Commonly used auxotrophic markers

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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).

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