TABLE 6.
Synthetic oligonucleotides used in this study
| Primer | 5′ → 3′ sequencea | Position(s) | Purpose |
|---|---|---|---|
| PtetR1-XbaI | CAATCTAGATTCGGCAGGCTATGCCGCTG | −394 to −1 | Amplification of the SCO3201 promoter region for promoter probing (xylE fusion) |
| PtetR1-HindIII | CAAAAGCTTCGGATGCCGCGTGACGTG | ||
| PtetR2 | CACTTCGGCAGGCTATGCC | −240 to +3 | Amplification of the SCO3201 promoter region for EMSA |
| PtetR2′ | ACCGAAGACCACGTCCCGAC | ||
| UtetR-BamHI | CGGGATCCCGCAAGGGCTTCAAGTTCTC | −999 to −1 | Amplification of the 1-kb fragment located upstream of SCO3201 |
| UtetR-XbaI | GCTCTAGATTCGGCAGGCTATGCCGCTG | ||
| DtetR-HindIII | CCAAGCTTGGCACGCGGTCGAGGGCCTG | +754 to +1711 | Amplification of the 1-kb fragment located downstream of SCO3201 |
| DtetR-XbaI | GCTCTAGAGGTCGCTCCGTCGGGGGTGA | ||
| ItetR1 | ACCGAAGACCACGTCCCGAC | −240 | Verification of the interruption of SCO3201 |
| ItetR2 | CGGATCTCGGCCCAGTTGAC | ||
| GSP1 | CTCTCGGCCAGACGGATGAG | +416 | Gene-specific primer (GSP) for 5′-RACE PCR |
| GSP2 | GACGGCCTCTTCCTTGGTGGCTGG | +240 | |
| GSP3 | CGATGTCCTCGGCC | +179 | |
| ExpTetR1-NdeI | CAACATATGGTGAGCAGCACCATTCCAGCACTTC | +1 to +708 | Amplification of SCO3201 for protein expression |
| ExpTetR2-XhoI | CAACTCGAGCCCCTCTTCCGCGGGCCC | ||
| RT-hrdB1 | AAGGAAGACGGCGAGCTTCT | +481 to +1060 | RT-PCR |
| RT-hrdB2 | GCACCGGGATACGGATGGTG | ||
| RT-scbA1 | GATCAATTCTGCGTCCGATG | +68 to +557 | RT-PCR |
| RT-scbA2 | GTAGACTTGAGGACTGGTG | ||
| RT-scbR1 | CAAGCAGGACCGGGCGATC | +130 to +664 | RT-PCR |
| RT-scbR2 | CTTCTGCAGCAGCGCGTAGC | ||
| RT-cpkO1 | GTCCACTCGAGGTGTTGTCC | +55 to +546 | RT-PCR |
| RT-cpkO2 | GGTAGTCCTCCAGGACATCG | ||
| Plabel | AGCCAGTGGCGATAAG | Cy5 labeling | |
| PscbA1 | AGCCAGTGGCGATAAGCCAGGAATCATGTGATGCCG | −230 to +38 | Amplification of the scbA promoter region for EMSA |
| PscbA2 | AGCCAGTGGCGATAAGCCTTGGACTGGAAGTGGAAG | ||
| PscbR1 | AGCCAGTGGCGATAAGGGCCATCAGGAAGTGGTAGC | −303 to +10 | Amplification of the scbR promoter region for EMSA |
| PscbR2 | AGCCAGTGGCGATAAGACCCATGCCCGAAGCAGTAG | ||
| PcpkO1 | AGCCAGTGGCGATAAGCATCCGGGACACCGACGGAG | −315 to +67 | Amplification of the cpkO promoter region for EMSA |
| PcpkO2 | AGCCAGTGGCGATAAGCACCTCGAGTGGACCGAGC |
a
Engineered restriction enzyme sites are in bold. Underlined nucleotides show no homology to the template; they were used for Cy5 labeling.