TABLE 1.

Bacterial strains, plasmids, cosmids, and oligonucleotides used in this study

Strain, plasmid, cosmid, or oligonucleotideRelevant characteristic(s), description, or sequenceReference and/or source
Strains
    HE300Positive for papA papC fimH fyuA iroN iha bmaE gafD issThis study; UPEC isolatea
    DH10BF mcrAΔ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 ΔlacX74 endA1 recA1 deoR (ara leu)7697 araD139 galU galK nupG rpsL λInvitrogen
    S17-1Streptomycin resistance (Strr); trimethoprim resistance (Tmpr); λpir; hsdR pro recA23
    XL-1 Blue MR′Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 supE44 thi-1 recA1 gyrA96 relA1 lacStratagene
    TH2supE44 hsdS20 (rBmB) recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1 thi trpR624Takara Shuzo Co., Ltd.
    TH2 specSpontaneous spectinomycin mutantThis study
    H5058aroB malT tsx thi cir fiu fepA4
Plasmids and cosmids
    p300Wild-type plasmid of E. coli HE300; Tcr; Tpr; carrying iroBCDEN genesThis study
    SuperCos 1Cosmid vector; 7.6 kb; Apr KmrStratagene
    pJS332SuperCos 1 with 31.7 kb of p300 carrying iroBCDEN genesThis study
    pCR4-TOPOTA cloning vector; 3.9 kb; Apr KmrInvitrogen
    pJS11pCR4-TOPO with 196-bp fragment of subtractive cloning (AA107)This study
    pJS12pCR4-TOPO with 3.8 kb of p300 carrying iroEN genesThis study
    pJS13pCR4-TOPO with 8.6 kb of p300 carrying iroBCDE genesThis study
    pJS14pJS12 with 0.8-kb Tpr cassette in iroN geneThis study
    pJS15pJS12 with 0.8-kb Tpr cassette in iroE geneThis study
Oligonucleotides (position [nt])
    ydfB.for (6808)5′-ATATCACGGGAAAGGAAGCAC-3′This study
    ydfB.rev (7215)5′-GTCCGGCAAGGTTTATCA-3′This study
    ORF14.for (12886)5′-TGGTCAGGTTGCGGAGGCTAT-3′This study
    iroN1.for (13464)5′-CCGACGATGATAATGACGAGA-3′This study
    iroN.rev (13806)5′-TGTTCCGGTGGCACCCAGTTG-3′This study
    iroN2.for (14668)5′-AGATAACATTGAGCCGGTTCC-3′This study
    iroE.for (15734)5′-GCATTGACGCCTTTATCTTTC-3′This study
    iroD.rev (16680)5′-CTGATTGACGGGATTGGTT-3′This study
    ORF20. rev (23257)5′-GCGAAGGCGAGACTATCAGGA-3′This study
    iroB.for (22565)5′-CGAGCGGAGGGTAGATGATGA-3′This study
  • a UPEC, uropathogenic E. coli.