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.
• 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
• ara-14 = cannot metabolize arabinose
• araD = mutation in L-ribulose-phosphate 4-epimerase blocks arabinose metabolism
• 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 abolished; high recombination efficiency; DNA repair turned on
• dcm = cytosine methylation at second C of 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
• dut1 = dUTPase activity abolished, leading to increased dUTP concentrations, allowing uracil instead of thymine incorporation in DNA. Stable U incorporation requires ung gene 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 = mutant more resistant to phage P1 infection
• galK/U = 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
• hflA150 = protease mutation stabilizing phage cII protein; 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). Carried on the e14 prophage (q.v.)
• mcrB = Mutation eliminating restriction of DNA methylated at the sequence R^mC
• metB = requires methionine
• metC = 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.
• mutS - mutation inhibits DNA repair of mismatches in unmethylated newly synthesized strands
• nupG = altered nucleoside uptake
• 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 is present in some strains.
• pLysS= contains pLysS plasmid carrying tetracycline resistance and phage T7 lysozyme, effective at lowering concentrations of T7 RNA polymerase, for better inhibition of expression under non-induced conditions.
• proA/B = requires proline
• recA1 = For reduced occurrence of unwanted recombination in cloned DNA; cells UV sensitive, deficient in DNA repair
• recA13 = as for recA1, but inserts 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 = blocked rhamose metabolism
• 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
• thyA = requires thymidine
• 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 transfer factor; prevents transfer of F plasmid
• trxB = mutation in thioredoxin reductase; enhances disulphide bond formation in the cytoplasm
• tyrT = suppression of amber (UAG) stop codons by insertion of tyrosine; needed for some phage infection such as λgt11.
• tsx = outer membrane protein mutation conveying resistance to phage T6 and colicin K
• ung1 = allows uracil to exist in plasmid DNA
• xyl-5 = blocked xylose metabolism

Methylation Issues in E. coli

• Type I methylation systems:
  • E. coli K-12 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 protectiing the sequence TGA^*[N8]TGCT or AGCA^*[N8]TCA.
• The mcrA gene restricts DNA which is methylated in C^mCWGG or ^mCG sequences (methylation by the dcm gene product).
• The mcrBC genes restrict R^mC sequences.
• 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."

Commonly used strains

BL21(DE3) (Novagen)

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

• an E. coli B strain with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacI^q
• 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^-) λ(DE3) pLysS(cm^R)

• pLys plasmid chloramphenicol resistant; grow with Cm to retain plasmid
• Chloramphenicol resistant

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

D1210

HB101 lacI^q lacY⁺

DB3.1

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

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

DH1

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

• parent of DH5α
• more efficient at transforming large (40-60Kb) plasmids
• nalidixic acid resistant

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.
• Promega also lists phoA
• nalidixic acid resistant
• 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)

F^- 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
• Promega also lists deoR (but see Top10 cell genotype)
• Streptomycin resistant

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
• 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

HB101

F^- mcrB mrr hsdS20(r_B^- m_B^-) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20(Sm^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
• 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
• 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.
  • Lacks S and Greenberg JR (1977) J Mol Biol 114:153.

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

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.
  
• Sigma lists e14-
• nalidixic acid resistant
• 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)

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

• 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.
• CGSC does not like this strain number -- tk 12/7/05

LE392

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

• Sigma lists F- e14-

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 e14-

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)

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.

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)

endA1 glnV44 thi-1 gyrA98 relA1 lac recB recJ sbcC umuC::Tn5 uvrC e14- Δ(mcrCB-hsdSMR-mrr)171 F'[ proAB⁺ lacI^q lacZΔM15 Tn10]

• uncertain status of TraD36 in F plasmid
• increased stability for inverted repeats and Z-DNA
• nalidixic acid resistant
• kanamycin resistant
• tetracycline resistant

TOP10 (Invitrogen)

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

• Very similar to DH10B with the addition of deoR
• streptomycin resistant

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⁺)

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

Other genotype information sources

• NEB
• Teknova
• Promega
• EMBL
• Novagen/EMD
• Sigma