Table I. UPS or UTS associated targets identified as preferentially ubiquitinated with K0 Ub. Ubiquitinated proteins enriched in K0 Ub expressing cells from supplemental Table S1 that are documented to be associated with ubiquitin, either as ubiquitin proteasome system components and substrates, or as ubiquitin trafficking system components. Light-to-Heavy (L/H) ratio represents abundance of each target in K0 Ub-expressing cells relative to WT. Protein description and links to protein trafficking or Rsp5 are based on SGD http://www.yeastgenome.org/.
| Systematic name | Protein | Ratio L/H | Protein description | Role in protein trafficking/sorting | Rsp5 association |
|---|---|---|---|---|---|
| YER094C | PUP3 | 14.1 | Beta subunit of the 20S proteasome involved in ubiquitin-dependent catabolism | ||
| YJL151C | SNA3a | 8.4 | Integral membrane protein has a possible role in either cell wall synthesis or protein-vacuolar targeting | + | + |
| YDR054C | CDC34 | 4.8 | Ubiquitin-conjugating enzyme (E2) and catalytic subunit of SCF ubiquitin-protein ligase complex | ||
| YPL084W | BRO1 | 4.7 | Class E vacuolar protein sorting factor that coordinates deubiquitination | + | + |
| YBL058W | SHP1 | 4.6 | UBX domain-containing protein that regulates Glc7p phosphatase activity | + | |
| YNR006W | VPS27 | 4.4 | Endosomal protein that forms a complex with Hse1p; required for recycling Golgi proteins | + | + |
| YML097C | VPS9 | 4.3 | A guanine nucleotide exchange factor involved in vesicle-mediated vacuolar protein transport | + | |
| YOR042W | CUE5 | 4.2 | Protein containing a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitination | + | + |
| YDL126C | CDC48 | 4.1 | ATPase in ER, nuclear membrane and cytosol | + | |
| YMR275C | BUL1 | 3.9 | Ubiquitin-binding component of the Rsp5p E3-ubiquitin ligase complex | + | + |
| YFL009W | CDC4 | 3.9 | F-box protein required for G1/S and G2/M transition | ||
| YDR320C | SWA2 | 3.9 | Auxilin-like protein involved in vesicular transport | + | |
| YOL038W | PRE6 | 3.9 | 20S proteasome alpha-type subunit | ||
| YEL037C | RAD23 | 3.9 | Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA | ||
| YDR177W | UBC1 | 3.7 | Ubiquitin-conjugating enzyme (E2) | ||
| YOR261C | RPN8 | 3.7 | Essential, non-ATPase regulatory subunit of the 26S proteasome | ||
| YDR092W | UBC13 | 3.7 | Ubiquitin-conjugating enzyme (E2) | ||
| YDL161W | ENT1 | 3.4 | Epsin-like protein involved in endocytosis and actin patch assembly | + | + |
| YLR421C | RPN13 | 3.3 | Subunit of the 19S regulatory particle of the 26S proteasome lid | ||
| YEL012W | UBC8 | 3.2 | Ubiquitin-conjugating enzyme (E2) | ||
| YJL172W | CPS1 | 3.2 | Vacuolar carboxypeptidase yscS | + | + |
| YGR135W | PRE9 | 3.1 | 20S proteasome beta-type subunit | ||
| YOR018W | ROD1/ART4 | 3.0 | Membrane protein; contains 2 PY motifs, which are required for Rod1p interaction with Rsp5p | + | + |
| YCR030C | SYP1 | 2.8 | Protein with a potential role in actin cytoskeletal organization | + | |
| YOR322C | LDB19/ART1/CVS7 | 2.8 | Protein involved in regulating the endocytosis of plasma membrane proteins | + | + |
| YKL213C | DOA1 | 2.7 | WD repeat protein required for ubiquitin-mediated protein degradation | ||
| YBL101C | ECM21/ART2 | 2.7 | Protein involved in regulating the endocytosis of plasma membrane proteins | + | + |
| YLR392C | ART10 | 2.7 | Protein of unknown function that contains 2 PY motifs and is ubiquinated by Rsp5p | + | + |
| YLR206W | ENT2 | 2.7 | Epsin-like protein required for endocytosis and actin patch assembly | + | + |
| YFR010W | UBP6 | 2.6 | Ubiquitin-specific protease situated in the base subcomplex of the 26S proteasome | ||
| YGR068C | ART5 | 2.6 | Protein proposed to regulate the endocytosis of plasma membrane proteins | + | + |
| YER125W | RSP5 | 2.6 | Ubiquitin-protein ligase (E3) | + | + |
| YJL084C | ALY2/ART3 | 2.5 | Protein proposed to regulate the endocytosis of plasma membrane proteins | + | + |
| YKL145W | RPT1 | 2.4 | One of six ATPases of the 19S regulatory particle of the 26S proteasome | ||
| YBR082C | UBC4 | 2.4 | Ubiquitin-conjugating enzyme (E2) | ||
| YHR200W | RPN10 | 2.4 | Non-ATPase base subunit of the 19S regulatory particle of the 26S proteasome | + | |
| YBL057C | PTH2 | 2.2 | Mitochondrially-localized peptidyl-tRNA hydrolases; negatively regulates the ubiquitin-proteasome pathway | ||
| YDL007W | RPT2 | 2.2 | One of six ATPases of the 19S regulatory particle of the 26S proteasome | ||
| YBR058C | UBP14 | 2.2 | Ubiquitin-specific protease that specifically disassembles unanchored ubiquitin chains | ||
| YOR124C | UBP2 | 2.2 | Ubiquitin-specific protease that removes ubiquitin from ubiquitinated proteins | + | |
| YNL243W | SLA2 | 2.1 | Transmembrane actin-binding protein involved in membrane cytoskeleton assembly and cell polarization | + | + |
| YDR388W | RVS167 | 2.1 | Actin-associated protein, interacts with Rvs161p to regulate actin cytoskeleton, endocytosis, and viability | + | + |
| YGL045W | RIM8/ART9 | 2.1 | Protein involved in proteolytic activation of Rim101p in response to alkaline pH | + | + |
| YMR304W | UBP15 | 2.0 | Ubiquitin-specific protease that may play a role in ubiquitin precursor processing | ||
| YHR108W | GGA2 | 2.0 | Golgi-localized protein with homology to gamma-adaptin | + | |
| YML111W | BUL2 | 2.0 | Component of the Rsp5p E3-ubiquitin ligase complex, involved in intracellular amino acid permease sorting | + | + |
| YGR048W | UFD1 | 2.0 | Involved in recognition of polyubiquitinated proteins and their presentation to the 26S proteasome | ||
| YKL010C | UFD4 | 1.9 | Ubiquitin-protein ligase (E3) | + | |
| YBL047C | EDE1 | 1.9 | Key endocytic protein involved in a network of interactions with other endocytic proteins | + | + |
| YML013W | UBX2/SEL1 | 1.9 | Protein involved in ER-associated protein degradation | + | |
| YHR027C | RPN1 | 1.6 | Non-ATPase base subunit of the 19S regulatory particle of the 26S proteasome | ||
| YPR103W | PRE2 | 1.6 | 20S proteasome beta-type subunit, responsible for the chymotryptic activity of the proteasome | ||
| YDL190C | UFD2 | 1.6 | Ubiquitin chain assembly factor (E4) | + | |
| YDL097C | RPN6 | 1.6 | Essential, non-ATPase regulatory subunit of the 26S proteasome | ||
| YIL075C | RPN2 | 1.5 | Subunit of the 26S proteasome | ||
| YDL140C | RPB1 | 1.5 | RNA polymerase II largest subunit B220, part of central core | + |
a Identified by one peptide only.