Table I. The Nuclear p32-associated proteins that are involved or expected to be involved in ribosome biogenesis. The nuclear p32-associated proteins involved or expected to be involved in ribosome biogenesis are indicated. Proteins are classified into functional groups based on SwissProt classification. Proteins were identified by LC-MS/MS (LTQ-Orbitrap XL or Q-Tof2) and/or immunoblot analysis (IB), as described in Supplementary Tables I and II, and Figs. 1C and 1D. Proteins detected in mock are not listed in this table. Uniprot KB accession numbers, entry names, protein names as well as gene symbols are shown. For proteins having yeast orthologs, the gene names are indicated (obtained by Blink analysis of the NCBI database). Cellular localization is also indicated: No, nucleoli; Nm, nuclear membrane; Np, nucleoplasm; Nu, nucleus; Cy, cytoplasm; CBs, Cajal bodies.
| Uniprot KB accession | Uniprot KB entry name | Protein name | Gene symbol | ID method |
Cellular localization | Yeast homologs | aFunction | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LTQ-Orbtrap XL | Q-Tof2 | IB | ||||||||
| pre-rRNAs modification and processing | ||||||||||
| 1 | P22087 | FBRL_HUMAN | rRNA 2∼-O-methyltransferase fibrillarin (FBL)b | FBL | ○ | ○ | ○ | No/CBs | NOP1 | Pre-90S, pre-60S, boxC/D snoRNP, SSU processome, methyltransferase |
| 2 | O00567 | NOP56_HUMAN | Nucleolar protein 56 (Nop56) | NOP56 | ○ | ○ | No | NOP56 | Pre-90S, boxC/D snoRNP, SSU processome | |
| 3 | Q9Y2X3 | NOP58_HUMAN | Nucleolar protein 58 (Nop58) | NOP58 | ○ | No | NOP5 | Pre-90S, boxC/D snoRNP, SSU processome | ||
| 4 | Q96G21 | IMP4_HUMAN | U3 small nucleolar ribonucleoprotein protein IMP4 | IMP4 | ○ | No | IMP4 | Pre-90S, U3 snoRNP, SSU processome | ||
| 5 | O00566 | MPP10_HUMAN | U3 small nucleolar ribonucleoprotein protein MPP10 | MPHOSPH10 | ○ | ○ | No | MPP10 | Pre-90S, U3 snoRNP, SSU processome | |
| 6 | Q9BVI4 | NOC4L_HUMAN | Nucleolar complex protein 4 homolog | NOC4L | ○ | No | NOC4 | Pre-90S, SSU processome, Noc4-Nop14 complex function unknown in mammals | ||
| 7 | P78316 | NOP14_HUMAN | Nucleolar protein 14 | NOP14 | ○ | No | NOP14 | Pre-90S, SSU processome, Noc4-Nop14 complex function unknown in mammals | ||
| 8 | Q9NQZ2 | SAS10_HUMAN | Something about silencing protein 10 | UTP3 | ○ | Nu | UTP3 | Pre-90S, SSU processome, function unknown in mammals | ||
| 9 | Q9Y3A4 | RRP7A_HUMAN | Ribosomal RNA-processing protein 7 homolog A | RRP7A | ○ | - | RRP7 | Pre-90S, function unknown in mammals | ||
| 10 | P19338 | NUCL_HUMAN | Nucleolin (NCL) | NCL | ○ | No | NSR1 | Pre-90S, pre-60S | ||
| 11 | Q9NR30 | DDX21_HUMAN | Nucleolar RNA helicase 2 (Guα) | DDX21 | ○ | ○ | ○ | No | DBP1 | Pre-60S, DEAD box RNA helicase |
| 12 | Q8N8A6 | DDX51_HUMAN | ATP-dependent RNA helicase DDX51 | DDX51 | ○ | No | DBP6 | Pre-60S, DEAD box RNA helicase | ||
| 13 | Q8IZL8 | PELP1_HUMAN | Proline-, glutamic acid- and leucine-rich protein 1 | PELP1 | ○ | No/Nu/Cy | RIX1 | Pre-60S, RIX1 complex, SENP3-sensitive target of SUMO | ||
| 14 | Q9NXF1 | TEX10_HUMAN | Testis-expressed sequence 10 protein | TEX10 | ○ | No/Nu/Nm | IPI1 | Pre-60S, RIX1 complex | ||
| 15 | Q9BV38 | WDR18_HUMAN | WD repeat-containing protein 18 | WDR18 | ○ | - | IPI3 | pre-60S, RIX1 complex | ||
| 16 | Q9Y4W2 | LAS1L_HUMAN | Protein LAS1 homolog | LAS1L | ○ | ○ | No | LAS1 | Pre-60S, associated with human RIX1 complex, SENP3-sensitive target of SUMO | |
| 17 | Q9NU22 | MDN1_HUMAN | Midasin | MDN1 | ○ | Nu | REA1 | Pre-60S, associated with human RIX1 complex | ||
| 18 | Q9H4L4 | SENP3_HUMAN | Sentrin-specific protease 3 | SENP3 | ○ | No/Np | ULP1 | Pre-60S, associated with human RIX1 complex | ||
| 19 | Q5SY16 | NOL9_HUMAN | Nucleolar protein 9 | NOL9 | ○ | No | GRC3 | Pre-60S | ||
| 20 | P56182 | RRP1_HUMAN | Ribosomal RNA processing protein 1 homolog A (Nop52) | RRP1 | ○ | ○ | ○ | No | RRP1 | Pre-60S, function unknown in mammals |
| 21 | Q8TDD1 | DDX54_HUMAN | ATP-dependent RNA helicase DDX54 | DDX54 | ○ | No | DBP10 | Pre-60S, DEAD box RNA helicase, function unknown in mammals | ||
| 22 | Q9NY93 | DDX56_HUMAN | Probable ATP-dependent RNA helicase DDX56 | DDX56 | ○ | No | DBP9 | Present in 65S preribosomal particles, DEAD box RNA helicase | ||
| 23 | Q9H6W3 | NO66_HUMAN | Lysine-specific demethylase NO66 | C14orf169 | ○ | ○ | No/Np | - | Present in large preribosomal particles | |
| 24 | Q5JTH9 | RRP12_HUMAN | RRP12-like protein | RRP12 | ○ | ○ | No/Nm | RRP12 | Nuclear export of pre-40S and pre-60S, function unknown in mammals | |
| 25 | Q9BQ39 | DDX50_HUMAN | ATP-dependent RNA helicase DDX50 (Guβ) | DDX50 | ○ | ○ | ○ | No | DBP1 | DEAD box RNA helicase |
| 26 | Q01780 | EXOSX_HUMAN | Exosome component 10 (PM/Scl-100) | EXOSC10 | ○ | No/Cy | RRP6 | Exosome | ||
| 27 | Q9NQT5 | EXOS3_HUMAN | Exosome complex exonuclease RRP40 | EXOSC3 | ○ | No/Cy | RRP40 | Exosome | ||
| 28 | Q9UI43 | RRMJ2_HUMAN | Putative ribosomal RNA methyltransferase 2 (FTSJ2) | FTSJ2 | ○ | No | MRM2 | Methyltransferase | ||
| Nucleolar Protein | ||||||||||
| 29 | Q9BQG0 | MBB1A_HUMAN | Myb-binding protein 1A | MYBBP1A | ○ | No/Cy | POL5 | |||
| 30 | Q5C9Z4 | NOM1_HUMAN | Nucleolar MIF4G domain-containing protein 1 | NOM1 | ○ | ○ | No | SGD1 | ||
| 31 | Q14684 | RRP1B_HUMAN | Ribosomal RNA processing protein 1 homolog Bb | RRP1B | ○ | No | RRP1 | |||
a Known roles in ribosome biogenesis and/or associated pre-ribosome particles for yeast homologs or for human proteins are indicated.
b The proteins known to be associated with p32.