E. coli genotypes

This information should be verified further. It was copied and pasted and edited by hand and so formatting/human errors may have been introduced. If sources are not cited, it is because this list was compiled prior to the wiki and the information source wasn't recorded.

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.
• r_B/K^+/- = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the restriction system. Courtesy of Sean Moore.
• m_B/K^+/- = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the modification (methylation) system. Courtesy of Sean Moore.
• 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
• ara = cannot metabolize arabinose
• Δ( ) = chromosomal deletion of genes between the listed genes (may include unlisted genes!)
• dam = adenine methylation at GATC sequences abolished; high recombination efficiency; DNA repair turned on
• dcm = cytosine methylation at CCWGG sites abolished
• deoR = regulatory gene that allows constitutive expression of deoxyribose synthesis genes; permits uptake of large plasmids
• dnaJ = one of the chaparonins inactivated; stabilizes some mutant proteins
• dut = dUTPase activity abolished; allows uracil incorporation in DNA
• 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
• galK/U = cannot metabolize galactose
• glnV = suppression of amber (UAG) stop codons by insertion of glutamine; required for some phage growth
• gyrA = mutation in DNA gyrase; conveys nalidixic acid resistance
• hflA = high frequency of lysogenization by λ
• lacI^q = overproduction of the lac repressor protein
• lacY = deficient in lactose transport; deletion of lactose permease (M protein)
• lacZΔM15 = partial deletion of the lacZ gene that allows α complementation of the β-galactosidase gene; required for blue/white selection on XGal plates
• leuB = requires leucine
• Δlon = deletion of the lon protease
• malA = cannot metabolize maltose
• mcrA = Mutation eliminating restriction of DNA methylated at the sequence C^mCGG (possibly ^mCG).
• mcrB = Mutation eliminating restriction of DNA methylated at the sequence R^mC
• metB = requires methionine
• mrr = Mutation eliminating restriction of DNA methylated at the sequence C^mAG or G^mAC
• mtlA = cannot metabilize mannitol
• (Mu) = Mu prophage present. Muδ means the phage is defective.
• nupG = altered nucleoside uptake
• (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 is present in some strains.
• proA/B = requires proline
• recA1 = For reduced occurrence of unwanted recombination in cloned DNA; cells UV sensitive, deficient in DNA repair
• recBCD = Exonuclease V; mutation in RecB or RecC reduces general recombination by a factor of 100; impaired DNA repair; UV sensitive
• recJ Exonuclease involved in alternate recombination
• relA = relaxed phenotype; permits RNA synthesis in absence of protein synthesis
• rspL = mutation in ribosomal protein S12 conveying streptomycin resistance; also called strA
• sbcBC = ExoI activity abolished; usually present in recBC strains; recombination proficient, stable inverted repeats
• supE = glnV
• supF = tyrT
• thi = requires thiamine
• tonA = Mutation in outer membrane protein conveying resistance to phage T1 and phage T5
• traD = Mutation eliminating transfer factor; prevents transfer of F plasmid
• tyrT = suppression of amber (UAG) stop codons by insertion of tyrosine; needed for some phage infection such as λgt11.
• xyl5 = cannot metaboize xylose
• Tn10 = transposon normally carrying Tetracycline resistance
• Tn5 = transposon normally carrying Kanamycin resistance

Methylation Issues in E. coli

E. coli K-12 restricts DNA which is not protected by adenine methylation at sites AAC[N6]GTGC or GCAC[N6]GTT, encoded by the hsdRMS genes. Deletions in these genes removes either the restriction or methylation or both of these functions. EcoBI derivative strains contain an hsdRMS system restricting and protectiing the sequence TGA[N8]TGCT or AGCA[N8]TCA. The mcrA gene restricts DNA which is methylated in C^mCWGG or ^mCG sequences. The mcrBC genes restrict R^mC sequences. E. coli methylates the adenine in GATC sites.

Commonly used strains

BL21(DE3) (Novagen)

F^– ompT gal dcm lon hsdS B(r_B^- m_B^-); an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene.

• Derived from B834 (Wood, 1966) by transducing to Met⁺.
• See the original Studier paper for more details.

BL21 (DE3) pLysS

F^- ompT gal dcm lon hsdS B(r_B^- m_B^-) (DE3) pLysS (cmR)

BNN93

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

• Some C600 strains are really BNN93

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 lacIq. 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)

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 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

DB3.1

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

• useful for propagating plasmids containing the ccdB operon.
• gyrA462 enables ccdB containing plasmid propagation

DH5α

endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR F^- Φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(r_K^- m_K⁺), λ–

• From a GIBCO BRL list of competent cells.
• Another source also mentioned phoA
• Reference: FOCUS (1986) 8:2, 9.
• Reference: Hanahan, D. (1985) in DNA Cloning: A Practical Approach (Glover, D.M., ed.), Vol. 1, p. 109, IRL Press, McLean, Virginia.

DH10B (Invitrogen)

endA1 recA1 galU galK nupG rpsL ΔlacX74 Φ80lacZΔM15 araD139 Δ(ara,leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) λ^-

• suitable for cloning methylated cytosine or adenine containing DNA
• blue/white selection

DH12S (Invitrogen)

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

• host for phagemid and M13 vectors
• useful for generating genomic libraries containing methylated cytosine or adenine residues
• 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.

D1210

HB101 lacI^q lacY⁺

DM1 (Invitrogen)

F- dam-13::Tn9(CmR) 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 Note: Chloramphenicol resistant

HB101

F^- mcrB mrr hsdS20(R_B^- m_B^-) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20(SmR) 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
• Host for pBR322 and many plasmids
• Streptomycin resistant
• 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.

JM101

glnV44 thi-1 glnV 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]

• References: Hanahan, D. (1983) J. Mol. Biol. 166:557-80.
• NEB says this strain encodes a prophage encoded EcoP1 endonuclease.

JM105

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

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

JM109

endA1 glnV44 thi-1 relA1 gyrA96 recA1 mcrB⁺ Δ(lac-proAB) glnV44 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.
  

recA1, endA1, gyrA96, thi, hsdR17, upE44, relA1, &lambda^-, Δ(lac-proAB), [F^', traD36, proAB, lacI^qZΔM15]

• 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: 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 we have) does NOT appear to be lacI^Q unless there is an undocumented extra copy of lacI somewhere on the genome or F' plasmid. 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)

JM2.300

Some folks have been using this strain (i.e., Elowitz, Gardner) and it took me too long to find the CGSC#.
The CGSC# is 5002. Check it out if you need.

Mach1

ΔrecA1398 endA1 tonA Φ80ΔlacM15 ΔlacX74 hsdR(r_K^- m_K⁺)

• From Invitrogen
• Doubling time approx. 50 min and supposedly fastest growing chemically competent cloning strain available
• Mach1 cells are derivatives of E. coli W strains, rather than E. coli K-12. This may have implications for BL-1 status for some facilities (apparently not for MIT).

MC4100

F^- araD139 Δ(argF-lac)U169* rspL150 relA1 flbB5301 fruA25‡ deoC1 ptsF25

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 fruB-yeiR. This means fruA is present but its promoter has been deleted.

The paper also showed that fimB is deleted in MC4100. The e14 element in MG1655 which is responsible for restriction and modification is also missing in MC4100. 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.

MG1655

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
• Blattner FR, et al. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462, 1997. PubMed: 9278503

RR1

HB101 recA⁺

STBL2 (Invitrogen)

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

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

TOP10 (Invitrogen)

F- mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK rpsL (StrR) endA1 nupG

W3110

F^- λ^- rph-1 INV(rrnD, rrnE)

• See CGSC#4474
• See ATCC 39936

XL1-Blue (Stratagene)

endA1 gyrA9(nal^R) thi-1 recA1 relA1 lac glnV44 F'[ ::Tn10 proAB⁺ lacI^q Δ(lacZ)M15] hsdR17(r_K^- m_K⁺)

Other genotype information sources

• NEB
• Teknova