Escherichia coli/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.