Escherichia coli/Nomenclature & Abbreviations

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 80: Line 80:
*'''xyl-5''' = blocked xylose metabolism
*'''xyl-5''' = blocked xylose metabolism
*'''Sm<sup>R</sup>''' = Streptomycin resistance
*'''Sm<sup>R</sup>''' = Streptomycin resistance; mutation of gene rpsL; synonyms '''rpsL135(strR)''', '''strA135''' [] *'''[[User:Karmella Haynes|---Karmella]] 13:27, 21 October 2012 (EDT)''':
[[Category:Escherichia coli]]
[[Category:Escherichia coli]]

Revision as of 13:27, 21 October 2012

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 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
  • 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 (complete deletion is Δcod-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)
  • 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).
  • LAM- or λ- = lambda lysogen deletion; approximate map location: 17.40; information from CGSC *---Karmella 13:02, 21 October 2012 (EDT):
  • 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
  • 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; mutation of gene rpsL; synonyms rpsL135(strR), strA135 [1] *---Karmella 13:27, 21 October 2012 (EDT):
Personal tools