TABLE 3.
Primers used in this study
| Primer name | Primer sequence (5′ to 3′) | Target |
|---|---|---|
| 18672-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGAGAAGGTGATTTGGCAGTGCGATGTA | 18672 deletion mutant |
| 18672-P2 | CTTTATGGGGTGACGTACACACCCAGAGTTGATAAAG | |
| 18672-P3 | AACTCTGGGTGTGTACGTCACCCCATAAAGCGGCGACAATT | |
| 18672-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTTAAATGCAGTCAAGGGGTAGCGTCC | |
| 18672-OUT-F | AGGATCGCTTTCCCCTGCTCTGCCG | |
| 18672-OUT-R | AGAACCGCCGATGGAATGT | |
| 18672-IN-F | ATGGATAAATTAACAAGCATGAAGG | |
| 18672-IN-R | CGACCAAGGTACGGTTTTTAAGGGA | |
| 02325-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGATCAGCCACGCATTGCGAATAGAACG | 02325 deletion mutant |
| 02325-P2 | TACACTCGCGTTCAAGTGCTGTGCTTCTCGTAATTGTCTT | |
| 02325-P3 | CGAGAAGCACAGCACTTGAACGCGAGTGTAAGAACCTGCCT | |
| 02325-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTGTATTCATCCTGATAACCCCTCTGT | |
| 02325-OUT-F | ATGCAAACCGTATTGAACCGAAAAG | |
| 02325-OUT-R | CGGCGAATGCGGTAAAAAGTGAAAG | |
| 02325-IN-F | ATGGAAATCGCACAGTCATTACAAC | |
| 02325-IN-R | TTACAACGTGTTGAGGACATCCGCG | |
| soxR-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGATTCTTGGGTGAAGGCATTGTTGGTC | soxR deletion mutant |
| soxR-P2 | GAATAGAGATAATCGCCTTGACTCCCTGTGTATCAA | |
| soxR-P3 | CACAGGGAGTCAAGGCGATTATCTCTATTCTTTGTCGAA | |
| soxR-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTTAGCAAGCGAATAATGGAATAAACA | |
| soxR-OUT-F | AAGCAAACTCTTTCATACCCCACAT | |
| soxR-OUT-R | GATTTACTTGCCGAAGAACGAGACC | |
| soxR-IN-F | TTCTGGAGTGAAAGTATCTGCCCTA | |
| soxR-IN-R | CCGAGTGGTCTTTCCCTAATACATC | |
| asnC-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGAGAGTGGTCACTGACGATGAGAACTT | asnC deletion mutant |
| asnC-P2 | ATTTACGTTTCGGTTACTATGATTTCCGTTAGGGATAGAG | |
| asnC-P3 | AACGGAAATCATAGTAACCGAAACGTAAATCCGT | |
| asnC-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTAAGAGAAAGTCGCGGTAGTT | |
| asnC-OUT-F | GTTGTTTTAGATCGATGATGCTGTC | |
| asnC-OUT-R | TATTTTGCGTCAGCTAGAATTCGGC | |
| asnC-IN-F | GCGCAATATTAAAAACACTGATGGC | |
| asnC-IN-R | GTTCTGCAACGATATCAATGTCTCC | |
| 06711-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGATCTGCAATCCAATCAAAATGAACAA | 06711 deletion mutant |
| 06711-P2 | TCACTGATAAAATGTGATTTGACACAACCAATAAATGAATTC | |
| 06711-P3 | TGGTTGTGTCAAATCACATTTTATCAGTGAGCGTC | |
| 06711-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTTTCTAAGACCGCTTTTCCAAATGGG | |
| 06711-OUT-F | ACGCTCAGACTTCGCAAGGGTAA | |
| 06711-OUT-R | ACAACCGATAACATTCACGAAGCCG | |
| 06711-IN-F | GTATGTCGATTAAGGCATTAGAGAA | |
| 06711-IN-R | GCTCAATTTATCTGCTAACCACGTC | |
| 01665-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGAACCTAAGCGAGATTGCAGCAGTTCA | 06115 deletion mutant |
| 01665-P2 | GCGAAATTATCGAGGATTTCGTACTCCAGTTCGAATTGCG | |
| 01665-P3 | ACTGGAGTACGAAATCCTCGATAATTTCGCCATCACTGCG | |
| 01665-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTAAGTGGAAGCTGGTATGGTTGCGAAG | |
| 01665-OUT-F | ATTTGTTCAAGCGTTCCATCGTGAG | |
| 01665-OUT-R | TACTTTCTTTATGTTGTTGTTCGGT | |
| 01665-IN-F | TGTCTTTTGCCCAACGCCTA | |
| 01665-IN-R | TCTTTATGGAGAGATAGGAAGGTCG | |
| metR-P1 | AGTACGCGTCACTAGTGGGGCCCTTCTAGAACCATTTGGTCATATCCGATGC | metR deletion mutant |
| metR-P2 | CATAACCCAAATCTTGAATTCCTTTCATCCTTTGTTGCTC | |
| metR-P3 | GGATGAAAGGAATTCAAGATTTGGGTTATGAAAGGCTTAGCG | |
| metR-P4 | TAACAATTTGTGGAATTCCCGGGAGAGCTGTCGATGACGAGCCTGCAAGGTTTA | |
| metR-OUT-F | GCGGCCAGCTCACTTCAAACGTATC | |
| metR-OUT-R | GCCGATCTTGCTGTCTTTAGCTATG | |
| metR-IN-F | AGCTAAAACATTTGCGGACACTCAC | |
| metR-IN-R | CGCGGTTGCGAAAAAAGCTTGTAAG | |
| 18672-Flag-F | CCATACCCGTTTTTTTGGGCTAGCGAATTCACAGGAGGAATTAACCATGAAATTAGATGACTTAAACCTG | 18672 expressed in pBAD33-mob |
| 18672-Flag-R1 | TCGTCGTCCTTGTAGTCTGAGCCACCGCCACCGTTGTTCACTTTTAGCTTTTGGAAG | |
| 18672-Flag-R2 | GGTCAGCATGGGTACCTTTCTCCTCTTTAATTACTTGTCGTCGTCGTCCTTGTAGTCTGA | |
| 18672-Flag2-F | AGAGGACACAATGGATAAATTAACAAGCATGAAGG | |
| pBAD33mob-C'Flag-R | CTTGCATGCCTGCAGGTCGATTACTTGTCGTCGTCGTCCTTGTAGTCTGA | |
| P18672-luxAB-F | ATTGCTGCAGGTCGACGGATCCGGGGAATTCAGCAACCGCGTACAGTTCACTCTT | Fluorescence assay |
| P18672-luxAB-R | GTCGACCTGCAGCCCAAGCTTATCGATTCGTACACACCCAGAGTTGATAAAG | |
| PaphA-luxAB-F | ATTGCTGCAGGTCGACGGATCCGGGGAATTAGCAGAGCTGCTATACCGCACGCGT | |
| PaphA-luxAB-R | GTCGACCTGCAGCCCAAGCTTATCGATTCGGCTACTTATACTTTCAGCTGCGCTC | |
| luxAB-pDM8-P4 | GTCGACCTGCAGCCCAAGCTTATCGATTCGTTACGAGTGGTATTTGACGATGTTG | |
| P18672-F | TGCCTGCAGGTCGACGATTCGGCATTCATTTTCAGTTCGGCGG | EMSA or DNase I footprinting |
| P18672-R | CATGGTCGGTGAAATATCAAAGTGG | |
| PluxR-F | AGTCGCACGCAAACGATCACC | |
| PluxR-R | ATCCATTTTCCTTGCCATTTG | |
| PaphA-F | ACTCCCGGGAGCAGAGCTGCTATACCGCACGCGT | |
| PaphA-R | ACTCCCGGGGCTACTTATACTTTCAGCTGCGCTC | |
| Pasp-F | TGCCTGCAGGTCGACGATAATCCATTCAGCATAGCAATCG | |
| Pasp-R | TTGCCCTATTCCTTATTTGAGC | |
| PluxRΔCBS-1 | CATCTGTAGAACAATTTATATACAG | PluxR ΔCBS |
| PluxRΔCBS-2 | TGATTATTTTAATAGTTGCTTAAAGCAGTGACATCTGTAGAACAATTTA | |
| PluxRΔCBS-3 | ATCCATTTTCCTTGCCATTTGAGTTGATATTGGGGGTAACCCCCTAATTGATTATTTTAATAGTTGCTT | |
| PaphAΔCBS-1 | AATTACCCTAAGTTTTTTATTCTTTTATTTTGGTAT | PaphA ΔCBS |
| PaphAΔCBS-2 | ATAAAAAACTTAGGGTAATTTTGTCCTACTATTC | |
| PaspΔCBS-1 | GATCATTCAATTAAAAATTATCTACAAAACCTTATAAAGC | Pasp ΔCBS |
| PaspΔCBS-2 | GATAATTTTTAATTGAATGATCTTTTGTACAAATTTG | |
| P18672ΔCBSI/II-1 | GAAATAACTAAAATTACAGTGGACGTATGATTAAGAA | P18672 ΔCBSI/II |
| P18672ΔCBSI/II-2 | CGTCCACTGTAATTTTAGTTATTTCATGGATAAATTAACAAGCATGAAGG | |
| P18672MRBS-1 | TCCGTATCAAGCATCGGAGCCAGAACCACAACGTGTGATT | P18672MRBS |
| P18672MRBS-2 | GCTTGATACGGATAGGTACCGCACCCCGCTTCGCTTTG | |
| P18672MABS-1 | GGTCGCGTACCCTATCAGCGGGGTGCTTGCAAGCGAAT | P18672MABS |
| P18672MABS-2 | GATAGGGTACGCGACCGGCAAAATTGTTCAATGGCTTCAACCA | |
| P18672MCBSI-1 | TACTCTGGGCGACCGACCCGTCTTGGCATTACAGTGGACGTATGATT | P18672MCBSI |
| P18672MCBSI-2 | CGGTCGCCCAGAGTATTTAGTTATTTCTTTATCAAC | |
| P18672MCBSII-1 | GTACACAAACTCTGGTCGCCCGAAATAACTAAAGCAGAGTT | P18672MCBSII |
| P18672MCBSII-2 | ACCAGAGTTTGTGTACATGGATAAATTAACAAGCATGA | |
| aphA-RT-F | GAAAGCAAGCCACCAACAGG | qRT-PCR |
| aphA-RT-R | CGACCAGCGTCTGTAATGGA | |
| luxR-RT-F | CCTACACGCGAAGACTTGGT | |
| luxR-RT-R | TCTTGGCTGACAAGCTCGAT | |
| 18672-RT-F | CCTTGAGCAACATGCCCCTA | |
| 18672-RT-R | ATCGGGTGTTGCTGTTTCCA | |
| asp-RT-F | TGCTCAGCGAAACGACTTCA | |
| asp-RT-R | TAGTACCAGCAACGCGGTTT | |
| 16sRNA-F | AAAGCACTTTCAGTCGTGAGGAA | |
| 16sRNA-R | TGCGCTTTACGCCCAGTAAT | |
| RACE-adapter | GCGCGAATTCCTGTAGAACGAAC | 5′-RACE |
| 18672-RACE-nested-1 | ACGGTTGATCAGCGTCTGG | |
| 18672-RACE-nested-2 | GATCAGCGTCTGGATCAGGTT | |
| 18672-RACE | TTACAGTTCCGGTTGGACGG | |
| RNA-Linker | AUAUGCGCGAAUUCCUGUAGAACGAACACUAGAAGAAA | |
| pBXcmT-F | CCTCGGACTGAACACGTTGGCT | BIH |
| pBXcmT-R | GTGTAAAGCCCGGGGTGCCTAA | |
| pTRG-LuxR-F | CGGGATCCATGGCAAGGAAAATGGATATGGACT | |
| pTRG-LuxR-R | CGGAATTCACAGCAGACAATAAAAAGCCCA | |
| pTRG-18672-F | CGGGATCCATGGATAAATTAACAAGCATGA | |
| pTRG-18672-R | CGGAATTCTTATGGATTCACATGAGAAAGA | |
| pTRG-02325-F | CGGGATCCATGGAAATCGCACAGTCATTAC | |
| pTRG-02325-R | CGGAATTCTTACAACGTGTTGAGGACATCC | |
| pTRG-06711-F | CGGGATCCATGAACTTAACTCAAGTAGAAG | |
| pTRG-06711-R | CGGAATTCTTAGAAGTCAAATAAATACTCG | |
| pTRG-AsnC-F | CGGGATCCATGAAATTAGATGACTTAAACCTG | |
| pTRG-AsnC-R | GGAATTCGTGAATGTTATAAGCGATCA | |
| pTRG-01665-F | CGGGATCCATGTCTTTTGCCCAACGCCTAGCCA | |
| pTRG-01665-R | CGGAATTCTCAAAGTGACTCGTTTTTAGATTCT | |
| pTRG-MetR-F | CGGGATCCATGATAGAGCTAAAACATTTGC | |
| pTRG-MetR-R | CGGAATTCTTAAGCCACCTTGATTCCGTCA | |
| pTRG-SoxR-F | CGGGATCCATGGAAATCAGCGTAGGAGAAG | |
| pTRG-SoxR-R | CGGAATTCCTACTCTTCTTCTAACGTTAAG | |
| pTRG-F | TGGCTGAACAACTGGAAGCT | |
| pTRG-R | ATTCGTCGCCCGCCATAA |