Table III

Selected list of proteins in SARS-CoV-infected or uninfected Vero E6 cells based on ICAT analysis

L, light; H, heavy; MuSK, muscle-specific tyrosine kinase; NSF, N-ethylmaleimide-sensitive factor.

Protein descriptionGI no.Subcellular locationPeptide hitsUnique peptidesRatio, ICAT (L:H; E6:E6-V)Peptide sequence (charge/Xcorr/ΔCn)a
Actin network protein
Anillin, actin-binding proteingi‖31657094‖Cytoskeletal111:0.25R.FGERC*QEHSKESPAR.S (2+/2.05/0.20)
α-Actinin 3 (F-actin cross-linking protein)gi‖728751‖Cytoskeletal111:0.38K.C*QLEINFNTLQTK.L (2+/3.16/0.36)
Destrin (actin-depolymerizing factor)gi‖5802966‖Cytoskeletal411:2.77K.HEC*QANGPEDLNR.A (3+/3.34/0.37)
Channel or transporter protein
Potassium channel-modulatory factor 1gi‖31543383‖No annotation111:2.59R.HEGVSC*DAC*LK.G5 (2+/2.90/0.43)
Potassium channel subfamily K member 15gi‖24636282‖Membrane111:2.97K.VFC*MFYALLGIPLTLVTFQSLGER.L (3+/2.52/0.11)
Sodium bicarbonate transporter 4 isoform agi‖15042959‖No annotation111:8.84R.FFGGLC*LDIK.R (2+/2.19/0.20)
Chromosome-associated protein
DEK proteingi‖544150‖Nuclear111:12.45K.C*PEILSDESSSDEDEKK.N (3+/2.90/0.20)
High mobility group protein 4gi‖20138144‖Nuclear111:2.20K.RPPSGFFLFC*SEFRPK.I (3+/3.70/0.34)
Condensin subunit 2gi‖30172801‖Cytoplasmic and nuclear111:2.21K.TAASFDEC*STAGVFLSTLHC*QDYR.S (3+/4.73/0.54)
Heat shock protein
HSP 90-αgi‖123678‖Cytoplasmic311:2.08K.HGLEVIYMIELIDKYC*VQQLK.E (3+/3.58/0.11)
Stress-induced phosphoprotein 1gi‖400042‖No annotation211:2.18K.DC*EEC*IQLEPTFIK.G (2+/2.54/0.25)
Heterogeneous nuclear ribonucleoproteinb
hnRNP D0gi‖13124489‖Nuclear411:1.51R.GFC*FITFK.E (2/2.27/0.41)
hnRNP Ugi‖6226894‖Nuclear411:1.77K.TC*NC*ETEDYGEK.F (2+/2.68/0.37)
hnRNP core protein A1gi‖133254‖Nuclear611:1.90K.YHTVNGHNC*EVR.S (2+/3.58/0.24)
hnRNP Igi‖131528‖Nuclear211:1.95K.LSLDGQNIYNAC*C*TLR.I (2+/3.37/0.41)
hnRNP K isoform agi‖14165437‖Cytoplasmic and nuclear411:2.00K.LFQEC*C*PHSTDR.V (2+/3.55/0.45)
hnRNP A0gi‖8134660‖Nuclear111:2.04R.GHFEAFGTLTDC*VVVVNPQTK.R (3+/2.98/0.43)
hnRNP D-likegi‖4885423‖No annotation811:2.18R.RGFC*FITYTDEEPVKK.L (3+/4.30/0.43)
hnRNP E2gi‖6707736‖Nuclear111:2.27R.INISEGNC*PER.I (2+/2.84/0.29)
Intracellular trafficking protein
Translocation protein SEC63 homologgi‖18203500‖Endoplasmic reticulum111:0.50R.APTLASLENCMKLSQMAVQGLQQFK.S (3+/2.74/0.29)
Synaptophysin-like protein isoform a; pantophysingi‖5803185‖Vesicular111:2.28K.GQTEIQVNC*PPAVTENKTVTATFGYPFR.L (3+/2.71/0.21)
α-Soluble NSF attachment proteingi‖6226705‖Membrane111:9.51K.C*LLKVAGYAALLEQYQK.A (3+/2.66/0.13)
Metabolic enzyme
Vacuolar ATP synthase catalytic subunit Agi‖22096378‖Endoplasmic reticulum111:0.36R.FCPFYKTVGMLSNMIAFYDMARR.A (3+/3.26/0.21)
Pyruvate dehydrogenase E1 component α subunitgi‖129063‖Mitochondrial111:0.36K.LPCIFICENNR.Y (2+/2.13/0.23)
FK506-binding protein 4gi‖399866‖Cytoplasmic and nuclear211:0.41K.VGEVCHITCKPEYAYGSAGSPPK.I (3+/2.86/0.23)
Alanine-glyoxylate aminotransferase 2gi‖17432913‖Mitochondrial111:0.45K.CLQHFNTFGGNPMACAIGSAVLEVIK.E (3+/2.77/0.16)
GMP reductase 2gi‖25008511‖No annotation111:2.10K.GHIISDGGC*SC*PGDVAK.A (3+/2.63/0.16)
Succinyl-CoA synthetase, α chaingi‖20141765‖Mitochondrial611:2.16R.LIGPNC*PGVINPGEC*K.I (2+/3.78/0.52)
Thioredoxin-like protein p46gi‖29839560‖Endoplasmic reticulum1921:2.44 ± 0.45K.VDC*TAHSDVC*SAQGVR.G (2+/4.18/0.50); K.VDC*TQHYELC*SGNQVR.G (3+/4.27/0.35)
UDP-glucose 6-dehydrogenasegi‖6175086‖No annotation111:3.56R.AVQALC*AVYEHWVPR.E (3+/2.60/0.30)
Protein degradation
Ovochymasegi‖34419641‖No annotation111:2.03R.YLLDYRGRLEC*SWVLR.V (3+/2.62/0.17)
Proteasome subunit P50gi‖20532406‖Cytoplasmic and nuclear311:2.22R.C*TDDFNGAQC*K.A (2+/3.16/0.45)
Ribosomal proteinb
Ribosomal protein S4gi‖4506725‖Ribosomal1121:1.52 ± 0.33K.LREC*LPLIIFLR.N (3+/3.82/0.32)
60 S ribosomal protein L10agi‖15431288‖Ribosomal611:1.58K.FSVC*VLGDQQHC*DEAK.A (2+/2.97/0.37)
40 S ribosomal protein S15agi‖14165469‖Ribosomal111:1.61K.C*GVISPR.F (2+/2.10/0.16)
40 S ribosomal protein S21gi‖4506699‖Ribosomal211:1.65K.TYAIC*GAIR.R (2+/2.27/0.25)
40 S ribosomal protein S26gi‖15011936‖Ribosomal611:1.66K.LHYCVSCAIHSK.V (3+/3.10/0.53)
40 S ribosomal protein S12gi‖14277700‖Ribosomal921:1.66 ± 0.12K.LVEALC*AEHQINLIK.V (2+/4.17/0.19); R.KVVGC*SC*VVVK.D (2+/2.72/0.21)
40 S ribosomal protein S11gi‖4506681‖Ribosomal1311:2.03R.DVQIGDIVTVGEC*RPLSK.T (2+/4.65/0.53)
40 S ribosomal protein SAgi‖125969‖Ribosomal411:2.06R.ADHQPLTEASYVNLPTIALC*NTDSPLR.Y (3+/5.15/0.49)
40 S ribosomal protein S27agi‖4506713‖Ribosomal721:2.18 ± 0.23K.C*C*LTYC*FNKPEDK.- (2+/3.35/0.40); R.EC*PSDEC*GAGVFMASHFDR.H (3+/4.17/0.45)
Signaling protein
Cell division protein kinase 6gi‖266423‖No annotation111:0.17R.ADQQYECVAEIGEGAYGK.V (3+/2.51/0.13)
Ectodysplasin A receptor-associated adapter proteingi‖21362527‖Cytoplasmic111:0.40K.ENCTCSSCLLR.A (2+/2.25/0.15)
Transducin β chain 5gi‖38258891‖No annotation111:0.45R.YYPSGDAFASGSDDATCRLYDLR.A (3+/2.51/0.22)
Phosphoinositide-3-kinase, regulatory subunit 4, p150gi‖23943912‖No annotation111:0.49K.PVIPVLSSTILPSTYQIRITTC*K.T (3+/2.55/0.12)
Galectin-1gi‖126155‖No annotation2321:2.07 ± 0.35K.DSNNLC*LHFNPR.F (2+/3.34/0.32); R.FNAHGDANTIVC*NSK.D (2+/4.70/0.59)
Receptor tyrosine kinase MuSKgi‖5031927‖No annotation111:2.18R.EYC*LAVKELFC*AKEWLVMEEK.T (3+/2.82/0.15)
Fibroblast growth factor-9gi‖544290‖Secreted111:2.42R.QLYCRTGFHLEIFPNGTIQGTR.K (3+/2.78/0.22)
Apoptotic chromatin condensation inducer in the nucleusgi‖7662238‖Nuclear111:2.47K.FLC*ADYAEQDELDYHR.G (3+/3.36/0.42)
Testingi‖17380320‖No annotation211:2.52K.NHAVVC*QGC*HNAIDPEVQR.V (3+/3.03/0.37)
Tenascin X precursorgi‖9087217‖Secreted111:3.68R.VRGEESEVTVGGLEPGC*K.Y (3+/3.58/0.11)
Transcription or replication factor
DNA ligase Igi‖118773‖Nuclear111:0.38K.GLFVACRHSEARFIAR.S (3+/2.65/0.22)
Cleavage- and polyadenylation-specific factor 6, 68-kDa subunitgi‖5901928‖Nuclear111:2.01K.RELHGQNPVVTPC*NK.Q (3+/2.69/0.40)
DNA helicase homologgi‖5523990‖Nuclear111:4.31R.QQLPLQLAWAMSIHKSQGMTLDC*VEISLGR.V (3+/3.08/0.12)
Translation factorb
eIF-1gi‖1174483‖No annotation821:1.56 ± 0.08K.FAC*NGTVIEHPEYGEVIQLQGDQR.K (3+/4.16/0.38); K.NICQFLVEIGLAK.D (2+/2.20/0.15)
eIF-5gi‖27735202‖No annotation111:1.60K.FVLCPECENPETDLHVNPK.K (3+/2.93/0.27)
eIF-5A2 proteingi‖9966867‖No annotation111:1.76K.KYEDIC*PSTHNMDVPNIK.R (3+/3.42/0.41)
EF-Tu, mitochondrial precursorgi‖1706611‖Mitochondrial411:2.17R.HYAHTDC*PGHADYVK.N (3+/3.96/0.49)
Other function protein
WD repeat domain 17 isoform 1gi‖31317311‖No annotation111:0.42R.IWDYTQDACINILNGHTAPVR.G (3+/2.52/0.15)
Ran-binding protein 2gi‖1709217‖Nuclear311:2.03K.C*IAC*QNPGK.Q (2+/2.86/0.43)
Hyaluronan-binding protein 4gi‖24307947‖No annotation111:2.06R.YGGNDKIAVRTEDNMGGC*GVR.T (3+/2.60/0.17)
Metallothionein IIgi‖127397‖No annotation111:2.51K.CAQGCICK.G (2+/2.20/0.15)
  • a Select list of the peptides with the best assignment scores for protein identification and quantification by ICAT analysis. C/C*, ICAT light/heavy reagent-labeled cysteine-including peptide, respectively.

  • b For heterogeneous nuclear ribonucleoproteins, ribosomal proteins, and translation factors, proteins with at least 1.5-fold alteration are listed. The MS and MS/MS spectra for identification and quantitation of these proteins are shown in Supplemental Figs. 4–24.