TABLE 1.
Bacterial strains and plasmids used in this study
| Plasmid or strain | Relevant genotype or feature(s) | Source, construction, or reference |
|---|---|---|
| Plasmids | ||
| pRK24 | Tra+ Mob+ bla, tet | 78 |
| pJK02 | E. coli-C. difficile shuttle vector; catP, cas9, pyrE sgRNA, pyrE homology region | 40 |
| pMC123 | E. coli-C. difficile shuttle vector; bla catP | 29 |
| pMC211 | pMC123 PcprA | 77 |
| pMC358 | pMC123 ::phoZ | 75 |
| pMC367 | pMC123 PcprA-rstA (CD3668) | 14 |
| pMC533 | pMC123 PcprA-rstA (C. sordellii ATCC 9714) | This study |
| pMC543 | pMC123 PrstA489::phoZ | 14 |
| pMC559 | pMC123 PrstAA-27T::phoZ | This study |
| pMC560 | pMC123 PrstAT-23A::phoZ | This study |
| pMC561 | pMC123 PrstAT-19A::phoZ | This study |
| pMC562 | pMC123 PrstAA-18T::phoZ | This study |
| pMC563 | pMC123 PrstAT-17A::phoZ | This study |
| pMC573 | pMC123 PrstAA-27C::phoZ | This study |
| pMC574 | pMC123 PrstAA-24G::phoZ | This study |
| pMC575 | pMC123 PrstAA-21C::phoZ | This study |
| pMC576 | pMC123 PrstAT-19G::phoZ | This study |
| pMC660 | pMC123 PrstA115::phoZ | This study |
| pMC675 | pMC123 PcprA-rstA-3XFLAG | This study |
| pMC676 | pMC123 PrstAIR(380 bp)::phoZ | This study |
| pMC677 | pMC123 PrstA231::phoZ | This study |
| pMC678 | pMC123 PrstA291::phoZ | This study |
| pMC682 | pMC123 PcprA-rstAΔHTH-3XFLAG | This study |
| pMC713 | pMC123 PtcdR::phoZ | This study |
| pMC726 | pJK02 with rstA homology region | This study |
| pMC729 | pMC726 with rstA sgRNA (oMC1724) | This study |
| pMC752 | pMC123 PtcdR(σA-92 bp)::phoZ | This study |
| pMC753 | pMC123 PtcdR(σD)::phoZ | This study |
| pMC754 | pMC123 PtcdR(P2 σTcdR)::phoZ | This study |
| pMC755 | pMC123 PtcdR(P1 σTcdR)::phoZ | This study |
| pMC780 | pMC123 PcprA-rstA (C. perfringens S13) | This study |
| pMC787 | pMC123 PcprA-rstA (C. acetobutylicum ATCC 824) | This study |
| pMC795 | pMC123 PtcdA::phoZ | This study |
| pMC796 | pMC123 PtcdB::phoZ | This study |
| pMC798 | pMC123 PcprA-rstACpHTHCdCterminal-3XFLAG | This study |
| pMC812 | pMC123 PtcdR(σA-76 bp)::phoZ | This study |
| pMC817 | pRT1824 PflgB (630)::phoZ | This study |
| pMC818 | pRT1824 PflgB (R20291)::phoZ | This study |
| pMC828 | pMC123 PcprA-rstA-3XFLAG (C. acetobutylicum ATCC 824) | This study |
| pMC829 | pMC123 PcprA-rstA-3XFLAG (C. perfringens S13) | This study |
| pMC830 | pMC123 PcprA-rstA-3XFLAG (C. sordellii ATCC 9714) | This study |
| pMC888 | pMC123 PrstA::phoZ PcprA-rstA-3XFLAG | This study |
| pMC889 | pMC123 PrstAT-19A/A-21C::phoZ | This study |
| pRPF144 | pMLT960 Pcwp2-gusA | 79 |
| pRT1824 | pMLT960 ::phoZ | This study |
| pSigD | pMC123 PcprA-sigD | 11 |
| E. coli strains | ||
| HB101 pRK24 | F− mcrB mrr hsdS20(rB− mB−) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20 pRK24 | B. Dupuy |
| C. difficile strains | ||
| 630Δerm | Erms derivative of strain 630 | Nigel Minton; 80 |
| MC282 | 630Δerm pMC211 | 77 |
| MC310 | 630Δerm spo0A::erm | 77 |
| MC391 | 630Δerm rstA::erm | 14 |
| MC448 | 630Δerm pMC358 | 75 |
| MC480 | 630Δerm rstA::erm pMC367 | 14 |
| MC505 | 630Δerm rstA::erm pMC211 | 14 |
| MC506 | 630Δerm sigD::erm pMC211 | This study |
| MC762 | 630Δerm rstA::erm pMC533 | This study |
| MC773 | 630Δerm pMC543 | 14 |
| MC774 | 630Δerm rstA::erm pMC543 | 14 |
| MC830 | 630Δerm pMC559 | This study |
| MC831 | 630Δerm rstA::erm pMC559 | This study |
| MC832 | 630Δerm pMC560 | This study |
| MC833 | 630Δerm rstA::erm pMC560 | This study |
| MC834 | 630Δerm pMC561 | This study |
| MC835 | 630Δerm rstA::erm pMC561 | This study |
| MC836 | 630Δerm pMC562 | This study |
| MC837 | 630Δerm rstA::erm pMC562 | This study |
| MC838 | 630Δerm pMC563 | This study |
| MC839 | 630Δerm rstA::erm pMC563 | This study |
| MC856 | 630Δerm pMC573 | This study |
| MC857 | 630Δerm rstA::erm pMC573 | This study |
| MC858 | 630Δerm pMC574 | This study |
| MC859 | 630Δerm rstA::erm pMC574 | This study |
| MC860 | 630Δerm pMC575 | This study |
| MC861 | 630Δerm rstA::erm pMC575 | This study |
| MC862 | 630Δerm pMC576 | This study |
| MC863 | 630Δerm rstA::erm pMC576 | This study |
| MC979 | 630Δerm pMC660 | This study |
| MC980 | 630Δerm rstA::erm pMC660 | This study |
| MC1004 | 630Δerm rstA::erm pMC675 | This study |
| MC1008 | 630Δerm pMC676 | This study |
| MC1009 | 630Δerm rstA::erm pMC676 | This study |
| MC1010 | 630Δerm pMC677 | This study |
| MC1011 | 630Δerm rstA::erm pMC677 | This study |
| MC1012 | 630Δerm pMC678 | This study |
| MC1013 | 630Δerm rstA::erm pMC678 | This study |
| MC1028 | 630Δerm rstA::erm pMC682 | This study |
| MC1088 | 630Δerm pMC713 | This study |
| MC1089 | 630Δerm rstA::erm pMC713 | This study |
| MC1118 | 630Δerm ΔrstA | This study |
| MC1133 | 630Δerm pMC729 | This study |
| MC1143 | 630Δerm pMC752 | This study |
| MC1144 | 630Δerm rstA::erm pMC752 | This study |
| MC1145 | 630Δerm pMC753 | This study |
| MC1146 | 630Δerm rstA::erm pMC753 | This study |
| MC1147 | 630Δerm pMC754 | This study |
| MC1148 | 630Δerm rstA::erm pMC754 | This study |
| MC1149 | 630Δerm pMC755 | This study |
| MC1150 | 630Δerm rstA::erm pMC755 | This study |
| MC1193 | 630Δerm sigD::erm pMC729 | This study |
| MC1224 | 630Δerm ΔrstA pMC211 | This study |
| MC1225 | 630Δerm ΔrstA pMC367 | This study |
| MC1249 | 630Δerm pMC795 | This study |
| MC1250 | 630Δerm rstA::erm pMC795 | This study |
| MC1251 | 630Δerm pMC796 | This study |
| MC1252 | 630Δerm rstA::erm pMC796 | This study |
| MC1257 | 630Δerm rstA::erm pMC798 | This study |
| MC1278 | 630Δerm ΔrstA sigD::erm | This study |
| MC1281 | 630Δerm ΔrstA sigD::erm pMC211 | This study |
| MC1282 | 630Δerm ΔrstA sigD::erm pMC367 | This study |
| MC1283 | 630Δerm ΔrstA sigD::erm pSigD | This study |
| MC1285 | 630Δerm pMC812 | This study |
| MC1286 | 630Δerm rstA::erm pMC812 | This study |
| MC1294 | 630Δerm pMC817 | This study |
| MC1295 | 630Δerm rstA::erm pMC817 | This study |
| MC1296 | 630Δerm pMC818 | This study |
| MC1297 | 630Δerm rstA::erm pMC818 | This study |
| MC1323 | 630Δerm rstA::erm pMC828 | This study |
| MC1324 | 630Δerm rstA::erm pMC829 | This study |
| MC1325 | 630Δerm rstA::erm pMC830 | This study |
| MC1433 | 630Δerm pMC889 | This study |
| MC1434 | 630Δerm rstA::erm pMC889 | This study |
| MC1435 | 630Δerm rstA::erm pMC888 | This study |
| RT1075 | 630Δerm sigD::erm | 81 |
| Other strains | ||
| ATCC 824 | Clostridium acetobutylicum | ATCC |
| ATCC 9714 | Clostridium sordellii | ATCC |