Commonly used auxotrophic markers

This table describes some commonly used auxotrophic markers (along with some novel useful markers); it is based on a table in Brachmann et al. (1998) "Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications." Yeast 14:115-132. Please send e-mail to the curators at SGD at sgd-helpdesk@lists.stanford.edu if you would like to suggest additions or modifications.

Allele	Deleted ORF?	Reverts?	Notes	Molecular Descriptiona	Reference
ade1-14	no	yes	red colonies	TGG-to-TGA nonsense change at codon 244; GGA-to-GAA missense change at codon 185	Nakayashiki et al. 2001
ade1-101	no		simple point mutation causing a requirement for adenine		Botstein et al. 1979
ade2-1	no	yes	ochre mutation	TTA-to-TTG silent change at codon 9, GAA-to-TAA ochre nonsense change at codon 64, AGA-to-GGA missense change at codon 101, GTT-to-GTC silent change at codon 124, ACG-to-ACA silent change at codon 539	Rodney Rothstein, Personal communication to SGD
ade2-101	no	yes	ochre mutation, red colonies	G to T transversion at nucleotide 190, changing codon 64 from a Glu to a Stop	Gai and Voytas, 2005
ade2-BglII	no	no	red colonies	frameshift (BglII site filled in at position 592)	Engebrecht and Roeder 1990
can1-100	no	yes	ochre mutation	AAA-to-TAA ochre nonsense change at codon 47	Rodney Rothstein, Personal communication to SGD
his3delta200	yes	no	Cold sensitive; high frequency of petite formation, especially during transformation. Note that this deletion damages the PET56 promoter. See Zhang et al. (2003) for a discussion of this issue.	1 kb deletion (-205 to 835)	Struhl 1985; Fasullo and Davis 1988
his3delta1	partial	no	chemically constructed deletion; reversion is undetectable (< 10(E-9) revertants in a culture). Causes histidine to be required for growth; allows selection of vectors carrying the HIS3 gene.	187 bp HindIII-HindIII internal deletion (305 to 492)	Scherer and Davis 1979 Botstein et al. 1979
his3-11,15	no	no	double mutant	G deletion at nucleotide 208, G deletion at nucleotide 319	Rodney Rothstein, Personal communication to SGD
his3delta	yes	no	In the S288C background, the his3 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
leu2delta1	partial	no		EcoRI-ClaI internal deletion (163 to 649, 0.6 kb)	Sikorski and Hieter 1989
leu2-3,112	no	no	double mutant; leu2-3 and leu2-112 are each frameshift mutations; the double mutants revert very infrequently (less than 10(E-8) revertants in a culture) and cause leucine to be required for growth. This allows the selection of vectors carrying the LEU2 gene.	GTC-to-GTT silent change at codon 56, GTT-to-GCT missense change at codon 69, G insertion at nucleotide 249, G insertion at nucleotide 792, GTT-to-GTC silent change at codon 299, GAC-to-AAC missense change at codon 300	Hinnen et al. 1978; Gaber and Culbertson 1982; Meira LB et al., 1995; Rodney Rothstein, Personal communication to SGD Botstein et al. 1979
leu2delta	yes	no	In the S288C background, the leu2 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
lys2-801	no	yes	amber mutation
lys2delta202	partial	no		XhoI-HpaI internal deletion (1813 to 2864, 1.0 kb)	Winston et al. 1995
lys2delta	yes	no	In the S288C background, the lys2 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
trp1delta1	yes	no	cold sensitiveb, weak galactose inducer (deletes GAL3 UAS), removes ARS1, also called trp1-901	1.45 kb deletion, EcoRI-EcoRI (-102 to 1352)	Sikorski and Hieter 1989
trp1delta63	partial	no	cold sensitiveb	0.6 kb deletion, EcoRI-HindIII (-102 to 513)	Sikorski and Hieter 1989
trp1-1	no	yes	amber mutation	GAG-to-TAG amber nonsense change at codon 83	McDonald et al. 1997
trp1-1	no	yes	cold sensitiveb	C to T at residue 403 of the coding sequence, changing residue 135 from glutamine to an amber stop codon	Brian Green and Joachim Li, unpublished results
trp1delta	yes	no	In the S288C background, the trp1 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
trp1-289	no	yes	Reverts at low frequency (about 10(E-7) revertants in a culture) and causes tryptophan to be required for growth.	Allows the selection of vectors carrying the TRP1 gene.	Botstein et al. 1979
trp5delta	yes	no	In the S288C background, the trp5 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
ura3-52	no	no		Ty1 insertion (transcribing left to right) at pos. 121	Rose and Winston 1984
ura3-1	no	yes		G to A transition at residue 701 of the coding sequence, changing residue 234 from glycine to glutamate	Yan Li, Glenn Manthey, and Adam Bailis, unpublished results
ura3delta	yes	no	In the S288C background, the ura3 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013
ura4delta	yes	no	In the S288C background, the ura4 null mutation confers sensitivity to acetic acid.	complete deletion	Ding et al. 2013

The alleles listed below are described in Brachmann et al. 1998.

Allele	Deleted ORF?	Reverts?	Notes	Molecular Descriptiona	Reference
ade2delta::hisG	no	no			(Aparicio et al. 1991)
leu2delta0	yes	no	designer deletion		Brachmann et al. 1998
lys2delta0	yes	no	designer deletion		Brachmann et al. 1998
met15delta0	yes	no	designer deletion		Brachmann et al. 1998
ura3delta0	yes	no	designer deletion		Brachmann et al. 1998

^aThe sequence coordinates are relative to the first ATG of the selectable marker ORF, in which the A residue is defined as +1.

^bAll trp- strains are cold sensitive (Singh and Manney 1974).