TABLE 1.
The names and functions of yeast proteins bound to TBSV p33
| Genea | Binding of corresponding protein tob:
|
Protein functionc | |||
|---|---|---|---|---|---|
| p33 | p33N | p33C | p92C | ||
| ALA1 | ++ | − | − | − | Cytoplasmic alanyl-tRNA synthetase |
| ARP8* | ++ | − | + | − | Nuclear actin-related protein involved in chromatin remodeling |
| BFR1 | ++ | − | − | − | Component of mRNP complexes associated with polyribosomes |
| BUD21 | ++ | − | − | − | Component of SSU processosome |
| CDC34 | ++ | − | ++++ | − | Ub-conjugating enzyme or E2 |
| DDR48 | ++ | ++ | ++ | ++ | DNA damage-responsive protein; expression is increased in response to heat shock stress |
| EFB1* | ++ | − | − | − | Translation elongation factor 1 beta |
| ELF1* | ++ | − | ++ | ++ | A conserved zinc finger containing transcription elongation factor; deletion inhibits BMV gene expression |
| EMI2 | + | + | − | − | Protein of unknown function |
| ERB1 | ++++ | ++ | ++ | ++ | Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S preribosomal particles; homologous to mammalian Bop1 |
| ERR2 | ++ | + | − | − | Protein of unknown function; has similarity to enolases |
| FOX2 | ++++ | − | − | − | Multifunctional enzyme of the peroxisomal fatty acid beta-oxidation pathway |
| FMP40 | + | + | − | − | Protein of unknown function |
| GIM3 | ++ | − | − | − | Subunit of the heterohexameric cochaperone prefoldin complex, which binds specifically to cytosolic chaperonin and transfers target proteins to it |
| GPH1 | ++ | ++ | + | − | Glycogen phosphorylase |
| GSY2* | + | + | ++ | ++ | Glycogen synthase |
| HBS1* | ++ | − | ++ | − | GTP binding protein with sequence similarity to the elongation factor class of G proteins, EF-1alpha and Sup35p |
| HOR2 | ++ | + | − | − | dl-Glycerol-3-phosphatase |
| IPI3 | ++ | − | − | − | Protein of unknown function; a possible role in assembly of the ribosomal large subunit |
| ISN1 | ++ | − | − | − | IMP-specific 5′ nucleotidase |
| IWR1* | ++++ | − | ++++ | ++++ | Protein of unknown function |
| JJJ1* | ++ | − | ++ | ++++ | Protein that may function as a cochaperone |
| JJJ3 | ++ | ++ | − | − | Protein of unknown function, contains a J-domain |
| MAM33 | ++ | − | + | − | Acidic protein of the mitochondrial matrix involved in oxidative phosphorylation |
| NAP1* | ++ | + | ++++ | − | Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics |
| PDI1 | ++ | + | − | − | Protein disulfide isomerase, multifunctional protein resident in the endoplasmic reticulum lumen; essential for the formation of disulfide bonds in secretory and cell surface proteins |
| PLP2 | ++ | − | − | − | Similarity to phosducins, which are GTPase inhibitors |
| POL30 | + | − | − | − | PCNA |
| PYC1 | ++ | − | + | − | Pyruvate carboxylase isoform |
| QCR6 | ++ | − | ++ | ++ | Subunit 6 of the ubiquinol cytochrome-c reductase complex; highly acidic protein |
| RIB2 | + | − | − | − | DRAP deaminase; cytoplasmic tRNA pseudouridine synthase |
| RPL8A* | ++ | − | ++++ | ++++ | Ribosomal protein L4 of the large (60S) ribosomal subunit |
| RSP5 | + | − | − | − | Ub-protein ligase involved in Ub-mediated protein degradation |
| RTT106 | ++ | − | ++ | − | Protein of unknown function |
| SAS10* | ++++ | − | ++++ | ++++ | Component of the SSU processosome |
| SHO1 | ++ | − | − | − | Transmembrane osmosensor |
| STM1* | + | − | ++ | ++ | Protein that binds G4 quadruplex and purine motif triplex nucleic acid |
| SPT16* | ++++ | + | ++++ | ++++ | Pol II transcription elongation factor activity |
| TIF1* | + | − | − | − | Translation initiation factor eIF4A; identical to Tif2p; DEA(D/H)-box RNA helicase |
| TIF11* | + | − | − | + | Translation initiation factor eIF1A; essential protein that forms a complex with Sui1p (eIF1) and the 40S ribosomal subunit and scans for the start codon |
| TOM71 | ++ | − | ++ | ++ | Mitochondrial outer membrane protein; minor component of the TOM |
| TRM1* | ++++ | − | ++++ | ++++ | tRNA methyltransferase; localizes to both nucleus and mitochondrion to produce the modified base N2,N2-dimethylguanosine in tRNAs in both compartments |
| TRZ1 | + | − | + | − | tRNase Z; involved in RNA processing; has two putative nucleotide triphosphate-binding motifs (P-loop) and a conserved histidine motif; homolog of the human candidate prostate cancer susceptibility gene ELAC2 |
| TSR2 | ++++ | − | − | − | Protein with a potential role in pre-rRNA processing |
| UBA1 | + | + | − | − | Ub-activating enzyme involved in Ub-mediated protein degradation |
| UBP10* | + | − | ++ | ++ | UBP that deubiquitinates Ub-protein moieties |
| UBP15* | ++++ | ++ | ++ | − | UBP that may play a role in Ub precursor processing |
| URN1 | ++ | + | − | ++ | Pre-mRNA splicing factor associated with the U2-U5-U6 snRNPs, the RES complex, and the Prp19-associated complex (NTC) |
| YCR016W | ++ | − | ++++ | ++++ | Unknown; involved in ribosome biogenesis |
| YDR161W | ++ | − | − | − | Unknown; involved in ribosome biogenesis |
| YGL242C | ++ | − | ++++ | ++ | Unknown |
| YGR017W | ++ | + | ++ | ++ | Unknown |
| YGR027W | ++++ | − | − | − | Retrotransposon TYA Gag gene |
| YHL013C/OTU2 | + | − | − | + | member of the OTU superfamily of predicted cysteine proteases |
| YHR009C | + | − | + | − | Unknown |
| YLR125W | + | − | − | − | Unknown |
| YOR251C | + | + | − | − | Thiosulfate sulfurtransferase activity |
a
Genes corresponding to proteins binding specifically to various regions of TBSV p33 and p92. Boldface data indicate yeast proteins that interacted with recombinant p33C in an in vitro protein-binding assay (Fig. 2). Host proteins that interacted with p33 in the split-Ub assay (Fig. 3) are marked with asterisks.
b
Binding of the yeast protein to p33, p33N (the N-terminal 82-aa region), p33C, and p92C was calculated according to the following formula: (signal − background signal/amount of the selected protein on the array) × 10,000. Relative binding values are indicated as follows: ++++, above 1,000; ++, between 350 and 1000; +, between 150 and 350; −, below 150. The values were derived from repeated experiments.
c
Documented functions of the yeast proteins are based on the Saccharomyces Genome Database at http://www.yeastgenome.org/. SSU, small ribosomal subunit; PCNA, proliferating cell nuclear antigen; Pol II, polymerase II; TOM, translocase of outer membrane; OTU, ovarian tumor-like; IMP, inosine 5′-monophosphate.