Table 3.
Mutations that confer Ino− phenotypes
| ORF | Gene | I− C− 30°C |
I−C+ 30°C |
I−C+ 37°C |
References |
|---|---|---|---|---|---|
| A. Protein complexes involved in transcription regulation | |||||
| A1. Subunits of the SWI/SNF chromatin remodeling complex | |||||
| YOR290C | SNF2 | + | VW | VW | (Peterson and Herskowitz 1992) |
| YBR289W | SNF5 | S | S | S | (Peterson and Herskowitz 1992) |
| YHL025W | SNF6 | S | S | S | (Peterson and Herskowitz 1992) |
| YPL016W | SWI1a | NS | NS | NS | (Peterson and Herskowitz 1992) |
| YJL176C | SWI3 | W | S | S | (Peterson and Herskowitz 1992) |
| A2. Subunits of the remodel the structure of chromatin (RSC) complex | |||||
| YGR056W | RSC1 | VW | VW | S | This study |
| YLR357W | RSC2 | VW | W | S | This study |
| A3. Subunits and proteins associated with the Ino80 chromatin remodeling complex | |||||
| YNL059C | ARP5a | NG | NG | NG | (Shen et al. 2003a) |
| YOR141C | ARP8 | W | S | NG | (Shen et al. 2003a) |
| YFL013C | IES1 | + | + | S | This study |
| YNL215W | IES2 | W | W | NG | This study |
| YOR189W | IES4 | VW | W | S | This study |
| YER092W | IES5 | + | + | S | This study |
| YEL044W | IES6 | S | S | NG | (Fernandez-Murray et al. 2009) |
| YGL150C | INO80a | NS | NS | NS | (Ebbert et al. 1999) |
| YDL002C | NHP10 | + | + | S | This study |
| A4. Subunits and proteins associated with the ADA and SAGA complexes | |||||
| YDR448W | ADA2 | S | W | W | This study |
| YGR252W | GCN5 | VW | VW | VW | This study |
| YPL254W | HFI1a | NG | NG | NG | (Horiuchi et al. 1997) |
| YDR176W | NGG1 | VW | W | W | This study |
| YGL066W | SGF73 | W | W | S | This study |
| YOL148C | SPT20a | NG | NG | NG | (Roberts and Winston 1996) |
| YDR392W | SPT3 | VW | W | S | This study |
| YBR081C | SPT7a | NS | NS | NS | (Gansheroff et al. 1995) |
| YLR055C | SPT8 | + | + | S | This study |
| A5. Subunit of a histone deacetylase (HAD1) complex | |||||
| YPR179C | HAD3 | + | + | S | This study |
| A6. Subunits of the Set3 deacetylase complex | |||||
| YGL194C | HOS2 | W | W | S | (Cohen et al. 2008) |
| YOL068C | HST1 | VW | VW | VW | This study |
| YKR029C | SET3 | + | W | S | (Cohen et al. 2008) |
| YBR103W | SIF2 | W | W | S | (Cohen et al. 2008) |
| YCR033W | SNT1 | W | S | S | (Cohen et al. 2008) |
| A7. Subunits of the RNA polymerase II SRB/mediator complex | |||||
| YHR041C | SRB2 | S | S | S | (Koleske et al. 1992) |
| YNL236W | SIN4 | S | S | NG | This study |
| YGR104C | SRB5 | VW | VW | NG | (Betz et al. 2002) |
| YGL127C | SOH1 | VW | W | S | This study |
| YGL025C | PGD1 | S | S | S | This study |
| A8. Subunits and proteins associated with the Paf1 complex | |||||
| YLR418C | CDC73 | S | S | S | This study |
| YOL145C | CTR9a | NS | NS | NS | (Betz et al. 2002) |
| YOR123C | LEO1 | W | W | S | This study |
| YBR279W | PAF1 | S | S | NG | (Betz et al. 2002) |
| YGL244W | RTF1 | VW | W | S | (Betz et al. 2002) |
| A9. Subunits and proteins associated with the CCR4-NOT complex | |||||
| YKR036C | CAF4 | + | VW | W | This study |
| YAL021C | CCR4 | + | + | W | (Betz et al. 2002) |
| YGR092W | DBF2 | W | S | S | This study |
| A10. Subunits of the COMPASS (Set1C) complex | |||||
| YLR015W | BRE2 | + | + | VW | This study |
| YDR469W | SDC1 | VW | VW | W | This study |
| YPL138C | SPP1 | + | + | S | This study |
| YAR003W | SWD1 | + | + | S | This study |
| YBR175W | SWD3 | VW | + | S | This study |
| A11. Subunits of the H2B ubiquitination complex | |||||
| YDL074C | BRE1 | W | W | S | This study |
| YPL055C | LGE1 | + | W | S | This study |
| YGL058W | RAD6 | VW | W | S | This study |
| B. Ribosomal biogenesis pathway | |||||
| B1. Components of the small (40S) ribosomal subunit | |||||
| YLR048W | RPS0B | W | W | W | This study |
| YOR096W | RPS7A | VW | VW | W | This study |
| YBR189W | RPS9B | + | W | W | This study |
| YDL083C | RPS16B | + | + | S | This study |
| YOL121C | RPS19A | + | + | S | This study |
| B2. Components of the large (60S) ribosomal subunit | |||||
| YKL006W | RPL14A | VW | W | S | This study |
| YBL027W | RPL19B | + | VW | W | This study |
| YMR242C | RPL20A | + | VW | W | This study |
| YBR191W | RPL21A | + | VW | W | This study |
| YLR061W | RPL22A | W | W | VW | This study |
| YGL031C | RPL24A | + | + | VW | This study |
| YHR010W | RPL27A | W | S | S | This study |
| YDL191W | RPL35A | W | W | S | This study |
| YPR043W | RPL43A | VW | VW | VW | This study |
| B3. Component of small ribosomal subunit (SSU) processosome | |||||
| YOR078W | BUD21 | + | VW | VW | This study |
| B4. Methyltransferase required for rRNA processing and nuclear export of 40S ribosomal subunits | |||||
| YCR047C | BUD23 | + | + | S | This study |
| B5. Components of the ribosomal stalk | |||||
| YDL081C | RPP1A | + | + | S | This study |
| YDL130W | RPP1B | + | + | S | This study |
| B6. Component of eukaryotic eIF3 and required for processing of 20S pre-rRNA | |||||
| YLR192C | HCR1 | + | + | S | This study |
| B7. Elongation factor 2 (EF-2), also encoded by EFT1 | |||||
| YDR385W | EFT2 | + | + | S | This study |
| C. Protein modification pathways | |||||
| C1. Glycosyltransferases of the ER, involved in N-linked protein glycosylation | |||||
| YOR002W | ALG6 | + | S | This study | |
| YOR067C | ALG8 | + | S | This study | |
| YNL219C | ALG9 | + | + | W | This study |
| YGR227W | DIE2 | + | + | S | This study |
| C2. Glycosyltransferases of the Golgi involved in branched glycosylation | |||||
| YJR075W | HOC1 | + | + | W | This study |
| YBR015C | MNN2 | + | + | W | This study |
| C3. Glycosyltransferases of the ER, involved in O-linked protein mannosylation | |||||
| YDL095W | PMT1 | + | VW | S | This study |
| YAL023C | PMT2 | W | W | S | This study |
| C4. GPI-anchored glycoproteins | |||||
| YCR089W | FIG 2 | + | + | W | This study |
| YMR307W | GAS1 | + | VW | S | This study |
| YNL322C | KRE1 | + | + | S | This study |
| YER150W | SPI1 | + | + | W | This study |
| YEL040W | UTR2 | + | + | W | This study |
| C5. Subunits of the N-terminal acetyltransferase NatA (Nat1p, Ard1p, Nat5p) | |||||
| YHR013C | ARD1 | W | S | S | This study |
| YDL040C | NAT1 | VW | W | S | This study |
| C6. Subunit of a palmitoyltransferase complex composed of Shr5p and Erf2p | |||||
| YOL110W | SHR5 | + | + | S | This study |
| D. Membrane trafficking pathways | |||||
| D1. Proteins involved in translocation into the ER (Translocon) | |||||
| YLR292C | SEC72 | + | + | S | This study |
| YKL065C | YET1 | W | S | S | (Wilson and Barlowe 2010) |
| YDL072C | YET3 | S | S | S | (Wilson and Barlowe 2010) |
| YLR242C | ARV1 | W | W | S | This study |
| D2. Proteins involved in COPII vesicle trafficking from the ER to the Golgi | |||||
| YGL054C | ERV14 | W | W | S | This study |
| YLR208W | SEC13a | NS | NS | NS | (Gilstring et al. 1999) |
| YLR268W | SEC22 | W | W | S | This study |
| D3. Proteins involved in Golgi to ER retrival | |||||
| YGL020C | GET1 | + | W | S | This study |
| YER083C | GET2 | W | W | NG | This study |
| D4. Proteins involved in protein ubiquitination/deubiquitination and degradation via proteosome and vacuole | |||||
| YDR069C | DOA4 | S | S | NG | (Henry and Patton-Vogt 1998) |
| YMR276W | DSK2 | + | VW | S | This study |
| YEL037C | RAD23 | + | + | W | This study |
| YBL058W | SHP1 | + | + | W | This study |
| YLL039C | UBI4 | + | + | S | This study |
| YBR058C | UBP14 | + | VW | S | This study |
| YMR304W | UBP15 | + | + | W | This study |
| YFR010W | UBP6 | W | W | S | This study |
| YML013W | UBX2 | VW | VW | S | This study |
| YMR067C | UBX4 | + | + | S | This study |
| YDL190C | UFD2 | + | + | S | This study |
| YDR057W | YOS9 | + | + | W | This study |
| D5. Proteins involved in COPI vesicle intra-Golgi trafficking and the COG complex | |||||
| YNL051W | COG5 | VW | VW | VW | This study |
| YNL041C | COG6 | W | W | W | This study |
| YML071C | COG8 | W | W | W | This study |
| YOR216C | RUD3 | VW | W | W | This study |
| YOL107W | YOL107 W | + | + | S | This study |
| D6. Proteins involved in late secretory trafficking | |||||
| YIL044C | AGE2 | + | + | S | This study |
| YDL192W | ARF1 | + | W | S | This study |
| YCR094W | CDC50 | + | + | W | This study |
| YAL026C | DRS2 | + | + | S | This study |
| YER122C | GLO3 | W | VW | W | This study |
| YGR166W | KRE11 | + | + | S | This study |
| YNL323W | LEM3 | + | VW | W | This study |
| YJL204C | RCY1 | + | VW | S | This study |
| YMR079W | SEC14a | NS | NS | NS | (Kearns et al. 1997) |
| YEL048C | TCA17 | + | + | S | This study |
| D7. Proteins involved in vacuole targeting | |||||
| YOR106W | VAM3 | + | + | S | This study |
| YDL077C | VAM6 | + | + | W | This study |
| YDR080W | VPS41 | + | VW | W | This study |
| YPR139C | VPS66 | + | W | S | This study |
| D8. Proteins involved in retrograde trafficking, from early and late endosomes, to the TGN | |||||
| YLR039C | RIC1 | VW | W | NG | (Kodaki et al. 1995) |
| YOL018C | TLG2 | VW | VW | VW | This study |
| YLR262C | YPT6 | + | + | VW | This study |
| D9. Proteins involved in endocytic trafficking, from plasma membrane to the MVB and vacuole | |||||
| YPL065W | VPS28 | + | + | S | This study |
| YDR486C | VPS60 | + | + | S | This study |
| D10. Subunits of the vacuolar H(+)-ATPase complex and associated proteins with vacuolar acidification | |||||
| YEL027W | CUP5 | S | S | S | This study |
| YMR123W | PKR1 | + | VW | W | This study |
| YHR026W | PPA1 | S | S | S | This study |
| YDL185W | TFP1 | W | S | S | This study |
| YPR036W | VMA13 | S | S | S | This study |
| YBR127C | VMA2 | S | S | S | This study |
| YGR105W | VMA21 | VW | W | S | This study |
| YHR060W | VMA22 | W | W | S | This study |
| YGR020C | VMA7 | VW | W | S | This study |
| YEL051W | VMA8 | S | S | S | This study |
| YOR270C | VPH1 | + | + | W | This study |
| YKL119C | VPH2 | W | S | S | This study |
| E. Stress response pathways | |||||
| E1. Components and associated proteins involved in the PKC–CWI signaling pathway | |||||
| YDL203C | ACK1 | + | + | S | This study |
| YJL095W | BCK1 | S | S | S | (Nunez et al. 2008) |
| YER167W | BCK2 | + | + | W | This study |
| YLR342W | FKS1 | VW | VW | S | This study |
| YLR332W | MID2 | + | VW | W | This study |
| YPL140C | MKK2 | + | + | W | This study |
| YBL105C | PKC1a | NS | NS | NS | (Nunez et al. 2008) |
| YPL089C | RLM1 | + | VW | S | This study |
| YLR371W | ROM2 | VW | W | S | This study |
| YDR389W | SAC7 | W | W | S | This study |
| YOR008C | SLG1 | VW | W | S | This study |
| YHR030C | SLT2 | VW | S | S | (Nunez et al. 2008) |
| YGR229C | SMI1 | + | + | S | This study |
| YLL021W | SPA2 | + | + | S | This study |
| YOL109W | ZEO1 | + | + | S | This study |
| E2. Components and associated proteins involved in the HOG signaling pathway | |||||
| YLR113W | HOG1 | W | W | W | This study |
| YGR014W | MSB2 | + | VW | W | This study |
| YDR162C | NBP2 | + | + | S | This study |
| YDL006W | PTC1 | W | W | NG | This study |
| YER118C | SHO1 | + | + | W | This study |
| YCL032W | STE50 | + | + | S | This study |
| E3. Components and associated proteins involved in the cell cycle progression | |||||
| YBR135W | CKS1a | NS | NS | NS | (Yu and Reed 2004) |
| YAL040C | CLN3 | + | + | W | This study |
| YBR133C | HSL7 | + | + | S | This study |
| YLR079W | SIC1 | + | W | S | This study |
| E4. Components and associated proteins involved in the TOR signaling pathway | |||||
| YMR068W | AVO2 | + | + | S | This study |
| YKR007W | MEH1 | + | + | S | This study |
| YIL105C | SLM1 | + | + | S | This study |
| YBR077C | SLM4 | + | + | W | This study |
| YJR066W | TOR1 | + | + | S | This study |
| YDL077C | VAM6 | + | + | W | This study |
| YMR104C | YPK2 | W | W | W | This study |
| E5. Components and associated proteins involved in the calcineurin signaling pathway | |||||
| YKL190W | CNB1 | VW | VW | W | This study |
| YNL307C | MCK1 | + | VW | W | This study |
| YHR206W | SKN7 | + | + | S | This study |
| E6. Components and associated proteins involved in the cAMP-PKA signaling pathway | |||||
| YER177W | BMH1 | + | VW | S | This study |
| YOR371C | GPB1 | + | + | W | This study |
| YAL056W | GPB2 | + | + | S | This study |
| YMR016C | SOK2 | + | + | S | This study |
| F. Lipid and glycerol metabolic pathways | |||||
| F1. Proteins involved in phospholipid metabolism | |||||
| YJL153C | INO1 | S | S | S | (Culbertson and Henry 1975) |
| YDR123C | INO2 | S | S | S | (Donahue and Henry 1981) |
| YOL108C | INO4 | S | S | S | (Donahue and Henry 1981) |
| YML059C | NTE1 | + | W | S | (Nunez et al. 2008) |
| YPR113W | PIS1a | NS | NS | NS | (Nikawa et al. 1987) |
| YER120W | SCS2 | W | W | S | (Kagiwada et al. 1998) |
| YGL126W | SCS3 | VW | S | S | (Hosaka et al. 1994) |
| F2. Proteins involved in glycerol metabolism | |||||
| YLL043W | FPS1 | + | VW | NG | This study |
| YDL022W | GPD1 | + | + | W | This study |
| YOL059W | GPD2 | W | W | W | This study |
| YHR104W | GRE3 | VW | W | S | This study |
| YBL011W | SCT1 | VW | W | S | This study |
| YDR368W | YPR1 | + | + | W | This study |
| F3. Proteins involved in phosphoinositides and inositol polyphosphates metabolism | |||||
| YDR173C | ARG82 | S | S | NG | This study |
| YFR019W | FAB1 | S | S | NG | This study |
| YDR017C | KCS1 | W | W | S | This study |
| YKL212W | SAC1 | S | S | S | (Whitters et al. 1993) |
| F4. Proteins involved in sphingolipids and ceramides metabolism | |||||
| YBR183W | YPC1 | VW | + | W | This study |
| YDR297W | SUR2 | + | + | W | This study |
| YJL134W | LCB3 | VW | W | S | This study |
| YDR294C | DPL1 | + | + | W | This study |
| YMR272C | SCS7 | VW | W | VW | This study |
| F5. Proteins involved in sterols metabolism | |||||
| YMR202W | ERG2 | W | W | S | This study |
| YLR056W | ERG3 | W | W | S | This study |
| YGL012W | ERG4 | + | W | S | This study |
| YMR015C | ERG5 | + | + | S | This study |
| YML008C | ERG6 | W | W | S | This study |
Table 3 contains only the mutations conferring an Ino− phenotype that were mentioned in the “Introduction”, “Results” or “Discussion” sections, in the approximate order in which they are described in the text. A complete list of all mutants exhibiting inositol auxotrphy detected in this study or previously reported is contained in Table S1. Phenotypes were scored as follows: mutants that grew well on I+C− medium at a given temperature, but whose growth was visibly weaker on either I−C− or I−C+ media, were scored as very weak (VW). Mutants exhibiting very reduced but still detectable growth in I−C− or I−C+ media were scored as weak (W). Mutants exhibiting no visible growth on I−C− or I−C+ media were scored as strong (S) (See Fig. 1). A score of “+” indicates no growth reduction in any inositol lacking media, and compared to growth on I+C− medium at the corresponding temperature. A score of “NS” indicates that the mutant conferring the Ino− phenotype was not present in the homozygous diploid strain collection, and hence was not screened. A score of “NG” (no growth) indicates that the deletion mutant from the homozygous diploid collection failed to grow in either I+C+, I+C− and/or YPD medium at a given temperature. Underlined gene names indicate deletions of essential genes for which conditional alleles have been reported to confer an Ino− phenotype. References are provided for those mutations previously shown to confer an Ino− phenotype
a
Mutations previously shown to confer an Ino− phenotype that were not confirmed in this study