Escherichia coli/Nomenclature & Abbreviations

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*'''endA1''' = For cleaner preparations of DNA and better results in downstream applications due to the elimination of non-specific digestion by Endonuclease I
*'''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
*'''(e14)''' = excisable prophage like element containing mcrA gene; present in K-12 but missing in many other strains
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*'''galE''' = mutations are associated with high competence and increased resistance to phage P1 infection.  galE mutations result 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.  --[[User:Dcekiert|Dcekiert]] 16:56, 23 January 2008 (CST)
+
*'''galE''' = mutations are associated with high competence and increased resistance to phage P1 infection.  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.  --[[User:Dcekiert|Dcekiert]] 16:56, 23 January 2008 (CST)
*'''galK/U''' = cannot metabolize galactose.  galK16 is an IS2 insertion ~170bp downstream of the galK start codon.
*'''galK/U''' = cannot metabolize galactose.  galK16 is an IS2 insertion ~170bp downstream of the galK start codon.
*'''gor''' = mutation in glutathione reductase; enhances disulphide bond formation
*'''gor''' = mutation in glutathione reductase; enhances disulphide bond formation

Revision as of 18:43, 23 January 2008

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.
  • 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 abolished; high recombination efficiency; DNA repair turned on
  • dcm = cytosine methylation at second C of CCWGG sites abolished
  • deoR = regulatory gene that allows constitutive expression of deoxyribose synthesis genes; permits uptake of large plasmids. See Hanahan D, US Patent 4,851,348.
  • 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 and increased resistance to phage P1 infection. 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. --Dcekiert 16:56, 23 January 2008 (CST)
  • galK/U = cannot metabolize galactose. galK16 is an IS2 insertion ~170bp downstream of the galK start codon.
  • 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
  • Δ(lac)X74 = Deletion of the entire lac operon as well as some flanking DNA.
  • 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).
  • 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 lacIq, 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.
  • 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
  • srl = 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 λgt11.
  • ung1 = allows uracil to exist in plasmid DNA
  • xyl-5 = blocked xylose metabolism
  • SmR = Streptomycin resistance
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