Escherichia coli/Nomenclature & Abbreviations

A listed gene name means that gene carries a loss of function mutation, a &Delta; 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, &lambda;, 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.
 * 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
 * &Delta; = 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
 * 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, "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.  --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 &lambda;
 * &Delta;(lac)X74 = Deletion of the entire lac operon as well as some flanking DNA (complete deletion is &Delta;cod-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)
 * lacZ&Delta;M15 = partial deletion of the lacZ gene that allows &alpha; complementation of the &beta;-galactosidase gene; required for blue/white selection on XGal plates. Deletes the amino portion of lacZ (aa 11-41).
 * leuB = requires leucine
 * &Delta;lon = 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. Mu&delta; 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+ &lambda;
 * (&phi;80) = Cell carries the lambdoid prophage &phi;80. 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 &phi;80 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.
 * 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
 * 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
 * sbcBC = ExoI activity abolished; usually present in recBC strains; recombination proficient, stable inverted repeats
 * sr1 = cannot metabolize sorbitol
 * 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
 * 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 &lambda;gt11.
 * ung1 = allows uracil to exist in plasmid DNA
 * xyl-5 = blocked xylose metabolism


 * SmR = Streptomycin resistance