Primers used in this study
| Type of analysis and primer | Sequence (5′–3′) |
|---|---|
| Construction of expression plasmid for PhoP expression in E. coli | |
| SCPhoPEX_F | AATGGATCCGTGCTCGTCGTCGAGGACGA |
| SCPhoPEX_R | AATGAATTCTACGGCTCGAACTTGTAAC |
| DNase I footprinting assay | |
| SCamtBFP(M13F) | GTAAAACGACGGCCAGTCCATGCCAGGTCATTCGGAG |
| SCamtBFP(M13R) | CAGGAAACAGCTATGACGGCGGAGCAGATGAGCATGA |
| M13F-FAM | GTAAAACGACGGCCAGT (5'-FAM labeled) |
| M13R-FAM | CAGGAAACAGCTATGAC (5'-FAM labeled) |
| RT-PCR | |
| hrdB-F | GAGTCCGTCTCTGTCATGGCG |
| hrdB-R | TCGTCCTCGTCGGACAGCACG |
| amtB-F | ATCCTCGTCATCGGCAAGC |
| amtB-R | TTGAAGCCGAACCAGCCGAA |
| egfp-F | GAAGAAGATGGTGCGCTCCT |
| egfp-R | GATGTTGCCGTCCTCCTTGA |
| Introducing mutations in amtB promoter for egfp fusion | |
| For wild-type amtBP | |
| amtBP-1 | CGGGATCCAACCCGAGGAGAGCACCGTG |
| amtBP-2 | GGGAATTCCATATGCGGCGTCTCCTCGTCGT |
| For a3-b3 site mutation | |
| amtBP-3 | CGGCCGGGGCCGGTCGTCGT |
| amtBP-4 | CCTGTCCACGCACGGTACGCACCGTGCCTTCGTCAC |
| For a1-b1 site mutation | |
| amtBP-6 | GAAGGCACGGTGCGTGTTAC |
| amtBP-7 | ACTGTGGCGGCAGGGTAACGAGGGGCTTCCACCGAA |
| For a2-b2 site mutation | |
| amtBP-8 | TCGTTGTTTCGCCGCCGTGA |
| amtBP-9 | GAAATCTCCACCAGGGTCGCGCTGCGTCAATGTCGT |
| Synthesizing mutants of amtB promoter by oligonucleotides for EMSA | |
| For the wild-type oWT | |
| oWTp1 | ACGACGACGACCGGCCCCGGCCGTTCACCCACGCGTAACACGCACCGTGCCTTC |
| oWTp2 | CACGACATTGACGCAGCGCGGTTTCGGTGGAAGCCCCTCGTTGTTTCGCCGCCGTGACGAAGGCACGGTGCGT |
| For oM3, mutagenesis at a3-b3 site | |
| oM3p1 | ACGACGACGACCGGCCCCGGCCGCCTGTCCACGCACGGTACGCACCGTGCCTTC |
| oM3p2 | Same as oWTp2 |
| For oM1, mutagenesis at a1-b1 site | |
| oM1p1 | Same as oWTp1 |
| oM1p2 | CACGACATTGACGCAGCGCGGTTTCGGTGGAAGCCCCTCGTTAGGGTGCCGCCACAGTGAAGGCACGGTGCGT |
| For oM2, mutagenesis at a2-b2 site | |
| oM2p1 | Same as oWTp1 |
| oM2p2 | CACGACATTGACGCAGCGCGACCCTGGTGGAGATTTCTCGTTGTTTCGCCGCCGTGACGAAGGCACGGTGCGT |