Difference between revisions of "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 [ | + | This table describes some commonly used auxotrophic markers (along with some novel useful markers); it is based on a table in [https://www.yeastgenome.org/reference/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. |
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− | + | {| border="1" class="wikitable" | |
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− | |||
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− | {| | ||
|- | |- | ||
!|Allele!!Deleted ORF?!!Reverts?!!Notes!!Molecular Description<sup>a</sup>!!Reference | !|Allele!!Deleted ORF?!!Reverts?!!Notes!!Molecular Description<sup>a</sup>!!Reference | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ade1 <em>ade1-14</em>] |
| | | | ||
no | no | ||
Line 24: | Line 18: | ||
GGA-to-GAA missense change at codon 185 | GGA-to-GAA missense change at codon 185 | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000060944 Nakayashiki et al. 2001] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [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 | no | ||
Line 44: | Line 52: | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ade2 <em>ade2-101</em>] |
| | | | ||
no | no | ||
Line 54: | Line 62: | ||
G to T transversion at nucleotide 190, changing codon 64 from a Glu to a Stop | G to T transversion at nucleotide 190, changing codon 64 from a Glu to a Stop | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000087056 Gai and Voytas, 2005] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ade2 <em>ade2-BglII</em>] |
| | | | ||
no | no | ||
Line 67: | Line 75: | ||
frameshift (BglII site filled in at position 592) | frameshift (BglII site filled in at position 592) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000049198 Engebrecht and Roeder 1990] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/can1 <em>can1-100</em>] |
| | | | ||
no | no | ||
Line 83: | Line 91: | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/his3 <em>his3delta200</em>] |
| | | | ||
yes | yes | ||
Line 89: | Line 97: | ||
no | no | ||
| | | | ||
− | Cold sensitive; high frequency of petite formation, especially during transformation. Note that this deletion damages the PET56 promoter. See [ | + | Cold sensitive; high frequency of petite formation, especially during transformation. Note that this deletion damages the PET56 promoter. See [https://www.yeastgenome.org/reference/S000074003 Zhang et al. (2003)] for a discussion of this issue. |
| | | | ||
1 kb deletion (-205 to 835) | 1 kb deletion (-205 to 835) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000042846 Struhl 1985]; [https://www.yeastgenome.org/reference/S000046453 Fasullo and Davis 1988] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/his3 <em>his3delta1</em>] |
| | | | ||
partial | partial | ||
Line 102: | Line 110: | ||
no | 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) | 187 bp HindIII-HindIII internal deletion (305 to 492) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000040818 Scherer and Davis 1979] |
+ | [http://www.yeastgenome.org/reference/395030 Botstein et al. 1979] | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/his3 <em>his3-11,15</em>] |
| | | | ||
no | no | ||
Line 123: | Line 132: | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [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 | partial | ||
Line 133: | Line 156: | ||
EcoRI-ClaI internal deletion (163 to 649, 0.6 kb) | EcoRI-ClaI internal deletion (163 to 649, 0.6 kb) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000044428 Sikorski and Hieter 1989] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/leu2 <em>leu2-3,112</em>] |
| | | | ||
no | no | ||
Line 142: | Line 165: | ||
no | no | ||
| | | | ||
− | double mutant | + | 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, | GTC-to-GTT silent change at codon 56, | ||
Line 151: | Line 174: | ||
GAC-to-AAC missense change at codon 300 | GAC-to-AAC missense change at codon 300 | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000043265 Hinnen et al. 1978]; |
− | [ | + | [https://www.yeastgenome.org/reference/S000042541 Gaber and Culbertson 1982]; |
− | [ | + | [https://www.yeastgenome.org/reference/S000069760 Meira LB et al., 1995]; |
[http://wiki.yeastgenome.org/index.php/CommunityW303.html Rodney Rothstein, Personal communication to SGD] | [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/ | + | [http://www.yeastgenome.org/locus/lys2 <em>lys2-801</em>] |
| | | | ||
no | no | ||
Line 170: | Line 208: | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/lys2 <em>lys2delta202</em>] |
| | | | ||
partial | partial | ||
Line 180: | Line 218: | ||
XhoI-HpaI internal deletion (1813 to 2864, 1.0 kb) | XhoI-HpaI internal deletion (1813 to 2864, 1.0 kb) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000047446 Winston et al. 1995] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [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 | yes | ||
Line 193: | Line 245: | ||
1.45 kb deletion, EcoRI-EcoRI (-102 to 1352) | 1.45 kb deletion, EcoRI-EcoRI (-102 to 1352) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000044428 Sikorski and Hieter 1989] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/trp1 <em>trp1delta63</em>] |
| | | | ||
partial | partial | ||
Line 206: | Line 258: | ||
0.6 kb deletion, EcoRI-HindIII (-102 to 513) | 0.6 kb deletion, EcoRI-HindIII (-102 to 513) | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000044428 Sikorski and Hieter 1989] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/trp1 <em>trp1-1</em>] |
| | | | ||
no | no | ||
Line 219: | Line 271: | ||
GAG-to-TAG amber nonsense change at codon 83 | GAG-to-TAG amber nonsense change at codon 83 | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000041995 McDonald et al. 1997] |
|- | |- | ||
+ | |||
+ | |||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/trp1 <em>trp1-1</em>] |
| | | | ||
no | no | ||
Line 235: | Line 289: | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [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 | ||
Line 245: | Line 338: | ||
Ty1 insertion (transcribing left to right) at pos. 121 | Ty1 insertion (transcribing left to right) at pos. 121 | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000043686 Rose and Winston 1984] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ura3 <em>ura3-1</em>] |
| | | | ||
no | no | ||
Line 260: | Line 353: | ||
Yan Li, Glenn Manthey, and Adam Bailis, unpublished results | 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 [ | + | The alleles listed below are described in [https://www.yeastgenome.org/reference/S000041186 Brachmann et al. 1998]. |
− | + | ||
− | + | {| | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | {| | ||
|- | |- | ||
!|Allele!!Deleted ORF?!!Reverts?!!Notes !!Molecular Description<sup>a</sup>!!Reference | !|Allele!!Deleted ORF?!!Reverts?!!Notes !!Molecular Description<sup>a</sup>!!Reference | ||
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ade2 <em>ade2delta::hisG</em>] |
| | | | ||
no | no | ||
Line 289: | Line 402: | ||
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− | [ | + | [https://www.yeastgenome.org/reference/S000048958 (Aparicio et al. 1991)] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/leu2 <em>leu2delta0</em>] |
| | | | ||
yes | yes | ||
Line 302: | Line 415: | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000041186 Brachmann et al. 1998] |
|- | |- | ||
+ | |||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/lys2 <em>lys2delta0</em>] |
| | | | ||
yes | yes | ||
Line 315: | Line 429: | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000041186 Brachmann et al. 1998] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/met15 <em>met15delta0</em>] |
| | | | ||
yes | yes | ||
Line 328: | Line 442: | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/S000041186 Brachmann et al. 1998] |
|- | |- | ||
| | | | ||
− | [http://www.yeastgenome.org/ | + | [http://www.yeastgenome.org/locus/ura3 <em>ura3delta0</em>] |
| | | | ||
yes | yes | ||
Line 341: | Line 455: | ||
| | | | ||
− | [ | + | [https://www.yeastgenome.org/reference/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>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 ([ | + | <sup>b</sup>All trp- strains are cold sensitive ([https://www.yeastgenome.org/reference/S000057172 Singh and Manney 1974]). |
Latest revision as of 12:34, 11 July 2019
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 |
---|---|---|---|---|---|
no |
yes |
red colonies |
TGG-to-TGA nonsense change at codon 244; GGA-to-GAA missense change at codon 185 |
||
no |
simple point mutation causing a requirement for adenine |
||||
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 | |
no |
yes |
ochre mutation, red colonies |
G to T transversion at nucleotide 190, changing codon 64 from a Glu to a Stop |
||
no |
no |
red colonies |
frameshift (BglII site filled in at position 592) |
||
no |
yes |
ochre mutation |
AAA-to-TAA ochre nonsense change at codon 47 |
Rodney Rothstein, Personal communication to SGD | |
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) |
||
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) |
||
no |
no |
double mutant |
G deletion at nucleotide 208, G deletion at nucleotide 319 |
Rodney Rothstein, Personal communication to SGD | |
yes |
no |
In the S288C background, the his3 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
partial |
no |
EcoRI-ClaI internal deletion (163 to 649, 0.6 kb) |
|||
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 | |
yes |
no |
In the S288C background, the leu2 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
no |
yes |
amber mutation |
|||
partial |
no |
XhoI-HpaI internal deletion (1813 to 2864, 1.0 kb) |
|||
yes |
no |
In the S288C background, the lys2 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
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) |
||
partial |
no |
cold sensitiveb |
0.6 kb deletion, EcoRI-HindIII (-102 to 513) |
||
no |
yes |
amber mutation |
GAG-to-TAG amber nonsense change at codon 83 |
||
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 | |
yes |
no |
In the S288C background, the trp1 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
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. |
||
yes |
no |
In the S288C background, the trp5 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
no |
no |
Ty1 insertion (transcribing left to right) at pos. 121 |
|||
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 | ||
yes |
no |
In the S288C background, the ura3 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
yes |
no |
In the S288C background, the ura4 null mutation confers sensitivity to acetic acid. |
complete deletion |
||
The alleles listed below are described in Brachmann et al. 1998.
Allele | Deleted ORF? | Reverts? | Notes | Molecular Descriptiona | Reference |
---|---|---|---|---|---|
no |
no |
||||
yes |
no |
designer deletion |
|||
yes |
no |
designer deletion |
|||
yes |
no |
designer deletion |
|||
yes |
no |
designer deletion |
|||
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).