TABLE 2.
Primers used in this study
| Primer function or corresponding gene | Sequencea (5′-3′) |
|---|---|
| Primers for gene deletion | |
| atmB up | CAGTTATACTAAAGAGCGTGCC |
| CCAACCAACCAACCAACCGCTAAAGCCAATCCTAAAAGACC | |
| atmB down | CTGTTGAAGCAGATTCTTCAGCTCC |
| CCTTCCTTCCTTCCTTCCCTGCCAAAGGCGTTGATGAACCTG | |
| atmBCDE up | CAGTTATACTAAAGAGCGTGCC |
| CCAACCAACCAACCAACCGCTAAAGCCAATCCTAAAAGACC | |
| atmBCDE down | CCTGTCCGACACGATTAACAGC |
| CCTTCCTTCCTTCCTTCCCGCTAACTCGAAAAGTAAGTCATCG | |
| cysD up | GGAATCACGCGAGCGGAACAAATGC |
| CCAACCAACCAACCAACCCTCCATTCTACTCCATTATTCGGT | |
| cysD down | GCGATGGCTCTAACAGGAGAACCTG |
| CCTTCCTTCCTTCCTTCCCGAAGATTTGCGCCTAGCACTTGA | |
| metE up | GTCAACATTCCAATGGCAGCTATC |
| CCAACCAACCAACCAACCGTCATTTCGTCCTCCTCTTAGCC | |
| metE down | CATTACCAAGTTACTAAAAGCTTCC |
| CCTTCCTTCCTTCCTTCCGCTGCAACTAAGGAAGTTCGTC | |
| metR up | CTTCCAAAATCACCGCATCTTTGTTGGC |
| CCAACCAACCAACCAACCACGCATGCCTTTATTTTAGCACA | |
| metR down | GCTTAATGTTGATTTTCTCTTTCAGAAC |
| CCTTCCTTCCTTCCTTCCTAGTATGCAAAAAGGCGACAGC | |
| smu.1487 up | CAACCGTCAGGTCAAACAAGCG |
| CCAACCAACCAACCAACCGTGTCATATACATGCCTCTTTCTAG | |
| smu.1487 down | GTCAACTGCGGTAGATGAATCAG |
| CCTTCCTTCCTTCCTTCCCAAACAAGGCCAAGAAATCGCTAAG | |
| Primers for gene amplification | |
| eryR | GGTTGGTTGGTTGGTTGGCAGCAAAGAATGGCGGAAACG |
| GGAAGGAAGGAAGGAAGGCTACATTCCCTTTAGTAACGTG | |
| metR-His8 | TTGTGCTAAAATAAACATATGCGTATTCAACAG |
| AATAAAAAATGCATCTACTAATGGTGATGGTGATGGTGATGGT GTTTATCAAATTTAACTTCT | |
| Primers for QRT-PCR analysis of S. mutans | |
| atmB | GCTCGTAATTTAGCATCCGTTG |
| CCATTGTTTAGAGCCTTCGTTC | |
| cysD | GCGTGCAGTACCAATCTATCAG |
| CGGCTGTAGTCGGATTAGTGAT | |
| metA | GAATATGACCGAGAAACCTTGG |
| CGAGATTCCAACGCATAATAGG | |
| metE | TGGGTCCAATCTTATGGTTCTC |
| CAGGACGATCAGTCAGACTTTG | |
| metR | TGACCAGGGTATCCATAACTCC |
| ATAGCCGTCAAGACCAATCATC | |
| luxS | AGTTTGGACCTAAAGGCGATCT |
| TGACGAATCAGCTTAGCCAGTA | |
| urk | AGCGCGGTCGTAGTTTAGATAG |
| AACGAGATTGCTGACACCTTCT | |
| smu.1387c | ACTCTGCCAATACAGCCATGAT |
| AGCAATGCTAGTATCACGCTCA | |
| smu.1486c | GATGAAGTGGCAGATATGGACA |
| ATCAACCGTCAGGTCAAACAAG | |
| smu.1487 | GTTGGATCTCTTCTTCGTCCAG |
| TCTGCTGTTTCTGTTTCACGAT | |
| smu.1936c | GTTTGGCAGGTGTTATGATTGA |
| TAGTTGTTTCTGCCGTCTGATG | |
| tuf | CAGCGTCGATTGAAGCGTAGTC |
| TTACGGAACATTTCAACACCAG | |
| Primers for QRT-PCR analysis of S. thermophilus | |
| atmB | GAATTGGCTAAAGACAAGGGTG |
| GGAAAGCATTAACGTCGATTTC | |
| metE | AGATTACACACGTTTACCGGCT |
| CTTAGTTTGAGGGAATGAACCG | |
| tuf | CATTGGTACAATCGGACACGTTG |
| CAGCGTCGATTGAAGCGTAGTC | |
| Primers for promoter amplification | |
| metE | GTCAACATTCCAATGGCAGCTATC |
| GTCATTTCGTCCTCCTCTTAGCC | |
| metE with box 1 deletion | GTCAACATTCCAATGGCAGCTATC |
| AGTATTTGTTACAGTTTTCATCTCTAA | |
| GTCATTTCGTCCTCCTCTTAGCC | |
| TTAGAGATGAAAACTGTAACAAATACT | |
| metE with box 2 deletion | GTCAACATTCCAATGGCAGCTATC |
| GTATATGTACAGTTTTAAGCTCTATATG | |
| GTCATTTCGTCCTCCTCTTAGCC | |
| CATATAGAGCTTAAAACTGTACATATAC | |
| metE with box 1 and 2 deletions | GTCAACATTCCAATGGCAGCTATC |
| GTACAGTTTTAAGCTCTATATGTAGTAT | |
| TTGTTACAGTTTTCATCTCTAA | |
| GTCATTTCGTCCTCCTCTTAGCC | |
| TTAGAGATGAAAACTGTAACAAATACTA | |
| CATATAGAGCTTAAAACTGTAC | |
| metE with box 1 and 2 and P2 deletions | GAACCTGAAATGTTTTTGAATACAAG |
| GTCAACATTCCAATGGCAGCTATC | |
| metE with P2 deletion | GTTTCAAGGGTTTTTGTGTTTTTATG |
| GTCAACATTCCAATGGCAGCTATC | |
| Primers for transcription start site mapping | |
| atmB | GCTTTATTCGGCTGTGAATAATCTG |
| CGGACTGATATATGTCTCAGCTAC | |
| cysD | CTGCTGCCATACCAGAAGCTGTTG |
| GATGAGCAGTATCGCCAATTTGCC | |
| metA | CAAGATACTCATGGGCCGAATATCC |
| GAATGATGACTCGTCATGTAGAG | |
| metE | GACCATTCGGGAACAATATAGTG |
| GTCTAAACGCAGTTCCTTAGCACCAGC | |
| urk | CACTGCGTGTATGCTGTGTGTAGTC |
| CGAATGTCATCATCGGTATCAAC | |
| smu.1387 | GGCAGCTTGCCTGCCAGTAAATCCTTC |
| GGATAGGAATTCCTTAATAAGAAGGAG | |
| smu.1486c | GCTAGGTTGTGGTCGATCATCTTGTG |
| CAACCGTCAGGTCAAACAAGCG | |
| smu.1487 | GTGTAGCCGTGGTCTGCAATGTAACG |
| TCTGCTGTTTCTGTTTCACGAT | |
| smu.1936c | CCTGTCTGAGCCAACTCCCGGATC |
| CGTTTAGTCGCTACAGATCCAGC | |
| Primers for gel retardation probe | |
| atmB | CCTTGGAGGAAGCTATCTTCCAG |
| GCTAAAGCCAATCCTAAAAGACC | |
| cysD | TAGCGTTCACGGGATTAGAC |
| GCTCTCCTTTTATTATTAATTAGCTCC | |
| cysK | GTTAACACTACTATTTATGTGG |
| CTTCAGGAACAACATTGTTGAG | |
| metA | GGCAACCATTGAAATGATTGAAAGG |
| GAGTAATTGGCATGAAAATATCTCC | |
| metE | GTCACTTGAAATGATAAGAGGAG |
| GTCATTTCGTCCTCCTCTTAGCC | |
| metR | CCTTACCAACTAACTGGCAAGGTTAC |
| GGCAGCCTCATTCATGCTGCCAG | |
| smu.1487 | GTGTGTAAATGGTTATCGCG |
| GTCAAGCAGATCAGCTGGAC | |
| metE with box 1 and 2 deletions | GTCACTTGAAATGATAAGAGGAG |
| GTACAGTTTTAAGCTCTATATGTAGTAT | |
| TTGTTACAGTTTTCATCTCTAA | |
| GTCATTTCGTCCTCCTCTTAGCC | |
| TTAGAGATGAAAACTGTAACAAATACT | |
| ACATATAGAGCTTAAAACTGTAC |
a
Upper and lower sequences correspond to primer pairs.