Brought to you by and meticulously curated by Shyam. See OpenWetWare for a guide to genotype abbreviations.
Standing on the Shoulders of a Tiny Giant ; EcoSal Plus Journal

Base Strains

...

Name	Genotype / Phenotype	Features	Resistances	Auxotrophies	Non-utilizations

MG1655	str. 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 allele variations MG1655 physiology

Genome paper (old), paper (new). Essential genome. Genome. BioCyc. Allele variations. Allele table.

—


NEB Turbo	str. K-12 F′[traD36 proAB ⁺ lacI ^q lacZΔM15 fhuA2] glnV44(supE44) thi-1

∆

Δ(lac-proAB) galE15 galK16 R(zgb-210::Tn10)Tet^S endA1 Δ(hsdS-mcrB)5

,

(r_K ^– m_K ^–)

F′[proA⁺B⁺ lacI^qlacZΔM15/fhuA2]endonuclease^–

= str. K-12 TG1[JM101 Δ(hsdS-mcrB)5 (r_K ^– m_K ^–)] endA1]	endonuclease I-deficient. lacI ^q. 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.	Nit^R 2dGal^R	Thiamine	Galactose, Lactose
DH10B (Invitrogen) = TOP10 (Thermo) ≈ NEB 10-beta	str. K-12 F^– Δ(ara-leu)7697

araD139 ΔlacX74 duplication

Δ(rapA'-cra')] Δ(lac)X74[Δ('yahH-mhpE)] DUP(514341-627601)[nmpC-gltI] galK16 galE15

deoR⁺

e14^– (icd ^WT mcrA)

mcrA galU⁺

φ80dlacZΔM15 recA1 relA1 endA1 Tn10.10 nupG rpsL150(Str^R) rph ⁺ spoT1 Δ(mrr-hsdRMS-mcrBC)(r_K ^– m_K ^–) 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. lacI ^q. Clones large plasmids. Exceptional competence (galE^– ).

P1 phage-resistance

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.

Str^R 2dGal^R

Leucine

Arabinose, Lactose,

(?)

Galactose
NEB Stable	str. K-12 NEB 10-beta F′[proAB lacI^q Δ(lacZ)M15 zzf::Tn10(Tet^R)]	Shown to exceed performance of Stbl3 in maintenance of repetitive DNAs. Reported genotype is identical to 10-beta except with additional F′ plasmid and Tet^R.	Str^R Tet^R 2dGal^R	Leucine	Arabinose, Lactose, Galactose
DH5α ≈ NEB 5-alpha	str. K-12 F^– endA1 glnV44(supE44) thi-1 recA1 relA1 gyrA96(Nal^R)

deoR⁺

nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169

,

hsdR17(r_K ^– m_K ⁺) λ^–

NEB 5-alpha: str. K-12 F^– fhuA2::IS2 Δ(mmuP-mhpD)169 ΔphoA8 glnX44 ϕ80d[ΔlacZ58(M15)] rfbD1 gyrA96(Nal^R) luxS11 recA1 endA1 relA^WT rph^WT nupG^WT thiE1 hsdR17(r_K^– m_K⁺)

,

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.

Nal^R

Thiamine

, Arginine

	Lactose
Mach1	str. W ΔrecA1398 endA1 fhuA

Φ80Δ(lac)

φ80d lacZ ΔM15 Δ(lac)X74 hsdR(r_K ^– m_K ⁺)

Recombination-deficient. Endonuclease I-deficient. lacI^– .

lacZα-complementer

Blue/ white-screening with lacZα. T1/T5/Φ80 phage-resistant. Blue/white-screening with lacZα.
Derivative of str. W (ATCC 9637). Patent: construction/

propertie

properties.Genome

.Genome paper

(str. W parent). BioCyc.

		Lactose
BW25113	str. K-12 F^– Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) λ^– rph-1 Δ(rhaD-rhaB)568 hsdR514(r_K

^–m_K

⁺)

lacI ⁺

Keio

Keio collection background. Parent: BD792
Genome

.

paper. Genome. BioCyc.			Arabinose, Rhamnose, Lactose
DB3.1	str. K-12 F^– gyrA462(CcdB^R) endA1 glnV44 Δ(sr1-recA) mcrB mrr hsdS20(r_B ^–

,

m_B ^–)

ara14

araC14 galK2 lacY1

proA2

Δ(gpt-proA)62 rpsL20(

Sm

Str^R)

xyl5 leu(

xylA5 leuB6(Am)

?) mtl1

mtl-1 lacI^– ?

CcdB-resistant by gyrase mutation, not CcdA. Recombination-deficient. Endonuclease

^–

I-deficient. Amber suppressor UAG>CAG(Gln). Parent: HB101.

CcdB^R Str^R 2dGal^R

Proline, Leucine

Galactose, Lactose

, Arabinose

, Xylose, Mannitol, Arabinose?

BW29655

OmniMAX2

str. K-12

F^– Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) λ^– Δ(envZ-ompR)520(::FRT) Δ(rhaD-rhaB)568 hsdR514(r_K^–m_K⁺) rph-1?lacI⁺ Arabinose, Lactose, Rhamnose

Shyam Can Obtain:

NameGenotype / PhenotypeFeaturesResistancesAuxotrophiesNon-utilizationsDH1str. K-12 F^– λ^– endA1 recA1 relA1 gyrA96(Nal^R) thi-1 glnV44(supE44) hsdR17(r_K^–m_K^–)Recombination-deficient. Relaxed. Endonuclease^–. Efficient 40–60kb plasmid transformer. Amber suppressor UAG>CAG(Gln)
DH5α parentNal^RThiamine JM109

F′[proAB⁺ lacI ^q lacZΔM15 Tn10(Tet^R) ΔccdAB] mcrA Δ(mrr-hsdRMS-mcrBC)(r_K ^– m_K ^–) φ80dlacZΔ M15 Δ(lacZYA-argF)U169 endA1 thi-1 recA1 relA1 gyrA96(Nal^R) fhuA2 panD	CcdB-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?	Tet^R Nal^R	Thiamine, Pantothenate	Lactose
XL1-Blue	str. K-12 F′[proAB ⁺ lacI ^q lacZΔM15 Tn10(Tet^R) recA1 endA1 gyrA96(Nal^R) thi-1 hsdR17 glnV44(supE44) relA1 lac	Recombination-deficient. Relaxed. Endonuclease I-deficient. lacI ^q. Amber suppressor UAG>CAG(Gln). Blue/white-screening with lacZα.	Tet^R Nal^R	Thiamine
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(Tet^S) endA1 rspL136(Str^R) dam13::Tn9(Chl^R) xylA5 mtl-1 thi-1 mcrB1 hsdR2	Host 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 Kan^R mutations. ColE1 replicons are suppressed in dam^– strains.	Chl^R Str^R Nit^R Cka^R 2dGal^R	Thiamine, Histidine	Galactose, Xylose, Arabinose, Mannitol
ET12567 (ATCC BAA-525)	str. K-12 F^– dam-13::Tn9(Chl^R) dcm-6 hsdM hsdR zjj(opgB)-202::Tn10(Tet^R) recF143 galK2 galT22 ara-14 lacY1 xyl-5 leuB6 thi-1 tonA31 rpsL136(Str^R) hisG4 tsx-78 mtl-1 glnV44	Host 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).	Chl^R Str^R Tet^R	Leucine, Thiamine, Histidine	Arabinose, Galactose, Mannitol
JTK165EK (DIAL strain)	str. K-12 MC1061 Δupp:(pir folA(Tmp^R)) Δ(rfbB–wbbL)::repA 1) Δupp::(P_con(BBa_J23100)-rbs(?)-pir_R6K -BBa_B0015(rrfBt-T7.TE) - FRT - P_con(BBa_J23119)-4krbs-folA(Tmp^R)-tR2 - FRT) 2) Δ(rfbB–wbbL')::(P_con(BBa_J23119)-rbs(?)-repA_ColE2-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.	Str^R Tmp^R	Leucine	Galactose, Lactose, Arabinose
EC100D	str. 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(Str^R) deoR(?) pir ⁺ -folA(Tmp^R)	pir ⁺: Replicates conditional ori _R6Kγ plasmids using genomic pir at medium copy ≈15. Recombination-deficient. Endonuclease I-deficient.	Str^R Tmp^R 2dGal^R		Galactose, Lactose, Arabinose
BW25141	Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) Δ(phoB-phoR)580 λ^– galU95 ΔuidA3::pir ⁺ recA1 ΔendA9::FRT rph-1 Δ(rhaD-rhaB)568 hsdR514(r_K ^– m_K ⁺)	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
BW23474	Δ(argF-lac)169 ΔuidA4::pir-116 recA1 rpoS396(Am) ΔendA9::FRT rph-1 hsdR514(r_K ^– m_K ⁺) rob-1 creC510	pir ⁺: Replicates conditional ori _R6Kγ plasmids using genomic pir-116 at high copy. Recombination-deficient. Endonuclease I-deficient. CGSC.			Lactose
MFDpir	MG1655 glvB::[RP4-2 Tet^R::Mu ΔMu1::aac(3′)IV(Apr^R) Δaph(3′)VIII (Kan^S) Δnic35 ΔMu2::ble(Zeo^R)] ΔdapA::(ermB-pir-116)(Ery^R) ΔrecA	IncP(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.	Ery^R Apr^R Zeo^R	DAP
Syn61Δ3(ev5)	MDS42 recoded(TCG,TCA,TAG) ΔserT ΔserU ΔprfA	0.7 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.		–	?
BW29655	str. K-12 F^– Δ(araBAD)567 ΔlacZ4787(::rrnB-3) λ^– Δ(envZ-ompR)520(::FRT) Δ(rhaBAD)568 hsdR514(r_K ^– m_K ⁺) 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*)(Chl^R)	DH10B with Marionette transcription factor cluster.	low Chl^{R 5 mg/L}	Leucine	Arabinose, Lactose, Galactose
Marionette-Pro sAJM.1505	str. BL21 glvC::(Marionette cluster*)(Chl^R)	BL21 with Marionette transcription factor cluster. (no DE3 and T7 RNAP.)	low Chl^{R 5 mg/L}		Galactose
Marionette-Wild sAJM.1506	str. K-12 MG1655 glvC::(Marionette cluster)(Chl^R) [hisIt P_J23119-phlF^AM-cymR^AM-luxR-vanR^AM araC_UTR P_lacI-lacI^AM-tetR-araC^AM-araE ihfAt P_J23100 -betI^AM-ttgR^AM-pcaU^AM-nahR^AM-cinR^AM hisLt cat(Chl^R)]	MG1655 with Marionette transcription factor cluster*.	low Chl^{R 5 mg/L}

str. K-12 endA1 recA1 relA1 gyrA96(Nal^R) thi-1 glnV44(supE44) Δ(lac-proAB) hsdR17(r_K^–m_K⁺) F′ [traD36 proAB⁺ lacI^q lacZΔM15]Recombination-deficient. Relaxed. Endonuclease^–. Amber suppressor UAG>CAG(Gln)Nal^RThiamine



BL21(DE3)	str. B F^– ompT gal dcm lon hsdS_B (r_B ^– m_B ^–) λ(DE3[lacI P_lacUV5-T7p07 ind1 sam7 nin5]) [malB ⁺]_K-12(λ^S)

proteases^–;

lac-inducible T7 RNAP

GalactoseBL21(DE3) pLysSstr

.

BL21(DE3) pLysS[T7p20 ori_p15A](Chl^R)proteases^–; lac-inducible T7 RNAP
pLysS encodes T7 lysozyme, inhibitor of T7 polymerase, which almost eliminates expression from uninduced T7 promoter.Chl^R

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](Chl^R)

proteases^–;

lac-inducible T7 RNAP. proteases^–. dcm^–.
pLysSRARE Expresses rare-codon tRNA^{Arg, Ile, Gly, Leu}

and

^{, Pro}

-tRNAs,

: 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.

Chl^R

		Galactose
BLIM	str. B BL26 Blue F^– ompT hsdS(r_B ^– m_B ^–) gal dcm lac T₁ ^R Parent strain BL26 Blue additionally had F′[proAB lacI ^q lacZΔM15::Tn10(Tet^R)]	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[P_N25-tetR P_tetO2-gam-bet-exo-dam] SS7::cymR ^q P_CP8-araE P_con-araC ΔaraBAD lacI ^q1 dnaG _Q576A ΔrecJ ΔsbcB	TetR-controlled recombination system. Mutations to stabilize ssDNA. Constitutive lacI, araC, tetR, cymR. Linear ara induction from constitutive araE. Faster minimal media growth from ilvG+.	Biotin	Arabinose

Nissle 1917	pMUT1[ori _ColE1] pMUT2[ori _ColE2]	Wild, gut-colonizing strain used as a probiotic. Has native ColE1 and ColE2 plasmids. History. Nissle engineering. Genome. BioCyc.		?

Galactose

Shyam Can Obtain:
Name	Genotype / Phenotype	Features	Resistances	Auxotrophies	Non-utilizations
DH1	str. K-12 F^– λ^– endA1 recA1 relA1 gyrA96(Nal^R) thi-1 glnV44(supE44) hsdR17(r_K ^– m_K ^–)	Recombination-deficient. Relaxed. Endonuclease I-deficient. Efficient 40–60kb plasmid transformer. Amber suppressor UAG>CAG(Gln). DH5α parent	Nal^R	Thiamine
JM109	str. K-12 endA1 recA1 relA1 gyrA96(Nal^R) thi-1 glnV44(supE44) Δ(lac-proAB) hsdR17(r_K ^– m_K ⁺) F′[traD36 proAB ⁺ lacI ^q lacZΔM15]	Recombination-deficient. Relaxed. Endonuclease I-deficient. Amber suppressor UAG>CAG(Gln). Blue/ white-screening with lacZα.	Nal^R	Thiamine

BLR(DE3) (Novagen®)

str. B F^– ompT hsdS _B(r_K ^– m_B ^–) gal dcm (DE3) Δ(srl-recA)306::Tn10 (Tet^R)

lac -inducible T7 RNAP. protease OmpT^–. Recombination-deficient. dcm^–.

Tet^R

	Galactose
BLR(DE3) pRIL (Novagen®)	str. B F^– ompT hsdS _B(r

_K

_B ^– m_B ^–) gal dcm λ(DE3 [lacI P_lacUV5-T7p07 ind1 sam7 nin5]) Δ(srl-recA)306::Tn10(Tet^R) pRIL[argU ileY leuW ori _p15A](Chl^R)

lac-inducible T7 RNAP. protease OmpT^–. Recombination-deficient. dcm^–.

Overexpresses

pRIL overexpresses rare-codon tRNA^{Arg, Ile, Leu} argU (AGA, AGG), ileY (AUA), leuW (CUA) from a p15A replicon.

Chl^R Tet^R

		Galactose
DP10	str. DH10B Δ(araFGH) φ(ΔaraEp P_cp8-araE(araE ^q)	Deletion of Arabinose consumption genes. Constitutive araE. Others, see DH10B.	Str^R	Leucine	Arabinose, Lactose
RU1012	str. MH215[MH70[MC4100 [F^– [araD139]B/r Δ( lacZYA-argF

-lac

)

169

U169 e14^– flhD5301 Δ(fruK-yeiR)725(fruA25) relA1 rpsL150(Str^R) rbsR22 Δ(fimB-fimE)632::IS1 deoC1 λ^–] malQ7] Φ(ompC-lacZ)10-25] ΔenvZ::Kan^R

Relaxed

Str^R Kan^R

Arginine

	Lactose, Fructose
JTK165JJ (DIAL strain)	str. MC1061 Δupp:(pir

dhfr

folA(Tmp^R)) Δ(rfbB–wbbL)::repA

1) Δupp::(P_con(BBa_J23100)-rbs(?)-pir-BBa_B0015(rrfBt-T7

_

.TE) - FRT - P_con(BBa_J23119)-4krbs-

dhfr

folA(Tmp^R)-tR2 - FRT)
2) Δ(rfbB–wbbL')::(P_con(BBa_J23119)-rbs(?)-repA-BBa_B0015(rrfBt-T7_TE) - FRT)

relaxed. lacI^– . Propagates R6K and ColE2 replicons. Improved cloning 5-mC DNA.

Str^R Tmp^R

Leucine

Galactose, Lactose, Arabinose

DGF-298

3.62 Mbp source strainstr. K-12 W3110, Δ(recC ptr recB recD)::P_lac-bet exo kan ilvG⁺ rph⁺ Δ(hella shit)2.98 Mbp reduced genome (from 4.6 Mbp)---

BW27783

str. K-12 BW25113 F^– λ^– Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) Δ(araH-araF)570(::FRT) ΔaraEp-532::FRT φP_cp8-araE535 rph-1 Δ(rhaD-rhaB)568 hsdR514(r_K ^–)

Constitutive araE (ara transporter) expression, expanding dynamic range of araBp (P_BAD) induction

--

.

Arabinose, Rhamnose, Lactose

RE630EcNR1[MG1655 bla bio λ-Red1] ilvG⁺ dam@λTerm tetO₂-pTet<>{kil, λ cI}cymR<>SS7 araE^q araC^q lacI^q-1 recJ sbcB dnaG-Q576AaTc-inducible recombination machinery. Recombination-deficient. Mutations to stabilize ssDNAAmp^RBiotin

DGF-298

str. K-12 W3110, Δ(recC ptr recB recD)::P_lac -bet-exo(Kan^R) ilvG ⁺ rph ⁺ Δ(hella shit)

35% reduced genome (2.98 Mbp from WT 4.6 Mbp). 3.62 Mbp parent strain

Syn61Δ3(ev5)

...

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Key

Base Strains

Name

Genotype / Phenotype

Features

Resistances

Auxotrophies

Non-utilizations

Shyam Can Obtain:

Shyam Can Obtain:

Syn61Δ3(ev5)

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Versions Compared

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Key

Base Strains

Name

Genotype / Phenotype

Features

Resistances

Auxotrophies

Non-utilizations

Shyam Can Obtain:

Shyam Can Obtain:

Syn61Δ3(ev5)