View source for 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 [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 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.


{| border="1"   class="wikitable"
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!|Allele!!Deleted ORF?!!Reverts?!!Notes!!Molecular Description<sup>a</sup>!!Reference
|- 
|
[http://www.yeastgenome.org/locus/ade1 <em>ade1-14</em>]
|
no
|
yes
|
red colonies
|
TGG-to-TGA nonsense change at codon 244;
GGA-to-GAA missense change at codon 185
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000060944 Nakayashiki et al. 2001] 
|- 
|
[http://www.yeastgenome.org/locus/ade1 <em>ade1-101</em>]
|
no
|

|
simple point mutation causing a requirement for adenine
|

|
[http://www.yeastgenome.org/reference/395030 Botstein et al. 1979]
|- 

|
[http://www.yeastgenome.org/locus/ade2 <em>ade2-1</em>]
|
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, [http://wiki.yeastgenome.org/index.php/CommunityW303.html Personal communication to SGD] 
|- 
|
[http://www.yeastgenome.org/locus/ade2 <em>ade2-101</em>]
|
no
|
yes
|
ochre mutation, red colonies
|
G to T transversion at nucleotide 190, changing codon 64 from a Glu to a Stop
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000087056 Gai and Voytas, 2005] 
|- 
|
[http://www.yeastgenome.org/locus/ade2 <em>ade2-BglII</em>]
|
no
|
no
|
red colonies
|
frameshift (BglII site filled in at position 592)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000049198 Engebrecht and Roeder 1990] 
|- 
|
[http://www.yeastgenome.org/locus/can1 <em>can1-100</em>]
|
no
|
yes
|
ochre mutation
|
AAA-to-TAA ochre nonsense change at codon 47
|
Rodney Rothstein, [http://wiki.yeastgenome.org/index.php/CommunityW303.html Personal communication to SGD] 
|- 
|
[http://www.yeastgenome.org/locus/his3 <em>his3delta200</em>]
|
yes
|
no
|
Cold sensitive; high frequency of petite formation, especially during transformation. Note that this deletion damages the PET56 promoter. See [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000074003 Zhang et al. (2003)] for a discussion of this issue.
|
1 kb deletion (-205 to 835)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042846 Struhl 1985]; [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000046453 Fasullo and Davis 1988] 
|- 
|
[http://www.yeastgenome.org/locus/his3 <em>his3delta1</em>]
|
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)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000040818 Scherer and Davis 1979] 
[http://www.yeastgenome.org/reference/395030 Botstein et al. 1979]
|- 
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[http://www.yeastgenome.org/locus/his3 <em>his3-11,15</em>]
|
no
|
no
|
double mutant
|
G deletion at nucleotide 208,
G deletion at nucleotide 319
|
Rodney Rothstein, [http://wiki.yeastgenome.org/index.php/CommunityW303.html Personal communication to SGD] 
|- 
|
[http://www.yeastgenome.org/locus/his3 <em>his3delta</em>]
|
yes
|
no
|
In the S288C background, the his3 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 

|
[http://www.yeastgenome.org/locus/leu2 <em>leu2delta1</em>]
|
partial
|
no
|

|
EcoRI-ClaI internal deletion (163 to 649, 0.6 kb)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski and Hieter 1989] 
|- 
|
[http://www.yeastgenome.org/locus/leu2 <em>leu2-3,112</em>]
|
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
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043265 Hinnen et al. 1978];
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000042541 Gaber and Culbertson 1982];
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000069760 Meira LB et al., 1995];
[http://wiki.yeastgenome.org/index.php/CommunityW303.html Rodney Rothstein, Personal communication to SGD] 
[http://www.yeastgenome.org/reference/395030 Botstein et al. 1979]
|- 
|
[http://www.yeastgenome.org/locus/leu2 <em>leu2delta</em>]
|
yes
|
no
|
In the S288C background, the leu2 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 

|
[http://www.yeastgenome.org/locus/lys2 <em>lys2-801</em>]
|
no
|
yes
|
amber mutation
|

|
 
|- 
|
[http://www.yeastgenome.org/locus/lys2 <em>lys2delta202</em>]
|
partial
|
no
|

|
XhoI-HpaI internal deletion (1813 to 2864, 1.0 kb)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000047446 Winston et al. 1995] 
|- 
|
[http://www.yeastgenome.org/locus/lys2 <em>lys2delta</em>]
|
yes
|
no
|
In the S288C background, the lys2 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 

|
[http://www.yeastgenome.org/locus/trp1 <em>trp1delta1</em>]
|
yes
|
no
|
cold sensitive<sup>b</sup>, weak galactose inducer (deletes <em>GAL3</em> UAS), removes <em>ARS1</em>, also called <em>trp1-901</em>
|
1.45 kb deletion, EcoRI-EcoRI (-102 to 1352)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski and Hieter 1989] 
|- 
|
[http://www.yeastgenome.org/locus/trp1 <em>trp1delta63</em>]
|
partial
|
no
|
cold sensitive<sup>b</sup>
|
0.6 kb deletion, EcoRI-HindIII (-102 to 513)
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044428 Sikorski and Hieter 1989] 
|- 
|
[http://www.yeastgenome.org/locus/trp1 <em>trp1-1</em>]
|
no
|
yes
|
amber mutation
|
GAG-to-TAG amber nonsense change at codon 83
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041995 McDonald et al. 1997] 
|- 


|
[http://www.yeastgenome.org/locus/trp1 <em>trp1-1</em>]
|
no
|
yes
|
cold sensitive<sup>b</sup>
|
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 
|- 
|
[http://www.yeastgenome.org/locus/trp1 <em>trp1delta</em>]
|
yes
|
no
|
In the S288C background, the trp1 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 
|
[http://www.yeastgenome.org/locus/trp1 <em>trp1-289</em>]
|
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.
|
[http://www.yeastgenome.org/reference/395030 Botstein et al. 1979] 
|- 
|
[http://www.yeastgenome.org/locus/trp5 <em>trp5delta</em>]
|
yes
|
no
|
In the S288C background, the trp5 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 
|
[http://www.yeastgenome.org/locus/ura3 <em>ura3-52</em>]
|
no
|
no
|

|
Ty1 insertion (transcribing left to right) at pos. 121
|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043686 Rose and Winston 1984] 
|- 
|
[http://www.yeastgenome.org/locus/ura3 <em>ura3-1</em>]
|
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 

|- 
|
[http://www.yeastgenome.org/locus/ura3 <em>ura3delta</em>]
|
yes
|
no
|
In the S288C background, the ura3 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 
|
[http://www.yeastgenome.org/locus/ura4 <em>ura4delta</em>]
|
yes
|
no
|
In the S288C background, the ura4 null mutation confers sensitivity to acetic acid.
|
complete deletion
|
[http://www.yeastgenome.org/reference/23828602 Ding et al. 2013]
|- 

|
|}

The alleles listed below are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al. 1998].
 

{| 
|-
!|Allele!!Deleted ORF?!!Reverts?!!Notes !!Molecular Description<sup>a</sup>!!Reference
|- 
|
[http://www.yeastgenome.org/locus/ade2 <em>ade2delta::hisG</em>]
|
no
|
no
|

|

|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048958 (Aparicio et al. 1991)] 
|- 
|
[http://www.yeastgenome.org/locus/leu2 <em>leu2delta0</em>]
|
yes
|
no
|
designer deletion
|

|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al. 1998] 
|- 

|
[http://www.yeastgenome.org/locus/lys2 <em>lys2delta0</em>]
|
yes
|
no
|
designer deletion
|

|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al. 1998] 
|- 
|
[http://www.yeastgenome.org/locus/met15 <em>met15delta0</em>]
|
yes
|
no
|
designer deletion
|

|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al. 1998] 
|- 
|
[http://www.yeastgenome.org/locus/ura3 <em>ura3delta0</em>]
|
yes
|
no
|
designer deletion
|

|
[http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000041186 Brachmann et al. 1998] 

|- 
|
|}



<sup>a</sup>The sequence coordinates are relative to the first ATG of the selectable marker ORF, in which the A residue is defined as +1.

<sup>b</sup>All trp- strains are cold sensitive ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000057172 Singh and Manney 1974]).