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Base Strains

Name

Genotype / Phenotype

Features

Resistances

Auxotrophies

Non-utilizations

MG1655str. K-12 F– λ– ilvG– rfb-50 rph-1 fnr?Prototypical K-12 strain.
Valine toxicity in absence of isoleucine, due to ilvG frameshift.
Partial pyrimidine starvation from polar effects of rph-1 on pyrE causes 9–13% slower growth in minimal medium.
Slow growth in M9 galactose (t d=200–300 min). Some strain variants have an fnr deletion that causes defects in anaerobic respiration.
P1 phage susceptible due to IS in rfb O-antigen biosythesis gene cluster.
Genome paper (old), paper (new). Essential genome.  Genome. BioCyc. Allele variations. Allele table.		———
NEB Turbostr. K-12 F′[traD36 proAB+ lacIq lacZΔM15 fhuA2] glnV44(supE44) thi-1 Δ(lac-proAB) galE15 galK16 R(zgb-210::Tn10)TetS endA1 Δ(hsdS-mcrB)5 (rK– mK–)
= str. K-12 TG1[JM101 Δ(hsdS-mcrB)5 (rK– mK–)] endA1]		endonuclease I-deficient. lacIq. Exceptional competence (galE–). Amber suppressor UAG>CAG(Gln). T1 phage resistant. Blue/white-screening with lacZα. Non-conjugative F′ (traD36).
Parent: TG1. Grandparent: JM101. Genome.		NitR 2dGalRThiamineGalactose, Lactose
DH10B (Invitrogen)
= TOP10 (Thermo)
≈ NEB 10-beta		str. K-12 F– Δ(ara-leu)7697 Δ(rapA'-cra')] Δ(lac)X74[Δ('yahH-mhpE)] DUP(514341-627601)[nmpC-gltI] galK16 galE15 e14–(icdWT mcrA) φ80dlacZΔM15 recA1 relA1 endA1 Tn10.10 nupG rpsL150(StrR) rph+ spoT1 Δ(mrr-hsdRMS-mcrBC)(rK– mK–) λ–
Missense(dnaA glmS glyQ lpxK mreC murA) Nonsense(chiA gatZ fhuA? yigA ygcG) Frameshift(flhC mglA fruB)
NEB 10-beta: [DH10B fhuA]		Recombination-deficient. Relaxed. Endonuclease I-deficient. lacIq. Clones large plasmids. Exceptional competence (galE–). Blue/white-screening with lacZα. Improved cloning 5-mC DNA. P1 phage-resistance.
Parent: MC1061
Tandem duplication of genes b0553–b0655; double gene dosage.
Genome paper. Genome. BioCyc.		StrR 2dGalRLeucineArabinose, Lactose, Galactose
NEB Stablestr. K-12 NEB 10-beta F′[proAB lacIq Δ(lacZ)M15 zzf::Tn10(TetR)]Shown to exceed performance of Stbl3 in maintenance of repetitive DNAs. Reported genotype is identical to 10-beta except with additional F′ plasmid and TetR.StrR TetR 2dGalRLeucineArabinose, Lactose, Galactose
DH5α
≈ NEB 5-alpha

str. K-12 F– endA1 glnV44(supE44) thi-1 recA1 relA1 gyrA96(NalR) nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169 hsdR17(rK– mK+) λ–

NEB 5-alpha: str. K-12 F– fhuA2::IS2 Δ(mmuP-mhpD169 ΔphoA8 glnX44 φ80d[ΔlacZ58(M15)] rfbD1 gyrA96(NalR) luxS11 recA1 endA1 relAWT rphWT nupGWT thiE1 hsdR17(rK– mK+) λ–

Recombination-deficient. Relaxed (except NEB's). Endonuclease I-deficient. Clones large plasmids. Amber suppressor UAG>CAG(Gln). Slow growth in M9 from purB-20. Blue/white-screening with lacZα. Methylates EcoKI sites.
DH5α genome A, B, C.
 NEB 5-alpha genome paper. NEB 5-alpha genome. BioCyc. Genetic properties.

NalRThiamineLactose
Mach1str. W ΔrecA1398 endA1 fhuA φ80d lacZ ΔM15 Δ(lac)X74 hsdR(rK– mK+)Recombination-deficient. Endonuclease I-deficient. lacI–. Blue/ white-screening with lacZα. T1/T5/Φ80 phage-resistant. Blue/white-screening with lacZα.
Derivative of str. W (ATCC 9637). Patent: construction/ properties. Genome (str. W parent). BioCyc.

Lactose
BW25113str. K-12 F– Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) λ– rph-1 Δ(rhaD-rhaB)568 hsdR514(rK+)lacI+  Keio collection background. Parent: BD792
Genome paper. Genome. BioCyc.

Arabinose, Rhamnose, Lactose
DB3.1str. K-12 F– gyrA462(CcdBR) endA1 glnV44 Δ(sr1-recA) mcrB mrr hsdS20(rB– mB–) araC14 galK2 lacY1 Δ(gpt-proA)62 rpsL20(StrR) xylA5 leuB6(Am) mtl-1 lacI–?CcdB-resistant by gyrase mutation, not CcdA. Recombination-deficient. Endonuclease I-deficient. Amber suppressor UAG>CAG(Gln). Parent: HB101.CcdBR StrR 2dGalRProline, LeucineGalactose, Lactose, Xylose, Mannitol, Arabinose?
OmniMAX2str. K-12 F′[proAB+ lacIq lacZΔM15 Tn10(TetR) ΔccdAB] mcrA Δ(mrr-hsdRMS-mcrBC)(rK– mK–) φ80dlacZΔ M15 Δ(lacZYA-argF)U169 endA1 thi-1 recA1 relA1 gyrA96(NalR) fhuA2 panDCcdB-hypersensitive. T1/T5/Φ80 phage resistant. Recombination-deficient. Relaxed. Endonuclease I-deficient. Clones large plasmids. Blue/white-screening with lacZα. Parent: DH5α. Thus amber suppressor?TetR NalRThiamine, PantothenateLactose
XL1-Bluestr. K-12 F′[proAB+ lacIq lacZΔM15 Tn10(TetR) recA1 endA1 gyrA96(NalR) thi-1 hsdR17 glnV44(supE44) relA1 lacRecombination-deficient. Relaxed. Endonuclease I-deficient. lacIq. Amber suppressor UAG>CAG(Gln). Blue/white-screening with lacZα.TetR NalRThiamine
NEB dam– /dcm–
= ER2925		str. K-12 ara-14 leuB6(Am) fhuA31 lacY1 tsx78 glnV44(supE44) galK2 galT22 mcrA dcm6 hisG4 rfbD1 R(zgb210::Tn10(TetS) endA1 rspL136(StrR) dam13::Tn9(ChlR) xylA5 mtl-1 thi-1 mcrB1 hsdR2Host for isolating plasmids free of Dam/Dcm methylation for transformation into methylation-sensitive hosts. Increased mutation rate as a side-effect.
Endonuclease I-deficient. T1/T5/Φ80/T6 phage-resistant. Amber suppressor UAG>CAG(Gln).
Low but noticeable frequency of KanR mutations. ColE1 replicons are suppressed in dam– strains.		ChlR StrR NitR CkaR 2dGalRThiamine, HistidineGalactose, Xylose, Arabinose, Mannitol
ET12567
(ATCC BAA-525)		str. K-12 F– dam-13::Tn9(ChlR) dcm-6 hsdM hsdR zjj(opgB)-202::Tn10(TetR) recF143 galK2 galT22 ara-14 lacY1 xyl-5 leuB6 thi-1 tonA31 rpsL136(StrR) hisG4 tsx-78 mtl-1 glnV44Host for isolating plasmids for transformation into Streptomyces or other organisms that have E. coli methylation-sensitive restriction systems. UV-sensitive (recF). ColE1 replicons are suppressed in dam– strains. Phage T6 and ColK-resistant (tsx). Amber suppressor UAG>CAG(Gln).ChlR StrR TetRLeucine, Thiamine, HistidineArabinose, Galactose, Mannitol
JTK165EK
(DIAL strain)		str. K-12 MC1061 Δupp:(pir folA(TmpR)) Δ(rfbB–wbbL)::repA
1) Δupp::(Pcon(BBa_J23100)-rbs(?)-pirR6K -BBa_B0015(rrfBt-T7.TE) - FRT - Pcon(BBa_J23119)-4krbs-folA(TmpR)-tR2 - FRT)
2) Δ(rfbB–wbbL')::(Pcon(BBa_J23119)-rbs(?)-repAColE2-P9 -BBa_B0015(rrfBt-T7_TE) - FRT)		pir+ repA+: Replicates conditional oriV R6Kγ and oriV ColE2 plasmids. Relaxed. lacI–. Improved cloning 5-mC DNA. Obtained by Shyam Cas9-curing plasmid from Addgene #85150 .StrR TmpRLeucineGalactose, Lactose, Arabinose
EC100Dstr. K-12 F– mcrA Δ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 Δ(lac)X74[Δ('yahH-mhpE)] recA1 endA1 araD139 Δ(ara-leu)7697 galU galK λ– rpsL(StrR) deoR(?) pir+ folA(TmpR)

pir+: Replicates conditional ori R6Kγ plasmids using genomic pir at medium copy ≈15.
Recombination-deficient. Endonuclease I-deficient.

StrR TmpR 2dGalR
Galactose, Lactose, Arabinose
BW25141Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) Δ(phoB-phoR)580 λ– galU95 ΔuidA3::pir+ recA1 ΔendA9::FRT rph-1 Δ(rhaD-rhaB)568 hsdR514(rK– mK+)pir+: Replicates conditional ori R6Kγ plasmids using genomic pir at medium copy ≈15. Deletion of phoBR. Recombination-deficient. Endonuclease I-deficient. Paper.

Arabinonse, Rhamnose, Lactose
BW23474Δ(argF-lac)169 ΔuidA4::pir-116 recA1 rpoS396(Am) ΔendA9::FRT rph-1 hsdR514(rK– mK+) rob-1 creC510pir+: Replicates conditional ori R6Kγ plasmids using genomic pir-116 at high copy. Recombination-deficient. Endonuclease I-deficient. CGSC.

Lactose
MFDpir MG1655 glvB::[RP4-2 TetR::Mu ΔMu1::aac(3′)IV(AprR) Δaph(3′)VIII (KanS) Δnic35 ΔMu2::ble(ZeoR)] ΔdapA::(ermB-pir-116)(EryR) ΔrecAIncP(RK2/RP4) non-self-transmissable conjugation donor. DAP (diaminopimelate) auxotroph. Recombination-deficient. pir+ : Replicates conditional ori R6Kγ plasmids using genomic pir-116 at high copy. Paper. Genome.EryR AprR ZeoRDAP
Syn61Δ3(ev5)MDS42 recoded(TCG,TCA,TAG) ΔserT ΔserU ΔprfA0.7 MB-shortened, IS/prophage-free strain MDS42 recoded with synonymous CDS mutations for serine codons TCG, TCA and amber stop TAG. Deleted of corresponding tRNA and release factor. Evolved for improved growth rate. Paper.
–?
BW29655str. K-12 F– Δ(araBAD)567 ΔlacZ4787(::rrnB-3) λ– Δ(envZ-ompR)520(::FRT) Δ(rhaBAD)568 hsdR514(rK– mK+) rph+
=str. K-12 BW25113 rph+ Δ(envZ-ompR)520(::FRT)		Base strain for refactored light systems. Described in this study. lacI+ .

Arabinose, Lactose, Rhamnose






Marionette-Clo sAJM.1504

str. DH10B glvC::(Marionette cluster*)(ChlR)DH10B with Marionette transcription factor cluster.low ChlR 5 mg/LLeucineArabinose, Lactose, Galactose
Marionette-Pro sAJM.1505str. BL21 glvC::(Marionette cluster*)(ChlR)BL21 with Marionette transcription factor cluster. (no DE3 and T7 RNAP.)low ChlR 5 mg/L
Galactose
Marionette-Wild sAJM.1506

str. K-12 MG1655 glvC::(Marionette cluster*)(ChlR)

*[hisIt PJ23119-phlFAM-cymRAM-luxR-vanRAM araCUTR PlacI-lacIAM-tetR-araCAM-araE ihfAt PJ23100 -betIAM-ttgRAM-pcaUAM-nahRAM-cinRAM hisLt cat(ChlR)]

MG1655 with Marionette transcription factor cluster*.low ChlR 5 mg/L







BL21(DE3)str. B F– ompT gal dcm lon hsdSB (rB– mB–) λ(DE3[lacI PlacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)

lac-inducible T7 RNAP. proteases– dcm– motility–.
Genome paper1, paper2a, paper2b, paper2c. Genome. Biocyc.



Galactose
Rosetta™(DE3)pLysS (Novagen)str. B BL21(DE3) pLysSRARE[T7p20 ileX argU thrU tyrU glyT thrT argW metT leuW proL cat ori p15A](ChlR)lac-inducible T7 RNAP. proteases–.  dcm–.
pLysSRARE Expresses rare-codon tRNA Arg, Ile, Gly, Leu, Pro : argU(AGG, AGA), ileX(AUA), leuW(CUA), proL(CCC), glyT(GGA), in addition to T7 lysozyme, with a p15A ori.
T7 lysozyme reduces T7 RNAP background activity and facilitates lysis.		ChlR
Galactose
BLIMstr. B BL26 Blue F– ompT hsdS(rB– mB–) gal dcm lac T1R
Parent strain BL26 Blue additionally had F′[proAB lacIq lacZΔM15::Tn10(TetR)]		Parent strain BL26 Blue (Novagen) was cured of F plasmid and made T1 phage-resistant, according to source.
Proline?Galactose, Lactose






BioDesignER (RE1000)str. K-12 MG1655 ilvG+ ΔbioAB::λred[PN25-tetR PtetO2-gam-bet-exo-dam] SS7::cymRq PCP8-araE Pcon-araC ΔaraBAD lacIq1 dnaG Q576A ΔrecJ ΔsbcBTetR-controlled recombination system. Mutations to stabilize ssDNA. Constitutive lacI, araC, tetR, cymR. Linear ara induction from constitutive araE. Faster minimal media growth from ilvG+.
BiotinArabinose






Crooks (ATCC 8739)
Used for antimicrobial and bioresistance testing. Genome.?

Nissle 1917pMUT1[ori ColE1] pMUT2[ori ColE2]Wild, gut-colonizing strain used as a probiotic. Has native ColE1 and ColE2 plasmids.
History. Nissle engineering. Genome. BioCyc.		?

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