TABLE 1

Bacterial strains and plasmids used in this study

Strain or plasmidDescriptionReference or source
Strain name or genotype
    Clostridium difficile
        630Epidemic type X38
        630 ΔermErythromycin-sensitive mutant of C. difficile 63087
        pilA1630 Δerm CD3513-474s::CTThis study
        pilB1630 Δerm CD3512-786s::CTThis study
        sigD630 Δerm CD0266-228s::TTThis study
    E. coli CA434HB101 carrying plasmid R70288
Plasmids
    pCR2.1-TATA cloning vectorLife Technologies
    pCR2.1-Rb3513srpCR2.1-TA with transcription template for Cdi2_4 c-di-GMP-II riboswitchThis study
    pCR2.1-Rb3513sr-a70cpCR2.1-Rb3513 with A-to-C substitution at nucleotide 70This study
    pCR2.1-Rb3513sr-a70gpCR2.1 with with A-to-G substitution at nucleotide 70This study
    pMTL007C-E5-CD3513-474/475spMTL007C-E5 with the Ll.ltrB intron retargeted to insert after base 474 in the 630 Δerm CD3513 ORFThis study
    pMTL007C-E5-CD3512-786/787spMTL007C-E5 with the Ll.ltrB intron retargeted to insert after base 786 in the 630 Δerm CD3512 ORFThis study
    pBL64pCR2.1-intron template part A48
    pBL65pCR2.1-intron template part B48
    pBL100::sigD::ermBpBL100 with the group II intron-TargeTron (TT) retargeted to insert after base 228 in the 630 Δerm CD0266 ORFThis study
    pMC-PcprcprK promoter cloned into pMC123 E. coli- C. difficile shuttle vector; bla catP31
    pDccApMC-Pcpr with DccA downstream of Pcpr31
    pDccAmutpMC-Pcpr with DccA(AADEF) downstream of Pcpr31
    pDccA-RB-pilA1pDccA with CD3513 and 497 bp upstream including the Cdi2_4 riboswitchThis study
    pDccAmut -RB-pilA1pDccAmut with CD3513 and 497 bp upstream including the c-di-GMP riboswitchThis study
    pDccA-RBA70C-pilA1pDccA-RB-pilA1 with - to-C substitution at nucleotide 70 in Cdi2_4This study
    pDccA-RBA70G-pilA1pDccA-RB-pilA1 with A-to-G substitution at nucleotide 70 in Cdi2_4This study
    pDccA-RB-pilA1G9YpDccA-RB-pilA1 with G- to-Y substitution at amino acid 9 in PilA1This study