Table 1 SMM-sensitive heterozygous deletion mutants
ORF IDGeneSGD DescriptionPhenotypes
Transcription
 YEL009CGCN4bZIP transcriptional activator of amino acid biosynthetic genes; activator responds to amino acid starvationM+, E, C, v
 YPR104CFHL1Regulator of ribosomal protein (RP) transcription; has forkhead associated domain that binds phosphorylated proteins; recruits coactivator Ifh1p or corepressor Crf1p to RP gene promotersM+, C, i
 YBL014CRRN6Component of the core factor (CF) rDNA transcription factor complex; CF is required for transcription of 35S rRNA genes by RNA polymerase I and is composed of Rrn6p, Rrn7p, and Rrn11pM+, C, i
 YBL005WPDR3Transcriptional activator of the pleiotropic drug resistance network; regulates expression of ATP-binding cassette (ABC) transportersM+, E, C, v
 YDL020CRPN4Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responsesM+, C, v
 YHR143W-ARPC10RNA polymerase subunit ABC10-α, found in RNA pol I, II, and IIIM+, i
 YPL254WHFI1Adaptor protein required for structural integrity of the SAGA complex, a histone acetyltransferase-coactivator complex that is involved in global regulation of gene expression through acetylation and transcription functionsM, C, v
 YOL148CSPT20Subunit of the SAGA transcriptional regulatory complexM, C, va
 YDR145WTAF12Subunit (61/68 kD) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2AM+, E, C, i
 YBR198CTAF5Subunit (90 kDa) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modificationM+, E, C, i
 YPL129WTAF14Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes; involved in RNA polymerase II transcription initiation and in chromatin modificationM+, E, C, v
 YMR091CNPL6Component of the RSC chromatin remodeling complexM+, C, v
 YNR052CPOP2RNase of the DEDD superfamily; subunit of the Ccr4-Not complex that mediates 3′–5′ mRNA deadenylationM, C, vb
 YBR095CRXT2Component of the histone deacetylase Rpd3L complexM+, E, C, v
mRNA processing/export
 YDR364CCDC40Pre-mRNA splicing factorM+, E, C, vb
 YNL004WHRB1Poly(A+) RNA-binding protein; key surveillance factor for the selective export of spliced mRNAs from the nucleus to the cytoplasmM, v
 YDR228CPCF11mRNA 3′ end processing factor; essential component of cleavage and polyadenylation factor IA (CF IA), involved in pre-mRNA 3′ end processing and in transcription terminationM+, i
 YMR061WRNA14Component of the cleavage and polyadenylation factor 1 (CF1); CF1, composed of the CF1A complex (Rna14p, Rna15p, Clp1p, Pcf11p) and Hrp1, is involved in cleavage and polyadenylation of mRNA 3′ endsM, C, i
 YLR293CGSP1Ran GTPase; GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transportM+, C, i
Translation
 YKL009WMRT4Protein involved in mRNA turnover and ribosome assemblyM, C, v
 YPL143WRPL33ARibosomal 60S subunit protein L33A; nearly identical to RPL33BM+, E, C, i
 YDR500CRPL37BRibosomal 60S subunit protein L37B; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; nearly identical to RPL37AM+, E, C, v
 YDR064WRPS13Protein component of the small (40S) ribosomal subunitM+, E, i
 YOR182CRPS30BProtein component of the small (40S) ribosomal subunit; identical to RPS30AM+, E, C, v
 YPL090CRPS6AProtein component of the small (40S) ribosomal subunit; identical to RPS6BM, v
 YOR096WRPS7AProtein component of the small (40S) ribosomal subunit; nearly identical to RPS7BM+, E, C, v
 YPL183W-ARTC6Protein involved in translation; mutants have defects in biogenesis of nuclear ribosomes; sequence similar to prokaryotic ribosomal protein L36M, C, v
Protein kinase and phosphatase subunits
 YER133WGLC7Type 1 S/T protein phosphatase catalytic subunit; cleavage and polyadenylation factor (CPF) componentM+, E, C, i
 YDR028CREG1Regulatory subunit of type 1 protein phosphatase Glc7pM+, v
 YAR018CKIN3Nonessential serine/threonine protein kinase; possible role in DNA damage responseM, C, v
 YBL046WPSY4Regulatory subunit of protein phosphatase PP4; presence of Psy4p in the PP4 complex is required for dephosphorylation of the histone variant H2AX during recovery from the DNA damage checkpointM+, E, C, v
Protein degradation
 YDR049WVMS1Component of a Cdc48p-complex involved in protein quality control; contributes to ER-associated degradation (ERAD) of specific substrates; forms a mitochondrially-associated complex with Cdc48p and Npl4p under oxidative stress that is required for ubiquitin-mediated mitochondria-associated protein degradation (MAD)M, C, v
 YGL116WCDC20Activator of anaphase-promoting complex/cyclosome (APC/C); APC/C is required for metaphase/anaphase transitionM+, E, C, i
Vacuole/V0 ATPase
 YPL234CVMA11Vacuolar ATPase V0 domain subunit c′; involved in proton transport activity; N and C termini are in the vacuolar lumenM, C, v
 YHR026WVMA16Subunit c′′ of the vacuolar ATPase; v-ATPase functions in acidification of the vacuole; one of three proteolipid subunits of the V0 domainM, C, v
 YEL027WVMA3Proteolipid subunit c of the V0 domain of vacuolar H+ ATPase; required for vacuolar acidification and important for copper and iron metal ion homeostasisM+, C, v
 YCL005W-AVMA9Vacuolar H+ ATPase subunit e of the V-ATPase V0 subcomplex; essential for vacuolar acidification; involved in V0 biogenesisM+, va
Protein trafficking
 YDL193WNUS1Forms dehydrodolichyl diphosphate syntase complex with RER2 or SRT1; Nus1p may be involved in protein traffickingM+, E, C, i
 YDR483WKRE2α1,2-mannosyltransferase of the Golgi; involved in protein mannosylationM, C, v
 YBR290WBSD2Heavy metal ion homeostasis protein; facilitates trafficking of Smf1p and Smf2p metal transporters to vacuole where they are degraded; controls metal ion transport, prevents metal hyper-accumulation, functions in copper detoxificationM+, C, v
Metabolic pathway
 YCL009CILV6Regulatory subunit of acetolactate synthase; acetolactate synthase catalyzes the first step of branched-chain amino acid biosynthesis; enhances activity of the Ilv2p catalytic subunitM+, v
 YLR303WMET15O-acetyl homoserine-O-acetyl serine sulfhydrylase; required for Methionine and cysteine biosynthesisM, v
 YFR055WIRC7β-lyase involved in the production of thiolsM+, v
 YDR531WCAB1Pantothenate kinase, ATP:D-pantothenate 4′-phosphotransferase; catalyzes the first committed step in the universal biosynthetic pathway for synthesis of coenzyme A (CoA)M, i
 YJL130CURA2Bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase; catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidinesM+, E, v
 YHR128WFUR1Uracil phosphoribosyltransferase; synthesizes UMP from uracil; involved in the pyrimidine salvage pathwayM+, C, i
Drug resistance
 YDR011WSNQ2Plasma membrane ATP-binding cassette (ABC) transporter; multidrug transporter involved in multidrug resistance and resistance to singlet oxygen speciesM+, v
Cytoskeleton
 YNR035CARC35Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patchesM, C, i
 YML085CTUB1α-tubulin; associates with β-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubulesM+, C, i
Amino acid sensor
 YNL008CASI3Subunit of the nuclear inner membrane Asi ubiquitin ligase complex; acts with Asi1p and Asi2p to ensure the fidelity of SPS-sensor signalingM, C, v
 YFR029WPTR3Component of the SPS plasma membrane amino acid sensor system; senses external amino acid concentration and transmits intracellular signals that result in regulation of expression of amino acid permease genesM, C, i
Unfolded protein
 YJL008CCCT8Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivoM+, C, i
 YJL082WIML2Protein required for clearance of inclusion bodies; localizes to the inclusion bodies formed under protein mis-folding stressM+, C, v
 YBL075CSSA3ATPase involved in protein folding and the response to stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocationM, C, v
Other
 YBR156CSLI15Subunit of the conserved chromosomal passenger complex (CPC); complex regulates kinetochore-microtubule attachments, activation of the spindle tension checkpoint, and mitotic spindle disassemblyM+, E, v
 YNL012WSPO1Meiosis-specific prospore protein; required for meiotic spindle pole body duplication and separationM, C, v
 YNL013CYNL013CDubious open reading frame; partially overlaps the verified ORF HEF3/YNL014WM, C, v
 YER177WBMH114-3-3 protein, major isoform; controls proteome at posttranscriptional level, binds proteins and DNA, involved in regulation of exocytosis, vesicle transport, Ras/MAPK and rapamycin-sensitive signaling, aggresome formation, spindle position checkpointM, v
 YGL110CCUE3Protein of unknown function; has a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitinationM, C, v
 YDR516CEMI2Nonessential protein of unknown function; required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulationM+, E, v
 YGL168WHUR1Protein of unknown function; reported null mutant phenotype of hydroxyurea sensitivity may be due to effects on overlapping PMR1 geneM+, E, C, v
 YGR289CMAL11High-affinity maltose transporter (α-glucoside transporter); broad substrate specificity that includes maltotrioseM+, E, C, va
 YBR185CMBA1Membrane-associated mitochondrial ribosome receptorM, C, v
 YBR100WMMS4Subunit of structure-specific Mms4p-Mus81p endonuclease; cleaves branched DNA; involved in recombination, DNA repair, and joint molecule formation/resolution during meiotic recombinationM+, E, C, v
 YPL142CYPL142CDubious open reading frame; completely overlaps the verified ORF RPL33A/YPL143W, a component of the large (60S) ribosomal subunitM+, E, C, i
 YNL028WYNL028WDubious open reading frame; partly overlaps verified ORF KTR5/YNL029C, a putative mannosyltransferaseM, C, v
 YBR221W-AYBR221W-APutative protein of unknown function; identified by expression profiling and mass spectrometryM, v
 YHL015W-AYHL015W-APutative protein of unknown functionM, v
 YBR196C-AYBR196C-APutative protein of unknown function; identified by fungal homology and RT-PCRM, C, v
 YCR061WYCR061WProtein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate patternM+, C, v
 YBL065WYBL065WDubious open reading frame; partially overlaps verified ORF SEF1/YBL066C; YBL065W is a nonessential geneM+, E, C, v
 YJR039WYJR039WPutative protein of unknown function; the authentic, nontagged protein is detected in highly purified mitochondria in high-throughput studiesM+, E, C, va
  • Genes are grouped into general functional categories. SGD descriptions are derived from the Saccharomyces Genome Database. Phenotypes are: M, Met (methionine auxotroph); M+, Met+ (methionine prototroph); E, ethionine sensitive (only M+ strains can be tested for ethionine sensitivity); C, canavanine sensitive; i, reported on SGD to be an inviable null mutation in large-scale surveys; v, reported on SGD to be a viable null deletion in large-scale surveys.

  • a Viability not stated on SGD, but the haploid deletion and homozygous null strains exist.

  • b Data in large-scale surveys include both viable and inviable phenotypes. Cells with a deletion of the CDC40 or POP2 genes in the S288C background that BY4743 was derived are viable.