TABLE 2.

Primers used in this study

PrimerCloneGene designationaFragment sizeb (bp)Sequencec
Promoter fusions and EMSA
    CD6.1-A1CD-1Zn-dependent alcohol dehydrogenase244*5′-GGCGTCGACGTTGGATCACTACCAGC-3′
    CD6.1-A25′-GGCGGATCCGGGGAATTCAGTAGCAG-3′
    CD6.2-A2CD-2secY330*5′-GGCGGATCCGCCATGAGTGGCAACTCC-3′
    CD6.2-B15′-GGCGTCGACGCTAAAACCGTGGCTGG-3′
    CD6.2-C1CD-2secY5265′-GGCGTCGACGCCATGAGTGGCAACTCC-3′
    CD6.2-C25′-GGCGGATCCCCGCATCTCGGAATGCC-3′
    CD6.3-A1CD-3Transcriptional regulator of ABC iron transport system4955′-GGCGTCGACTTCCTAGAAATAGCAGG-3′
    CD6.3-A25′-GGCGGATCCCCTTCTTAGCGGGAGCC-3′
    CD6.3-B1243*5′-GGCGTCGACCGCTATTGAAGAACTGTG-3′
    CD6.4-A1CD-4recA5695′-GGCGTCGACGCAGATACTGTACTGCG-3′
    CD6.4-A25′-GGCGGATCCGTTGGTTGCTGCGTCTTAC-3′
    CD6.4-B1342*5′-GGCGTCGACCTGGTTTGATTTGTGCG-3′
    CD7.4-A1CD-7-4ywjA380*5′-GGCGTCGACCGAACATATATGACCGACC-3′
    CD7.4-A25′-GGCGGATCCGATCGCACAGTTGAGTCC-3′
    CD7.20-A1CD-20piuB150*5′-GGCGTCGACCATAACGTTGAAATATAGAC-3′
    CD7.20-A25′-GGCGGATCCCTGCTTCTCGGCGGACG-3′
    CD7.40-A1CD-40chtA211*5′-GGCGTGGACGAGTTGTGGTCTAGGTGG-3′
    CD7.40-A25′-GGCGGATCCCAAAGACGTAAGTGTTGC-3′
    HtaA-1CD-50htaA319*5′-GGCGGATCCGCAGCAGCCATTAGTCC-3′
    HtaA-25′-GGCGTCGACGGGGAGGCTGTGGGCAGG-3′
    HtaC-1CD-50htaC3195′-GGCGGATCCGGGGAGGCTGTGGGCAGG-3′
    HtaC-25′-GGCGTCGACGCAGCAGCCATTAGTCC-3′
    FrgA-1CD-frgfrgA236*5′-GGCGGATCCATGATTACAAGGAAAGTG-3′
    FrgA-25′-GGCGTCGACCTTGAGCGTTAGTCGAGG-3′
    FrgD-1CD-frgfrgD2365′-GGCGTCGACATGATTACAAGGAAAGTG-3′
    FrgD-25′-GGCGGATCCCTTGAGCGTTAGTCGAGG-3′
    SidA-1CD-sidsidA499*5′-GGCGTCGACCGGGGCCGGTGGCGGCG-3′
    SidA-25′-GGCGGATCCGGCGGTGAGAATTTCGG-3′
    TprT-1CD-sidTranscriptional regulator4995′-GGCGGATCCCGGGGCCGGTGGCGGCG-3′
    TprT-25′-GGCGTCGACGGCGGTGAGAATTTCGG-3′
Vector integration mutants
    SidA-C1CD-sidC-terminal sidA mutant7115′-GGCGGATCCCGTCCACtACTGAGCAACGAT-3′
    SidA-C25′-GGCGTCGACGGCGAATTCGCATaGTTCCAATTGCGTGCA-3′
    SidA-2CD-sidN-terminal sidA mutant8195′-GGCGTCGACGGCGAATTCGCCATATAgGGCCCCGTCGACCC-3′
    SidA-35′-GGCGGATCCGTCcTAAGTCATCTCGGCTAG-3′
    SidB-1CD-sidsidB mutant8105′-GGCGTCGACGGCGAATTCGAATGCtGATTCCCAGGCATCC-3′
    SidB-25′-GGCGGATCCCACCTaAGCATGTGCGTGCATCGA-3′
    CdtP-2CD-sidcdtP mutant6305′-GGCGTCGACGGCGAATTCCGCTAgATCCACGGACGCTGGCCG-3′
    CdtP-35′-GGCGGATCCGTCCTaACCCACGCGGTTGAACAC-3′
  • a The first gene in the operon is specified.

  • b Asterisks indicate PCR product was used in EMSA.

  • c Bold letters identify restriction sites and lowercase letters identify base changes to insert in-frame stop codons.