor 1-γ 1 (EF-1-γ 1)50.410.0640.4450.0320.733Yes
    (P07282) 40S ribosomal protein S25 precursor (S31) (YS23) (RP45)50.4120.0660.4520.0210.739Yes
    (P38693) Acid phosphatase PHO12 precursor (EC 3.1.3.2)40.4140.0980.4160.050.744
    (P39939) 40S ribosomal protein S26-B40.4150.0490.4770.00550.749Yes
    (P06106) MET17 protein [includes O-acetylhomoserine sulfhydrylase (EC 2.5.1.49)]80.4160.0850.4740.0240.75Yes
    (P14832) Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (rotamase)90.4160.0550.5240.050.751Yes
    (P23254) Transketolase 1 (EC 2.2.1.1) (TK 1)110.4170.0550.4780.040.753Yes
    (P46990) 60S ribosomal protein L17-B (YL17-B)30.4180.0430.4870.0270.757Yes
    (P05740) 60S ribosomal protein L17-A (YL17-A)90.4190.0370.4580.0350.761Yes
    (P07281) 40S ribosomal protein S19-B (S16B) (YS16) (RP55)20.4190.00820.4550.0120.762Yes
    (P04912) Histone H2A.220.420.0050.3790.0510.763Yes
    (P25631) Hypothetical 24.7-kDa protein in ARE1-THR4 intergenic region30.420.060.5090.0140.763Yes
Upf1Δ-up
    (P22768) Argininosuccinate synthase (EC 6.3.4.5) (citrulline-aspartate ligase)30.6110.0050.5720.0161.435Yes
    (P04076) Argininosuccinate lyase (EC 4.3.2.1) (arginosuccinase) (ASAL)40.6420.0540.5690.0611.417Yes
    (P00812) Arginase (EC 3.5.3.1)30.6140.0190.5670.0321.404Yes
    (P30822) Exportin 1 (chromosome region maintenance protein 1)20.570.0740.5650.0681.397Yes
    (Q04636) Hypothetical 63.0-kDa protein in DAK1-ORC1 intergenic region20.5910.0290.5630.0481.383
    (P00815) Histidine biosynthesis trifunctional protein40.6720.1210.5620.0441.377Yes
    (P07215) Metallothionein precursor (Cu-MT) (copper chelatin)30.350.0560.5620.0241.376Yes
    (P53337) Hypothetical 35.0-kDa protein in BGL2-ZUO1 intergenic region20.5630.0560.5570.0341.348
    (P38886) 26S proteasome regulatory subunit RPN1040.5330.0840.5550.0551.34Yes
    (P53111) Hypothetical 38.1-kDa protein in RCK1-AMS1 intergenic region20.5820.1550.5540.0431.33Yes
    (P42940) Probable electron transfer flavoprotein β-subunit (β-ETF)20.6010.0430.5530.0871.326
    (P13587) Sodium transport ATPase 1 (EC 3.6.3.7)20.5490.0170.5480.0221.301
    (P03965) Carbamoyl-phosphate synthase, arginine-specific, large chain (EC 6.3.5.5)110.6820.0410.5460.051.29Yes
    (P06208) 2-isopropylmalate synthase (EC 2.3.3.13) (α-isopropylmalate synthase)150.680.0470.5460.0381.287Yes
    (P14906) Translocation protein (NPL1 protein)20.5350.0390.5460.0461.285Yes
    (P49089) Asparagine synthetase [glutamine-hydrolyzing] 1 (EC 6.3.5.4)110.5610.0540.5420.0251.268Yes
    (P32179) 3′(2′),5′-bisphosphate nucleotidase20.5640.0710.5410.0491.264Yes
    (P10591) Heat shock protein SSA1 (heat shock protein YG100)60.5810.0750.540.0381.257
    (P04046) Amidophosphoribosyltransferase (EC 2.4.2.14)20.5860.0230.540.011.257Yes
    (P38066) GTP cyclohydrolase II (EC 3.5.4.25)30.5150.0850.5390.0671.249
    (P38891) Branched-chain amino acid aminotransferase, mitochondrial precursor110.5270.0570.5380.0311.246Yes
    (P07274) Profilin20.5750.0190.5380.0391.244Yes
    (P00498) ATP phosphoribosyltransferase (EC 2.4.2.17)50.6280.0540.5370.0371.243Yes
    (P46992) Hypothetical 43.0-kDa protein in CPS1-FPP1 intergenic region20.6490.0110.5370.0071.242
    (P38009) Bifunctional purine biosynthesis protein ADE1720.7010.1270.5370.0481.241
    (P23776) Glucan 1,3-β-glucosidase I/II precursor (EC 3.2.1.58)40.7320.0210.5360.0661.235Yes
    (P38080) Probable serine/threonine-protein kinase YBR059C (EC 2.7.1.-)30.5460.0190.5350.0561.232
    (Q04182) ATP-dependent permease PDR1520.5640.0450.5350.0161.23
    (P25294) SIS1 protein20.4420.0190.5350.0461.229
    (P38765) Hypothetical 32.6-kDa protein in DAP2-SLT2 intergenic region20.5230.0050.5340.0581.227Yes
    (P48353) HLJ1 protein30.5440.0590.5340.021.226
    (P38777) Hypothetical 27.3-kDa protein in AAP1-SMF2 intergenic region40.6090.0690.5340.0271.225
    (P39676) Flavohemoprotein (hemoglobin-like protein) (flavohemoglobin)80.5130.0830.5340.0131.223Yes
    (P31539) Heat shock protein 104100.6120.0410.5340.031.223Yes
    (P33734) Imidazole glycerol phosphate synthase hisHF (IGP synthase)30.5840.0460.5330.0191.219
    (P41895) Transcription initiation factor IIF, α subunit (TFIIF-α)20.5120.0390.5330.0641.219
    (P32454) Aminopeptidase II (EC 3.4.11.-) (YscII)20.5980.0610.5320.0271.215Yes
    (P36013) Probable NAD-dependent malic enzyme (EC 1.1.1.38) (NAD-ME)70.560.0420.5310.0471.211Yes
    (P07273) Transcription elongation factor S-II (DNA strand transfer protein α)30.610.0940.5310.0111.208Yes
    (P38998) Saccharopine dehydrogenase [NAD+, l-lysine forming] (EC 1.5.1.7)20.550.0180.530.0071.205Yes
    (P13663) Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)120.5330.0460.530.0251.204Yes
    (P10962) MAK16 protein20.5330.0160.5290.0841.2Yes
    (P07264) 3-isopropylmalate dehydratase (EC 4.2.1.33) (isopropylmalate isomerase)260.4860.0610.5290.0271.199Yes
    (Q06142) Importin β-1 subunit (karyopherin β-1 subunit) (importin 95)40.5480.0450.5290.0261.198
    (P36112) Hypothetical 61.1-kDa protein in YPT52-DBP7 intergenic region20.5240.0210.5280.0531.195Yes
    (P10659) S-adenosylmethionine synthetase 1 (EC 2.5.1.6)130.5020.0530.5280.0231.193Yes
    (P32381) Actin-like protein ARP220.5230.0140.5280.051.193Yes
    (P15891) Actin binding protein70.5630.0610.5280.0671.192Yes
    (P51401) 60S ribosomal protein L9-B (L8) (YL11) (RP25)20.5180.0090.5270.0081.191Yes
    (P47079) T-complex protein 1, τ subunit (TCP-1-τ) (CCT-τ)50.5480.0630.5270.0481.189Yes
    (P40482) Protein transport protein Sec24 (abnormal nuclear morphology 1)20.6150.0750.5250.051.179Yes
    (P06168) Ketol-acid reductoisomerase, mitochondrial precursor (EC 1.1.1.86)180.6130.0990.5250.0571.177Yes
    (P34227) Hypothetical 29.5-kDa protein in SEF1-KIP1 intergenic region20.580.0380.5240.0331.176
    (P14832) Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (rotamase)90.4160.0550.5240.0511.173
    (P07342) Acetolactate synthase, mitochondrial precursor (EC 2.2.1.6)100.5560.0450.5230.0251.172
    (Q06252) Hypothetical 22.2-kDa protein in TFS1-SAM1 intergenic region20.4590.0870.5230.0271.17Yes
    (P32563) Vacuolar ATP synthase 95-kDa subunit (vacuolar ATPase 95-kDa subunit)60.550.0560.5230.051.169
    (P23542) Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (transaminase A)50.5850.0440.5230.0211.169Yes
    (P43555) 47-kDa endomembrane protein precursor (endosomal P44 protein)20.5340.0430.5230.0381.168
    (P47176) Branched-chain amino acid aminotransferase, cytosolic (EC 2.6.1.42)60.5210.0730.5220.0271.165Yes
    (Q08965) Ribosome biogenesis protein BMS120.6250.0160.5210.0141.159
Upf1Δ-down
    (Q03667) Hypothetical 16.7-kDa protein in CDC5-MVP1 intergenic region20.4690.180.3440.0840.549Yes
    (P43579) Hypothetical 78.8-kDa protein in HSP12-HXT10 intergenic region20.5770.0270.3760.0320.634
    (P04912) Histone H2A.220.420.0050.3790.0510.642
    (P87108) Mitochondrial import inner membrane translocase subunit TIM1020.5020.0440.410.0120.732Yes
    (P38693) Acid phosphatase PHO12 precursor (EC 3.1.3.2)40.4140.0980.4160.050.751Yes
    (P15565) N(2),N(2)-dimethylguanosine tRNA methyltransferase, mitochondrial prec.20.5160.1250.4170.0050.753Yes
    (P32591) Transcription regulatory protein SWI3 (SWI/SNF complex component SWI3)20.4520.1180.4170.0870.755
    (P02309) Histone H440.4740.060.420.0380.762
    (P21538) DNA-binding protein REB1 (QBP)20.4990.0180.420.0230.762
    (P30624) Long-chain-fatty-acid-CoA ligase 1 (EC 6.2.1.3)20.5270.0010.4210.0510.768
    (P15019) Transaldolase (EC 2.2.1.2)30.4870.0570.4240.0350.775
    (P32386) ATP-dependent bile acid permease20.5130.0060.4250.0270.78
    (P25644) Topoisomerase II-associated protein PAT130.5030.0670.4250.0120.78
    (P07263) Histidyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.21)40.4850.0640.4260.0650.783Yes
    (P53720) SMM1 protein20.5780.0890.4270.0490.785
    (P19358) S-adenosylmethionine synthetase 2 (EC 2.5.1.6)30.4630.0510.4280.0920.79Yes
    (P02293) Histone H2B.120.3780.0290.4310.0440.801
    (Q04439) Myosin-5 isoform20.4930.0180.4320.0490.804Yes
    (P32610) Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit)30.5310.0140.4330.0660.807
    (Q04493) Prefoldin subunit 520.4890.0110.4340.0270.81Yes
    (P00942) Triosephosphate isomerase (EC 5.3.1.1) (TIM)140.4860.1450.4360.0390.817Yes
    (P00330) Alcohol dehydrogenase I (EC 1.1.1.1) (YADH-1)210.4890.1610.4380.0970.822Yes
    (P04911) Histone H2A.130.4270.030.4110.0320.735
  • a Number of top-ranked, significant peptides, including duplicate sequences from separate MS/MS spectra.

  • b Calculated as area(mutant)/(area(mutant) + area(wild type)), with expression change ranging from 0 to 1, where no change = 0.5.

  • c Fold changes were calculated with respect to the global peptide average, 0.503 for Xrn1Δ and 0.485 for Upf1Δ.

  • d Yes indicates that protein was identified in preliminary 2-plex experiments, as in Footnote 2.

  • e Yes indicates that protein was identified in ICAT experiments (16).