E. coli genotypes

Nomenclature & Abbreviations

A listed gene name means that gene carries a loss of function mutation, a Δ preceding a gene name means the gene is deleted. If a gene is not listed, it is not known to be mutated. Prophages present in wt K-12 strains (F, λ, e14, rac) are listed only if absent. E. coli B strains are naturally lon^– and dcm^–.

• F^– = Does not carry the F plasmid
• F⁺ = Carries the F plasmid. The cell is able to mate with F^- through conjugation.
• F′[ ] = Carries an F plasmid that has host chromosomal genes on it from a previous recombination event. This cell can also mate with F^- through conjugation. Chromosomal genes carried in the F plasmid are listed in brackets.
• ΔH1 = removes part of cro and all genes to the right of it
• r_B/K^+/- = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the restriction system.
• m_B/K^+/- = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the modification (methylation) system.
• hsdS = Both restriction and methylation of certain sequences is deleted from the strain. If you transform DNA from such a strain into a wild type strain, it will be degraded.
• hsdR' = For efficient transformation of cloned unmethylated DNA from PCR amplifications
• INV( ) = chromosomal inversion between locations indicated
• ahpC = mutation to alkyl hydroperoxide reductase conferring disulfide reductase activity
• ara-14 = cannot metabolize arabinose
• araD = mutation in L-ribulose-phosphate 4-epimerase blocks arabinose metabolism
• bio252 = removes all genes to the left of cIII
• cycA = mutation in alanine transporter; cannot use alanine as a carbon source
• dapD = mutation in succinyl diaminopimelate aminotransferase leads to succinate or (lysine + methionine) requirement
• Δ( ) = chromosomal deletion of genes between the listed genes (may include unlisted genes!)
• dam = adenine methylation at GATC sequences exist; high recombination efficiency; DNA repair turned on
• dcm = cytosine methylation at second C of CCWGG sites exist. dam & dcm are the default properties and always elided, while dam^- or dcm^- should be declare explicitly
• DE3 = Lysogen that encodes T7 RNA polymerase. Used to induce expression in T7-driven expression systems
• deoR = regulatory gene that allows constitutive expression of deoxyribose synthesis genes; permits uptake of large plasmids. See Hanahan D, US Patent 4,851,348. ***This has been called into question, as the DH10B genome sequence revealed that it is deoR⁺. See Durfee08, PMID 18245285.
• dnaJ = one of the chaparonins inactivated; stabilizes some mutant proteins
• DUP() = chromosomal duplication between locations indicated
• dut1 = dUTPase activity abolished, leading to increased dUTP concentrations, allowing uracil instead of thymine incorporation in DNA. Stable U incorporation requires ung mutation as well.
• endA1 = For cleaner preparations of DNA and better results in downstream applications due to the elimination of non-specific digestion by Endonuclease I
• (e14) = excisable prophage like element containing mcrA gene; present in K-12 but missing in many other strains
• galE = mutations are associated with high competence, increased resistance to phage P1 infection, and 2-deoxygalactose resistance. galE mutations block the production of UDP-galactose, resulting in truncation of LPS glycans to the minimal, "inner core". The exceptional competence of DH10B/TOP10 is thought to be a result of a reduced interference from LPS in the binding and/or uptake of transforming DNA. galE15 is a point mutation resulting in a Ser123 -> Phe conversion near the enzyme's active site. See van Die, et al. PMID 6373734, Hanahan, et al. PMID 1943786, and EcoSal ISBN 1555811647.
• galK = mutants cannot metabolize galactose and are resistant to 2-deoxygalactose. galK16 is an IS2 insertion ~170bp downstream of the galK start codon. See EcoSal ISBN 1555811647.
• galU = mutants cannot metabolize galactose
• gor = mutation in glutathione reductase; enhances disulphide bond formation
• glnV = suppression of amber (UAG) stop codons by insertion of glutamine; required for some phage growth
• gyrA96 = mutation in DNA gyrase; conveys nalidixic acid resistance
• gyrA462 = mutation in DNA gyrase; conveys resistance to CcdB colicin
• hflA150 = protease mutation stabilizing phage cII protein; high frequency of lysogenization by λ
• ΔlacX74 = Deletion of the entire lac operon as well as some flanking DNA (complete deletion is Δcod-mhpF; see Mol.Micro., 6:1335, and J.Bact., 179:2573)
• lacI^q = overproduction of the lac repressor LacI; -35 site in promoter upstream of lacI is mutated from GCGCAA to GTGCAA
• lacI^q1 = overproduction of the lac repressor LacI; contains a 15 bp deletion to create optimal -35 site in promoter upstream of lacI
• lacY = deficient in lactose transport; deletion of lactose permease LacY
• lacZΔM15 = partial deletion of the β-galactosidase lacZ gene (removing N-terminal aa 11–41), allowing α-complementation; required for blue/white selection on X-Gal plates using LacZ α subunit.
• λ^– or LAM^– = λ lysogen deletion; approximate map location: 17.40; information from CGSC
• lamR or malT1 or malT1(Lam^R) = mutation in malT1 conferring λ resistance [1]
• leuB = Mutation in leuB, disrupting leucine biosynthesis.
• Δlon = Mutation of the Lon protease
• malA = Mutation abolishing mannitol metabolism.
• mcrA = Mutation eliminating restriction of DNA methylated at the sequence C^mCGG (possibly ^mCG). Carried on the e14 prophage (q.v.)
• mcrB = Mutation eliminating restriction of DNA methylated at the sequence R^mC
• metB = Mutation in methionine biosynthesis enzyme MetB; methionine auxotroph
• metC = Mutation in methionine biosynthesis enzyme MetC; methionine auxotroph
• mrr = Mutation eliminating restriction of DNA methylated at the sequence C^mAG or G^mAC
• mtlA = Mutation in mannitol permease MtlA; cannot metabolize mannitol
• (Mu) = Mu prophage present. MuΔ; means the phage is defective.
• mutS = mutation inhibits DNA repair of mismatches in unmethylated newly synthesized strands
• nupG = same as deoR
• ompT = mutation in outer membrane protein protease VII, reducing proteolysis of expressed proteins
• (P1) = Cell carries a P1 prophage. Cells express the P1 restriction system.
• (P2) = Cell carries a P2 prophage. Allows selection against Red+ Gam+ λ
• (φ80) = Cell carries the lambdoid prophage φ80. A defective version of this phage carrying lacZM15 deletion (as well as wild-type lacI, lacYA, and flanking sequences) is present in some strains. The φ80 attachment site is just adjacent to tonB.
• pLysS = contains pLysS plasmid carrying chloramphenicol resistance and phage T7 lysozyme, effective at attenuating activity of T7 RNA polymerase, for better inhibition of expression under non-induced conditions. The sequence can be found here.
• proAB = mutation in proline biosynthesis enzymes; proline auxotroph, unless (as often) complemented by proAB⁺ on F plasmid
• recA1 = For reduced occurrence of unwanted recombination in cloned DNA; cells UV sensitive, deficient in DNA repair
• recA13 = as for recA1, but DNA constructs less stable.
• recBCD = exonuclease V; mutation in RecB or RecC reduces general recombination by a factor of 100; impaired DNA repair; UV sensitive, easier propagation of inverted repeats
• recJ exonuclease involved in alternate recombination
• relA = relaxed phenotype; permits RNA synthesis in absence of protein synthesis
• rha = cannot metabolize rhamnose
• rnc = encodes RNaseIII (rnc-14 is a common null mutant)
• rne = encodes RNaseE (rne-3071 is a common temperature sensitive mutant)
• rpsL = mutation in ribosomal protein S12 conveying streptomycin resistance; also called strA, rpsL135(Str^R), strA135 [2]
• sbcBC = ExoI activity abolished; usually present in recBC strains; recombination proficient, stablizes inverted repeats
• sr1 = cannot metabolize sorbitol
• supE = glnV
• supF = tyrT
• thi = thiamine auxotroph
• thyA = thymidine auxotroph
• Tn10 = transposon normally carrying Tetracycline resistance
• Tn5 = transposon normally carrying Kanamycin resistance
• tonA = mutation in outer membrane protein conveying resistance to phage T1 and phage T5
• traD = mutation eliminating F transfer factor; prevents transfer of F plasmid
• trxB = mutation in thioredoxin reductase; enhances disulphide bond formation in the cytoplasm
• tsx = outer membrane protein mutation conveying resistance to phage T6 and colicin K
• tyrT = suppression of amber (UAG) stop codons by insertion of tyrosine; needed for some phage infection such as λgt11.
• ung1 = allows uracil to exist in plasmid DNA
• xyl-5 = blocked xylose metabolism

Antibiotic resistance nomenclature based on ASM AAC conventions

• Amp^R = ampicillin resistance, usually by β-lactamase TEM (class A): bla. Older: Ap^R
• Apr^R = apramycin resistance, usually by aminoglycoside N3-acetyltransferase (AAC(3′)-IV): aacC4.
• Ble^R = bleomycin/phleomycin/Zeocin resistance, usually by bleomycin-binding protein: ble.
• Chl^R = chloramphenicol resistance, usually by chloramphenicol O-acetyltransferase A-1: cat. Older: Cm^R or Cam^R.
• Ery^R = erythromycin resistance, usually by macrolide 2'-phosphotransferase I (MPH(2′)-I): mphA.
• Gen^R = gentamicin resistance, usually by aminoglycoside-N3-acetyltransferase (AAC(3′)-I): aacC1. Older: Gm^R
• Kan^R = kanamycin resistance, usually by aminoglycoside 3′-phosphotransferase type I (APH(3′)-I): aphA1, nptI; or type II (aph(3′)-II): aphA2, nptII, neo. Older: Km^R
• Spt^R = spectinomycin resistance, usually by aminoglycoside (3″)9-O-adenylyltransferase:aadA1.
• Str^R = streptomycin resistance, usually by Spt^R gene aadA1 or by genomic rpsL mutation. Older: Sm^R
• Tet^R = tetracycline resistance, usually by a tetracycline efflux antiporter:tetA. Older: Tc^R
• Tmp^R = trimethoprim resistance, usually by dihydrofolate reductase type II (DHFR): dhfr.

Methylation Issues in E. coli

• Type I methylation systems:
  • E. coli K12 restricts DNA which is not protected by adenine methylation at sites AA^*C[N₆]GTGC or GCA^*C[N₆]GTT, encoded by the hsdRMS genes(EcoKI). Deletions in these genes removes either the restriction or methylation or both of these functions.
  • E. coli B derivative strains contain an hsdRMS system (EcoBI) restricting and protecting the sequence TGA^*[N₈]TGCT or AGCA^*[N₈]TCA.
• The mcrA gene (carried on the e14 prophage) restricts DNA which is methylated in C^mCWGG or ^mCG sequences (methylation by the dcm gene product).
• The mcrBC genes restrict R^mC sequences.
• The mrr gene product restricts adenine methylated sequences at CAG or GAC sites.
• E. coli methylates the adenine in GATC (and the corresponding A on the opposite strand) with the dam gene product.
• M.EcoKII methylates the first A at the palindromic site ATGCAT (as well as the corresponding A on the opposite strand), see (Kossykh VG (2004) J. Bact 186: 2061-2067 PMID 15028690) Note that this article has been retracted; the retraction appears to center on textual plagarism, not experimental results. The homology to AvaIII is real. I think I believe it. tk 20:28, 9 December 2005 (EST). Rich Roberts reports: "We have tried ourselves to detect activity with this gene product and cannot detect any methyltransferase activity. In our case we used antibodies able to detect N6-methyladenine or N4 methylcytosine in DNA. The ones we have are very sensitive and should have been able to detect 5-methyl groups in the whole E. coli chromosome. Nothing was detected in an over-expressing strain."
• For additional information see E. coli restriction-modification system and the NEB technical information on methylation.

Commonly used strains

NEB 10-beta (NEB)

K-12 str. DH10B fhuA

• NEB's DH10B version with fhuA–, imparting T1/T5/Φ80 phage-resistance.
• https://www.neb.com/products/c3019-neb-10-beta-competent-e-coli-high-efficiency

AG1

endA1 recA1 gyrA96 thi-1 relA1 glnV44 hsdR17(r_K^- m_K⁺)

AB1157

thr-1, araC14, leuB6(Am), Δ(gpt-proA)62, lacY1, tsx-33, qsr'-0, glnV44(AS), galK2(Oc), LAM-, Rac-0, hisG4(Oc), rfbC1, mgl-51, rpoS396(Am), rpsL31(strR), kdgK51, xylA5, mtl-1, argE3(Oc), thi-1

• Bachmann BJ: Derivation and genotypes of some mutant derivatives of Escherichia coli K-12.

Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology (Edited by: F C Neidhardt J L Ingraham KB Low B Magasanik M Schaechter H E Umbarger). Washington, D.C., American Society for Microbiology 1987, 2:1190-1219.
See CGSC#1157

B2155

thrB1004 pro thi strA hsdsS lacZD M15 (F′ lacZΔM15 lacI^q traD36 proAB⁺) ΔdapA::erm(Ery^R) pir::RP4 [::kan (Kan^R) from SM10]

• An E. coli strain carrying the pir sequence required for maintenance of plasmids containing R6K ori. Also, this strain is auxotrophic for DAP (diaminopimelic acid - a lysine precursor). The auxotrophy helps in removal of this strain from a bi-parental mating setup after conjugation.
• Ref: Maintenance of broad-host-range incompatibility group P and group Q plasmids and transposition of Tn5 in Bartonella henselae following conjugal plasmid transfer from Escherichia coli
  

Dehio, C. & Meyer, M. (1997) J. Bacteriol. 179, 538–540

BHB2688

F^- λ[Eam4 b2 red3 imm434 cIts Sam7] recA3 IN(rrnD-rrnE)1 rpsL200

• Streptomycin resistant
• The strain is meant for in vitro packaging of phage λ and cosmid DNA and is used for the preparation of freeze-thaw lysates (FTL).

See BCCM/GeneCorner Plasmid Collection #LMBP 8016

1. Hohn B. In vitro packaging of lambda and cosmid DNA. Methods Enzymol. 1979;68:299-309. DOI:10.1016/0076-6879(79)68021-7 |

BL21

E. coli B F^– ompT gal dcm lon hsdS_B(r_B^– m_B^–) [malB⁺]_K-12(λ^S)

• Galactose nonutilizing
• Deficient in Lon and OmpT proteases
• The "malB region" was transduced in from the K-12 strain W3110 to make the strain Mal⁺λ^S. See Studier et al. (2009) J. Mol. Biol. 394(4), 653 for a discussion of the extent of the transfer.
• Stratagene E. coli Genotype Strains

BL21[pT7POL26]

E. coli B F^– ompT gal dcm lon hsdS_B(r_B^–m_B^–) [malB⁺]_K-12(λ^S)

• Galactose nonutilizing
• This strain contains the low-copy auxiliary pT7POL26 vector for T7 promoter-driven protein expression, which is repressed until IPTG induction of T7 RNA polymerase expression occurs. The strain does not contain the lon protease and is also deficient in the outer membrane protease OmpT. The lack of two key proteases reduces the degradation of heterologous proteins expressed in the strain.

See BCCM/GeneCorner Plasmid Collection #LMBP 9558

BL21(AI)

E. coli B F^– ompT gal dcm lon hsdS_B(r_B^–m_B^–) [malB⁺]_K-12(λ^S) araB::T7RNAP-tetA

• an E. coli B strain carrying the T7 RNA polymerase gene in the araB locus of the araBAD operon^q.
• Transformed plasmids containing T7 promoter driven expression are repressed until L-arabinose induction of T7 RNA polymerase.
  • Maximal expression is lower than that of BL21(DE3) (customer support 10/2012)
• Derived from BL21.
• See the product page for more information.
• Brian Caliendo (Voigt lab) reported trouble getting the Datsenko and Wanner (2000) plasmid pCP20 to transform into this strain, when other strains transformed fine. Cause is unknown.

BL21(DE3)

E. coli str. B F^– ompT gal dcm lon hsdS_B(r_B^–m_B^–) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB⁺]_K-12(λ^S)

• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
• Derived from B834 (Wood, 1966) by transducing to Met⁺.
• Whole genome sequence available [3]

See BCCM/GeneCorner Plasmid Collection #LMBP 1455

2. Studier FW, Rosenberg AH, Dunn JJ, and Dubendorff JW. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990;185:60-89. DOI:10.1016/0076-6879(90)85008-c |

BL21(DE3) pLysS

E. coli str. B F^– ompT gal dcm lon hsdS_B(r_B^–m_B^–) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB⁺]_K-12(λ^S) pLysS[T7p20 ori_p15A](Cm^R)

• pLysS plasmid chloramphenicol resistant; grow with chloramphenicol to retain plasmid.
• Chloramphenicol resistant
• The pLysS plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.
• see Moffatt87 for details of pLysS and pLysE plasmids

See BCCM/GeneCorner Plasmid Collection #LMBP 2462

BL21(DE3) pLysE

E. coli str. B F^– ompT gal dcm lon hsdS_B(r_B^–m_B^–) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB⁺]_K-12(λ^S) pLysS[T7p20 ori_p15A](Cm^R)

• pLysE plasmid chloramphenicol resistant; grow with chloramphenicol to retain plasmid.
• Chloramphenicol resistant
• The pLysE plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which almost eliminates expression from transformed T7 promoter containing plasmids when not induced. pLysE produces higher amounts of T7 lysozyme than pLysS to further reduce basal level expression of recombinant genes by inhibiting basal levels of T7 RNA polymerase. This makes BL21(DE3)[pLysE] more suitable for expressing toxic genes
• see Moffatt87 for details of pLysS and pLysE plasmids

See BCCM/GeneCorner Plasmid Collection #LMBP 2468

BLR

F^– ompT gal dcm hsdS_B(r_K^–m_B^–) Δ(srl-recA)306::Tn10(Tet^R)

BNN93

F^- tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1 mcrB e14-(mcrA^-) hsdR(r_K^-m_K⁺) λ^-

• Some C600 strains are really BNN93

BNN97

• BNN93 (λgt11)
  • A λgt11 lysogen producing phage at 42C

BW25113

lacI⁺rrnB_T14 ΔlacZ_WJ16 hsdR514 ΔaraBAD_AH33 ΔrhaBAD_LD78 rph-1
Δ(araB–D)567 Δ(rhaD–B)568 ΔlacZ4787(::rrnB-3) hsdR514 rph-1

• Parent strain for Keio collection single-gene knockout strains
• Arabinose, rhamnose, lactose nonutilizing

BW26434, CGSC Strain # 7658

Δ(araD-araB)567, Δ(lacA-lacZ)514(::kan), lacIp-4000(lacI^q), λ^-, rpoS396(Am)?, rph-1, Δ(rhaD-rhaB)568, hsdR514

• This information is from a printout sent by the E. coli Genetic Stock Center with the strain.
• B.L. Wanner strain
• rph-1 is a 1bp deletion that results in a frameshift over last 15 codons and has a polar effect on pyrE leading to suboptimal pyrimidine levels on minimal medium. (Jensen 1993 J Bact. 175:3401)
• Δ(araD-araB)567 was formerly called ΔaraBAD_AH33 by Datsenko and Wanner
• Am = amber(UAG) mutation
• Reference: Datsenko and Wanner, 2000, PNAS, 97:6640

NOTE:

• This promoter driving the expression of lacI was sequenced in this strain using a primer in mhpR (upstream of lacI) and a primer in the opposite orientation in lacI. The lac promoter was found to be identical to wildtype. Thus, the -35 sequence was GCGCAA not GTGCAA as expected with lacI^q. Therefore this strain (or at least the version obtained from the E. coli Genetic Stock Center) does NOT appear to be lacI^q. According to Barry Wanner, this is an unexpected result. -Reshma 13:19, 5 May 2005 (EDT)
• "We have now confirmed that BW25113, BW25141, and BW26434 are all lacI⁺, and not lacI^q. We thank you for alerting us to the error with respect to BW26434. Apparently, the lacI region was restored to wild-type in a predecessor of BW25113." (from Barry Wanner November 18, 2005)
• The genotype has been corrected at the CGSC

BW313

Hfr ung-1 relA1 dut-1 spoT1 thi-1 See BCCM/GeneCorner Plasmid Collection #LMBP 1325

3. Kunkel TA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488-92. DOI:10.1073/pnas.82.2.488 |

C600

F^- tonA21 thi-1 thr-1 leuB6 lacY1 glnV44 rfbC1 fhuA1 λ^-

• There are strains circulating with both e14+(mcrA⁺) and e14-(mcrA^-)
• General purpose host

See BCCM/GeneCorner Plasmid Collection LMBP 8013
See CGSC#3004

• References: Appleyard, R.K. (1954) Genetics 39, 440; Hanahan, D. (1983) J. Mol. Biol. 166, 577.

C600 hflA150 (Y1073, BNN102)

F^- thi-1 thr-1 leuB6 lacY1 tonA21 glnV44 λ^- hflA150(chr::Tn10)

• host for repressing plaques of λgt10 when establishing cDNA libraries
• Reference Young R.A. and Davis, R. (1983) Proc. Natl. Acad. Sci. USA 80, 1194.
• Tetracycline resistance from the Tn10 insertion

CSH50

F^- λ^- ara Δ(lac-pro) rpsL thi fimE::IS1

• See CGSC#8085
• References: Miller, J.H. 1972. Expts.in Molec.Genetics, CSH 0:14-0; Blomfeld et al., J.Bact. 173: 5298-5307, 1991.

D1210

HB101 lacI^q lacY⁺

NEB dam^–/dcm^– (NEB)

K-12 ara-14 leuB6(Am) fhuA31 lacY1 tsx78 glnV44(supE44) galK2 galT22 mcrA dcm6 hisG4 rfbD1 R(zgb-210::Tn10)(Tet^S)) endA1 rspL-136(Str^R) dam13::Tn9(Chl^R) xylA5 mtl-1 thi-1 mcrB1 hsdR2

• Identical published genotype to strain ER2925; perhaps just renamed by NEB.
• Makes plasmids free of Dam/Dcm methylation; increases mutation rate.
• Endonuclease I-deficient.
• T1/T5/Φ80/T6 phage-resistant.
• Amber suppressor UAG>CAG(Gln).
• Low but noticeable frequency of Kan^R mutations.
• Thiamine and histidine auxotroph. May be leucine prototroph: leuB6(Am) should be complemented by glnV44.
• Galactose, Xylose, Arabinose, Mannitol non-utilizing (predicted by genotype).
• Resistant to streptomycin, chloramphenicol, nitrofurantoin, Colicin K, and 2–deoxygalactose
• References:
  • New England Biolabs, product catalogue number C2925H

DB3.1

F- gyrA462 endA1 glnV44 Δ(sr1-recA) mcrB mrr hsdS20(r_B^-, m_B^-) ara14 galK2 lacY1 proA2 rpsL20(Str^R) xyl5 Δleu mtl1

• useful for propagating plasmids containing the ccdB operon.
• gyrA462 enables ccdB containing plasmid propagation
• streptomycin resistant
• appears to NOT contain lacI (based on a colony PCR) --Austin Che 16:16, 18 June 2007 (EDT)

See BCCM/GeneCorner Plasmid Collection #LMBP 4098

4. Bernard P and Couturier M. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol. 1992 Aug 5;226(3):735-45. DOI:10.1016/0022-2836(92)90629-x |
5. Miki T, Park JA, Nagao K, Murayama N, and Horiuchi T. Control of segregation of chromosomal DNA by sex factor F in Escherichia coli. Mutants of DNA gyrase subunit A suppress letD (ccdB) product growth inhibition. J Mol Biol. 1992 May 5;225(1):39-52. DOI:10.1016/0022-2836(92)91024-j |

DC10B

mcrA Δmrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm

• DNA cytosine methyltransferase (dcm) negative mutant of E. coli K12 DH10B
• The strain is meant as a universal Staphylococcal cloning host
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9585

6. Monk IR, Shah IM, Xu M, Tan MW, and Foster TJ. Transforming the untransformable: application of direct transformation to manipulate genetically Staphylococcus aureus and Staphylococcus epidermidis. mBio. 2012;3(2). DOI:10.1128/mBio.00277-11 |

DH1

F^– λ^– endA1 recA1 relA1 gyrA96 thi-1 glnV44 hsdR17(r_K^–m_K^–)

• Parent of DH5α
• A Hoffman-Berling 1100 strain derivative (Meselson68)
• More efficient at transforming large (40-60Kb) plasmids
• Thiamine auxotroph
• Lactose nonutilizing
• Nalidixic acid resistant
• Recombination-deficient
• Relaxed phenotype
• Endonuclease A deficient

7. Meselson M and Yuan R. DNA restriction enzyme from E. coli. Nature. 1968 Mar 23;217(5134):1110-4. DOI:10.1038/2171110a0 |

DH5α

F^– endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(r_K^–m_K⁺), λ^–

• A Hoffman-Berling 1100 strain derivative (Meselson68)
• Promega also lists phoA
• Thiamine, arginine auxotroph
• Lactose nonutilizing
• Nalidixic acid resistant
• Recombination-deficient
• Relaxed phenotype
• Endonuclease A deficient
• Constitutive deoxyribose synthesis, good for cloning large plasmids.
• Amber suppressor UAG>CAG(Gln).
• Slow growth in M9 medium due to purB-20
• References:
  • FOCUS (1986) 8:2, 9.
  • Hanahan, D. (1985) in DNA Cloning: A Practical Approach (Glover, D.M., ed.), Vol. 1, p. 109, IRL Press, McLean, Virginia.
  • Grant, S.G.N. et al. (1990) Proc. Natl. Acad. Sci. USA 87: 4645-4649 PMID 2162051.
  • Meselson M. and Yuan R. (1968) Nature 217:1110 PMID 4868368.

DH5αF

F⁺ endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(r_K^–m_K⁺), λ^–

• This strain contains the F factor of NK3 and therefore can be used for infection with M13 or fd phages and derivatives.
• Thiamine, arginine auxotroph
• Lactose nonutilizing
• Nalidixic acid resistant
• Recombination-deficient
• Relaxed phenotype
• Endonuclease A deficient
• Constitutive deoxyribose synthesis, good for cloning large plasmids.

See BCCM/GeneCorner Plasmid Collection #LMBP 1596

DH5αF(λ)

F⁺ endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG purB20 φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(r_K^–m_K⁺), λ⁺

• This strain contains the F factor of NK3 and therefore can be used for infection with M13 or fd phages and derivatives.
• In addition the strain is lysogenic for wild-type phage λ; cultivate at 28°C to keep phage λ stably integrated.
• Thiamine, arginine auxotroph
• Lactose nonutilizing
• Nalidixic acid resistant
• Recombination-deficient
• Relaxed phenotype
• Endonuclease A deficient
• Constitutive deoxyribose synthesis, good for cloning large plasmids.

See BCCM/GeneCorner Plasmid Collection #LMBP 2846

DH5αpir

endA1 hsdR17 glnV44 (= supE44) thi-1 recA1 gyrA96 relA1 φ80dlacΔ(lacZ)M15 Δ(lacZYA-argF)U169 zdg-232::Tn10 uidA::pir+

• tetracyclin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 7962

8. Platt R, Drescher C, Park SK, and Phillips GJ. Genetic system for reversible integration of DNA constructs and lacZ gene fusions into the Escherichia coli chromosome. Plasmid. 2000 Jan;43(1):12-23. DOI:10.1006/plas.1999.1433 |
9. Grant SG, Jessee J, Bloom FR, and Hanahan D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4645-9. DOI:10.1073/pnas.87.12.4645 |
10. Sitaras C, Beyde A, Malekazari P, and Herrington MB. Light producing reporter plasmids for Escherichia coli K-12 that can be integrated into the chromosome. Plasmid. 2011 May;65(3):232-8. DOI:10.1016/j.plasmid.2011.02.005 |

DH5αpir116 variant

endA1 hsdR17 glnV44 (= supE44) thi-1 recA1 gyrA96 relA1 φ80dlacΔ(lacZ)M15 Δ(lacZYA-argF)U169 zdg-232 uidA::pir116

• tetracyclin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 7961

8. Platt R, Drescher C, Park SK, and Phillips GJ. Genetic system for reversible integration of DNA constructs and lacZ gene fusions into the Escherichia coli chromosome. Plasmid. 2000 Jan;43(1):12-23. DOI:10.1006/plas.1999.1433 |
9. Grant SG, Jessee J, Bloom FR, and Hanahan D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4645-9. DOI:10.1073/pnas.87.12.4645 |
10. Sitaras C, Beyde A, Malekazari P, and Herrington MB. Light producing reporter plasmids for Escherichia coli K-12 that can be integrated into the chromosome. Plasmid. 2011 May;65(3):232-8. DOI:10.1016/j.plasmid.2011.02.005 |

DH10B (Invitrogen)

str. K-12 F^– Δ(ara-leu)7697[Δ(rapA'-cra' )] Δ(lac)X74[Δ('yahH-mhpE)] duplication(514341-627601)[nmpC-gltI] galK16 galE15 e14^–(icd^WT mcrA) φ80dlacZΔM15 recA1 relA1 endA1 Tn10.10 nupG rpsL150(Str^R) rph⁺ spoT1 Δ(mrr-hsdRMS-mcrBC) λ^– Missense(dnaA glmS glyQ lpxK mreC murA) Nonsense(chiA gatZ fhuA? yigA ygcG) Frameshift(flhC mglA fruB)

• An MC1061 derivative (Casadaban80). Prepare cells for chemical transformation with CCMB80 buffer
• Thermo TOP10 and NEB 10-beta commercial strains are close derivatives.
• Recombination-deficient (recA1)
• Endonuclease I-deficient (endA1)
• Relaxed phenotype (relA1)
• Constitutive deoxyribose synthesis for improving cloning of large plasmids
• Suitable for cloning methylated cytosine or adenine containing DNA
• High competence (galE^–)
• Blue/white screening with lacZα.
• While DH10B has been classically reported to be galU galK, the preliminary genome sequence for DH10B indicates that DH10B (and by their lineage also TOP10 and any other MC1061 derivatives) is actually (galE galK galU)⁺. Dcekiert 16:37, 23 January 2008 (CST)
• Genome sequence indicates that DH10B is actually deoR⁺. Presumably TOP10 and MC1061 are also deoR⁺.
• Streptomycin-resistant and 2-deoxygalactose-resistant
• Leucine auxotroph
• Arabinose, lactose, and galactose non-utilizing
• References:
  • Casdaban, M. and Cohen, S. (1980) J Mol Biol 138:179 PMID 6997493.
  • Grant, S.G.N. et al. (1990) Proc. Natl. Acad. Sci. USA 87: 4645-4649 PMID 2162051.
  • E. coli Genetic Stock Center, MC1061 Record
  • Durfee, Tim, et al. "The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse." Journal of bacteriology 190.7 (2008): 2597-2606.
  • RefSeq genome
  • Genome with gene names

DH12S (Invitrogen)

mcrA Δ(mrr-hsdRMS-mcrBC) φ80d lacZΔM15 ΔlacX74 recA1 deoR Δ(ara, leu)7697 araD139 galU galK rpsL F' [proAB⁺ lacI^qZΔM15]

• host for phagemid and M13 vectors
• useful for generating genomic libraries containing methylated cytosine or adenine residues
• streptomycin resistant
• References: Lin, J.J., Smith, M., Jessee, J., and Bloom, F. (1991) FOCUS 13, 96.; Lin, J.J., Smith, M., Jessee, J., and Bloom, F. (1992) BioTechniques 12, 718.

DM1 (Invitrogen)

F- dam-13::Tn9(Cm^R) dcm- mcrB hsdR-M+ gal1 gal2 ara- lac- thr- leu- tonR tsxR Su0

• Host for pBR322 and other non-pUC19 plasmids; useful for generating plasmids that can be cleaved with dam and dcm sensitive enzymes
• Chloramphenicol resistant
• Promega lists as F' not F-
• Reference: Lorow-Murray D and Bloom F (1991) Focus 13:20

DP50

F^- fhuA53 dapD8 lacY1 or Δ(cod-lacI)6 glnX44(AS) Δ(galuvrB)47 λ^- gyrA29 ΔthyA57 hsdS3

• Resistant to diaminopimelic acid and nalidixic acid
• The strain is meant for propagation of phage λ and phage λ Charon.

See BCCM/GeneCorner Plasmid Collection #LMBP 8014

11. Leder P, Tiemeier D, and Enquist L. EK2 derivatives of bacteriophage lambda useful in the cloning of DNA from higher organisms: the lambdagtWES system. Science. 1977 Apr 8;196(4286):175-7. DOI:10.1126/science.322278 |

E. cloni(r) 5alpha (Lucigen)

fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80 Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17

• Common cloning strain.

E. cloni(r) 10G (Lucigen)

F- mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 Φ80dlacZΔM15 ΔlacX74 araD139 Δ(ara,leu)7697 galU galK rpsL nupG λ- tonA

• Common cloning strain.
• Resistant to phage T₁.

E. cloni(r) 10GF' (Lucigen)

[F´ pro A+B+ lacIqZΔM15::Tn10 (TetR)] /mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 Φ80dlacZΔM15 ΔlacX74 araD139 Δ(ara, leu)7697 galU galK rpsL nupGλ tonA

• Strain for cloning and single-strand DNA production.

EPI300 (Epicentre)

F^– λ^– mcrA Δ(mrr-hsdRMS-mcrBC) Φ80dlacZΔM15 Δ(lac)X74 recA1 endA1 araD139 Δ(ara, leu)7697 galU galK rpsL (Str^R) nupG' trfA dhfr

• Recombination-deficient
• Endonuclease A-deficient
• Inducible trfA for controlling oriV
• Improved cloning 5-mC DNA
• Streptomycin resistant
• Leucine auxotroph
• Arabinose, galactose, lactose
• References
  • Product page

ER2738 (NEB)

K-12 F′[proAB⁺ lacI^q lacZΔM15 zzf::Tn10(Tet^R)] fhuA2 glnV Δ(lac-proAB) thi-1 Δ(hsdS-mcrB)5

• Phage propagation strain
• Modified E. coli str. NM522, with fhuA2 and tet-selectable F′.
• Also available from Lucigen Corporation.
• https://www.neb.com/products/e4104-ecoli-k12-er2738

ER2566 (NEB)

B F^– λ^– fhuA2 [lon] ompT lacZ::T7.1 gal sulA11 Δ(mcrC-mrr)114::IS10 R(mcr-73::miniTn10)(Tet^S)2 R(zgb-210::Tn10)(Tet^S) endA1 [dcm]

• Host strain for the expression of a target gene cloned in the pTYB vectors.
• Carry a chromosomal copy of the T7 RNA polymerase gene inserted into lacZ gene and thus under the control of the lac promoter. In the absence of IPTG induction expression of T7 RNA polymerase is suppressed by the binding of lac I repressor to the lac promoter.
• Deficient in both lon and ompT proteases.
• https://www.neb.com/-/media/catalog/datacards-or-manuals/e4130datasheet-lot0121503.pdf?rev=2c30363fc97f4656b9bc302b2824b3a3&hash=88062530C5B91D0BB3F6896395E44F07

ER2267 (NEB)

K-12 F′[proAB⁺ lacI^q lacZΔM15 zzf::miniTn10(Kan^R)] Δ(argF-lacZ)U169 glnV44 e14^–(mcrA^–) rfbD1? recA1 relA1? endA1 spoT1? thi-1 Δ(mcrC-mrr)114::IS10

• Commonly used for titering M13 phage because of the strain's F' plasmid, which carries Kan^R, and its slow growth, which promotes easy visualization of plaques.
• https://www.neb.com/products/e4103-ecoli-k12-er2267

FHK12

F' lacIq lacZΔM15 proA+B+ ara Δ(lac-proAB) rpsL (ϕ80dlacZΔM15) attB::(ctx::lacZ)

• Resistant to ampicillin and streptomycin
• The ctx::lacZ fusion integrated at the attB site is tagged with the ampicillin resistance gene.

See BCCM/GeneCorner Plasmid Collection #LMBP 11202

12. Kolmar H, Hennecke F, Götze K, Janzer B, Vogt B, Mayer F, and Fritz HJ. Membrane insertion of the bacterial signal transduction protein ToxR and requirements of transcription activation studied by modular replacement of different protein substructures. EMBO J. 1995 Aug 15;14(16):3895-904. DOI:10.1002/j.1460-2075.1995.tb00061.x |

GM31

F^- thr-1 araC14 leuB6(Am) fhuA31 lacY1 tsx-78 glnX44(AS) galK2(Oc) galT22 λ^- dcm-6 hisG4(Oc) rpsL136 xylA5 mtl-1 thiE1

• Resistant to streptomycin
• The strain is dcm^-

See BCCM/GeneCorner Plasmid Collection #LMBP 4433

13. Marinus MG, Carraway M, Frey AZ, Brown L, and Arraj JA. Insertion mutations in the dam gene of Escherichia coli K-12. Mol Gen Genet. 1983;192(1-2):288-9. DOI:10.1007/BF00327681 |

GM124

F^- lacZ118(Oc) rpsL275 dam-4

• Resistant to streptomycin
• The strain is dam^-

See BCCM/GeneCorner Plasmid Collection #LMBP 4434

13. Marinus MG, Carraway M, Frey AZ, Brown L, and Arraj JA. Insertion mutations in the dam gene of Escherichia coli K-12. Mol Gen Genet. 1983;192(1-2):288-9. DOI:10.1007/BF00327681 |

GM2198

F^- thr-1 araC14 leuB6(Am) fhuA31 lacY1 tsx-78 glnX44(AS) galK2(Oc) λ^- dcm-6 hisG4(Oc) rpsL136 dam-13::Tn9 xylA5 mtl-1 thiE1

• Resistant to streptomycin and chloramphenicol
• The strain is dam^- and dcm^-.

See BCCM/GeneCorner Plasmid Collection #LMBP 4435

13. Marinus MG, Carraway M, Frey AZ, Brown L, and Arraj JA. Insertion mutations in the dam gene of Escherichia coli K-12. Mol Gen Genet. 1983;192(1-2):288-9. DOI:10.1007/BF00327681 |

H12R8a

Hfr Su+ supF

• phosphatase positive strain with H12 amber mutation in the phosphatase gene

See BCCM/GeneCorner Plasmid Collection #LMBP 4980

14. Garen A, Garen S, and Wilhelm RC. Suppressor genes for nonsense mutations. I. The Su-1, Su-2 and Su-3 genes of Escherichia coli. J Mol Biol. 1965 Nov;14(1):167-78. DOI:10.1016/s0022-2836(65)80238-8 |
15. Remaut E and Fiers W. Studies on the bacteriophage MS2. XVI. The termination signal of the A protein cistron. J Mol Biol. 1972 Nov 14;71(2):243-61. DOI:10.1016/0022-2836(72)90349-x |
16. Weigert MG, Lanka E, and Garen A. Amino acid substitutions resulting from suppression of nonsense mutations. II. Glutamine insertion by the Su-2 gene; tyrosine insertion by the Su-3 gene. J Mol Biol. 1965 Dec;14(2):522-7. DOI:10.1016/s0022-2836(65)80201-7 |

HB94

F^- Hfr gal-55 λ^- relA1 spoT1 thiE1 hsdR4

• r^- m_K⁺

See BCCM/GeneCorner Plasmid Collection #LMBP 7992

17. Boyer HW and Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459-72. DOI:10.1016/0022-2836(69)90288-5 |

HB101

F^- mcrB mrr hsdS20(r_B^- m_B^-) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20(Str^R) glnV44 λ^-

Please note that different sources have different genotypes so treat this information with caution.

• From a GIBCO BRL list of competent cells.

• Hybrid of E. coli K12 and E. coli B (but 98% K strain AB266 according to Smith et al.)
• Host for pBR322 and many plasmids
• Sigma lists the deletion Δ(gpt,proA). Check this.
• Promega does not list F-, mcrB, or mrr
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection LMBP 8015

• References:
  • Boyer, H.W. and Roulland-Dussoix, D. (1969) J. Mol. Biol. 41, 459.
  • Smith, M., Lorow, D., and Jessee, J. (1989) FOCUS 11, 56 - pdf version from Invitrogen
  • Lacks S and Greenberg JR (1977) J Mol Biol 114:153.

HMS174(DE3)

F- recA1 hsdR(rK12- mK12+) (DE3) (Rif R)

• HMS174 strains provide the recA mutation in a K-12 background. Like BLR, these strains may stabilize certain target genes whose products may cause the loss of the DE3 prophage.

• DE3 indicates that the host is a lysogen of lDE3, and therefore carries a chromosomal copy of the T7 RNA polymerase gene under control of the lacUV5 promoter. Such strains are suitable for production of protein from target genes cloned in pET vectors by induction with IPTG.

• Full genome sequence available LM993812 *J Mairhofer 07:36, 28 October 2014 (EDT):.

High-Control(tm) BL21(DE3) (Lucigen)

F^– ompT gal dcm hsdS_B(r_B^- m_B^-) (DE3)/Mini-F lacI^q1(Gent^r)

• The HI-Control BL21(DE3) cells contain a single-copy BAC plasmid harboring a specially engineered version of the lacI^q1 repressor allele. The lacI^q1 allele expresses ~170-fold more lac repressor protein than the wild-type lacI gene.
• The increased pool of lac repressor in HI-Control BL21(DE3) cells maintains tight control over the expression of T7 RNA polymerase from the lacUV5 promoter, reducing leaky expression of genes cloned under a T7 promoter.
• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.

High-Control(tm) 10G (Lucigen)

F- mcrA Δ(mrr-hsdRMS-mcrBC) endA1 recA1 Φ80dlacZΔM15 ΔlacX74 araD139 Δ(ara,leu)7697 galU galK rpsL nupG λ- tonA/Mini-F lacI^q1(Gent^r)

• The HI-Control 10G cells contain a single-copy BAC plasmid harboring a specially engineered version of the lacI^q1 repressor allele. The lacI^q1 allele expresses ~170-fold more lac repressor protein than the wild-type lacI gene.
• For stable cloning of T7 protein expression plasmids.
• Resistant to phage T₁.

IJ1126

E. coli K-12 recB21 recC22 sbcA5 endA gal thi Su+ Δ(mcrC-mrr)102::Tn10
See Endy:IJ1126

IJ1127

IJ1126 lacUV5 lacZ::T7p07-Knr
See Endy:IJ1127

IM01B

mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm ΩPhelp-hsdMS (CC1-2) ΩPN25-hsdS (CC1-1)

• DNA cytosine methyltransferase (dcm) negative mutant of E. coli K12 DH10B
• The hsdMS genes encoding methylase and specificity genes (from Staphylococcus aureus clonal complex 1 - MW2) were introduced into the chromosome at neutral locations via recombineering
• The strain can be transformed efficiently with large plasmids due to deoR (nupG) mutation
• Plasmids isolated from this E. coli strain transform S. aureus clonal complex 1 - MW2 at high efficiency
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9581

18. Monk IR, Tree JJ, Howden BP, Stinear TP, and Foster TJ. Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. mBio. 2015 May 26;6(3):e00308-15. DOI:10.1128/mBio.00308-15 |

IM08B

mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm ΩPhelp-hsdMS (CC8-2) ΩPN25-hsdS (CC8-1)

• DNA cytosine methyltransferase (dcm) negative mutant of E. coli K12 DH10B
• The hsdMS genes encoding methylase and specificity genes (from Staphylococcus aureus clonal complex 8 - NRS384) were introduced into the chromosome at neutral locations via recombineering
• The strain can be transformed efficiently with large plasmids due to deoR (nupG) mutation
• Plasmids isolated from this E. coli strain transform S. aureus clonal complex 8 - NRS384 at high efficiency
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9582

18. Monk IR, Tree JJ, Howden BP, Stinear TP, and Foster TJ. Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. mBio. 2015 May 26;6(3):e00308-15. DOI:10.1128/mBio.00308-15 |

IM30B

mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm ΩPhelp-hsdMS (CC30-2) ΩPN25-hsdS (CC30-1)

• DNA cytosine methyltransferase (dcm) negative mutant of E. coli K12 DH10B
• The hsdMS genes encoding methylase and specificity genes (from Staphylococcus aureus clonal complex 30 - MRSA252) were introduced into the chromosome at neutral locations via recombineering
• The strain can be transformed efficiently with large plasmids due to deoR (nupG) mutation
• Plasmids isolated from this E. coli strain transform S. aureus clonal complex 30 - MRSA252 at high efficiency
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9583

18. Monk IR, Tree JJ, Howden BP, Stinear TP, and Foster TJ. Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. mBio. 2015 May 26;6(3):e00308-15. DOI:10.1128/mBio.00308-15 |

IM93B

mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara-leu)7697 galU galK rpsL endA1 nupG Δdcm ΩPhelp-hsdMS (CC93-3) ΩPN25-hsdS/S (CC93-2/CC93-1)

• DNA cytosine methyltransferase (dcm) negative mutant of E. coli K12 DH10B
• The hsdMS genes encoding methylase and specificity genes (from Staphylococcus aureus sequence type 93-JKD6159) were introduced into the chromosome at neutral locations via recombineering
• The strain can be transformed efficiently with large plasmids due to deoR (nupG) mutation
• Plasmids isolated from this E. coli strain transform S. aureus sequence type 93-JKD6159 at high efficiency
• Streptomycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9584

18. Monk IR, Tree JJ, Howden BP, Stinear TP, and Foster TJ. Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. mBio. 2015 May 26;6(3):e00308-15. DOI:10.1128/mBio.00308-15 |

JK242

asnA31 asnB32 thi-1 relA spoT rpsL12

• The JK242 strain is auxotrophic for asparagine because of the inactivated asnA and asnB gene.
• It carries also the streptomycin-resistant allele, rpsL, a mutation leading to increased translational accuracy.

See BCCM/GeneCorner Plasmid Collection #LMBP 917

19. Parker J, Johnston TC, and Borgia PT. Mistranslation in cells infected with the bacteriophage MS2: direct evidence of Lys for Asn substitution. Mol Gen Genet. 1980;180(2):275-81. DOI:10.1007/BF00425839 |

JM83

rpsL ara Δ(lac-proAB) Φ80dlacZΔM15

• Sigma lists thi. Check this.
• streptomycin resistant

JM101

glnV44 thi-1 Δ(lac-proAB) F'[lacI^qZΔM15 traD36 proAB⁺]

• host for M13mp vectors
• recA⁺, r_K⁺
• original blue/white cloning strain
• has all wt restriction systems
• References: Messing, J. et al. (1981) Nucleic Acids Res. 9, 309; Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Gene 33, 103.

JM103

endA1 glnV44 sbcBC rpsL thi-1 Δ(lac-proAB) F'[traD36 proAB⁺ lacI^q lacZΔM15]

• streptomycin resistant
• References: Hanahan, D. (1983) J. Mol. Biol. 166:557-80.
• NEB says this strain encodes a prophage encoded EcoP1 endonuclease.
• Sigma lists (P1) (r_K^-m_K⁺ rP1⁺ mP1⁺)

JM105

endA1 glnV44 sbcB15 rpsL thi-1 Δ(lac-proAB) [F' traD36 proAB⁺ lacI^q lacZΔM15] hsdR4(r_K^-m_K⁺)

• Sigma lists sbcC
• streptomycin resistant
• References: Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Gene 33, 103.

JM106

endA1 glnV44 thi-1 relA1 gyrA96 Δ(lac-proAB) F^- hsdR17(r_K^-m_K⁺)

• References: Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Gene 33, 103.

JM107

endA1 glnV44 thi-1 relA1 gyrA96 Δ(lac-proAB) [F' traD36 proAB⁺ lacI^q lacZΔM15] hsdR17(R_K^- m_K⁺) λ^-

• host for M13mp vectors
• recA+, r_K+
• Sigma lists e14- (McrA-)
• nalidixic acid resistant
• References: Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Gene 33, 103.

JM108

endA1 recA1 gyrA96 thi-1 relA1 glnV44 Δ(lac-proAB) hsdR17 (r_K^- m_K⁺)

• nalidixic acid resistant
• deficient in expression of the lon protease due to IS186 transposon insertion -- J Mairhofer 18:59, 24 March 2010 (CET)

20. Mairhofer J, Cserjan-Puschmann M, Striedner G, Nöbauer K, Razzazi-Fazeli E, and Grabherr R. Marker-free plasmids for gene therapeutic applications--lack of antibiotic resistance gene substantially improves the manufacturing process. J Biotechnol. 2010 Apr 1;146(3):130-7. DOI:10.1016/j.jbiotec.2010.01.025 |

JM109

endA1 glnV44 thi-1 relA1 gyrA96 recA1 mcrB⁺ Δ(lac-proAB) e14- [F' traD36 proAB⁺ lacI^q lacZΔM15] hsdR17(r_K^-m_K⁺)

• From NEB
• Partly restriction-deficient; good strain for cloning repetitive DNA (RecA^–).
• Suppresses many amber mutations when glutamine is acceptable but not the S₁₀₀ or S₇ mutations of λ, e.g., λgt11.
• Can also be used for M13 cloning/sequencing and blue/white screening.
  
• Sigma lists e14-
• nalidixic acid resistant
• deficient in expression of the lon protease due to IS186 transposon insertion -- J Mairhofer 18:59, 24 March 2010 (CET)
• From C. Yanisch-Perron, J. Vieira, and J. Messing. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene, 33(1):103–19, 1985.
  
• Some information from Mary Berlyn at the E. coli Genetic Stock Center: One of the reasons the original curator of this collection did not accession the JM109, JM103, etc. strains was because she found it impossible to be sure of the derivation and therefore the details of the genotype. But I think it's safe to assume that the F' in this strain is derived from or similar to F128 which extends from the proBA region through the lac operon. It thus carries the wildtype genes for all loci in that region except those indicated as mutant for the genotype of the F'. So it carries the lacZ (alpha-complementation) deletion lacZ58(M150 and the lacI mutation lacIq, but it has the lacY+ gene also on the F-prime. On the chromosome it lacks all the lac operon genes.

NOTE: The promoter driving the expression of lacI was sequenced in this strain using a primer in mhpR (upstream of lacI) and a primer in the opposite orientation in lacI. The lac promoter was found to be identical to wildtype. Thus, the -35 sequence was GCGCAA not GTGCAA as expected with lacI^Q. Therefore this strain (or at least the version we have) does NOT appear to be lacI^Q unless there is another copy of lacI elsewhere. This result is somewhat confirmed by the fact that a lacI regulated promoter driving expression of YFP on a medium copy vector does not repress completely. -Reshma 13:48, 5 May 2005 (EDT)

JM109(DE3)

JM109 + λ(DE3)

• DE3 prophage carrying T7 polymerase expression cassette
• Same cassette as BL21(DE3) carrying a lac inducible T7 RNA polymerase and lacI^q
• nalidixic acid resistant

JM110

rpsL thr leu thi lacY galK galT ara tonA tsx dam dcm glnV44 Δ(lac-proAB) e14- [F' traD36 proAB⁺ lacI^q lacZΔM15] hsdR17(r_K^-m_K⁺)

• Sigma fails to list tonA tsx e14 fhuA hsdR17
• (e14-) status uncertain
• streptomycin resistant

JM2.300

lacI22, LAM-, e14-, rpsL135(strR), malT1(LamR), xyl-7, mtl-1, thi-1

• Some folks have been using this strain (i.e., Elowitz, Gardner) and it took me too long to find the CGSC#.
• This strain is no longer available from the CGSC
• This strain may also be F-. JM2.300 is described as F-, lacI22, λ-, e14-, rpsL135(StrR), thi-1 in K. Brenner, D. Karig, R. Weiss, F. Arnold, “Engineered biodirectional communication mediates a consensus in a microbial biofilm consortium,” in Proc. Natl. Acad. Sci. USA, 2007 Oct 30;104(44):17300-4.

JTK165

str. MC1061 Δupp:(pir dhfr(Tmp^R)) Δ(rfbB–wbbL')::repA

More detailed:
str. MC1061[K-12 F^– λ^– Δ(ara-leu)7697 [araD139]B/r Δ(codB-lacI)3 galK16 galE15 e14^– mcrA0 relA1 rpsL150(Str^R) spoT1 mcrB1 hsdR2(r^–m⁺)] Δupp::(P_con(BBa_J23100)-rbs(?)-pir-BBa_B0015(rrfBt(rrnBt)+T7t) - FRT - P_con(BBa_J23119)-4krbs-dhfr (Tmp^R)-tR2 - FRT) Δ(rfbB–wbbL')::(P_con(BBa_J23119)-rbs(?)-repA-BBa_B0015(rrfBt(rrnBt)+T7t) - FRT)

• Propagates R6K- and ColE2-origin plasmids by expressing pir and repA, respectively.
• Relaxed phenotype
• lacI^–
• Improved cloning 5-mC DNA
• Str^R Spc^R Tmp^R(FRT-flanked)
• Leucine auxotroph
• Galactose, lactose, arabinose nonutilizing
• Generic DIAL strain

21. Kittleson JT, Cheung S, and Anderson JC. Rapid optimization of gene dosage in E. coli using DIAL strains. J Biol Eng. 2011 Jul 25;5:10. DOI:10.1186/1754-1611-5-10 |

K12 3000

hfrH relA1 spoT1 thi-1

• This strain is designed for propagation of F+ specific phages

See BCCM/GeneCorner Plasmid Collection #LMBP 1393

22. Loomis WF Jr and Magasanik B. The catabolite repression gene of the lac operon in Escherichia coli. J Mol Biol. 1967 Feb 14;23(3):487-94. DOI:10.1016/s0022-2836(67)80120-7 |

K12ΔH1Δtrp

lacZam Δ(bio-uvrB) Δ(trpE-A)2 rpsL λ(Nam7Nam53 cI857 ΔH1)

• spectinomycin resistant
• Expression host for plasmids containing phage λ's PL or PR promoter. Induction is obtained by shifting the culture from 28°C to 42°C.
• The resident λ is a defective lysogen. .
• cI857 is ind-

See BCCM/GeneCorner Plasmid Collection #LMBP 69

23. Bernard HU, Remaut E, Hershfield MV, Das HK, Helinski DR, Yanofsky C, and Franklin N. Construction of plasmid cloning vehicles that promote gene expression from the bacteriophage lambda pL promoter. Gene. 1979 Jan;5(1):59-76. DOI:10.1016/0378-1119(79)90092-1 |
24. Remaut E, Stanssens P, and Fiers W. Plasmid vectors for high-efficiency expression controlled by the PL promoter of coliphage lambda. Gene. 1981 Oct;15(1):81-93. DOI:10.1016/0378-1119(81)90106-2 |

LE392

glnV44 supF58 (lacY1 or ΔlacZY) galK2 galT22 metB1 trpR55 hsdR514(r_K^-m_K⁺)

• Sigma lists F- e14-

LK111

F' lac-pro Δ(lacZ)M15 / thi-1 thr-1 leuB6 tonA lacI- Δ(lacZ)M15 lacY+ supE44 P1s

• r_k^- m_K⁺

See BCCM/GeneCorner Plasmid Collection #LMBP 4706

25. Zabeau M and Stanley KK. Enhanced expression of cro-beta-galactosidase fusion proteins under the control of the PR promoter of bacteriophage lambda. EMBO J. 1982;1(10):1217-24. DOI:10.1002/j.1460-2075.1982.tb00016.x |

M15 (Qiagen)

F-, Φ80ΔlacM15, thi, lac-, mtl-, recA+ , KmR

• From Qiagen
• E. coli M15 DZ291
• Qiagen variant includes the pREP4 plasmid which confers kanamycin resistance and constitutively expresses the lac repressor protein encoded by the lac I gene.
• M15 cannot be infected by lambda phages
• PL promoter introduced; however, is not active
• References:
  • QIAexpress® Data Sheet: E. coli strain M15 - (EN)
  • Villarejo, M.R. and Zabin, I. (1974) J. Bacteriol. 120, 466. PMID 4607501.

M5219

lacZam trpAam rpsL λ(bio252 cI857 ΔH1)

• streptomycin resistant
• Expression host for plasmids containing phage λ's PL or PR promoter. Induction is obtained by shifting the culture from 28°C to 42°C.
• The resident λ is a defective lysogen.
• cI857 is ind-

See BCCM/GeneCorner Plasmid Collection #LMBP 130

24. Remaut E, Stanssens P, and Fiers W. Plasmid vectors for high-efficiency expression controlled by the PL promoter of coliphage lambda. Gene. 1981 Oct;15(1):81-93. DOI:10.1016/0378-1119(81)90106-2 |

Mach1

str. W ΔrecA1398 endA1 fhuA Φ80Δ(lac)M15 Δ(lac)X74 hsdR(r_K^–m_K⁺)

• From Invitrogen
• lacZα-complementation ready
• T1/T5/Φ80 phage resistant
• Doubling time approx. 50 min and supposedly fastest growing chemically competent cloning strain available
• Derivatives of E. coli W strains (ATCC 9637, S. A. Waksman), rather than E. coli K-12. This may have implications for BL-1 status for some facilities (apparently not for MIT).
• See Bloom04 patent for details on the construction and properties of this strain.

MC1061

str. K-12 F^– λ^– Δ(ara-leu)7697 [araD139]B/r Δ(codB-lacI)3 galK16 galE15 e14^– mcrA0 relA1 rpsL150(Str^R) spoT1 mcrB1 hsdR2(r^–m⁺)

• Streptomycin resistant
• Relaxed phenotype
• Leucine auxotroph
• Galactose, lactose, arabinose nonutilizing
• The thr-leu region was transduced from an E. coli B/r strain (SB3118) in early steps of strain construction.
• Parent of DH10B/TOP10 and derived strains
• References:
  • E. coli Genetic Stock Center, MC1061 Record
  • BCCM/GeneCorner Plasmid Collection #LMBP 472
  • Complete DH10B sequence is available, see Durfee et al., 2008.

26. Casadaban MJ and Cohen SN. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179-207. DOI:10.1016/0022-2836(80)90283-1 |
27. Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörgo B, Pósfai G, Weinstock GM, and Blattner FR. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 Apr;190(7):2597-606. DOI:10.1128/JB.01695-07 |

MC1061(λ)

Δ(araA-leu)7697 [araD139]B/r Δ(codB-lacI)3 = Δlac74 galK16 galE15 e14- mcrA0 relA1 rpsL150 spoT1 mcrB1 hsdR2 λ+

• streptomycin resistant
• r_k^–m_k⁺
• recommended growth at 28°C

See BCCM/GeneCorner Plasmid Collection #LMBP 1061

28. Mertens N, Remaut E, and Fiers W. Versatile, multi-featured plasmids for high-level expression of heterologous genes in Escherichia coli: overproduction of human and murine cytokines. Gene. 1995 Oct 16;164(1):9-15. DOI:10.1016/0378-1119(95)00505-z |
29. Casadaban MJ and Cohen SN. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179-207. DOI:10.1016/0022-2836(80)90283-1 |

MC1061Rif

Δ(araA-leu)7697 [araD139]B/r Δ(codB-lacI)3 = Δlac74 galK16 galE15 e14- mcrA0 relA1 rpsL150 spoT1 mcrB1 hsdR2

• streptomycin resistant
• rifampicin resistant
• r_k^–m_k⁺

See BCCM/GeneCorner Plasmid Collection #LMBP 3319

29. Casadaban MJ and Cohen SN. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179-207. DOI:10.1016/0022-2836(80)90283-1 |

MC4100

F^- [araD139]_B/r Δ(argF-lac)169* &lambda^- e14- flhD5301 Δ(fruK-yeiR)725 (fruA25)‡ relA1 rpsL150(strR) rbsR22 Δ(fimB-fimE)632(::IS1) deoC1

• The thr-leu region was transduced from an E. coli B/r strain (SB3118) in early steps of strain construction.
• This paper compares MC4100 to MG1655 and describes the significant deletions.

• *The paper referenced above showed that this deletion was larger than previously known. The deletion now covers ykfD-b0350.

• ‡The fruA25 allele is attributed to the deletion of fruK-yeiR. This means fruA is present but its promoter has been deleted.

• The paper also shows that the e14 element is deleted in MC4100. One of the genes removed by this deletion is mcrA, which encodes an enzyme that restricts DNA containing methylcytosine. However, other E. coli K-12 restriction/modification systems are still present in MC4100. MC4100 still encodes the McrBC 5-methylcytosine=specific restriction enzyme and the HsdR/HsdS/HsdM type I restriction-modification complex.

• Table three of the paper lists all genes believed to be deleted in MC4100. The methods used in the paper can detect deletions but not loss of function mutations.

• See CGSC#6152
  

MFDpir

MG1655 RP4-2-Tc::[ΔMu1::aac(3)IV-ΔaphA-Δnic35-ΔMu2::zeo] ΔdapA::(erm-pir) ΔrecA

E. coli strain for performing biparental mating to transfer plasmids to other bacteria. This strain was constructed after noticing that the common conjugation strains, SM10 and S17-1, were Hfr+ and also transferring a Mu transposon to the recipient strain.

Refer >> Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008518/

MG1655

K-12 F^– λ^– ilvG^– rfb-50 rph-1

This is the "wild type" K-12 strain which was sequenced, and should be used when PCRing genes from the sequenced genome. It also looks very healthy under the microscope -- a dramatic difference from most of the cloning strains, which appear sick.

• See CGSC#6300
• See ATCC 700926

30. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, and Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. DOI:10.1126/science.277.5331.1453 |

• More accurate sequence correcting 243 errors in the original sequencing[31]. New Genbank accession number U00096.2
  • Latest genome sequence can be found with Genbank accession number U00096.3

MG1655 seqA-eYFP

K-12 F^– λ^– ilvG^– rfb-50 rph-1 seqA-eYFP:km^R

• The native seqA gene was fused at its 3' end to the fluorescent protein eYFP, separated with a linker (ASPPPGRSR) and followed by a kanamycin resistance marker. The entire cassette was integrated in the chromosome of E. coli K12 MG1655.
• This strain can be used to study the subcellular localization of the E. coli DNA binding protein SeqA.
• Kanamycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9776

32. Mika JT, Vanhecke A, Dedecker P, Swings T, Vangindertael J, Van den Bergh B, Michiels J, and Hofkens J. A study of SeqA subcellular localization in Escherichia coli using photo-activated localization microscopy. Faraday Discuss. 2015;184:425-50. DOI:10.1039/c5fd00058k |

MG1655 seqA-mEOS3.2

K-12 F^– λ^– ilvG^– rfb-50 rph-1 seqA-mEOS3.2:km^R

• The native seqA gene was fused at its 3' end to the fluorescent protein gene mEOS3.2, separated with a linker (ASPPPGRSR) and followed by a kanamycin resistance marker. The entire cassette was integrated in the chromosome of E. coli K12 MG1655.
• This strain can be used to study the subcellular localization of the E. coli DNA binding protein SeqA.
• Kanamycin resistant

See BCCM/GeneCorner Plasmid Collection #MBP 9777

32. Mika JT, Vanhecke A, Dedecker P, Swings T, Vangindertael J, Van den Bergh B, Michiels J, and Hofkens J. A study of SeqA subcellular localization in Escherichia coli using photo-activated localization microscopy. Faraday Discuss. 2015;184:425-50. DOI:10.1039/c5fd00058k |

MG1655 seqA-PAmCherry

K-12 F^– λ^– ilvG^– rfb-50 rph-1 seqA-PAmCherry:km^R

• The native seqA gene was fused at its 3' end to the fluorescent protein gene PAmCherry, separated with a linker (ASPPPGRSR) and followed by a kanamycin resistance marker. The entire cassette was integrated in the chromosome of E. coli K12 MG1655.
• PAmCherry is a photoactivatable variant of the red fluorescent protein mCherry. PAmCherry is not fluorescent until it is exposed to 350-400 nm light.
• This strain can be used to study the subcellular localization of the E. coli DNA binding protein SeqA.
• Kanamycin resistant

See BCCM/GeneCorner Plasmid Collection #LMBP 9778

32. Mika JT, Vanhecke A, Dedecker P, Swings T, Vangindertael J, Van den Bergh B, Michiels J, and Hofkens J. A study of SeqA subcellular localization in Escherichia coli using photo-activated localization microscopy. Faraday Discuss. 2015;184:425-50. DOI:10.1039/c5fd00058k |

OmniMAX2

From Invitrogen: "This strain constitutively expresses LacI (lacI^q). For blue/white screening, you will need to add IPTG to induce expression from the lacZp promoter. Strain is resistant to T₁ bacteriophage."

I called Thermo Fisher Scientific on 11/14/2019 to inquire about the parent strain of their OmniMax 2 cell line (listed generally here: https://www.thermofisher.com/us/en/home/life-science/cloning/competent-cells-for-transformation/chemically-competent.html), and they said that the parental genotype is DH5alpha. The "2" indicates an improvement over the original OmniMax strain, but it is still a DH5alpha parental strain. -AJVincelli

F′[proAB⁺ lacI^q lacZΔM15 Tn10(Tet^R) Δ(ccdAB)] mcrA Δ(mrr-hsdRMS-mcrBC) φ80(lacZ)ΔM15 Δ(lacZYA-argF)U169 endA1 recA1 glnV44 thi-1 gyrA96(Nal^R) relA1 tonA panD

• Thiamine auxotroph
• Pantothenate auxotroph
• Relaxed phenotype
• Recombination-deficient
• Endonuclease A-deficient
• Lactose-nonutilizing
• Tetracycline-resistant
• More susceptible(?) to CcdB through deletion of native ccdAB toxin-antitoxin system.

OverExpress(tm)C41(DE3) (Lucigen)

F^– ompT gal dcm hsdS_B(r_B^- m_B^-)(DE3)

• The OverExpress strains contain genetic mutations phenotypically selected for conferring tolerance to toxic proteins. The strain C41(DE3) was derived from BL21(DE3). This strain has at least one uncharacterized mutation, which prevents cell death associated with expression of many recombinant toxic proteins. The strain C43(DE3) was derived from C41(DE3) by selecting for resistance to a different toxic protein and can express a different set of toxic proteins to C41(DE3).
• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.

OverExpress(tm)C41(DE3)pLysS (Lucigen)

F^– ompT gal dcm hsdS_B(r_B^- m_B^-)(DE3)pLysS (Cm^r)

• The OverExpress strains contain genetic mutations phenotypically selected for conferring tolerance to toxic proteins. The strain C41(DE3) was derived from BL21(DE3). This strain has at least one uncharacterized mutation, which prevents cell death associated with expression of many recombinant toxic proteins. The strain C43(DE3) was derived from C41(DE3) by selecting for resistance to a different toxic protein and can express a different set of toxic proteins to C41(DE3).
• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
• The pLysS plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.

OverExpress(tm)C43(DE3) (Lucigen)

F^– ompT gal dcm hsdS_B(r_B^- m_B^-)(DE3)

• The OverExpress strains contain genetic mutations phenotypically selected for conferring tolerance to toxic proteins. The strain C41(DE3) was derived from BL21(DE3). This strain has at least one uncharacterized mutation, which prevents cell death associated with expression of many recombinant toxic proteins. The strain C43(DE3) was derived from C41(DE3) by selecting for resistance to a different toxic protein and can express a different set of toxic proteins to C41(DE3).
• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.

OverExpress(tm)C43(DE3)pLysS (Lucigen)

F^– ompT gal dcm hsdS_B(r_B^- m_B^-)(DE3)pLysS (Cm^r)

• The OverExpress strains contain genetic mutations phenotypically selected for conferring tolerance to toxic proteins. The strain C41(DE3) was derived from BL21(DE3). This strain has at least one uncharacterized mutation, which prevents cell death associated with expression of many recombinant toxic proteins. The strain C43(DE3) was derived from C41(DE3) by selecting for resistance to a different toxic protein and can express a different set of toxic proteins to C41(DE3).
• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
• The pLysS plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.

Rosetta™(DE3)pLysS

E. coli str. B F^– ompT gal dcm lon? hsdS_B(r_B^–m_B^–) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB⁺]_K-12(λ^S) pLysSRARE[T7p20 ileX argU thrU tyrU glyT thrT argW metT leuW proL ori_p15A](Cm^R)

• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
• Chloramphenicol resistant
• pLysSRARE contains tRNA genes argU, argW, ileX, glyT, leuW, proL, metT, thrT, tyrU, and thrU. The rare codons AGG, AGA, AUA, CUA, CCC, and GGA are supplemented.
• The pLysS plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.
• see Moffatt87 for details of pLysS and pLysE plasmids
• Novagen strain manual

Rosetta-gami(DE3)pLysS

Δ(ara-leu)7697 ΔlacX74 ΔphoA PvuII phoR araD139 ahpC galE galK rpsL (DE3) F'[lac⁺ lacI^q pro] gor522::Tn10 trxB pLysSRARE (Cam^R, Str^R, Tet^R)

• an E. coli K-12 strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• Transformed plasmids containing T7 promoter driven expression are repressed until IPTG induction of T7 RNA polymerase from a lac promoter.
• ahpC mutation allows trxB/gor double mutants to grow in the absence of reducing medium
• pLysSRARE contains tRNA genes argU, argW, ileX, glyT, leuW, proL, metT, thrT, tyrU, and thrU. The rare codons AGG, AGA, AUA, CUA, CCC, and GGA are supplemented.
• The pLysS plasmid encodes T7 phage lysozyme, an inhibitor for T7 polymerase which reduces and almost eliminates expression from transformed T7 promoter containing plasmids when not induced.
• see Moffatt87 for details of pLysS and pLysE plasmids
• Chloramphenicol resistant
• Kanamycin resistant
• Tetracycline resistant
• Streptomycin resistant
• Novagen strain manual

RR1

HB101 recA⁺

RV308

lacIq-, su-, ΔlacX74, gal IS II::OP308, strA K12 derivative used for industrial protein production. ATCC strain 31608, deposited by Genentech. Complete Genome Sequence available LM995446 *J Mairhofer 07:36, 28 October 2014 (EDT):.

S26

Hfr(PO2A) fhuA22 garB10 ompF627 fadL701 relA1 pit10 spoT1 metB1 mcrB1 cre-510 phoA4

• This is a phosphatase negative strain, carrying the S26 amber mutation (TAG) in the phosphatase gene

See BCCM/GeneCorner Plasmid Collection #LMBP 4977

14. Garen A, Garen S, and Wilhelm RC. Suppressor genes for nonsense mutations. I. The Su-1, Su-2 and Su-3 genes of Escherichia coli. J Mol Biol. 1965 Nov;14(1):167-78. DOI:10.1016/s0022-2836(65)80238-8 |

S26R1d

Hfr(PO2A) fhuA22 garB10 ompF627 fadL701 relA1 pit10 spoT1 metB1 mcrB1 cre-510 phoA4 supE

• This is a phosphatase negative strain, carrying the S26 amber mutation (TAG) in the phosphatase gene
• The strain carries the supE suppressor (insers glutamine at the amber position) and is therefore capable of suppressing the S26 phosphatase nonsense mutation, as well as amber mutations in other genes. However, the efficiency of suppression may vary considerably depending on the sequence context of the amber codon.

See BCCM/GeneCorner Plasmid Collection #LMBP 4979

14. Garen A, Garen S, and Wilhelm RC. Suppressor genes for nonsense mutations. I. The Su-1, Su-2 and Su-3 genes of Escherichia coli. J Mol Biol. 1965 Nov;14(1):167-78. DOI:10.1016/s0022-2836(65)80238-8 |

S26R1e

Hfr(PO2A) fhuA22 garB10 ompF627 fadL701 relA1 pit10 spoT1 metB1 mcrB1 cre-510 phoA4 supE

• This is a phosphatase negative strain, carrying the S26 amber mutation (TAG) in the phosphatase gene
• The strain carries the supD suppressor (insers serine at the amber position) and is therefore capable of suppressing the S26 phosphatase nonsense mutation, as well as amber mutations in other genes. However, the efficiency of suppression may vary considerably depending on the sequence context of the amber codon.

See BCCM/GeneCorner Plasmid Collection #LMBP 4978

14. Garen A, Garen S, and Wilhelm RC. Suppressor genes for nonsense mutations. I. The Su-1, Su-2 and Su-3 genes of Escherichia coli. J Mol Biol. 1965 Nov;14(1):167-78. DOI:10.1016/s0022-2836(65)80238-8 |

SG4044

lon-100 Δ(gal-pgl)324 lac thi rpsL

• StrR
• Lon^-
• non-mucoid
• The Lon protease plays a major role in the proteolytic machinery of E. coli. Lon mutants are highly pleioptropic and produce mucoid colonies that are difficult to handle. The (gal-pgl) deletion eliminates mucoidy and restores normal colony morphology.
• Lon mutants may be useful in stabilizing heterologous proteins expressed in E. coli.

See BCCM/GeneCorner Plasmid Collection #LMBP 670

33. Gottesman S, Halpern E, and Trisler P. Role of sulA and sulB in filamentation by lon mutants of Escherichia coli K-12. J Bacteriol. 1981 Oct;148(1):265-73. DOI:10.1128/jb.148.1.265-273.1981 |
34. Remaut E, Stanssens P, and Fiers W. Inducible high level synthesis of mature human fibroblast interferon in Escherichia coli. Nucleic Acids Res. 1983 Jul 25;11(14):4677-88. DOI:10.1093/nar/11.14.4677 |

SG4121

lon-100 Δ(gal-pgl)324 lac thi rpsL recA hsdR See BCCM/GeneCorner Plasmid Collection #LMBP 671

35. Keidel S, Rupp E, and Szardenings M. Recombinant human retinoic acid receptor alpha. Binding of DNA and synthetic retinoids to the protein expressed in Escherichia coli. Eur J Biochem. 1992 Mar 15;204(3):1141-8. DOI:10.1111/j.1432-1033.1992.tb16739.x |

SM10(λpir)

thi thr leu tonA lacY supE recA::RP4-2-Tc::Mu Km λpir See BCCM/GeneCorner Plasmid Collection #LMBP 3889

SOLR (Stratagene)

e14-(McrA-) Δ(mcrCB-hsdSMR-mrr)171 sbcC recB recJ uvrC umuC::Tn5 (Kan^r) lac gyrA96 relA1 thi-1 endA1 λ^R [F’ proAB lacI^qZ ΔM15]^C Su-

• Used in phagemid recovery (LambdaZap)
• Kanamycin resistant
• Stratagene E. coli Genotype Strains

SS320 (Lucigen)

F'[proAB+lacIqlacZΔM15 Tn10 (tet^r)]hsdR mcrB araD139 Δ(araABC-leu)7679 ΔlacX74 galUgalK rpsL thi

• Useful for phage display.
• Sidhu, S.S., Weiss, G.A., and Wells, J.A. (2000) J. Mol. Biol. 296, 487-495.

STBL2 (Invitrogen)

F- endA1 glnV44 thi-1 recA1 gyrA96 relA1 Δ(lac-proAB) mcrA Δ(mcrBC-hsdRMS-mrr) λ^-

• host for unstable sequences such as retroviral sequences and direct repeats
• nalidixic acid resistant
• References: Trinh, T., Jessee, J., Bloom, F.R., and Hirsch, V. (1994) FOCUS 16, 78.

===STBL3 (Invitrogen)===f F- glnV44 recA13 mcrB mrr hsdS20(rB-, mB-) ara-14 galK2 lacY1 proA2 rpsL20 xyl-5 leu mtl-1

• Streptomycin resistant
• endA+, use care in preparing DNA from this strain

STBL4

endA1 glnV44 thi-1 recA1 gyrA96 relA1 Δ(lac-proAB) mcrA Δ(mcrBC-hsdRMS-mrr) λ^- gal F'[ proAB⁺ lacI^q lacZΔM15 Tn10]

• Tetracycline resistant (from Tn10 insertion)
• STBL2 + blue/white selection

SURE (Stratagene)

F′[proAB⁺ lacI^q lacZΔM15 Tn10(Tet^R] endA1 glnV44 thi-1 gyrA96 relA1 lac recB recJ sbcC umuC::Tn5(Kan^R uvrC e14^–(mcrA^–) Δ(mcrCB-hsdSMR-mrr)171

• Uncertain status of TraD36 in F plasmid
• Increased stability for inverted repeats and Z-DNA
• Recombination-deficient
• Relaxed phenotype
• Endonuclease A-deficient
• Constitutive lac repressor expression
• Amber suppressor UAG>CAG(Gln)
• Improved cloning 5-mC DNA
• Nalidixic acid resistant
• Kanamycin resistant
• Tetracycline resistant

SURE2 (Stratagene)

endA1 glnV44 thi-1 gyrA96 relA1 lac recB recJ sbcC umuC::Tn5 uvrC e14- Δ(mcrCB-hsdSMR-mrr)171 F'[ proAB⁺ lacI^q lacZΔM15 Tn10 Amy Cm^R]

• increased stability for inverted repeats and Z-DNA
• nalidixic acid resistant
• kanamycin resistant
• tetracycline resistant
• chloramphenicol resistant for < 40 μg/ml, sensitive for > 100 μg/ml

TG1 (Lucigen)

K-12 glnV44 thi-1 Δ(lac-proAB) Δ(mcrB-hsdSM)5(r_K^–m_K^–) F′ [traD36 proAB⁺ lacI^q lacZΔM15]
= K-12 JM101 Δ(mcrB-hsdSM)5(r_K^–m_K^–)

• Useful for phage display.
• Fast-growing
• Thiamine auxotroph
• Lactose nonutilizing
• Amber suppressor UAG>CAG(Gln)
• Parent: JM101

TOP10 (Invitrogen)

F- mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 nupG recA1 araD139 Δ(ara-leu)7697 galE15 galK16 rpsL(Str^R) endA1 λ^-

• Very similar to DH10B
  • I actually emailed Invitrogen and asked if DH10B and TOP10 are the same strain or what. Their response: "Thank you for contacting Invitrogen Technical Support.TOP10 and DH10B competent cells are closely related. They have the same genotypes and can used for the same applications. You can also choose from those that are Chemically competent or electrocomp cells. I hope this information answers your questions." So either there is a difference that they don't want to put out there, or they have rebranded DH10B as TOP10 for marketing purposes... --Dcekiert 18:55, 23 January 2008 (CST)
• While DH10B has been classically reported to be galU galK, the preliminary genome sequence for DH10B indicates that DH10B (and by their lineage also TOP10 and any other MC1061 derivatives) is actually galE galK galU⁺. --Dcekiert 16:45, 23 January 2008 (CST)
• Previously reported to be deoR, but genome sequence indicates that DH10B is actually deoR⁺. Presumably TOP10 and MC1061 are also deoR⁺.
• Streptomycin resistant
• an MC1061 derivative [37]
• Prepare cells for chemical transformation with CCMB80 buffer Here
• Contain lacI based on a colony PCR (even though lacX74 supposedly deletes the lac operon) --Austin Che 16:16, 18 June 2007 (EDT)
  • φ80lacZΔM15 actually contains the entire lac operon, including lacI^q --Dcekiert 16:45, 23 January 2008 (CST)
    • Analysis of the published DH10B sequence (Genbank CP000948) suggests the φ80lacZΔM15 insertion has the wild-type lacI -35 sequence, not the lacI^q -35 sequence (gtgcaa) --BC 15:01, 29 March 2008 (EDT)
• leucine auxoroph (source)
• References:
  • E. coli Genetic Stock Center, MC1061 Record
  • DH10B Genome Sequencing Project, Baylor College of Medicine

9. Grant SG, Jessee J, Bloom FR, and Hanahan D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4645-9. DOI:10.1073/pnas.87.12.4645 |
37. Casadaban MJ and Cohen SN. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179-207. DOI:10.1016/0022-2836(80)90283-1 |
38. Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörgo B, Pósfai G, Weinstock GM, and Blattner FR. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 Apr;190(7):2597-606. DOI:10.1128/JB.01695-07 |

    Complete DH10B sequence is available

Top10F' (Invitrogen)

F'[lacI^q Tn10(tet^R)] mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 deoR nupG recA1 araD139 Δ(ara-leu)7697 galU galK rpsL(Str^R) endA1 λ^-

• Very similar to DH10B with F plasmid containing lacI^q and Tn10
• While DH10B has been classically reported to be galU galK, the preliminary genome sequence for DH10B indicates that DH10B (and by their lineage also TOP10 and any other MC1061 derivatives) is actually galE galK galU⁺. --Dcekiert 16:45, 23 January 2008 (CST)
• Previously reported to be deoR, but genome sequence indicates that DH10B is actually deoR⁺. Presumably TOP10 and MC1061 are also deoR⁺.
• Tetracycline resistant
• Streptomycin resistant
• an MC1061 derivative [37]
• References:
  • E. coli Genetic Stock Center, MC1061 Record
  • DH10B Genome Sequencing Project, Baylor College of Medicine
  • Complete DH10B sequence is available, see Durfee08, PMID 18245285.

NEB Turbo (NEB)

K-12 glnV44 thi-1 Δ(lac-proAB) galE15 galK16 R(zgb-210::Tn10)Tet^S endA1 fhuA2 Δ(mcrB-hsdSM)5(r_K^–m_K^–) F′[traD36 proAB⁺ lacI^q lacZΔM15]

• TG1 derivative, based on very similar genotype and very fast growth, with additional endA1 and fhuA2 mutations.
  • T₁ phage resistant
  • Thiamine auxotroph
  • Lactose nonutilizing
  • Constitutive lac repressor LacI
  • Rapid growth: visible colonies on agar, ~6.5–9 hours; shaking liquid culture OD 600 = 2.0 in ≈4 hours
• Endonuclease A-deficient
• Galactose-nonutilizing
• Nitrofurantoin-resistant
• References:
  • New England Biolabs, product catalogue number C2984H

W3110

F^- λ^- rph-1 INV(rrnD, rrnE)

• See CGSC#4474
• See ATCC 39936
• See [39]. Briefly, there are 8 site (9nt) differences between W3110 and MG1655. They reside in 7 orgs and one rRNA gene. Two are nonfunctional (rpoS and dcuA) and 5 are unknown missense mutations.
• New annotation has accession number DDBJ AP009048.

W3110 (λ857S7)

• Phenotype: ?
• See also the Talk page and the "W3110 (λ857S7)" section to discuss about this E. coli/K-12 strain.

WK6mutS(λ)

F' lacI^q Δ(lacZ)M15 proA⁺B⁺ traD36I Δ(lac-proB) galE rpsL mutS::Tn10 λ

• Streptomycin and tetracyclin resistant
• Useful strain for site-directed mutagenesis: isabled mismatch repair due to knocked-out mutS
• Not to be used as permanent storage host for plasmids because of the danger of accumulating spontaneous mutations.

See BCCM/GeneCorner Plasmid Collection #LMBP 1466

40. Zell R and Fritz HJ. DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues. EMBO J. 1987 Jun;6(6):1809-15. DOI:10.1002/j.1460-2075.1987.tb02435.x |

WM3064

thrB1004 pro thi rpsL hsdS lacZΔM15 RP4-1360 Δ(araBAD)567 ΔdapA1341::[erm pir]

Derived from B2155. Is auxotrophic to DAP (see strain information for B2155). This strain can be used for conjugation experiments and replication of plasmids that require pir protein.

Strain developed by William Metcalf at UIUC.

XL1-Blue (Stratagene)

endA1 gyrA96(nal^R) thi-1 recA1 relA1 lac glnV44 F'[ ::Tn10 proAB⁺ lacI^q Δ(lacZ)M15] hsdR17(r_K^- m_K⁺)

• nalidixic acid resistant
• tetracycline resistant (carried on the F plasmid)

XL1-Blue MRF' (Stratagene)

Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 supE44 thi-1 recA1 gyrA96 relA1 lac [F′ proAB lacI^qZΔM15 Tn10 (Tet^r)]

• Used in lambda phage infection, amplification, expression
• Tetracyline resistant
• Stratagene E. coli Genotype Strains

XL2-Blue (Stratagene)

endA1 gyrA96(nal^R) thi-1 recA1 relA1 lac glnV44 F'[ ::Tn10 proAB⁺ lacI^q Δ(lacZ)M15 Amy Cm^R] hsdR17(r_K^- m_K⁺)

• nalidixic acid resistant
• tetracycline resistant (carried on the F plasmid)
• chloramphenicol resistant for <40 μg/ml; sensitive for >100 μg/ml

XL2-Blue MRF' (Stratagene)

endA1 gyrA96(nal^R) thi-1 recA1 relA1 lac glnV44 e14- Δ(mcrCB-hsdSMR-mrr)171 recB recJ sbcC umuC::Tn5 uvrC F'[ ::Tn10 proAB⁺ lacI^q Δ(lacZ)M15 Amy Cm^R]

• Minus Restriction strain (minus mcrA mcrCB mcrF mrr hsdR)
• nalidixic acid resistant
• kanamycin resistant
• tetracycline resistant (carried on the F plasmid)
• chloramphenicol resistant <40 μg/ml, sensitive >100μg/ml

XL1-Red (Stratagene)

F- endA1 gyrA96(nal^R) thi-1 relA1 lac glnV44 hsdR17(r_K^- m_K⁺) mutS mutT mutD5 Tn10

• nalidixic acid resistant
• tetracycline resistant
• mutator strain, produces highly unstable DNA changes
• colonies grow and mutate so quickly that the strain is sick and mutated constructs must be moved rapidly to stable strains for plasmid isolation

XL10-Gold (Stratagene)

endA1 glnV44 recA1 thi-1 gyrA96 relA1 lac Hte Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 tet^R F'[proAB lacI^qZΔM15 Tn10(Tet^R Amy Cm^R)]

• Tetracycline and Chloramphenicol resistant
• Nalidixic acid resistant
• Hte phenotype allows high transformation with large plasmid inserts

XL10-Gold KanR (Stratagene)

endA1 glnV44 recA1 thi-1 gyrA96 relA1 lac Hte Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 tet^R F'[proAB lacI^qZΔM15 Tn10(Tet^R Amy Tn5(Kan^R)]

• Tetracycline and Kanamycin resistant
• Nalidixic acid resistant
• Hte phenotype allows high transformation with large plasmid inserts

Other genotype information sources

• Bachmann B, Bacteriol Rev. 1972 Dec;36(4):525-57. Pedigrees of some mutant strains of Escherichia coli K-12. PMID 4568763
  • History of the derivation of most lab strains of E. coli
• Strains at EcoliWiki.org
  • Provides information about common E. coli laboratory strains, allowing for annotation of the genotype, plasmids, phages and source information of a particular strain.

• E. coli Genetic Stock Center
• E. coli genotypes/Exhibit: Test of moving information on this page into a wiki database

• NEB strains Other NEB strains
• NEB genotype information
• Teknova
• Promega
• EMBL
• Novagen/EMD
• Sigma

• EcoCyc, EcoCyc Query Page, and EcoCyc Genome Browser
• EcoliWiki strains and EcoliWiki home
• Escherichia coli K12 genome browser

References

39. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, and Horiuchi T. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. DOI:10.1038/msb4100049 |
41. Novick RP, Clowes RC, Cohen SN, Curtiss R 3rd, Datta N, and Falkow S. Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev. 1976 Mar;40(1):168-89. DOI:10.1128/br.40.1.168-189.1976 |

42. Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Ananthara-man TS, and Witkin, EM. Inherited differences in sensitivity to radiation in Escherichia coli. Proc Natl Acad Sci USA 1946 32:59-68 (the original B strain reference).

43. Moffatt BA and Studier FW. T7 lysozyme inhibits transcription by T7 RNA polymerase. Cell. 1987 Apr 24;49(2):221-7. DOI:10.1016/0092-8674(87)90563-0 |