Table 10.
Bacteria, plasmids and phages employed.
| Bacterial strains | Characteristics or genotype | Source/Ref.’; Hayes lab #a |
|---|---|---|
| 594 | F-lac-3350 galK2 galT22 rpsL179 IN(rrnD-rrnE)1; see [97]; called R594 | [97], SH lab; B10 |
| TC600 | supE, Pm+ | SH lab, B8 |
| Ymel | supF, Pm+ | SH lab, B71 |
| DE407 | lexA3[Ind-] malB::Tn9 TetRsulA211 sfiA11, UVS | D. Ennis; B142 |
| FC40 (=SMR624) | Δ(srlR-recA)306::Tn10 TetR UVS | SM Rosenberg [98]; Y921 |
| AB2834 aroE | grpD55, thi tsxR λR at 42 ˚C from K552 | H. Uchida [32,33]; NB83 |
| W3874 malB5 | dnaB grpA80 lac- StrR λR at 42 ˚C | [32], NB81 |
| W3350 dnaB-grpD55 | grpD55 malF3089::Tn10 TetRλR at 42°C, λrepP22S | [33], NB15 |
| 594 dnaB-grpD55 | grpD55 allele malF3089::Tn10; TetR, λR at 42°C, λrepP22S | [34], NB295 |
| 594 lexA3[Ind-] malB::Tn9 | LexA repressor induction defective | CE, NB293 |
| 594 Δ(srlR-recA)306::Tn10 | deletion of recA TetR UVS | CE, B318 |
| W3350 | F- lac-3350 galK2 galT22 rpsL179 IN(rrnD-rrnE)1 | SH lab, B12 |
| Y836 | SA500(λbio275cI[Ts]857 Δ431) his- | [78,82], NY1049 |
| 594::nadA::Tn10 [~cIII-ren]λ | Tn10 [zbh29 at 16.8 min] bio+ transductant = 594 bio275 (λcIII-cI[Ts]857-O-P-ren) Δ431 | A. Chu, SH lab, NY1057 |
| Y836 P::kan(Bib11t) | SA500 (λbio275 cI[Ts]857 O+P::kan Δ431) his- KanR | SH, NY1153 |
| 594(λcI857Sam7) | λ lysogen defective for cell lysis | C. Marek, SH lab, Y1163 |
| 594(λcI857Sam7)[pcIpR-P-timm] | as above with transformed plasmid | SH lab, P509 |
| 594 clpP::kan | clpP-, KanR from SG22159 | S. Gottesman; [99], NB276 |
| Plasmids | Transformed into strain 594 | Source/Ref.’; Hayes lab #a |
| pUC19 | Wild type AmpR (New England Biolabs) | NP188 |
| pcIpR-P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 39582-40280 | CH, P466 |
| pcIpR-P::kan-timm | PCR BamHI-ClaI fragment from Y836 P::kan(Bib11t) strain NY1153 | KM, P510 |
| PcIpR-P-SPA-timm b | Replace D in P462 between BamHI and AscI sites with BamHI-P(λ bp’s 39582-40280)-AscI PCR fragment | KM, P467 |
| pcIpR-PΔ76-timm | In-frame deletion76 codons: λbp 39609-39836 in pcIpR-P-timm with HpaI, ligate | KM, P515 |
| pcIpR-Pπ-timm | BamHI-ClaI PCR fragment from λcI72π Lysate #3a, replacing D-CAP in P459 with λ bp’s 39582-40280 | KM, P505 |
| pcIpR-O-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38686-39582 | [36], CH, P465 |
| P434’pR-O-timm | Constitutive O expression; BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38686-39582 | [36], CH, P494 |
| pcIpR-O-P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38686-40280 | CH, P569 |
| pcIpR-O-36P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38686-39687 | CH, P565 |
| pcIpR-O-63P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38686-39768 | CH, P566 |
| pcIpR-oop#1-O-P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38559-40280 | CH, P567 |
| pcIpR-oop#2-O-P-timm | BamHI-ClaI PCR fragment from λcI857, replacing D-CAP in P459 with λ bp’s 38546-40280 | CH, P568 |
| pHB30 | λ bases 34499-34696, 36965-38103, 38814-40806 (see Section 3.2.) | [31,34], SH lab, P8 |
| Bacteriophage | Genotype | Hayes lab lysate # |
| λ wild type (wt) | λpapa | [78], 944,1001 |
| λcI72 | cI- | [78], 951, 999 |
| λnin5 | made from λ wt | [78], CH, 698 |
| Λvir | λv2v1v3 | [78], 260 |
| λcI857 | cI[Ts]857 | [100], 1002 |
| λcI857Sam7 | defective for cell lysis | [101], 963 |
| λimm434Pam3 | imm434, sequenced Pam3 mutation C to T, λ base 39786 (CAG to TAG) | [83], SH lab, 518, 664 |
| λimm434nin5 | imm434, Δnin5 region, forms very turbid plaques at 37˚C | [22], CH, 963 |
a: The strain numbers are from the Hayes laboratory collections. All gene inserts within the pcIpR-[ ]-timm plasmids were sequenced to confirm the genetic integrity of the inserted fragment.
b: Plasmid pcIpR-D-SPA-timm [20] (strain P462) was prepared from pcIpR-D-CAP-timm (strain P459), replacing 318 bp CAP from P459 by digestion with AscI and ClaI and replacing with 239 bp SPA tag from pMZS3F [72] (from J. Greenblatt) isolated via PCR with primers L-Asc-CBP & R-ClaI-FLAG. SPA is a 66 amino acid tag with 3X FLAG sequences.