Escherichia coli/Nomenclature & Abbreviations

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*'''mtlA''' = cannot metabilize mannitol
*'''mtlA''' = cannot metabilize mannitol
*'''(Mu)''' = Mu prophage present.  Muδ means the phage is defective.
*'''(Mu)''' = Mu prophage present.  Muδ means the phage is defective.
-
*'''mutS''' - mutation inhibits DNA repair of mismatches in unmethylated newly synthesized strands
+
*'''[[Ecoliwiki:mutS|mutS]]''' - mutation inhibits DNA repair of mismatches in unmethylated newly synthesized strands
-
*'''nupG''' = same as deoR
+
*'''[[[[Ecoliwiki:nupG|nupG]]''' = same as [[Ecoliwiki:deoR|deoR]]
-
*'''ompT''' = mutation in outer membrane protein protease VII, reducing proteolysis of expressed proteins
+
*'''[[Ecoliwiki:ompT|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.
*'''(P1)''' = Cell carries a P1 prophage.  Cells express the P1 restriction system.
*'''(P2)''' = Cell carries a P2 prophage.  Allows selection against Red+ Gam+ λ
*'''(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.
*'''(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 [http://www.emdbiosciences.com/docs/NDIS/69659-000.HTML here].
+
*'''[[Ecoliwiki:pLysS|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 [http://www.emdbiosciences.com/docs/NDIS/69659-000.HTML here].
*'''proA/B''' = requires proline
*'''proA/B''' = requires proline
*'''recA1''' = For reduced occurrence of unwanted recombination in cloned DNA; cells UV sensitive, deficient in DNA repair
*'''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.
*'''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
+
*'''[[Ecoliwiki:recBCD|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
+
*'''[[Ecoliwiki:recJ|recJ]]''' Exonuclease involved in alternate recombination
-
*'''relA''' = relaxed phenotype; permits RNA synthesis in absence of protein synthesis
+
*'''[[Ecoliwiki:relA|relA]]''' = relaxed phenotype; permits RNA synthesis in absence of protein synthesis
-
*'''rha''' = blocked rhamose metabolism
+
*'''[[Ecoliwiki:rha|rha]]''' = blocked rhamose metabolism
-
*'''rnc''' = encodes RnaseIII (rnc-14 is a common null mutant)
+
*'''[[Ecoliwiki:rnc|rnc]]''' = encodes RnaseIII (rnc-14 is a common null mutant)
-
*'''rne''' = encodes RnaseE (rne-3071 is a common temperature sensitive mutant)
+
*'''[[[[Ecoliwiki:rne|rne]]''' = encodes RnaseE (rne-3071 is a common temperature sensitive mutant)
-
*'''rpsL''' =  mutation in ribosomal protein S12 conveying streptomycin resistance; also called strA
+
*'''[[Ecoliwiki:rpsL|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
*'''sbcBC''' = ExoI activity abolished; usually present in recBC strains; recombination proficient, stable inverted repeats
-
*'''srl''' = cannot metabolize sorbitol
+
*'''[[Ecoliwiki:srl|sr1]]''' = cannot metabolize sorbitol
-
*'''supE''' = glnV
+
*'''supE''' = [[Ecoliwiki:glnV|glnV]]
-
*'''supF''' = tyrT
+
*'''supF''' = [[Ecoliwiki:tyrT|tyrT]]
-
*'''thi''' = requires thiamine
+
*'''[[Ecoliwiki:thi|thi]]''' = requires thiamine
-
*'''thyA''' = requires thymidine
+
*'''[[Ecoliwiki:thyA|thyA]]''' = requires thymidine
*'''Tn10''' = transposon normally carrying Tetracycline resistance
*'''Tn10''' = transposon normally carrying Tetracycline resistance
*'''Tn5''' = transposon normally carrying Kanamycin resistance
*'''Tn5''' = transposon normally carrying Kanamycin resistance
-
*'''tonA''' = Mutation in outer membrane protein conveying resistance to phage T1 and phage T5
+
*'''[[Ecoliwiki:tonA|tonA]]''' = Mutation in outer membrane protein conveying resistance to phage T1 and phage T5
-
*'''traD''' = Mutation eliminating transfer factor; prevents transfer of F plasmid
+
*'''[[Ecoliwiki:traD|traD]]''' = Mutation eliminating transfer factor; prevents transfer of F plasmid
-
*'''trxB''' = mutation in thioredoxin reductase; enhances disulphide bond formation in the cytoplasm
+
*'''[[Ecoliwiki:trxB|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
+
*'''[[Ecoliwiki:tsx|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.
+
*'''[[Ecoliwiki:tyrT|tryT]]''' = 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
*'''ung1''' = allows uracil to exist in plasmid DNA
*'''xyl-5''' = blocked xylose metabolism
*'''xyl-5''' = blocked xylose metabolism

Revision as of 00:53, 8 April 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. ***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 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 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.
  • 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
  • tryT = 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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