Commonly used strains

This page describes some of the most commonly used yeast lab strains. Much of the information is taken from F. Sherman (2002) Getting started with yeast, Methods Enzymol. 350, 3-41. Other useful papers for strain background information include:

• Mortimer and Johnston (1986) Genetics 113:35-43 - thoroughly describes the genealogy of strain S288C
• van Dijken et al. (2000) Enzyme Microb Technol 26:706-714 - compares various characteristics of commonly used lab strains
• Winzeler et al. (2003) Genetics 163:79-89 - uses SFP (single-feature polymorphisms) analysis to study genetic identity between common lab strains

S288C

Genotype: MATα SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6

Notes: Strain used in the systematic sequencing project, the sequence stored in SGD. S288C does not form pseudohyphae. In addition, since it has a mutated copy of HAP1, it is not a good strain for mitochondrial studies. It has an allelic variant of MIP1 which increases petite frequency. S288C strains are gal2- and they do not use galactose anaerobically.

The S288C genome was recently resequenced at the Sanger Institute.

References: Mortimer and Johnston (1986) Genetics 113:35-43.

Sources: ATCC:204508

BY4743

Genotype: MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met15Δ0/MET15 ura3Δ0/ura3Δ0

Notes: Strain used in the systematic deletion project, generated from a cross between BY4741 and BY4742, which are derived from S288C. As in S288c, this strain as well as haploid derivatives BY4741, and BY4742 have allelic variants of MIP1, SAL1 and CAT5 and these polymorphisms, described in the respective locus history notes for these genes (MIP1, SAL1 and CAT5) all contribute to the high observed petite frequency. Details regarding the contributions of these variants to petite formation are referenced in Dimitrov et al. (2009) Genetics 183(1):365-83. See the Brachmann et al., 1998 reference for details of strain construction.

References: Brachmann et al. (1998) Yeast 14:115-32.

Sources: Thermo Scientific:YSC1050

FY4

Genotype: MATa

Notes: Derived from S288C.

References: Winston et al. (1995) Yeast 11:53-55.

Brachmann et al. (1998) Yeast 14:115-32.

DBY12020

Genotype: MATa(P_GAL10+gal1)Δ::loxP, leu2Δ0::P_ACT1-GEV-NatMX, gal4Δ::LEU2, HAP1⁺

Notes: Derived from FY4.

Reference: McIsaac et al. (2011) Mol Biol Cell 22(22):4447-59.

DBY12021

Genotype: MATα(P_GAL10+gal1)Δ::loxP, leu2Δ0::P_ACT1-GEV-NatMX, gal4Δ::LEU2, HAP1⁺

Notes: Derived from FY4.

Reference: McIsaac et al. (2011) Mol Biol Cell 22(22):4447-59.

FY1679

Genotype: MATa/α ura3-52/ura3-52 trp1Δ63/TRP1 leu2Δ1/LEU2 his3Δ200/HIS3 GAL2/GAL

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

References: Winston et al. (1995) Yeast 11:53-55.

Sources: EUROSCARF:10000D

AB972

Genotype: MATα X2180-1B trp1₀ [rho ⁰]

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD. AB972 is an ethidium bromide-induced rho- derivative of the strain X2180-1B-trp1.

References: Olson MV et al. (1986) Proc. Natl. Acad. Sci. USA 83:7826-7830.

Sources: ATCC:204511

A364A

Genotype: MATa ade1 ade2 ura1 his7 lys2 tyr1 gal1 SUC mal cup BIO

Notes: Used in the systematic sequencing project, the sequence stored in SGD.

References: Hartwell (1967) J. Bacteriol. 93:1662-1670.

Sources: ATCC:208526

DC5

Genotype: MATa leu2-3,112 his3-11,15 can1-11

Notes: Isogenic to S288C; used in the systematic sequencing project, the sequence stored in SGD.

References: Broach et al. (1979) Gene 8:121-133

X2180-1A

Genotype: MATa SUC2 mal mel gal2 CUP1

Notes:S288c spontaneously diploidized to give rise to X2180. The haploid segregants X2180-1a and X2180-1b were obtained from sporulated X2180

References: Mortimer and Johnston

Sources: ATCC:204504

XJ24-24a

Genotype: MATa ho HMa HMα ade6 arg4-17 trp1-1 tyr7-1 MAL2

Notes: Derived from, but not isogenic to, S288C

References: Strathern et al. (1979) Cell 18:309-319

YNN216

Genotype: MATa/α ura3-52/ura3-52 lys2-801^amber/lys2-801^amber ade2-101^ochre/ade2-101^ochre

Notes: Congenic to S288C (see Sikorski and Hieter). Used to derive YSS and CY strains (see Sobel and Wolin).

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.

YPH499

Genotype: MATa ura3-52 lys2-801_amber ade2-101_ochre trp1-Δ63 his3-Δ200 leu2-Δ1

Notes: Contains nonrevertible (deletion) auxotrophic mutations that can be used for selection of vectors. Note that trp1-Δ63, unlike trp1-Δ1, does not delete adjacent GAL3 UAS sequence and retains homology to TRP1 selectable marker. gal2-, does not use galactose anaerobically. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:204679

YPH500

Genotype: MATα ura3-52 lys2-801_amber ade2-101_ochre trp1-Δ63 his3-Δ200 leu2-Δ1

Notes:MATα strain isogenic to YPH499 except at mating type locus. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:204680

YPH501

Genotype: MATa/MATα ura3-52/ura3-52 lys2-801_amber/lys2-801_amber ade2-101_ochre/ade2-101_ochre trp1-Δ63/trp1-Δ63 his3-Δ200/his3-Δ200 leu2-Δ1/leu2-Δ1

Notes: a/α diploid isogenic to YPH499 and YPH500. Derived from the diploid strain YNN216 (Johnston and Davis 1984; original source: M. Carlson, Columbia University), which is congenic with S288C.

References: Sikorski RS and Hieter P (1989) Genetics 122:19-27.
Sobel and Wolin (1999) Mol. Biol. Cell 10:3849-3862.
Johnston M and Davis RW (1984) Mol Cell Biol 4(8):1440-8.

Sources: ATCC:204681

Sigma1278b

Notes: Used in pseudohyphal growth studies. Detailed notes about the sigma strains have been kindly provided by Cora Styles.

Granek and Magwene, PLoS Genet. 2010 Jan 22;6(1):e1000823, established that certain lineages of the Sigma1278B background contain a nonsense mutation in RIM15, a G-to-T transversion at position 1216 that converts a Gly codon to an opal stop codon. This rim15 mutation interacts epistatically with mutations in certain other genes to affect colony morphology. The Sigma1278b genome is closely related to S288c, and shares some other genomic regions with W303 [1].

Annotation of the Sigma1278b genome and information about the systematic deletion collection can be found here.

SK1

Genotype: MATa/α HO gal2 cup^S can1^R BIO

Notes: Commonly used for studying sporulation or meiosis. Canavanine-resistant derivative.

The SK1 genome was sequenced at the Sanger Institute.

References: Kane SM and Roth J. (1974) Bacteriol. 118: 8-14

Sources: ATCC:204722

CEN.PK (aka CEN.PK2)

Genotype: MATa/α ura3-52/ura3-52 trp1-289/trp1-289 leu2-3_112/leu2-3_112 his3 Δ1/his3 Δ1 MAL2-8C/MAL2-8C SUC2/SUC2

Notes: CEN.PK possesses a mutation in CYR1 (A5627T corresponding to a K1876M substitution near the end of the catalytic domain in adenylate cyclase which eliminates glucose- and acidification-induced cAMP signalling and delays glucose-induced loss of stress resistance (Vanhalewyn et al., 1999; Dumortier et al., 2000).

References: van Dijken et al. (2000) Enzyme Microb Technol 26:706-714

Sources: EUROSCARF:30000D

W303

Genotype: MATa/MATα {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15} [phi⁺]

allele	locus	mutation (1)
ade2-1	YOR128C	nonsense, glu64STOP
trp1-1	YDR007W	nonsense, glu83STOP
can1-100	YEL063C	frameshift, lys47
leu2-3,112	YCL018W	frameshift, gly83
his3-11,15	YOR202W	2x frameshifts, ala70 and glu106

Notes: The W303 genome is to 85.4% derived from S288c, part of the other regions are similar to non-S288c regions of Sigma1278b. In total, some 800 CDS differ between W303 and S288c, but in most cases only one or two residues differ [2]. These include a bud4 mutation that causes haploids to bud with a mixture of axial and bipolar budding patterns. In addition, the original W303 strain contains the rad5-535 allele. As S288c, W303 has an allelic variant of MIP1 which increases petite frequency.

The W303 genome was sequenced at the Sanger Institute and by Ralser M. et al. (2012) Open Biol 2: 120093. 1 (DDBJ/EMBL/GenBank ALAV00000000).

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).
bud4 info: Voth et al. (2005) Eukaryotic Cell, 4:1018-28.
rad5-535 info: see detailed notes

Sources: Thermo Scientific:YSC1058

W303-1A

Genotype: MATa {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15}

Notes: W303-1A possesses a ybp1-1 mutation (I7L, F328V, K343E, N571D) which abolishes Ybp1p function, increasing sensitivity to oxidative stress.

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).
ybp1-1 info: Veal et al. (2003) J. Biol. Chem. 278:30896-904.

Sources: Thermo Scientific:YSC1058

W303-1B

Genotype: MATα {leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15}

References: W303 constructed by Rodney Rothstein (see detailed notes from RR and Stephan Bartsch).

Sources: Thermo Scientific:YSC1058

W303-K6001

Genotype: MATa; {ade2-1, trp1-1, can1-100, leu2-3,112, his3-11,15, GAL, psi+, ho::HO::CDC6 (at HO), cdc6::hisG, ura3::URA3 GAL-ubiR-CDC6 (at URA3)}

References: K6001 was created in Kim Nasmyth's lab Piatti at al (PMID: 7641697) and Bobola et al (PMID: 8625408). K6001 has become a popular model in yeast aging research, as it allows a replicative aging assay based on microcolonies (PMID: 15489200). Its genome has been sequenced by Timmermann et al (PMID: 20729566), Ralser et al [3].

DY1457

Genotype: MATa; {ade6 can1-100(oc) his3-11,15 leu2-3,112 trp1-1 ura3-52}

References: Askwith C, et al. (1994) Cell 76(2):403-10 PMID: 8293473

D273-10B

Genotype: MATα mal

Notes: Normal cytochrome content and respiration; low frequency of rho-. This strain and its auxotrophic derivatives were used in numerious laboratories for mitochondrial and related studies and for mutant screens. Good respirer that's relatively resistant to glucose repression.

References: Sherman, F. (1963) Genetics 48:375-385.

Sources: ATCC:24657

FL100

Genotype: MATa

References: Lacroute, F. (1968) J. Bacteriol. 95:824-832.

Sources: ATCC: 28383

SEY6210/SEY6211

Genotype: MATa/MATα leu2-3,112/leu2-3,112 ura3-52/ura3-52 his3-Δ200/his3-Δ200 trp1-Δ901/trp1-Δ901 ade2/ADE2 suc2-Δ9/suc2-Δ9 GAL/GAL LYS2/lys2-801

Notes: SEY6210/SEY6211, also known as SEY6210.5, was constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers, good growth properties and good sporulation.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:201392

SEY6210

Genotype: MATα leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 suc2-Δ9 lys2-801; GAL

Notes: SEY6210 is a MATalpha haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:96099

SEY6211

Genotype: MATa leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 ade2-101 suc2-Δ9; GAL

Notes: SEY6211 is a MATa haploid constructed by Scott Emr and has been used in studies of autophagy, protein sorting etc. It is the product of crossing with strains from 5 different labs (Gerry Fink, Ron Davis, David Botstein, Fred Sherman, Randy Schekman). It has several selectable markers and good growth properties.

References: Robinson et al. (1988) Mol Cell Biol 8(11):4936-48

Sources: ATCC:96100

JK9-3d

There are a, alpha and a/alpha diploids of JK9-3d with the following genotypes:

Genotypes: JK9-3da MATa leu2-3,112 ura3-52 rme1 trp1 his4

JK9-3dα has the same genotype as JK9-3da with the exception of the MAT locus

JK9-3da/α is homozygous for all markers except mating type

Notes: JK9-3d was constructed by Jeanette Kunz while in Mike Hall's lab. She made the original strain while Joe Heitman isolated isogenic strains of opposite mating type and derived the a/alpha isogenic diploid by mating type switching. It has in its background S288c, a strain from the Oshima lab, and a strain from the Herskowitz lab. It was chosen because of its robust growth and sporulation, as well as good growth on galactose (GAL+) (so that genes under control of the galactose promoter could be induced). It may also have a SUP mutation that allows translation through premature STOP codons and therefore produces functional alleles with many point mutations.

References: Heitman et al. (1991a) Science 253(5022):905-9 and Heitman et al. (1991b) Proc Natl Acad Sci U S A 88(5):1948-52

RM11-1a

Genotype: MATa leu2Δ0 ura3-Δ0 HO::kanMX

Notes: RM11-1a is a haploid derivative of RM11, which is a diploid derivative of Bb32(3), which is an ascus derived from Bb32, which is a natural isolate collected by Robert Mortimer from a California vineyard (Ravenswood Zinfandel) in 1993, as in Mortimer et al., 1994. It has high spore viability (80–90%) and has been extensively characterized phenotypically under a wide range of conditions. It has a significantly longer life span than typical lab yeast strains and accumulates age-associated abnormalities at a lower rate. It displays approximately 0.5–1% sequence divergence relative to S288c. More information is available at the Broad Institute website.

References: Brem et al. (2002) Science 296(5568):752-5

Y55

Genotype: MATa /MATalpha HO/HO

Notes: Y55 is a prototrophic, homothallic diploid strain that was originally isolated by Dennis Winge. Many auxotrophic mutant derivatives have been created by John McCusker by using ethidium bromide treatment to eliminate non-auxotrophs. Y55 background strains have been used to study the timing of meiotic recombination (Borts et al. 1984); to isolate almost all the subunits of the proteasome (McCusker and Haber 1988a, 1988b); to get mutations in PMA1 and related genes (McCusker 1986); and to do meiotic mapping and interference experiments (Malkova et al. 2004).