TABLE 1.
Bacterial strains and plasmids used in this study
| Strain or plasmid | Relevant characteristic(s) | Source or reference |
|---|---|---|
| E. coli DH5α | φ80 lacZΔM15 ΔlacU169 recA1 endA1 hsdR17 supE44 thi-1 gyrA relA1 | 16 |
| M. xanthus | ||
| DK1622 | Wild type | 22 |
| MDB01 | attB::pDB01 | 8 |
| MDY1727 | attB::pREG1727 | 56 |
| MDY101 | attB::pDY101 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY100)a | This study |
| MDY103 | attB::pDY103 (pREG1727 with 121-bp XhoI-BamHI fragment from pDO2) | This study |
| MDY104 | attB::pDY104 (pREG1727 with 111-bp XhoI-BamHI fragment from pDO3) | This study |
| MDY40 | attB::pDY40 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY39) | This study |
| MDY42 | attB::pDY42 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY41) | This study |
| MDY44 | attB::pDY44 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY43) | This study |
| MDY46 | attB::pDY46 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY45) | This study |
| MDY48 | attB::pDY48 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY47) | This study |
| MDY50 | attB::pDY50 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY49) | This study |
| MDY52 | attB::pDY52 (pREG1727 with 150-bp XhoI-BamHI fragment from pDY51) | This study |
| MDY106 | attB::pDY106 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY105) | This study |
| MDY108 | attB::pDY108 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY107) | This study |
| MDY110 | attB::pDY110 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY109) | This study |
| MDY112 | attB::pDY112 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY111) | This study |
| MDY114 | attB::pDY114 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY113) | This study |
| MDY116 | attB::pDY116 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY115) | This study |
| MDY118 | attB::pDY118 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY117) | This study |
| MDY120 | attB::pDY120 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY119) | This study |
| MDY122 | attB::pDY122 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY121) | This study |
| MDY124 | attB::pDY124 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY123) | This study |
| MDY126 | attB::pDY126 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY125) | This study |
| MDY128 | attB::pDY128 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY127) | This study |
| MDY130 | attB::pDY130 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY129) | This study |
| MDY132 | attB::pDY132 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY131) | This study |
| MDY134 | attB::pDY134 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY133) | This study |
| MDY136 | attB::pDY136 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY135) | This study |
| MDY138 | attB::pDY138 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY137) | This study |
| MDY140 | attB::pDY140 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY139) | This study |
| MDY142 | attB::pDY142 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY141) | This study |
| MDY144 | attB::pDY144 (pREG1727 with 268-bp XhoI-BamHI fragment from pDY143) | This study |
| DK5208 | csgA::Tn5-132 (Tcr) Ω205 | 46 |
| MDY5208-103 | csgA::Tn5-132 (Tcr) Ω205 attB::pDY103 | This study |
| MDY5208-134 | csgA::Tn5-132 (Tcr) Ω205 attB::pDY134 | This study |
| ΔsigD | ΔsigD | 51 |
| MDY4499.SD | attB::pDY101 | This study |
| ΔsigE | ΔsigE | 52 |
| MDY4499.SE | attB::pDY101 | This study |
| Plasmids | ||
| pGEM7Zf | Aprlacα | Promega |
| pREG1727 | Apr Kmr P1-inc attP ′lacZ | 9 |
| pMF0051 | pGEM7Zf with 3.2-kb PstI-BamHI fragment from pMF002 | 8 |
| pDY100 | pGEM7Zf with 268-bp fragment from −218 to +50 bp of Ω4499 DNA generated by PCR using pMF0051 as template, inserted as a XhoI-BamHI fragment | This study |
| pDO2 | pGEM7Zf with 121-bp fragment from −71 to +50 bp of Ω4499 DNA generated by PCR using pDY100 as a template, inserted as a XhoI-BamHI fragment | This study |
| pDO3 | pGEM7Zf with 111-bp fragment from −61 to +50 bp of Ω4499 DNA generated by PCR using pDY100 as a template, inserted as a XhoI-BamHI fragment | This study |
| pDY39 | pDY100 with C-to-A mutation at −36 bp | This study |
| pDY41 | pDY100 with C-to-A mutation at −32 bp | This study |
| pDY43 | pDY100 with C-to-A mutation at −31 bp | This study |
| pDY45 | pDY100 with CATTCCT-to-ACGGAAG mutation from −36 to −30 bp | This study |
| pDY47 | pDY100 with GAAC-to-TCCA mutation from −48 to −45 bp | This study |
| pDY49 | pDY100 with TCATTC-to-GACGGA mutation from −59 to −54 bp | This study |
| pDY51 | pGEM7Zf with 150-bp fragment from −100 to +50 bp of Ω4499 DNA generated by PCR using pDY100 as template, inserted as a XhoI-BamHI fragment | This study |
| pDY105 | pDY100 with CGA-to-TAT mutation from −12 to −10 bp | This study |
| pDY107 | pDY100 with T-to-G mutation at −25 bp | This study |
| pDY109 | pDY100 with T-to-G mutation at −30 bp | This study |
| pDY111 | pDY100 with T-to-G mutation at −33 bp | This study |
| pDY113 | pDY100 with T-to-G mutation at −34 bp | This study |
| pDY115 | pDY100 with A-to-C mutation at −35 bp | This study |
| pDY117 | pDY100 with C-to-A mutation at −37 bp | This study |
| pDY119 | pDY100 with T-to-G mutation at −44 bp | This study |
| pDY121 | pDY100 with CCTTC-to-AAGGA mutation from −53 to −49 bp | This study |
| pDY123 | pDY100 with TCA-to-GAC mutation from −59 to −57 bp | This study |
| pDY125 | pDY100 with CCGG-to-AATT mutation from −63 to −60 bp | This study |
| pDY127 | pDY100 with ACCA-to-CAAC mutation from −67 to −64 bp | This study |
| pDY129 | pDY100 with GGAC-to-TTCA mutation from −71 to −68 bp | This study |
| pDY131 | pDY100 with TCGCT-to-GATAG mutation from −76 to −72 bp | This study |
| pDY133 | pDY100 with GCCGC-to-TAATA mutation from −81 to −77 bp | This study |
| pDY135 | pDY100 with CATAC-to-ACGCA mutation from −86 to −82 bp | This study |
| pDY137 | pDY100 with GCGTT-to-TATGG mutation from −91 to −87 bp | This study |
| pDY139 | pDY100 with AGATT-to-CTCGG mutation from −96 to −92 bp | This study |
| pDY141 | pDY100 with CGAGG-to-ATCTT mutation from −101 to −97 bp | This study |
| pDY143 | pDY100 with CCC-to-AAA mutation from −29 to −27 bp | This study |
a
Where possible, the plasmid description is given in parentheses after the strain description.