Table 1. Vacuolar, endomembrane, and vesicle trafficking genes required for the downregulation of the Ribi gene NSR1 in stress.
| Name | Description | Loc | [NSR1] | Down TOR | Phys Net |
|---|---|---|---|---|---|
| VMA1 | Subunit A of the V1 peripheral membrane domain of V-ATPase | V | 2.2 | No | Yes |
| VMA2 | Subunit B of V1 peripheral membrane domain of vacuolar H+-ATPase | V | 2.3 | Yes | Yes |
| VMA3 | Proteolipid subunit c of the V0 domain of vacuolar H(+)-ATPase | V | 1.9 | No | Yes |
| VMA5 | Subunit C of the V1 peripheral membrane domain of V-ATPase | V | 2.2 | No | Yes |
| VMA6 | Subunit d of the V0 integral membrane domain of V-ATPase | V | 2.1 | No | Yes |
| VMA8 | Subunit D of the V1 peripheral membrane domain of V-ATPase | V | 2.1 | No | Yes |
| VMA11 | Vacuolar ATPase V0 domain subunit c’ | V | 1.5 | No | Yes |
| VMA16 | Subunit c’’ of the vacuolar ATPase | V | 1.9 | No | Yes |
| VMA21 | Integral membrane protein required for V-ATPase function | ER | 1.5 | No | Yes |
| VMA22 | Protein that is required for vacuolar H+-ATPase (V-ATPase) function | ER | 1.9 | No | Yes |
| PKR1 | V-ATPase assembly factor | ER | 1.9 | No | Yes |
| SLM4 | Component of the EGO and GSE complexes | V | 3.7 | No | Yes |
| MEH1 | Component of the EGO and GSE complexes | V | 1.5 | No | Yes |
| VTC1 | Subunit of the vacuolar transporter chaperone (VTC) complex | ER/V | 1.4 | No | Yes |
| VTC4 | Vacuolar membrane polyphosphate polymerase | ER/V | 2.3 | No | Yes |
| GAP1 | General amino acid permease | V | 1.9 | No | Yes |
| SYN8 | Endosomal SNARE related to mammalian syntaxin 8 | Endo | 1.8 | No | Yes |
| VAM3 | Syntaxin-like vacuolar t-SNARE | V | 2.6 | No | Yes |
| VAM7 | Vacuolar SNARE protein | V | 2.4 | No | Yes |
| YPT7 | Rab family GTPase | V | 2.5 | Yes | Yes |
| PEP5 | Histone E3 ligase, component of CORVET membrane tethering complex | V | 1.9 | No | Yes |
| RCR1 | Involved in chitin deposition; may function in endosomal-vacuolar trafficking | ER | 2.0 | No | No |
| YOP1 | Membrane protein that interacts with Yip1p to mediate membrane traffic | ER | 1.7 | No | Yes |
| GYP5 | GTPase-activating protein (GAP) for yeast Rab family members | G | 1.8 | No | Yes |
| RGP1 | Subunit of a Golgi membrane exchange factor (Ric1p-Rgp1p) | G | 1.4 | No | No |
| SYS1 | Integral membrane protein of the Golgi | G | 1.8 | No | Yes |
| TVP15 | Integral membrane protein; localized to late Golgi vesicles | G | 1.8 | No | Yes |
| TVP38 | Integral membrane protein; localized to late Golgi vesicles | G | 1.9 | No | Yes |
| VPS52 | Component of the GARP (Golgi-associated retrograde protein) complex | G | 1.3 | No | No |
| YIP5 | Protein that interacts with Rab GTPases; localized to late Golgi vesicles | G | 1.6 | No | Yes |
| EMP70 | Endosome-to-vacuole sorting | V | 1.6 | No | Yes |
| SNX4 | Sorting nexin; involved in the retrieval of late-Golgi SNAREs | Endo | 2.0 | No | Yes |
| SNX41 | Sorting nexin; involved in the retrieval of late-Golgi SNAREs | Endo | 2.0 | No | Yes |
| VFA1 | Protein that interacts with Vps4p and has a role in vacuolar sorting | Endo | 1.8 | No | Yes |
| VPS5 | Nexin-1 homolog; moves proteins from endosomal compartment to Golgi | Endo | 1.7 | No | Yes |
| PFA3 | Palmitoyltransferase for Vac8p | V | 2.4 | No | Yes |
| VAC8 | Phosphorylated and palmitoylated vacuolar membrane protein | V | 2.9 | No | Yes |
| LST4 | Protein possibly involved in a post-Golgi secretory pathway | 2.7 | Yes | No | |
| EDE1 | Scaffold protein involved in the formation of early endocytic sites | 1.6 | No | Yes | |
| ENT2 | Epsin-like protein required for endocytosis and actin patch assembly | 1.8 | No | Yes | |
| KIN2 | Serine/threonine protein kinase involved in regulation of exocytosis | 1.7 | ? | YES | |
| VAB2 | Subunit of the BLOC-1 complex involved in endosomal maturation | 2.4 | ? | YES | |
| MDR1 | Cytoplasmic GTPase-activating protein; regulation of Golgi secretory function | 2.4 | No | No | |
| APL4 | Gamma-adaptin | Endo | 1.8 | No | Yes |
| APM1 | Mu1-like medium subunit of the AP-1 complex | G | 1.8 | No | Yes |
| CHC1 | Clathrin heavy chain | 1.5 | ? | YES | |
| DYN1 | Cytoplasmic heavy chain dynein | 1.7 | ? | YES |
The top three groups of genes encode proteins highlighted in the top portion of the physical interaction (Phys Net) network shown in Figure 6; V-ATPase, EGO/VTC, and CORVET/SNARE, respectively. The fourth group lists other genes found in our screen encoding vacuolar, vesicle transport of endomembrane proteins. The third column lists the localization (Loc) of each protein. The fourth column [NSR1] lists the log2 NSR1/PEX6 expression ratio from the screen. The fifth column notes if the gene acts downstream of TORC1 (has log2 > 1 normalized NSR1/PEX6 ratio in rapamycin). The sixth column states whether the genes is part of the physical interaction network shown in Figure 6. V, vacuole; ER, endoplasmic reticulum; G, Golgi; Endo, other parts of the Endomembrane system. A question mark means that the protein/gene was not analyzed in the rapamycin subscreen.