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Table S3. Oligonucleotides used in this study. PCR target Sequence (5’-3’) Forward and reverse primer (a) Primers for PhoB-3xFLAG expressing strain (MG1655_PhoB_FLAG) phoB and pSUB11 5’-GACCGTGCGCGGTACAGGATATCGTTTTTCA phoB-pSUB11-F ACCCGCTTTGACTACAAAGACCATGACGG-3’ 5’-ATAAGCCCTGCTCTGCGTCCGATGAGCAAGG phoB-pSUB11-R CGTTAAAAGCATATGAATATCCTCCTTAG-3’ phoB phoB-check1122-F 5’-TGCCAGTCTGAGGTGTGAAG-3’ phoB-check1122-R 5’-GGCGCAATAAATTCCAGAAA-3’ (b) Primers for detection of inserts of pGL3 derivatives pGL3-basic vector pGL3_InsChk_F 5’-GGTACGGGAGGTACTTGGAGC-3’ pGL3_InsChK_R 5’-GGCCTTTCTTTATGTTTTTGGC-3’ (c) Primers for constructing PhoB-His fusion protein expressing vector phoB PhoB_His_F 5’-GCCCATGGCGAGACGTATTCTGGTCG-3’ PhoB_His_R 5’-GCAAGCTTAAAGCGGGTTGAAAAACGATATCCTG-3’ (d) Primers for constructing promoter::luciferase fusionsa phoB cusC cusR feaR mipA prpR sbcD ydfH yedX yegH phoB_FPB 5’-GCGCTAGCACGGTAGTATTGAGGAACGCC-3’ phoB_RPB 5’-GCCCATGGGATTTGCCCTGTTGTAATAAATAGG-3’ cusC_FPB 5’-GCGCTAGCCGCCAGCAGTTCAGCAAA cusC_RPB 5’-GCCCATGGAGGCTCATAATTTCTGGTGATTTTA cusR_FPB 5’-GCGCTAGCTTAAGATTACCGCTCCAGCTGC cusR_RPB 5’-GCCCATGGATTTCCTCCGCATGTTGCC feaR_FPB 5’-GCGCTAGCGTAGCAGAATACGTTCACGCTCTG feaR_RPB 5’-GCCCATGGGGCACGTTTTCGCTCTGT mipA_FPB 5’-GCGCTAGCTGCAGTGTGAACTCTTCGTCCT mipA_RPB 5’-GCCCATGGAATTAATCATTCCTTAAACAAATGTTTAG prpR_FPB 5’-GCGCTAGCTATCCGCATCCACCAGCA prpR_RPB 5’-GCCCATGGAGCGCACCGCAAAGTTAAG sbcD_FPB 5’-GCGCTAGCTGATATAGTCATCCGCGCCG sbcD_RPB 5’-GCCCATGGAACGGTTCCCTGGCGAAA ydfH_FPB 5’-GCGCTAGCCGCCGTCTTACCGGGTATG ydfH_RPB 5’-GCCCATGGTCGTTCTTGCTTGTGAGTGAGTTAA yedX_FPB 5’-GCGCTAGCGAATTCAAAGCGTGATGTTGC yedX_RPB 5’-GCCCATGGGTTTATATCCTTGTCATGTGAATGAGT yegH_FPB 5’-GCGCTAGCTGGTCTTTCAGGCATCCAGA yegH_RPB 5’-GCCCATGGAGTAAGTACAAAACCTATTCGTTGTATGA yhjC yhjC_FPB 5’-GCGCTAGCAAAGACTTAAGTAGTGGAAGGGTATTACC yhjC_RPB 5’-GCCCATGGTTCTTTGACCGATTGTTGTTCAC (e) Oligonucleotidesb for DNA binding assay mipA 5’-GCGTTACTGGCGAGCCTGGTCTTTACATT mipA_p AATTATGCAAAATTTATGGATGAGTTGTTGA-3’ 5’-TCAACAACTCATCCATAAATTTTGCATAAT mipA_c TAATGTAAAGACCAGGCTCGCCAGTAACGC-3’ yedX 5’-ATGTTATAGAAACAGCCTGGTTCATTACAA yedX_p AATTGTAATGCTGCTGTAAGGTTACCCTGG-3’ 5’-CCAGGGTAACCTTACAGCAGCATTACAAT yedX_c TTTGTAATGAACCAGGCTGTTTCTATAACAT-3’ ydfH 5’-GCGTAACTGCCGGGTTATTGCTTGTCACA ydfH_p AAAAAGTGGTAGACTCATGCAGTTAACTCAC-3’ 5’-GTGAGTTAACTGCATGAGTCTACCACTTT ydfH_c TTTGTGACAAGCAATAACCCGGCAGTTACGC-3’ cusR 5’-TGGCAATCGCTTATTGGCAAAATGACAAT cusR_p TTTGTCATTTTTCTGTCACCGGAAAATCAGA-3’ 5’-TCTGATTTTCCGGTGACAGAAAAATGACA cusR_c AAATTGTCATTTTGCCAATAAGCGATTGCCA-3’ yhjC 5’-TGAGAAATCGCCACATTCGGCATGACAAC yhjC_p ATTGTGAAACCCGGCATTAGATGTTAGAAAA-3’ 5’-TTTTCTAACATCTAATGCCGGGTTTCACAA yhjC_c TGTTGTCATGCCGAATGTGGCGATTTCTCA-3’ yegH 5’-CGATTTATCCATGATCGAATTGTGACATTT yegH_p GTCATACAACGAATAGGTTTTGTACTTACT-3’ 5’-AGTAAGTACAAAACCTATTCGTTGTATGAC yegH_c AAATGTCACAATTCGATCATGGATAAATCG-3’ feaR 5’-TCTGTGAAATGTATTTTTATTGTTGCATTT feaR_p GTGTTGCAATAAACGAAGCTAATGAGCCTG-3’ 5’-CAGGCTCATTAGCTTCGTTTATTGCAACA feaR_c CAAATGCAACAATAAAAATACATTTCACAGA-3’ prpR 5’-CCGAATATTGGGTTTAGTCTTGTTTCATAA prpR_p TTGTTGCAATGAAACGCGGTGAAACATTGC-3’ 5’-GCAATGTTTCACCGCGTTTCATTGCAACA prpR_c ATTATGAAACAAGACTAAACCCAATATTCGG-3’ yahA 5’-TATCCGCCACGGGGAGTAATAGTCACAGA yahA_p TATATTAATGATAATCACTATCACCATATCG-3’ 5’-CGATATGGTGATAGTGATTATCATTAATATA yahA_c TCTGTGACTATTACTCCCCGTGGCGGATA-3’ cof 5’-GTTTTCGTTATCAGATAATCGATGTCAAAA cof_p AAATGCCACTCGGCAGCGTCACCAAGATCT-3’ 5’-AGATCTTGGTGACGCTGCCGAGTGGCATT cof_c TTTTTGACATCGATTATCTGATAACGAAAAC-3’ yddV 5’-TTGCGATACGGTATTTCTTATCTGTAATAAA yddV_p AATTTCACCCGCAGACTTCTGTTATTCAA-3’ 5’-TTGAATAACAGAAGTCTGCGGGTGAAATT yddV_c TTTATTACAGATAAGAAATACCGTATCGCAA-3’ a For the construction of pGL3 derivative plasmids, the upstream region was around 500 bps in front of the translation start site of each gene. b For each binding candidate, complimentary oligonucleotide of 60 base pairs centered at the corresponding putative binding site were first end-labeled with biotin separately and then annealed before use.
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