Table 2.
Primers used in this work
| Primer name | Sequence | Purpose/PCR product |
|---|---|---|
| pdxR_acc_f | GTCAACCATGGCCAATTTGGGGAAGGTGGACTGATTTCCATGATTCCGGGGATCCGTCGACC | To amplify aac(3)IV for pdxR replacement |
| pdxR_acc_r | GCGGGCGGAGGTCCCCCGGCGGCCCCGCCGGACGCGCCCTATGTAGGCTGGAGCTGCTTC | |
| pdxST_f | AATAAAAGCTTACAAGACGTCTGTCATGACA | To amplify pdxST with 3-kb flanks |
| pdxST_r | AATAATCTAGACCAGTTCACTTGATTCTCCT | |
| pdxST_acc_f | CGTTGCTGCACAACCCCCCTTCTCCCCAGTGAGGTACCCGTGGATATCTCTAGATACCG | To amplify aac(3)IV for pdxST replacement |
| pdxST_acc_r | CTTCGCGTAACCCATCTCCTGCAACGAACGCAGGAATCCTAAACAAAAGCTGGAGCTC | |
| pdxR-cmpl-f | ATTGAAAGGATCCCATCGACAGCCCCGTGTGCT | To clone pdxR for complementation |
| pdxR-cmpl-r | ATTGAAATCTAGAGCGCCCTAGGCCACGAACGT | |
| pdxST-cmpl-f | AATAAGGATCCCTGCGCGAGCACCGCAAGGT | To clone pdxST for complementation |
| pdxST-cmpl-r | AATAATCTAGAATCTGCCTGTCTCCTTCGCG | |
| Gus-R-f | TCTGAATCTAGATTCAGGACGATGCCCGCCAC | pdxRp for pGUS |
| Gus-R-r | TCTGAAGGTACCCCAAATTGGCCATGGTTGAC | |
| Gus-ST-f | TCTGAATCTAGAAGGAACTCGCCACCTCCGGC | pdxSTp for pGUS |
| Gus-ST-r | TCTGAAGGTACCACTGGGGAGAAGGGGGGTTG | |
| RT_1523_f | ACATGATCGAGGGCATCATC | To check the trans-cription of pdxS |
| RT_1523_r | ATCTCGTTCTTGATCTGGCG | |
| RThrdB_f | CGAGGACGAGGCGACCGAGGAG | Positive RT control (hrdB) |
| RThrdB_r | CAGCTTGTCCTCGGCGAACAGA | |
| SCO1417NcoI-f | AAAACCATGGCGCAGTGGACCTCGGCCGTG | pdxR-ORF for protein production |
| SCO1417BamHIhis-r | AAAGGATCCTCAGTGGTGGTGGTGGTGGTGGGCCACGAACGTCCGCG | |
| R-f | CTGGTGCAGCACGTTCCA | pdxR promoter for EMSAs |
| R-r | ACTGCGCCATGGAAATCAGT | |
| ST-f | CCGCCGCTTCCACAACGA | pdxST promoter for EMSA |
| ST-r | TGCTGGACACGGGTACCTCA | |
| OTR1-f | TGGGGTGGTGGTAGTGGACTGCCACATGACACCCTGTGGCTTCAGAA | To generate ds-oligonucleotides with predicted rPdxR binding sites (bs) in pdxRp |
| OTR1-r | TTCTGAAGCCACAGGGTGTCATGTGGCAGTCCACTACCACCACCCCA | |
| OTR2-f | TCAACCATGGCCAATTTGGGGAAGGTGGACTGATTT | |
| OTR2-r | AAATCAGTCCACCTTCCCCAAATTGGCCATGGTTGA | |
| OTST-f | ACGAAAACGATCCACCGCCTTCTCATTGGCCCTTGCTGTGGCCTGCT | To generate ds-oligonucleotides carrying putative rPdxR bs in pdxSTp |
| OTST-r | AGCAGGCCACAGCAAGGGCCAATGAGAAGGCGGTGGATCGTTTTCGT | |
| OTST2-f | CTTCTCATTGGCCCTTGCTGTGGCCTGCTC | |
| OTST2-r | GAGCAGGCCACAGCAAGGGCCAATGAGAAG | |
| OTR1a-f | TGGGGTGGTGGTAAAAAACTGCCACATGACACCCTGTGGCTTCAGAA | To generate ds-oligonucleotides with mutated rPdxR bs in pdxRp |
| OTR1a-r | TTCTGAAGCCACAGGGTGTCATGTGGCAGTTTTTTACCACCACCCCA | |
| OTR1b-f | TGGGGTGGTGGTAGTGGACTGCCACATGACACCCTAAAACTTCAGAA | |
| OTR1b-r | TTCTGAAGTTTTAGGGTGTCATGTGGCAGTCCACTACCACCACCCCA | |
| OTR1c-f | TGGGGTGGTGGTAAAAAACTGCCACATGACACCCTAAAACTTCAGAA | |
| OTR1c-r | TTCTGAAGTTTTAGGGTGTCATGTGGCAGTTTTTTACCACCACCCCA | |
| OTR2a-f | TCAACCATGGCCAATTTGGGGAAGAAAAACTGATTT | |
| OTR2a-r | AAATCAGTTTTTCTTCCCCAAATTGGCCATGGTTGA | |
| OTR2b-f | TCAACCAAAACCAATTTGGGGAAGGTGGACTGATTT | |
| OTR2b-r | AAATCAGTCCACCTTCCCCAAATTGGTTTTGGTTGA | |
| OTR2c-f | TCAACCAAAACCAATTTGGGGAAGAAAAACTGATTT | |
| OTR2c-r | AAATCAGTTTTTCTTCCCCAAATTGGTTTTGGTTGA | |
| OTST2a-f | CTTCTCATTGGCCCTTGCTAAAACCTGCTC | To generate ds-oligonucleotides carrying matated rPdxR bs in pdxSTp |
| OTST2a-r | GAGCAGGTTTTAGCAAGGGCCAATGAGAAG | |
| OTST2b-f | CTTCTCAAAAACCCTTGCTGTGGCCTGCTC | |
| OTST2b-r | GAGCAGGCCACAGCAAGGGTTTTTGAGAAG | |
| OTST2c-f | CTTCTCAAAAACCCTTGCTAAAACCTGCTC | |
| OTST2c-r | GAGCAGGTTTTAGCAAGGGTTTTTGAGAAG | |
| Pnat-f | CAGGTGATCGTTACGGAGCGTAGAGAACCTATGTCCCTGAGTGACGATACTGG | To generate unspecific oligonucleotide probe |
| Pnat-r | CCAGTATCGTCACTCAGGGACATAGGTTCTCTACGCTCCGTAACGATCACCTG |