Table I

SUMO target proteins

Proteins identified by at least two arginine-containing peptides with a minimum SILAC cutoff ratio of 1.5 are presented here and include 25 SUMO-1 targets (top part), 19 SUMO-2 targets (middle part), and nine proteins conjugated to both SUMO family members (bottom part). 14 of the 25 SUMO-1 targets contain one or more zinc fingers (ZF). A complete list of identified arginine-containing peptides can be found in the supplemental dataset. RB, retinoblastoma susceptibility protein; KRAB, Krueppel-associated box.

Protein nameAccession numberFunctional classificationZinc fingersNo. Arg peptidesSUMO-1/controlaS.D.SUMO-2/controlbS.D.
SUMO-1 target proteins
    Zinc finger HIT domain-containing protein 4 Swiss-Prot:Q9C086 Cell cycleZF21.600.620.590.07
    Spectrin β chain, brain 1 Swiss-Prot:Q01082 Cytoskeleton81.510.141.090.11
    UDP-N-acetylglucosamine-peptide N Swiss-Prot:O15294 Glycosylation41.760.171.440.19
    Δ1-Pyrroline-5-carboxylate synthetase Swiss-Prot:P54886-1 Metabolism71.880.241.270.22
    (3-Methyl-2-oxobutanoate dehydrogenase (lipoamide)) kinase TrEMBL:Q96G95 Metabolism21.830.090.750.01
    Double-stranded RNA-specific editase B2 Swiss-Prot:Q9NS39 RNA editing21.640.200.200.07
    Protein phosphatase 1 regulator Swiss-Prot:Q96QC0 SignalingZF151.530.200.910.18
    Zinc finger protein 462 Swiss-Prot:Q96JM2-2 Transcriptional regulatorZF62.310.221.070.14
    Zinc finger motif enhancer-binding protein-1β TrEMBL:Q6BEP6 Transcriptional regulatorZF52.021.430.470.27
    AT-rich interactive domain-containing protein 5B Swiss-Prot:Q14865 Transcriptional regulator41.570.161.260.34
    ZMYND11 protein TrEMBL:Q5BJG6 Transcriptional regulatorZF41.530.350.990.31
    Zinc finger protein 592 Swiss-Prot:Q92610 Transcriptional regulatorZF31.940.120.480.04
    RB-associated KRAB repressor TrEMBL:Q9NYW8 Transcriptional regulatorZF31.750.181.280.09
    Zinc finger protein 96 Swiss-Prot:O43309 Transcriptional regulatorZF22.010.070.830.08
    Zinc finger protein 174 Swiss-Prot:Q15697 Transcriptional regulatorZF21.780.081.250.32
    Zinc finger protein 317 Swiss-Prot:Q96PQ6-2 Transcriptional regulatorZF21.650.130.210.04
    Chromodomain helicase DNA-binding protein 2 Swiss-Prot:O14647 Transcriptional regulator, helicase72.000.301.170.29
    Protein CXorf17 Swiss-Prot:Q9NX05-1 Transmembrane component23.650.100.750.10
    KIAA1441 protein TrEMBL:Q9P2A7 Uncharacterized novel proteinZF41.670.130.380.07
    Hypothetical protein TrEMBL:Q569L7 Uncharacterized novel proteinZF41.580.311.100.28
    Hypothetical protein FLJ12104 TrEMBL:Q9HA80 Uncharacterized novel protein31.870.170.930.23
    Novel protein TrEMBL:Q5T0B9 Uncharacterized novel proteinZF21.890.600.380.14
    Hypothetical protein TrEMBL:Q7Z7K6 Uncharacterized novel protein23.090.080.630.02
    WD-repeat protein 33 Swiss-Prot:Q9C0J8 Unknown61.560.130.840.20
    Zinc finger CCCH type domain-containing protein 1 Swiss-Prot:Q9H0J9 UnknownZF51.770.470.440.09
SUMO-2 target proteins
    DNA damage-binding protein 2 Swiss-Prot:Q92466 DNA repair161.400.122.410.48
    Probable helicase with zinc finger domain Swiss-Prot:P42694 HelicaseZF20.700.041.650.29
    α2-Macroglobulin receptor-associated protein precursor Swiss-Prot:P30533 Metabolism61.480.122.080.25
    Malonyl-CoA-acyl carrier protein transacylase Swiss-Prot:Q8IVS2 Metabolism20.900.192.290.08
    2-Oxoglutarate dehydrogenase E component Swiss-Prot:Q02218 Metabolism20.830.212.500.52
    Dual specificity protein kinase CLK3 Swiss-Prot:P49761-3 Signaling21.220.081.580.32
    Nuclear receptor co-repressor 2 Swiss-Prot:Q9Y618 Transcriptional regulator91.030.131.540.16
    AT-rich interactive domain-containing protein 1B Swiss-Prot:Q8NFD5 Transcriptional regulator91.050.201.520.35
    Homeobox protein Meis1 Swiss-Prot:O00470 Transcriptional regulator30.780.222.760.97
    PML protein TrEMBL:Q59FP9 Transcriptional regulatorZF21.210.254.350.27
    Zinc finger protein Rlf Swiss-Prot:Q13129 Transcriptional regulatorZF21.220.091.550.42
    Activating signal cointegrator 1 complex subunit 3 Swiss-Prot:Q8N3C0-1 Transcriptional regulator, helicase20.500.061.520.04
    Hypothetical protein FLJ10534 TrEMBL:Q8WUY5 Uncharacterized novel protein70.930.161.930.20
    Hypothetical protein FLJ13157 TrEMBL:Q9H8X6 Uncharacterized novel protein41.060.231.940.60
    Hypothetical protein DKFZp434D1319 TrEMBL:Q9NSV0 Uncharacterized novel protein31.190.341.840.35
    FMRP-interacting protein, 82 kDa Swiss-Prot:Q7Z417 Unknown110.980.211.570.37
    Ataxin-2-like protein Swiss-Prot:Q8WWM7 Unknown111.000.242.170.38
    Protein FAM98A Swiss-Prot:Q8NCA5 Unknown51.020.121.720.26
    Ataxin-2 Swiss-Prot:Q99700 Unknown21.090.022.690.13
SUMO-1,2 target proteins
    Erythrocyte band 7 integral membrane proteinSwiss-Prot:P27105Cation conductance32.790.582.391.28
    Ran GTPase-activating protein 1 Swiss-Prot:P46060 GTPase20.972.015.561.10
    DEAH (Asp-Glu-Ala-His) box polypeptide 30 TrEMBL:Q7L2E3 Helicase21.500.731.580.29
    Histone H2B.q Swiss-Prot:Q16778 Nucleosome24.731.962.490.65
    SART-1 TrEMBL:Q53GB5 Pre-mRNA splicing42.030.993.463.04
    Alkaline phosphatase Swiss-Prot:P05187 Signaling613.222.491.743.24
    Chromodomain helicase DNA-binding protein HELSNF1 Swiss-Prot:Q9HCK8 Transcriptional regulator, helicase91.770.271.800.39
    KIAA1553 protein TrEMBL:Q9HCL9 Uncharacterized novel protein24.353.4453.5053.09
    Zinc finger protein 106 homolog Swiss-Prot:Q9H2Y7 UnknownZF54.570.552.260.56
  • a SILAC enrichment ratios of Arg6-labeled peptides, indicating conjugation of proteins to SUMO-1.

  • b SILAC enrichment ratios of Arg10-labeled peptides, indicating conjugation of proteins to SUMO-2.