Table I Quantitative proteomics analysis of nucleolar sumoylated proteins upon proteasome inhibition

Proteins identified by at least two arginine- or lysine- containing peptides and enriched at least 0.8-fold in the heavy arginine or lysine form are shown. H/L, heavy/light ratio; FACT, facilitates chromatin transcription; TPR, translocated promoter region.

IPI accession numberSwiss-Prot accession numberProtein nameProtein scoreProtein massMatched peptidesProtein coverageH/L ratioAverageS.D.SUMO predictionsitesSubcellular localization
Experiment IExperiment IIExperiment III
Da%
IPI00296337P78527Isoform 1 of DNA-dependent protein kinase catalytic subunita2,499473,7497916.10.790.630.50.640.15IKSE 0.94, LKEE 0.91Nucleoli
IPI00004970O75691Small subunit processome component 20 homolog169320,84672.20.680.30.490.27IKED 0.94, VKDE 0.93Nucleoli
IPI00019502P35579Myosin-9a,b1,801227,6464221.80.820.650.660.710.10VKND 0.93, LKTD 0.91Nucleoli
IPI00783060P62988Ubiquitin1958,560560.50.20.090.030.110.09None
IPI00007928Q6P2Q9Pre-mRNA-processing-splicing factor 8a117274,73851.60.760.490.560.600.14IKVE 0.94, IKTE 0.94Nucleoli
IPI00009342P46940Ras GTPase-activating-like protein IQGAP1a377189,761147.80.790.660.730.09IKTD 0.94, VKED 0.93Cell membrane
IPI00420014O75643U5 small nuclear ribonucleoprotein 200-kDa helicasea,b336246,0061150.750.580.620.650.09VKLD 0.93, VKYD 0.93Nucleoli
IPI00218753P11388Isoform 3 of DNA topoisomerase 2-αa,b234179,398137.50.780.520.650.18IKNE 0.94Nucleus
IPI00024067Q00610Isoform 1 of clathrin heavy chain 11,032193,2602915.20.760.590.710.690.09IKAD 0.94, IKAD 0.94Cytosol
IPI00005024Q9BQG0Isoform 1 of Myb-binding protein 1Aa1,012149,7312616.80.740.370.640.580.19VKKD 0.93, LKAD 0.91Nucleoli
IPI00006702Q81ZL8Isoform 1 of proline-, glutamic acid-, and leucine-rich protein 1160120,87943.90.690.350.520.24IKEE 0.94, LKLD 0.91Nucleoli
IPI00449049P09874Poly(ADP-ribose) polymerase 1a393113,81188.60.870.470.80.710.21IKDE 0.94, VKAE 0.93Nucleus
IPI00100160Q86VP6Isoform 1 of Cullin-associated NEDD8-dissociated protein 1323137,999107.20.810.70.760.08IKLD 0.94, VKAD 0.93Nucleus
IPI00479217Q00839Isoform short of heterogeneous nuclear ribonucleoprotein Ua,b28689,66578.80.770.690.720.730.04LKEE 0.91, LKAE 0.91Nucleus
IPI00152890Q9H6R4Isoform 1 of nucleolar protein 6a221128,36875.40.740.350.550.28LKDG 0.73Nucleoli
IPI00300127Q9H0A0N-acetyltransferase 10a187116,54377.50.740.670.710.05IKQD 0.94, LKSD 0.91Nucleoli
IPI00297211O60264SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A178122,51364.80.790.680.740.08IKAD 0.94, IKNE 0.94Nucleus
IPI00654555Q3KQS4NOL1 proteina15493,20245.60.750.590.670.11LKKD 0.91Nucleoli
IPI00017297P43243Matrin-3a15295,07868.40.810.640.730.12IKNE 0.94, VKVD 0.93Nucleus
IPI00140420Q7KZF4Staphylococcal nuclease domain-containing protein 1a141102,61844.10.830.50.580.640.17IKCP 0.84Nucleus
IPI00444262P19338CDNA FLJ45706 fi, highly similar to nucleolin73365,9791316.70.620.560.710.630.08IKLE 0.94Nucleoli
IPI00015953Q9NR30Isoform 1 of nucleolar RNA helicase 2a,b41387,8041113.90.620.520.480.540.07IKQD 0.94Nucleoli
IPI00010740P23246Isoform long of splicing factor, proline- and glutamine-richa23576,21657.10.790.480.720.660.16IKLE 0.94Nucleoli
IPI00013214P25205DNA replication licensing factor MCM314391,55144.80.70.340.520.25AKAG 0.62Nucleoli
IPI00414676P08238Heat shock protein HSP 90-βb82585,1041719.70.530.370.480.460.08LKID 0.91, LKED 0.91Nucleoli
IPI00784295Q2VPJ6Heat shock protein HSP 90-αb65898,6701314.50.40.320.210.310.10LKED 0.91, IKLG 0.77Nucleoli
IPI00022774P55072Transitional endoplasmic reticulum ATPase38789,950810.90.550.890.420.620.24IKRE 0.94, VKRE 0.93Nucleus
IPI00396435O43143DEAH (Asp-Glu-Ala-His) box polypeptide 15b27893,5681011.70.740.620.80.720.09IKPE 0.94, IKRE 0.94Nucleus
IPI00001639Q14974Importin β-1 subunit20898,42079.50.710.490.880.690.20LKGD 0.91Nucleus
IPI00005154Q08945FACT complex subunit SSRP1b20081,36756.10.760.570.840.720.14IKSD 0.94, VKME 0.93Nucleoli
IPI00306369Q08J23NOL1/NOP2/Sun domain family 2 protein16987,21479.10.760.660.710.07LKYE 0.91Nucleoli
IPI00304925P08107Heat shock 70-kDa protein 1b53570,2941016.20.140.060.030.080.06AKLD 0.79Nucleus
Da%
IPI00003362P11021Isoform 1 of heat shock 70-kDa protein 540771,0821113.50.620.520.670.600.08AKFE 0.79Nucleoli
IPI00171903P52272Isoform 1 of heterogeneous nuclear ribonucleoprotein Ma,b27777,749612.10.730.680.770.730.05IKME 0.94, IKME 0.94Nucleoli
IPI00299904P33993Isoform 1 of DNA replication licensing factor MCM722581,88468.50.710.690.540.650.09FKYG 0.68Nucleoli
IPI00013174Q96PK6Isoform 1 of RNA-binding protein 14a10969,62044.90.670.520.600.11NoneNucleus
IPI00021405P02545Isoform A of lamin A/Ca,b90674,3803026.40.780.730.710.740.04MKEE 0.80Nucleoli
IPI00003865P11142Isoform 1 of heat shock cognate 71-kDa protein45971,0821012.10.490.530.310.440.12AKLD 0.79Nucleoli
IPI00017617P17844Probable ATP-dependent RNA helicase DDX5a,b45969,6181622.50.650.460.550.550.10LKRD 0.91Nucleoli
IPI00007765P38646Stress-70 protein, mitochondrial precursor37473,920912.50.840.710.790.780.07LKEE 0.91Nucleoli
IPI00411937O00567Nucleolar protein Nop56a15966,40889.30.730.530.630.14LKKE 0.91Nucleoli
IPI00220644P14618Isoform M1 of pyruvate kinase isozymes M1/M249158,5381022.40.670.60.610.630.04IKKP 0.84Cytosol
IPI00290770Q5SZY0Chaperonin containing TCP1, subunit 3 isoform b32460,994711.20.630.370.500.18LKPD 0.91Nucleus
IPI00304596Q15233Non-POU domain-containing octamer-binding proteina25954,3116140.760.770.770.01AKVE 0.79Nucleoli
IPI00440493P25705ATP synthase subunit α, mitochondrial precursor49159,8281321.90.790.690.810.760.06MKLE 0.80Mitochondrion
IPI00216049Q5T6W2Isoform 1 of heterogeneous nuclear ribonucleoprotein Kb39851,230920.50.730.840.790.08GKPD 0.67Nucleus
IPI00011200O43175d-3-Phosphoglycerate dehydrogenase25457,356510.50.630.60.620.02GKWE 0.67Cytosol
IPI00303476P06576ATP synthase subunit β, mitochondrial precursor43556,525718.70.820.710.690.740.07IKIP 0.84Nucleoli
IPI00218343Q9BQE3Tubulin α-6 chainb42750,548820.90.70.490.660.620.11VKCD 0.93Nucleoli
IPI00032140P05454Serpin H1 precursor32746,525719.40.460.380.220.350.12VKKP 0.82Endoplasmic reticulum
IPI00000875P26641Elongation factor 1-γb30050,429611.70.730.740.480.650.15AKEE 0.79Nucleoli
IPI00328328Q14240Isoform 1 of eukaryotic initiation factor 4A-II21646,601411.50.670.510.310.500.18VKEE 0.93Nucleoli
IPI00021440P63261Actin, cytoplasmic 286742,1082240.80.760.560.660.14LKYP 0.80Cytosol
IPI00549248P06748Isoform 1 of nucleophosminb35632,6111317.70.730.480.610.18LKAD 0.91Nucleoli
IPI00553164P0886540 S ribosomal protein SA24732,947616.30.740.830.790.06MKEE 0.80Nucleoli
IPI00455315P07355Annexin A253638,80815440.740.480.660.630.13VKGD 0.93Nucleoli
IPI00217466P16402Histone H1.336822,336734.40.860.830.850.02VKKP 0.82Nucleoli
IPI00219018P04406Glyceraldehyde-3-phosphate dehydrogenase32336,201825.40.840.760.130.580.39VKAE 0.93Nucleoli
IPI00220740P06748Isoform 2 of nucleophosminb24729,617613.60.680.480.580.14LKAD 0.91Nucleoli
IPI00215965P09651Isoform A1-B of heterogeneous nuclear ribonucleoprotein A116538,936311.80.860.630.750.16IKED 0.94Nucleoli
IPI00219217P07195l-Lactate dehydrogenase B chain37636,900925.70.730.510.620.16LKGE 0.91, LKDD 0.91Cytosol
IPI00419880P6124740 S ribosomal protein S3a34230,154932.60.640.650.650.01VKAP 0.82Nucleoli
IPI00030179P1812460 S ribosomal protein L7a29629,264830.60.70.630.670.05NoneNucleoli
IPI00329801P08758Annexin A523435,971515.60.710.810.760.07IKGD 0.94, LKSE 0.91Nucleoli
IPI00012772P6291760 S ribosomal protein L8a12628,235416.70.730.60.350.560.19VKLP 0.82Nucleoli
IPI00021840P6275340 S ribosomal protein S612028,834280.640.380.510.18VKKG 0.76Nucleoli
IPI00018534Q99880Histone H2B type 1-Lb37513,944945.20.810.750.780.04NoneNucleoli
IPI00026272P04908Histone H2A type 1-Bb21414,127637.70.680.720.700.03NoneNucleoli
IPI00013296P6226940 S ribosomal protein S1817217,7083250.750.580.670.12VKDG 0.76Nucleoli
IPI00221092P6224940 S ribosomal protein S1614816,5494260.740.640.690.07VKGG 0.76Nucleoli
Da%
IPI00026271P6226340 S ribosomal protein S1413616,434217.90.660.540.610.600.06VKAD 0.93Nucleoli
IPI00453473P62805Histone H4b47311,3601357.30.810.760.760.780.03NoneNucleus
IPI00328379Q5T1N8G-protein-signaling modulator 218876,66137.60.060.040.050.01NoneCytoplasm
IPI00025721Q9UNS2COP9 signalosome complex subunit 35347,87312.80.320.50.410.13NoneNucleus
IPI00003768B2RDF2Isoform 1 of Pescadillo homolog 1b6568,00222.90.450.30.380.11LKLE 0.91Nucleoli
IPI00742682P12270Nucleoprotein TPR355267,29084.10.570.460.520.08VKLE 0.93Nucleus
IPI00024279Q9H583HEAT repeat-containing protein 1393242,370104.90.570.640.610.05IKEE 0.94Nucleoli
IPI00003377Q16629Isoform 1 of splicing factor, arginine/serine-rich 74427,36623.80.690.480.590.15GKGE 0.67Nucleus
  • a In vitro identified SUMO-1 targets.

  • b Known SUMO-1 targets.