TABLE 2.
Oligonucleotide primers used in this study
| Primer application and name | Nucleotide sequence 5′-3′e | Restriction site |
|---|---|---|
| Cloning | ||
| CodSacFwd | GCGCGCCCGCGGAGGTCGTGCTGGTAAGTCAG | SacII |
| CodKpnRv | GCGCGCGGTACCGATGATTTTCAGGCCAGATG | KpnI |
| CodHindFwdinv | TACGAAGCTTTGAGTCTGCGGGGATTATTG | HindIII |
| CodPstRvinv | ATGCCTGCAGGTGCCATTTTTCACCTCGAA | PstI |
| CodKOrv | CATATTAGCCCCTTGAACGTAGTC | |
| Cod 5′ chrom | CATGTCAAGATTGCGGCTAA | |
| pcpA_L1 | GTTTCCCAGAAAGACTCTGG | |
| pcpA_L2a | CCACTAGTTCTAGAGCGGCGGAGTATCTGCTAGGATTGG | |
| pcpA_R1 | ATAAGAATACGGATTCGGACG | |
| pcpA_R2a | GCGTCAATTCGAGGGGTATCGATGGCTATCGAGTCAATGC | |
| pR412_L | GCCGCTCTAGAACTAGTGG | |
| pR412_R | GATACCCCTCGAATTGACGC | |
| Overexpression | ||
| CodY-NheI-H6-Fwb | CGGCTAGCCATCACCATCACCATCACGCACATTTATTAGAAAAAACT | NheI |
| CodYBamRv | CGCGCGGGATCCTTAGTAATCTCTTTTCTT | BamHI |
| EMSA | ||
| codY EMSA fw | TGCAAGTCAATAAGGAATTTTCA | |
| codY EMSA rv | GCCATTTTTCACCTCGAATT | |
| gdhA EMSA fw | CCAAAAACTGAATTGAAAGAATTT | |
| gdhA EMSA rv | CTTTAGCAGATGTCATATCGTTCTCC | |
| amiA EMSA fw | GACACTTCGAACGACAATTTG | |
| amiA EMSA rv | TGACAACCATTATATCACATTATCCA | |
| ilvB EMSA fw | CATAAATAAACGTTAAAATAGAAAATTCAG | |
| ilvB EMSA rv | CCCTTTCTTTCCTCTTAAAAATAAC | |
| ilvE EMSA fw | GAAATGAAGAATCAGTTCTAAGATGG | |
| ilvE EMSA rv | TCCCAATCAATCGTTACTGTCA | |
| livJ EMSA fw | CCCTTTGTGGGCAATCTTTA | |
| livJ EMSA rv | CAAGCGCCACAAACGATA | |
| psaR EMSA fw | TGAAAGAAGAGCTATTTTCGTCAT | |
| psaR EMSA rv | CTTTGTTTGGGGTCATTCGT | |
| livH EMSA fw | TCAACGTCGCCTTGGATTAT | |
| livH EMSA rv | CGAGGGTTTTCCCTCACTTT | |
| acuB EMSA fw | TTCAGAGCTCTTTTTGCTAGCTT | |
| acuB EMSA rv | CCTTGCGGGTCATAAAATCT | |
| asd EMSA fw | CCCTAGTCTAGCGACTGGGATT | |
| asd EMSA rv | GCGCCGACTACAGCAACT | |
| gapN EMSA fw | CGCCTTGACGTAGTGGATTT | |
| gapN EMSA rv | TCGGATGATTTCCATTTTCC | |
| aliB EMSA fw | TTGAACAATCTTTTAGGAGAACTTGA | |
| aliB EMSA rv | CATTTCCAGAACCTCCTGCT | |
| fatD EMSA fw | TCCCTCGAAGATATTATTTTATCAGA | |
| fatD EMSA rv | TTTCATACCCCGTCCTTTCA | |
| spr0140 EMSA fw | GACATTCTATTTAGAACGAGGATTGA | |
| spr0140 EMSA rv | ATTCCCCCAGTTCCATTTTT | |
| spr0141 EMSA fw | TCTATCAAAATCGCAAATAAGAAA | |
| spr0141 EMSA rv | TTCCATTGTTTCTGCAAATTGT | |
| spr0157 EMSA fw | AACAATGTTTTAGAAGCAAAGGTG | |
| spr0157 EMSA rv | GCTTGCGACATGATAAATACTCC | |
| spr0788 EMSA fw | GAGGAAGGCCTTGTCCAGTT | |
| spr0788 EMSA rv | CCCATAGAGCAACCTGTCGT | |
| spr1436 EMSA fw | TGCGTAAACTACGTGAGCAA | |
| spr1436 EMSA rv | TGACCTGCTTCTGACATTTGA | |
| spr1934 EMSA fw | CTCCGGTTGCTTGTCTCAGT | |
| spr1934 EMSA rv | AGCAGTCCCTCCACGTGATA | |
| spr1945 EMSA fw | TGTGTTTATGGAGAGATGACAATTT | |
| spr1945 EMSA rv | AACCGCAGCTGTAGTTAATGA | |
| spr1982 EMSA fw | CTTGGTCAGGGTCAAGGAAG | |
| spr1982 EMSA rv | TCGCCATAAGTGTGTTCCTG | |
| fake gdhA EMSA fw2c | GAATTGAAAGGGTCTCGAGCTGCTATCTGTTTTTTC | |
| psaR EMSA codY fw2d | GCTATTTTCAATTTTTAGAAAATTTCGTTTTTTC | |
| Footprinting | ||
| codY FP fw | GCAACTTGTCAATAGAAAAGGAA | |
| fake gdhA FP fw | GATATTTCCAAGAAAAACGTTCG | |
| RT-PCR | ||
| codYF | GATTGCCAGTACCGTTGT | |
| codYR | CACGGAGTTCGGAGTAAG | |
| gyrAF | TCTTGATTGCGCTAGACC | |
| gyrAR | ACGACGAAGACGCATATC |
a
The overlap with primers pR412_L and pR412_R is in bold.
b
The six-His tag is in bold.
c
The underlined sequence indicates random nucleotides used to replace the putative CodY box of the gdhA promoter.
d
The underlined sequence indicates the CodY box introduced into the psaR promoter.
e
Restriction sites are underlined.