Table 1. SMM-sensitive heterozygous deletion mutants.

ORF ID	Gene	SGD Description	Phenotypes
Transcription
YEL009C	GCN4	bZIP transcriptional activator of amino acid biosynthetic genes; activator responds to amino acid starvation	M+, E, C, v
YPR104C	FHL1	Regulator of ribosomal protein (RP) transcription; has forkhead associated domain that binds phosphorylated proteins; recruits coactivator Ifh1p or corepressor Crf1p to RP gene promoters	M+, C, i
YBL014C	RRN6	Component 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 Rrn11p	M+, C, i
YBL005W	PDR3	Transcriptional activator of the pleiotropic drug resistance network; regulates expression of ATP-binding cassette (ABC) transporters	M+, E, C, v
YDL020C	RPN4	Transcription 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 responses	M+, C, v
YHR143W-A	RPC10	RNA polymerase subunit ABC10-α, found in RNA pol I, II, and III	M+, i
YPL254W	HFI1	Adaptor 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 functions	M−, C, v
YOL148C	SPT20	Subunit of the SAGA transcriptional regulatory complex	M−, C, va
YDR145W	TAF12	Subunit (61/68 kD) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	M+, E, C, i
YBR198C	TAF5	Subunit (90 kDa) of TFIID and SAGA complexes; involved in RNA polymerase II transcription initiation and in chromatin modification	M+, E, C, i
YPL129W	TAF14	Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes; involved in RNA polymerase II transcription initiation and in chromatin modification	M+, E, C, v
YMR091C	NPL6	Component of the RSC chromatin remodeling complex	M+, C, v
YNR052C	POP2	RNase of the DEDD superfamily; subunit of the Ccr4-Not complex that mediates 3′–5′ mRNA deadenylation	M−, C, vb
YBR095C	RXT2	Component of the histone deacetylase Rpd3L complex	M+, E, C, v
mRNA processing/export
YDR364C	CDC40	Pre-mRNA splicing factor	M+, E, C, vb
YNL004W	HRB1	Poly(A+) RNA-binding protein; key surveillance factor for the selective export of spliced mRNAs from the nucleus to the cytoplasm	M−, v
YDR228C	PCF11	mRNA 3′ end processing factor; essential component of cleavage and polyadenylation factor IA (CF IA), involved in pre-mRNA 3′ end processing and in transcription termination	M+, i
YMR061W	RNA14	Component 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′ ends	M−, C, i
YLR293C	GSP1	Ran GTPase; GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport	M+, C, i
Translation
YKL009W	MRT4	Protein involved in mRNA turnover and ribosome assembly	M−, C, v
YPL143W	RPL33A	Ribosomal 60S subunit protein L33A; nearly identical to RPL33B	M+, E, C, i
YDR500C	RPL37B	Ribosomal 60S subunit protein L37B; required for processing of 27SB pre-rRNA and formation of stable 66S assembly intermediates; nearly identical to RPL37A	M+, E, C, v
YDR064W	RPS13	Protein component of the small (40S) ribosomal subunit	M+, E, i
YOR182C	RPS30B	Protein component of the small (40S) ribosomal subunit; identical to RPS30A	M+, E, C, v
YPL090C	RPS6A	Protein component of the small (40S) ribosomal subunit; identical to RPS6B	M−, v
YOR096W	RPS7A	Protein component of the small (40S) ribosomal subunit; nearly identical to RPS7B	M+, E, C, v
YPL183W-A	RTC6	Protein involved in translation; mutants have defects in biogenesis of nuclear ribosomes; sequence similar to prokaryotic ribosomal protein L36	M−, C, v
Protein kinase and phosphatase subunits
YER133W	GLC7	Type 1 S/T protein phosphatase catalytic subunit; cleavage and polyadenylation factor (CPF) component	M+, E, C, i
YDR028C	REG1	Regulatory subunit of type 1 protein phosphatase Glc7p	M+, v
YAR018C	KIN3	Nonessential serine/threonine protein kinase; possible role in DNA damage response	M−, C, v
YBL046W	PSY4	Regulatory 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 checkpoint	M+, E, C, v
Protein degradation
YDR049W	VMS1	Component 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
YGL116W	CDC20	Activator of anaphase-promoting complex/cyclosome (APC/C); APC/C is required for metaphase/anaphase transition	M+, E, C, i
Vacuole/V0 ATPase
YPL234C	VMA11	Vacuolar ATPase V0 domain subunit c′; involved in proton transport activity; N and C termini are in the vacuolar lumen	M−, C, v
YHR026W	VMA16	Subunit c′′ of the vacuolar ATPase; v-ATPase functions in acidification of the vacuole; one of three proteolipid subunits of the V0 domain	M−, C, v
YEL027W	VMA3	Proteolipid subunit c of the V0 domain of vacuolar H+ ATPase; required for vacuolar acidification and important for copper and iron metal ion homeostasis	M+, C, v
YCL005W-A	VMA9	Vacuolar H+ ATPase subunit e of the V-ATPase V0 subcomplex; essential for vacuolar acidification; involved in V0 biogenesis	M+, va
Protein trafficking
YDL193W	NUS1	Forms dehydrodolichyl diphosphate syntase complex with RER2 or SRT1; Nus1p may be involved in protein trafficking	M+, E, C, i
YDR483W	KRE2	α1,2-mannosyltransferase of the Golgi; involved in protein mannosylation	M−, C, v
YBR290W	BSD2	Heavy 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 detoxification	M+, C, v
Metabolic pathway
YCL009C	ILV6	Regulatory subunit of acetolactate synthase; acetolactate synthase catalyzes the first step of branched-chain amino acid biosynthesis; enhances activity of the Ilv2p catalytic subunit	M+, v
YLR303W	MET15	O-acetyl homoserine-O-acetyl serine sulfhydrylase; required for Methionine and cysteine biosynthesis	M−, v
YFR055W	IRC7	β-lyase involved in the production of thiols	M+, v
YDR531W	CAB1	Pantothenate kinase, ATP:D-pantothenate 4′-phosphotransferase; catalyzes the first committed step in the universal biosynthetic pathway for synthesis of coenzyme A (CoA)	M−, i
YJL130C	URA2	Bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase; catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines	M+, E, v
YHR128W	FUR1	Uracil phosphoribosyltransferase; synthesizes UMP from uracil; involved in the pyrimidine salvage pathway	M+, C, i
Drug resistance
YDR011W	SNQ2	Plasma membrane ATP-binding cassette (ABC) transporter; multidrug transporter involved in multidrug resistance and resistance to singlet oxygen species	M+, v
Cytoskeleton
YNR035C	ARC35	Subunit of the ARP2/3 complex; ARP2/3 is required for the motility and integrity of cortical actin patches	M−, C, i
YML085C	TUB1	α-tubulin; associates with β-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	M+, C, i
Amino acid sensor
YNL008C	ASI3	Subunit of the nuclear inner membrane Asi ubiquitin ligase complex; acts with Asi1p and Asi2p to ensure the fidelity of SPS-sensor signaling	M−, C, v
YFR029W	PTR3	Component 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 genes	M−, C, i
Unfolded protein
YJL008C	CCT8	Subunit of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivo	M+, C, i
YJL082W	IML2	Protein required for clearance of inclusion bodies; localizes to the inclusion bodies formed under protein mis-folding stress	M+, C, v
YBL075C	SSA3	ATPase involved in protein folding and the response to stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation	M−, C, v
Other
YBR156C	SLI15	Subunit of the conserved chromosomal passenger complex (CPC); complex regulates kinetochore-microtubule attachments, activation of the spindle tension checkpoint, and mitotic spindle disassembly	M+, E, v
YNL012W	SPO1	Meiosis-specific prospore protein; required for meiotic spindle pole body duplication and separation	M−, C, v
YNL013C	YNL013C	Dubious open reading frame; partially overlaps the verified ORF HEF3/YNL014W	M−, C, v
YER177W	BMH1	14-3-3 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 checkpoint	M−, v
YGL110C	CUE3	Protein of unknown function; has a CUE domain that binds ubiquitin, which may facilitate intramolecular monoubiquitination	M−, C, v
YDR516C	EMI2	Nonessential protein of unknown function; required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulation	M+, E, v
YGL168W	HUR1	Protein of unknown function; reported null mutant phenotype of hydroxyurea sensitivity may be due to effects on overlapping PMR1 gene	M+, E, C, v
YGR289C	MAL11	High-affinity maltose transporter (α-glucoside transporter); broad substrate specificity that includes maltotriose	M+, E, C, va
YBR185C	MBA1	Membrane-associated mitochondrial ribosome receptor	M−, C, v
YBR100W	MMS4	Subunit of structure-specific Mms4p-Mus81p endonuclease; cleaves branched DNA; involved in recombination, DNA repair, and joint molecule formation/resolution during meiotic recombination	M+, E, C, v
YPL142C	YPL142C	Dubious open reading frame; completely overlaps the verified ORF RPL33A/YPL143W, a component of the large (60S) ribosomal subunit	M+, E, C, i
YNL028W	YNL028W	Dubious open reading frame; partly overlaps verified ORF KTR5/YNL029C, a putative mannosyltransferase	M−, C, v
YBR221W-A	YBR221W-A	Putative protein of unknown function; identified by expression profiling and mass spectrometry	M−, v
YHL015W-A	YHL015W-A	Putative protein of unknown function	M−, v
YBR196C-A	YBR196C-A	Putative protein of unknown function; identified by fungal homology and RT-PCR	M−, C, v
YCR061W	YCR061W	Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern	M+, C, v
YBL065W	YBL065W	Dubious open reading frame; partially overlaps verified ORF SEF1/YBL066C; YBL065W is a nonessential gene	M+, E, C, v
YJR039W	YJR039W	Putative protein of unknown function; the authentic, nontagged protein is detected in highly purified mitochondria in high-throughput studies	M+, 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.

^aViability not stated on SGD, but the haploid deletion and homozygous null strains exist.

^bData 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.