E. coli genotypes

Contents

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1 Nomenclature & Abbreviations ? 2 Methylation Issues in E. coli ? 3 Commonly used strains

o 3.1 AG1 o 3.2 AB1157 o 3.3 B2155 o 3.4 BL21 o 3.5 BL21(AI) o 3.6 BL21(DE3)

o 3.7 BL21 (DE3) pLysS o 3.8 BNN93 o 3.9 BNN97

o 3.10 BW26434, CGSC Strain # 7658 o 3.11 C600

o 3.12 C600 hflA150 (Y1073, BNN102) o 3.13 CSH50 o 3.14 D1210 o 3.15 DB3.1 o 3.16 DH1 o 3.17 DH5α

o 3.18 DH5α Turbo (NEB) o 3.19 DH10B (Invitrogen) o 3.20 DH12S (Invitrogen) o 3.21 DM1 (Invitrogen)

o 3.22 E. cloni(r) 5alpha (Lucigen) o 3.23 E. cloni(r) 10G (Lucigen) o 3.24 E. cloni(r) 10GF' (Lucigen) o 3.25 E. coli K12 ER2738 (NEB) o 3.26 ER2566 (NEB) o 3.27 ER2267 (NEB) o 3.28 HB101

o 3.29 HMS174(DE3)

o 3.30 High-Control(tm) BL21(DE3) (Lucigen) o 3.31 High-Control(tm) 10G (Lucigen) o 3.32 IJ1126 o 3.33 IJ1127

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o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

3.34 JM83 3.35 JM101 3.36 JM103 3.37 JM105 3.38 JM106 3.39 JM107 3.40 JM108 3.41 JM109

3.42 JM109(DE3) 3.43 JM110 3.44 JM2.300 3.45 LE392 3.46 Mach1 3.47 MC1061 3.48 MC4100 3.49 MG1655 3.50 OmniMAX2

3.51 OverExpress(tm)C41(DE3) (Lucigen)

3.52 OverExpress(tm)C41(DE3)pLysS (Lucigen) 3.53 OverExpress(tm)C43(DE3) (Lucigen)

3.54 OverExpress(tm)C43(DE3)pLysS (Lucigen) 3.55 Rosetta(DE3)pLysS

3.56 Rosetta-gami(DE3)pLysS 3.57 RR1 3.58 RV308

3.59 SOLR (Stratagene) 3.60 SS320 (Lucigen) 3.61 STBL2 (Invitrogen) 3.62 STBL3 (Invitrogen) 3.63 STBL4

3.64 SURE (Stratagene) 3.65 SURE2 (Stratagene) 3.66 TG1 (Lucigen)

3.67 TOP10 (Invitrogen) 3.68 Top10F' (Invitrogen) 3.69 W3110 3.70 WM3064

3.71 XL1-Blue (Stratagene)

3.72 XL1-Blue MRF' (Stratagene) 3.73 XL2-Blue (Stratagene)

3.74 XL2-Blue MRF' (Stratagene) 3.75 XL1-Red (Stratagene) 3.76 XL10-Gold (Stratagene)

3.77 XL10-Gold KanR (Stratagene)

4 Other genotype information sources ? 5 References

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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-.

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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.

rB/K+/- = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the restriction system.

mB/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

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

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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

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 = 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, \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. --Dcekiert 16:56, 23 January 2008 (CST)

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. --Dcekiert 16:56, 23 January 2008 (CST)

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 gene product

hflA150 = protease mutation stabilizing phage cII protein; high frequency of lysogenization by λ

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Δ(lac)X74 = 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)

lacIq or lacIQ = overproduction of the lac repressor protein; -35 site in promoter upstream of lacI is mutated from GCGCAA to GTGCAA lacIQ1 = overproduction of the lac repressor protein; contains a 15 bp deletion to create optimal -35 site in promoter upstream of lacI

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. Deletes the amino portion of lacZ (aa 11-41). LAM- or λ- = lambda lysogen deletion; approximate map location: 17.40; information from CGSC *---Karmella 13:02, 21 October 2012 (EDT): LamR = mutation in malT1 conferring lambda resistance; synonym malT1(LamR) [1] *---Karmella 13:35, 21 October 2012 (EDT): leuB = requires leucine

Δlon = deletion of the lon protease malA = cannot metabolize maltose

mcrA = Mutation eliminating restriction of DNA methylated at the

sequence CmCGG (possibly mCG). Carried on the e14 prophage (q.v.) mcrB = Mutation eliminating restriction of DNA methylated at the sequence RmC

metB = requires methionine metC = requires methionine

mrr = Mutation eliminating restriction of DNA methylated at the sequence CmAG or GmAC

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 = 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