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

Work on me. Many abbreviations can be found in the NEB catalog.

• A gene name means that gene carries a loss of function mutation, a Δ preceding a gene name means the gene is deleted.
• 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.
• 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
• mcrA = For efficient transformation of methylated DNA from genomic preparations
• lacZΔM15 = For blue/white color screening recombinants
• endA1 = For cleaner preparations of DNA and better results in downstream applications due to the elimination of non-specific digestion by Endonuclease I
• recA1 = For reduced occurrence of unwanted recombination in cloned DNA
• tonA = Resistance to T1 and T5 phage

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.

DH5α

F^-, Φ80dlacZΔM15Δ(lacZYA-argF)U169, deoR, recA1, endA1, hsdR17(r_K^- m_K⁺), supE44, λ–, thi-1, gyrA96, relA1

• From a GIBCO BRL list of competent cells.
• Another source also mentioned phoA
• Reference: FOCUS (1986) 8:2, 9.

DB3.1

F- gyrA462 endA1 Δ(sr1-recA) mcrB mrr hsdS20(rB-, mB-) supE44 ara14 galK2 lacY1proA2 rpsL20(Smr) xyl5 Δleu mtl1

D1210

HB101 lacI^q, lacY⁺

JM109

F^'traD36, proA⁺B⁺, lacI^q Δ(lacZ)M15/ Δ(lac-proAB), glnV44, e14-, gyrA96, recA1, relA1, endA1, thi, hsdR17

• 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.

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)

MC4100

F^-, araD139δ(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.

Miscellaneous strains

HB101

Please note that different sources have different genotypes so treat this information with caution.
supE44, Δ(mcrC-mrr), recA13, ara-14, proA2, lacY1, galK2, rpsL20, xyl-5, mtl-1, leuB6, thi-1
F^-, mcrB, mrr, hsdS20(r_B^- m_B^-), recA13, leuB6, ara-14, proA2, lacY1, galK2, xyl-5, mtl-1, rpsL20(Sm^r), supE44, λ^-

• From a GIBCO BRL list of competent cells.

BL21 (DE3)pLysS

F-ompT hsdS B(r_B^- m_B^-)gal dcm (DE3) pLysS (cam R)

XL1-Blue (Stratagene)

15 F' ::Tn 10 proA+ B+ lacI^q, Δ(lacZ)M15/recA1, endA1, gyrA96, (Nalr), thi, hsdR17(r_K^- m_K⁺), glnV44, relA1, lac

TOP10

F- mcrA Δ(mrr-hsdRMS-mcrBC) f80lacZΔM15 ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK rpsL (StrR) endA1 nupG

• From Invitrogen

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).