TABLE 1.

Oligonucleotides used to construct and verify deletion strains

Gene(s)NameOligonucleotide sequence (5′ to 3′)aEnzymeb
evgASNoaaggaaaaaagcggccgCTGAATACGTGCTGAAGCGACTTCNotI
NiggagccgctatttaCATAGATTATTCCCTTTGCAATGAAGCATC
CigcaaagggaataatctatgTAAATAGCGGCTCCCACAATGTTC
CocgcacgcatgtcgaCGCTAAAAGATGCTCCTGCCTACSalI
acrBNoaaggaaaaaagcggccgCATCAGTAAGCAAGAGTACGATCAGGNotI
NigattacacgttgtatcaCATGTCTTAACGGCTCCTGTTT
CigagccgttaagacatgTGATACAACGTGTAATCACTAAGGCCG
CocgcacgcatgtcgacTAAAGGTGTCATCCAGATATTCGTCGSalI
appCBANoaaggaaaaaagcggccGCGTGCCTCATGAGCGAAACNotI
NigctcttttttatgcattACATGCGCACTCCTGTAGGC
CiggagtgcgcaTGTAATGCATAAAAAAGAGCATTCAGTTACCTG
CocgcggatccAAGCGTTGAACGTGGTGCTTGBamHI
gadCNoaaggaaaaaagcggccgcAGTTGTTTATGGACCCGAAACGCNotI
NiccattcagacatggttaCATATTATCCCCCTAAAACGGTATTCCTG
CigttttagggggataatatgTAACCATGTCTGAATGGTTATAAGACAAGG
CocgcacgcatgtcgacGCTAACACCAAATTCGACTCCCSalI
ydeP-b1500-ydeONoaaggaaaaaagcggccgcAAACCTGGTACAAGGCTCAGCNotI
NictcgttagcaaataatcaCATCTACTTATCCTGTGTGGAAATGAATTATTAGG
CiacacaggataagtagatgTGATTATTTGCTAACGAGTAGTCAACCAC
CocgcacgcatgtcgaCGTTTGTTTATCTTCCGGTACCGSalI
ydePNoaaggaaaaaagcggccgcAAACCTGGTACAAGGCTCAGCNotI
NiaaatgagaagaggcattaTTTTTTCTTCATCTACTTATCCTGTGTGG
CigataagtagatgaagaaaaaaTAATGCCTCTTCTCATTTCTTCTGCTG
CocgcacgcatgtcgaCTTCAACAGGCTTTCACTGATGTACAGSalI
b1500NoaaggaaaaaagcggccgcGGACGTAGCGAGATTGACATGCNotI
NicccatttctgaaatacTCGCATGCATTTCAAATATGTTTATTTAGCGG
CitttgaaatgcatgcGAGTATTTCAGAAATGGGTCGCATTG
CocgcacgcatgtcgacGCAAGTGCATAAATATGTGATGGATGTCSalI
ydeONoaaggaaaaaagcggccgCTATAACCAGCGCATCCGTCATCNotI
NictcgttagcaaataatcaAGAACAAACGAGCGACATTTTATCTCC
CitcgctcgtttgttcTTGATTATTTGCTAACGAGTAGTCAACCAC
CocgcacgcatgtcgaCGTTTGTTTATCTTCCGGTACCGSalI
yegR-b2084-yegZNoaaggaaaaaagcggccgCATCGTTAATTAACGCGTTCGGACNotI
NigataaaataaaaacatcaACGACACTCTCTAGTGTTTAAATATAATAATGGC
CiactagagagtgtcgtTGATGTTTTTATTTTATCTGTTTGTTTTGTAAGGG
CocgcacgcatgtcgacTTTACCGCAAAGCTATCGATGACGSalI
yfdXWUVENoaaggaaaaaagcggccgCACAACAGTCTTGCATTTAACATGCTGNotI
NicagcacatcttacatttaCATACTTACCTCATTCTTTAACAGTTTTAGAAAACG
CiaagaatgaggtaagtatgTAAATGTAAGATGTGCTGGTAAATAGCTCC
CocgcacgcatgtcgacATCGCAGGAAGAACAACAACAACTGSalI
slp-yhiFNoaaggaaaaaagcggccgcTACCAATGCTGCATGCAGTGAATGNotI
NigtaagcctgaaattcaTGTCATGTTCATGTTACTATCCTTATCAAC
CiagtaacatgaacatgacaTGAATTTCAGGCTTACGGTGAGTC
CocgcacgcatgtcgaCGTTGGCAGCCAATGAATCCSalI
yhiDNoaaggaaaaaagcggccgCTAATTGCAGTATCTGATGCATCTGTAACTCNotI
NictgccacacagattACATATAAAAATGCAAAAAGGAGCAGCAAGATG
CicctttttgcatttttatatgTAATCTGTGTGGCAGCGTAGC
CocgcacgcatgtcgacGCTTCCTTGATCCAGTGAACTATCGSalI
hdeBNoaaggaaaaaagcggccgCAATGGCAAAAATGCCCAGCTCNotI
NiggtatcgccacctttACCCATTCAATATAGAGATTATATATGAACAGGAGG
CitctctatattgaatgggTAAAGGTGGCGATACCGTTACTTTAAATG
CocgcacgcatgtcgaCAACGGAAGATATTCTGGAGAAACTGSalI
hdeANoaaggaaaaaagcggccgcGTTTGAAATGGCTAATTTGCCATAGAGTGNotI
NicattcccggaattaCATCGTAATATCCTCAACTATAAAGTGAAAGAGC
CigttgaggatattacgATGTAATTCCGGGAATGCGTTACATC
CocgcacgcatgtcgacTGCTGCTTAAACCAGTCGAGCSalI
hdeD-yhiENoaaggaaaaaagcggccgCCTCATTAATTCGGCAAGTCATTAGATGCNotI
NittgcttatgtcctgactaCATAGAACCACCCTATAAAATTAAGAAGAAAATCC
CitagggtggttctatgTAGTCAGGACATAAGCAACTGAAATTGATG
CocgcacgcatgtcgaCGTAAGAAATCTTGCACCGACTGCSalI
hdeDNoaaggaaaaaagcggccgCCTCATTAATTCGGCAAGTCATTAGATGCNotI
NicaaccggggtaattACATAGAACCACCCTATAAAATTAAGAAGAAAATCC
CitagggtggttctatgTAATTACCCCGGTTGTCACCC
CocgcacgcatgtcgacTTCTCTCGGCATCTAATTTCTCCAGSalI
yhiENoaaggaaaaaagcggccgcGAGTTGGTATCGTCAGCGTTCAATGNotI
NittgcttatgtcctgactaCATAACTTGCTCCTTAGCCGTTATCG
CictaaggagcaagttatgTAGTCAGGACATAAGCAACTGAAATTGATG
CocgcacgcatgtcgaCGTAAGAAATCTTGCACCGACTGCSalI
Gene(s)NameOligonucleotide sequence (5′ to 3′)aEnzymeb
yhiUVNoaaggaaaaaagcggccGCTTTTGGCAGTTGAAAGATAATCACGNotI
NicttactctcatttacacgttaCATTTTAGTCCCTGAAAATTCTTGAGAAATAACG
CitcagggactaaaatGTAACGTGTAAATGAGAGTAAGGTTGAACATG
CocgcggatcCTTCAATGAATCCGGGGTAAATTCACBamHI
yiiSNoaaggaaaaaagcggccgcTTACTTGCAGCACGAGTGAGATTGNotI
NicccctccagatcCATAGGGCACCTCTGTATATTCGC
CicagaggtgccctatGGATCTGGAGGGGCAAGTTG
CocgcacgcatgtcgacGGATTCTTTGTGCTCGATGAAGTGSalI
yjdENoaaggaaaaaagcggcCGCTTTTTTTTGCCTGTTATTTATCCTGNotI
NitgaccacataacctcCATAATTAAACTCCTGCGAAGGCGAG
CicgcaggagtttaattatgGAGGTTATGTGGTCATTTGTCACC
CocgcacgcatgtcgacGGTTAGTTTCACGCGGGTAGCSalI
emrKYNoaaggaaaaaagcggccgcTTTGGGACTTATGTACTGCAATCACAAGNotI
NiccctccttttatcatcaCTGTTCCACTATTATCTCTCATTTCTCATAGATG
CiagagataatagtggaacaGTGATGATAAAAGGAGGGGGTTATAGC
CocgcacgcatgtcgaCAAAAGCATTTCCTGAAACTGCTGCSalI
tolCNoaaggaaaaaagcggccgcTGCTAAACAGTATCGCAACCAGTCNotI
NitcgtcgtcatcaCATTCCTTGTGGTGAAGCAGTATTTAGC
CicaccacaaggaatgTGATGACGACGACGGGGC
CocgcacgcatgtcgaCTCGTATAGTGACGTTGGCGTATCSalI
  • a Sequences complementary to the amplified regions are represented by capital letters, and newly added sequences are represented by lowercase letters. Incorporated cutting sites for restriction enzymes (No and Co) and start and stop codons of the gene or tandem group of the genes to be disrupted (Ni and Ci) are underlined.

  • b Restriction enzyme for cutting the amplified fragment.