Table 1.
Selected Entries for Putative Nucleolar SUMO1 Substrates from MaxQuant Analysis
| Number in Figure 1 | Protein Names | Gene Names | Uniprot | ELUATE Seq. Cov. (%) | ELUATE Log2 M/L Norm. | ELUATE M/L Sign. A | ELUATE M/L Count | INPUT Whole M/L Sign. B | SUMO Site? | Other Ref. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Alkaline phosphatase; tissue-nonspecific isozyme | ALPL | P05186 | 15.6 | 0.768 | 7.45E-03 | 3 | 0.359 | No | – |
| 2 | H/ACA ribonucleoprotein complex subunit 4 | DKC1 | A8MUT5 | 24.5 | 1.40 | 3.78E-06 | 10 | 0.234 | Yes | Manza et al., 2004; Blomster et al., 2009 |
| 3 | H/ACA ribonucleoprotein complex subunit 2 | NHP2 | Q9NX24 | 39.9 | 3.79 | 4.42E-34 | 3 | 0.150 | Yes | Blomster et al., 2009; Golebiowski et al., 2009 |
| 4 | Nucleolar phosphoprotein p130 | NOLC1 | Q14978 | 8.2 | 2.83 | 7.41E-20 | 7 | 0.358 | Yes | Golebiowski et al., 2009 |
| 5 | Nucleolar protein 58 | NOP58 | Q9Y2X3 | 53.7 | 1.81 | 3.64E-09 | 101 | 0.148 | Yes | Zhao et al., 2004; Manza et al., 2004; Schimmel et al., 2008; Golebiowski et al., 2009 |
| 6 | Alkaline phosphatase; placental type | ALPP | P05187 | 28.5 | 1.03 | 5.24E-04 | 18 | 5.84E-09 | Yes | Vertegaal et al., 2006 |
| 7 | Caveolin | CAV1 | Q59E85 | 13.4 | 0.848 | 3.54E-03 | 2 | 2.81E-04 | Yes | – |
| 8 | Cytochrome b5 type B | CYB5B | O43169 | 28.7 | 0.748 | 8.87E-03 | 3 | 0.136 | Yes | – |
| 9 | DNA damage-binding protein 2 | DDB2 | Q92466 | 44.3 | 0.909 | 1.94E-03 | 20 | – | No | Vertegaal et al., 2006; Pungaliya et al., 2007 |
| 10 | Nucleolar RNA helicase 2 | DDX21 | Q9NR30 | 3.1 | 2.25 | 3.35E-13 | 2 | 0.466 | Yes | Matafora et al., 2009 |
| 11 | Exosome component 10 | EXOSC10 | Q01780 | 28.2 | 3.82 | 1.05E-34 | 21 | 0.374 | Yes | Zhao et al., 2004; Golebiowski et al., 2009 |
| 12 | Four and a half LIM domains 1 variant | FHL1 | Q53FI7 | 43.6 | 1.30 | 1.74E-05 | 14 | 3.85E-06 | No | Wang et al., 2007 |
| 13 | Lanosterol synthase | LSS | P48449 | 4.9 | 0.938 | 1.44E-03 | 3 | – | No | – |
| 14 | Protein arginine N-methyltransferase 5 | PRMT5 | O14744 | 7.7 | 0.805 | 5.32E-03 | 3 | 2.58E-02 | Yes | – |
| 15 | Retinol dehydrogenase 10 | RDH10 | Q8IZV5 | 23.8 | 1.03 | 5.27E-04 | 5 | 1.22E-03 | Yes | – |
| 16 | Small ubiquitin-related modifier 1 | SUMO1 | P63165 | 46.9 | 4.55 | 3.17E-48 | 37 | 3.53E-139 | No | – |
| 17 | Transferrin receptor protein 1 | TFRC | P02786 | 3.9 | 1.07 | 3.26E-04 | 2 | 5.08E-04 | Yes | Golebiowski et al., 2009 |
| 18 | Transmembrane protein 109 | TMEM109 | Q9BVC6 | 9.1 | 0.805 | 5.32E-03 | 3 | 9.24E-03 | No | – |
| 19 | Tubulin–tyrosine ligase-like protein 12 | TTLL12 | Q14166 | 3.9 | 0.764 | 7.66E-03 | 2 | 9.71E-02 | Yes | Golebiowski et al., 2009 |
The first entry of each column for protein groups with Ratio M/L Significance A < 0.01 (ratio count >1) is shown. Reverse, contaminant, and unnamed protein groups are not included. “–” indicates a missing value in the MaxQuant output. All columns were derived from Ni2+-NTA pull-downs except for “INPUT Whole M/L Significance B,” which is based on analysis of mixed lysates prior to fractionation (Figure 1B). Protein sequences that contain a high probability SUMOylation site are indicated (SUMOplot). snoRNP-related proteins are highlighted. The complete MaxQuant output is given in Tables S1 and S2.