E. coli genotype

출처: http://openwetware.org/wiki/E._coli_genotypes

 

Nomenclature & Abbreviations

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 operon as well as some flanking DNA (complete deletion is Δcod-mhpF; see Mol.Micro., 6:1335, and J.Bact., 179:2573)

  lac

• lacIq or lacIQ = overproduction of the lac repressor protein; -35 site in promoter upstream of is mutated from GCGCAA to GTGCAA

  lacI

• 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):

• LamR = mutation in malT1 conferring lambda resistance; synonym malT1(LamR) [1] *---Karmella 13:35, 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 CCGG (possibly CG). Carried on the e14 prophage (q.v.)

  m

  m

• mcrB = Mutation eliminating restriction of DNA methylated at the sequence RC

  m

• metB = requires methionine

• metC = requires methionine

• mrr = Mutation eliminating restriction of DNA methylated at the sequence CAG or GAC

  m

  m

• 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, rpsL135(strR), strA135 [2] *---Karmella 13:27, 21 October 2012 (EDT):

• 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