Escherichia coli/Nomenclature & Abbreviations

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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
  • 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
  • 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)
  • lacIq = overproduction of the lac repressor LacI; -35 site in promoter upstream of lacI is mutated from GCGCAA to GTGCAA
  • lacIq1 = 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(LamR) = 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 CmCGG (possibly mCG). Carried on the e14 prophage (q.v.)
  • mcrB = Mutation eliminating restriction of DNA methylated at the sequence RmC
  • 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 CmAG or GmAC
  • 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(StrR), 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 conventions

  • AmpR = ampicillin resistance, usually by β-lactamase gene bla. Older: ApR
  • AprR = apramycin resistance, usually by aminoglycoside N3-acetyltransferase gene aac(3′)-IV = aacC4.
  • ChlR = chloramphenicol resistance, usually by chloramphenicol O-acetyltransferase A-1 gene cat. Older: CmR or CamR.
  • GenR = gentamicin resistance, usually by aminoglycoside-N3-acetyltransferase gene aac(3′)-I = aacC1. Older: GmR
  • KanR = kanamycin resistance, usually by aminoglycoside 3′-phosphotransferase type I (aphA1 = aph(3′)-I = nptI) or type II (aphA2 = aph(3′)-II = nptII = neo). Older: KmR
  • SptR = spectinomycin resistance, usually by aminoglycoside 3″-adenylyltransferase gene aadA1.
  • StrR = streptomycin resistance, usually as by SptR or by genomic rpsL mutation. Older: SmR
  • TetR = tetracycline resistance, usually by a tetracycline efflux antiporter gene tetA. Older: TcR