Escherichia coli/Nomenclature & Abbreviations: Difference between revisions
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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 | 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''<sup>–</sup> and ''dcm''<sup>–</sup>. | ||
*'''F<sup> | *'''F<sup>–</sup>''' = Does not carry the F plasmid | ||
*'''F<sup>+</sup>''' = Carries the F plasmid. The cell is able to mate with F<sup>-</sup> through conjugation. | *'''F<sup>+</sup>''' = Carries the F plasmid. The cell is able to mate with F<sup>-</sup> 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<sup>-</sup> through conjugation. Chromosomal genes carried in the F plasmid are listed in brackets. | ||
*'''ΔH1''' = removes part of cro and all genes to the right of it | |||
*'''r<sub>B/K</sub><sup>+/-</sup>''' = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the restriction system. | *'''r<sub>B/K</sub><sup>+/-</sup>''' = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the restriction system. | ||
*'''m<sub>B/K</sub><sup>+/-</sup>''' = The (B/K) defines the strain lineage. The +/- indicates whether the strain has or hasn't got the modification (methylation) system. | *'''m<sub>B/K</sub><sup>+/-</sup>''' = 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. | *'''[[Ecoliwiki:hsdS|''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 | *'''[[Ecoliwiki:hsdR|''hsdR']]''' = For efficient transformation of cloned unmethylated DNA from PCR amplifications | ||
*'''INV( )''' = chromosomal inversion between locations indicated | *'''INV( )''' = chromosomal inversion between locations indicated | ||
*'''ahpC''' = mutation to alkyl hydroperoxide reductase conferring disulfide reductase activity | *'''[[Ecoliwiki:ahpC|''ahpC'']]''' = mutation to alkyl hydroperoxide reductase conferring disulfide reductase activity | ||
*'''ara-14''' = cannot metabolize arabinose | *'''''ara-14''''' = cannot metabolize arabinose | ||
*'''araD''' = mutation in L-ribulose-phosphate 4-epimerase blocks arabinose metabolism | *'''[[Ecoliwiki:araD|''araD'']]''' = mutation in L-ribulose-phosphate 4-epimerase blocks arabinose metabolism | ||
*'''cycA''' = mutation in alanine transporter; cannot use alanine as a carbon source | *'''''bio252''''' = removes all genes to the left of cIII | ||
*'''dapD''' = mutation in succinyl diaminopimelate aminotransferase leads to succinate or (lysine + methionine) requirement | *'''[[Ecoliwiki:cycA|''cycA'']]''' = mutation in alanine transporter; cannot use alanine as a carbon source | ||
*''' | *'''[[Ecoliwiki:dapD|''dapD'']]''' = mutation in succinyl diaminopimelate aminotransferase leads to succinate or (lysine + methionine) requirement | ||
*'''dam''' = adenine methylation at GATC sequences | *'''Δ( )''' = chromosomal deletion of genes between the listed genes (may include unlisted genes!) | ||
*'''dcm''' = cytosine methylation at second C of CCWGG sites | *'''[[Ecoliwiki:dam|''dam'']]''' = adenine methylation at GATC sequences exist; high recombination efficiency; DNA repair turned on | ||
*'''deoR''' = regulatory gene that allows constitutive expression of deoxyribose synthesis genes; permits uptake of large plasmids. See Hanahan D, [http://patft.uspto.gov/netacgi/nph-Parser?u=/netahtml/srchnum.htm&Sect1=PTO1&Sect2=HITOFF&p=1&r=1&l=50&f=G&d=PALL&s1=4851348.WKU.&OS=PN/4851348&RS=PN/4851348 US Patent 4,851,348]. | *'''[[Ecoliwiki:dcm|''dcm'']]''' = cytosine methylation at second C of CCWGG sites exist. dam & dcm are the default properties and always elided, while dam<sup>-</sup> or dcm<sup>-</sup> should be declare explicitly | ||
*'''dnaJ''' = one of the chaparonins inactivated; stabilizes some mutant proteins | *'''[http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/Transformation/expression-competent-cells.html DE3]''' = Lysogen that encodes T7 RNA polymerase. Used to induce expression in T7-driven expression systems | ||
*''' | *'''[[Ecoliwiki:deoR|''deoR'']]''' = regulatory gene that allows constitutive expression of deoxyribose synthesis genes; permits uptake of large plasmids. See Hanahan D, [http://patft.uspto.gov/netacgi/nph-Parser?u=/netahtml/srchnum.htm&Sect1=PTO1&Sect2=HITOFF&p=1&r=1&l=50&f=G&d=PALL&s1=4851348.WKU.&OS=PN/4851348&RS=PN/4851348 US Patent 4,851,348]. ***This has been called into question, as the DH10B genome sequence revealed that it is ''deoR''<sup>+</sup>. See Durfee08, PMID 18245285. | ||
*'''endA1''' = For cleaner preparations of DNA and better results in downstream applications due to the elimination of non-specific digestion by Endonuclease I | *'''[[Ecoliwiki:dnaJ|''dnaJ'']]''' = one of the chaparonins inactivated; stabilizes some mutant proteins | ||
*'''DUP()''' = chromosomal duplication between locations indicated | |||
*'''[[Ecoliwiki:dut|''dut'']]1''' = dUTPase activity abolished, leading to increased dUTP concentrations, allowing uracil instead of thymine incorporation in DNA. Stable U incorporation requires ''ung'' mutation as well. | |||
*'''[[Ecoliwiki:endA|''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 | ||
*'''galE''' = | *'''[[Ecoliwiki:galE|''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. | ||
*'''galK | *'''[[Ecoliwiki:galK|''galK'']]''' = mutants cannot metabolize galactose and are resistant to 2-deoxygalactose. ''galK16'' is an IS''2'' insertion ~170bp downstream of the ''galK'' start codon. See EcoSal ISBN 1555811647. | ||
*'''gor''' = mutation in glutathione reductase; enhances disulphide bond formation | *'''[[Ecoliwiki:galU|''galU'']]''' = mutants cannot metabolize galactose | ||
*'''glnV''' = suppression of amber (UAG) stop codons by insertion of glutamine; required for some phage growth | *'''[[Ecoliwiki:gor|''gor'']]''' = mutation in glutathione reductase; enhances disulphide bond formation | ||
*'''gyrA96''' = mutation in DNA gyrase; conveys nalidixic acid resistance | *'''[[Ecoliwiki:glnV|''glnV'']]''' = suppression of amber (UAG) stop codons by insertion of glutamine; required for some phage growth | ||
*'''gyrA462''' = mutation in DNA gyrase; conveys resistance to | *'''[[Ecoliwiki:gyrA|''gyrA96'']]''' = mutation in DNA gyrase; conveys nalidixic acid resistance | ||
*'''hflA150''' = protease mutation stabilizing phage cII protein; high frequency of lysogenization by | *'''''gyrA462''''' = mutation in DNA gyrase; conveys resistance to CcdB colicin | ||
*''' | *'''''hflA150''''' = protease mutation stabilizing phage cII protein; high frequency of lysogenization by λ | ||
*' | *'''Δ''lacX74''''' = Deletion of the entire ''lac'' operon as well as some flanking DNA (complete deletion is Δ''cod-mhpF''; see Mol.Micro., 6:1335, and J.Bact., 179:2573) | ||
*'''lacI<sup> | *'''''lacI''<sup>q</sup>''' = overproduction of the ''lac'' repressor LacI; -35 site in promoter upstream of ''lacI'' is mutated from GCGCAA to GTGCAA | ||
*'''lacY''' = deficient in lactose transport; deletion of lactose permease | *'''''lacI''<sup>q1</sup>''' = overproduction of the ''lac'' repressor LacI; contains a 15 bp deletion to create optimal -35 site in promoter upstream of ''lacI'' | ||
*''' | *'''''lacY''''' = deficient in lactose transport; deletion of lactose permease LacY | ||
*'''leuB''' = | *'''''lacZΔM15''''' = partial deletion of the β-galactosidase ''lacZ'' gene (removing N-terminal aa 11–41), allowing α-complementation; required for blue/white selection on X-Gal plates using LacZ α subunit. | ||
*'''Δlon''' = | * '''λ<sup>–</sup>''' or '''LAM<sup>–</sup>''' = λ lysogen deletion; approximate map location: 17.40; information from [http://cgsc.biology.yale.edu/Mutation.php?ID=4499 CGSC] | ||
*'''malA''' = | * '''''lamR''''' or '''''malT1''''' or '''''malT1''(Lam<sup>R</sup>)''' = mutation in ''malT1'' conferring λ resistance [http://cgsc.biology.yale.edu/Mutation.php?ID=4749] | ||
*'''mcrA''' = Mutation eliminating restriction of DNA methylated at the sequence C<sup>m</sup>CGG (possibly <sup>m</sup>CG). Carried on the e14 prophage (q.v.) | *'''[[Ecoliwiki:leuB|''leuB'']]''' = Mutation in ''leuB'', disrupting leucine biosynthesis. | ||
*'''mcrB''' = Mutation eliminating restriction of DNA methylated at the sequence R<sup>m</sup>C | *'''Δ[[Ecoliwiki:lon|''lon'']]''' = Mutation of the Lon protease | ||
*'''metB''' = | *'''[[Ecoliwiki:malA|''malA'']]''' = Mutation abolishing mannitol metabolism. | ||
*'''metC''' = | *'''[[Ecoliwiki:mcrA|''mcrA'']]''' = Mutation eliminating restriction of DNA methylated at the sequence C<sup>m</sup>CGG (possibly <sup>m</sup>CG). Carried on the e14 prophage (q.v.) | ||
*'''mrr''' = Mutation eliminating restriction of DNA methylated at the sequence C<sup>m</sup>AG or G<sup>m</sup>AC | *'''[[Ecoliwiki:mcrB|''mcrB'']]''' = Mutation eliminating restriction of DNA methylated at the sequence R<sup>m</sup>C | ||
*'''mtlA''' = cannot | *'''[[Ecoliwiki:metB|''metB'']]''' = Mutation in methionine biosynthesis enzyme MetB; methionine auxotroph | ||
*'''(Mu)''' = Mu prophage present. | *'''[[Ecoliwiki:metC|''metC'']]''' = Mutation in methionine biosynthesis enzyme MetC; methionine auxotroph | ||
*'''mutS''' | *'''[[Ecoliwiki:mrr|''mrr'']]''' = Mutation eliminating restriction of DNA methylated at the sequence C<sup>m</sup>AG or G<sup>m</sup>AC | ||
*'''nupG''' = same as deoR | *'''''mtlA''''' = Mutation in mannitol permease MtlA; cannot metabolize mannitol | ||
*'''ompT''' = mutation in outer membrane protein protease VII, reducing proteolysis of expressed proteins | *'''(Mu)''' = Mu prophage present. MuΔ; means the phage is defective. | ||
*'''[[Ecoliwiki:mutS|''mutS'']]''' = mutation inhibits DNA repair of mismatches in unmethylated newly synthesized strands | |||
*'''[[Ecoliwiki:nupG|''nupG'']]''' = same as [[Ecoliwiki:deoR|deoR]] | |||
*'''[[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''. | ||
*'''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]. | ||
*''' | *'''''proAB''''' = mutation in proline biosynthesis enzymes; proline auxotroph, unless (as often) complemented by ''proAB''<sup>+</sup> on F plasmid | ||
*'''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 | *'''''recA13''''' = as for ''recA1'', but DNA constructs less stable. | ||
*'''recBCD''' = | *'''[[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''' | *'''[[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''' = | *'''[[Ecoliwiki:rha|''rha'']]''' = cannot metabolize rhamnose | ||
*'''rnc''' = encodes | *'''[[Ecoliwiki:rnc|''rnc'']]''' = encodes RNaseIII (''rnc-14'' is a common null mutant) | ||
*'''rne''' = encodes | *'''[[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'', ''rpsL135''(Str<sup>R</sup>), strA135 [http://cgsc.biology.yale.edu/Mutation.php?ID=5280] | ||
*'''sbcBC''' = ExoI activity abolished; usually present in recBC strains; recombination proficient, | *'''''sbcBC''''' = ExoI activity abolished; usually present in ''recBC'' strains; recombination proficient, stablizes 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''' = | *'''[[Ecoliwiki:thi|''thi'']]''' = thiamine auxotroph | ||
*'''thyA''' = | *'''[[Ecoliwiki:thyA|''thyA'']]''' = thymidine auxotroph | ||
*''' | *'''Tn''10''''' = transposon normally carrying Tetracycline resistance | ||
*''' | *'''Tn''5''''' = transposon normally carrying Kanamycin resistance | ||
*'''tonA''' = | *'''[[Ecoliwiki:tonA|''tonA'']]''' = mutation in outer membrane protein conveying resistance to phage T1 and phage T5 | ||
*'''traD''' = | *'''[[Ecoliwiki:traD|''traD'']]''' = mutation eliminating F 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 | *'''[[Ecoliwiki:tyrT|''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 | *'''''ung1''''' = allows uracil to exist in plasmid DNA | ||
*'''xyl-5''' = blocked xylose metabolism | *'''''xyl-5''''' = blocked xylose metabolism | ||
*'''Sm<sup>R</sup>''' = | '''Antibiotic resistance nomenclature based on [https://journals.asm.org/journal/aac/abbreviations ASM AAC conventions]''' | ||
*'''Amp<sup>R</sup>''' = ampicillin resistance, usually by β-lactamase TEM (class A): ''bla''. Older: Ap<sup>R</sup> | |||
*'''Apr<sup>R</sup>''' = apramycin resistance, usually by aminoglycoside N3-acetyltransferase (AAC(3′)-IV): ''aacC4''. | |||
*'''Ble<sup>R</sup>''' = bleomycin/phleomycin/Zeocin resistance, usually by bleomycin-binding protein: ''ble''. | |||
*'''Chl<sup>R</sup>''' = chloramphenicol resistance, usually by chloramphenicol O-acetyltransferase A-1: ''cat''. Older: Cm<sup>R</sup> or Cam<sup>R</sup>. | |||
*'''Ery<sup>R</sup>''' = erythromycin resistance, usually by macrolide 2'-phosphotransferase I (MPH(2′)-I): ''mphA''. | |||
*'''Gen<sup>R</sup>''' = gentamicin resistance, usually by aminoglycoside-N3-acetyltransferase (AAC(3′)-I''): ''aacC1''. Older: Gm<sup>R</sup> | |||
*'''Kan<sup>R</sup>''' = kanamycin resistance, usually by aminoglycoside 3′-phosphotransferase type I (APH(3′)-I): ''aphA1'', ''nptI''; or type II (aph(3′)-II): ''aphA2'', ''nptII'', ''neo''. Older: Km<sup>R</sup> | |||
*'''Spt<sup>R</sup>''' = spectinomycin resistance, usually by aminoglycoside (3″)9-''O''-adenylyltransferase:''aadA1''. | |||
*'''Str<sup>R</sup>''' = streptomycin resistance, usually by Spt<sup>R</sup> gene ''aadA1'' or by genomic ''rpsL'' mutation. Older: Sm<sup>R</sup> | |||
*'''Tet<sup>R</sup>''' = tetracycline resistance, usually by a tetracycline efflux antiporter:''tetA''. Older: Tc<sup>R</sup> | |||
*'''Tmp<sup>R</sup>''' = trimethoprim resistance, usually by dihydrofolate reductase type II (DHFR): ''dhfr''. | |||
[[Category:Escherichia coli]] | [[Category:Escherichia coli]] |
Latest revision as of 03:30, 7 October 2021
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.
- ΔH1 = removes part of cro and all genes to the right of it
- 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
- bio252 = removes all genes to the left of cIII
- 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
- DUP() = chromosomal duplication between locations indicated
- dut1 = dUTPase activity abolished, leading to increased dUTP concentrations, allowing uracil instead of thymine incorporation in DNA. Stable U incorporation requires ung 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.
- 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.
- 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
- hflA150 = protease mutation stabilizing phage cII protein; high frequency of lysogenization by λ
- ΔlacX74 = 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 = overproduction of the lac repressor LacI; -35 site in promoter upstream of lacI is mutated from GCGCAA to GTGCAA
- lacIq1 = overproduction of the lac repressor LacI; contains a 15 bp deletion to create optimal -35 site in promoter upstream of lacI
- lacY = deficient in lactose transport; deletion of lactose permease LacY
- lacZΔM15 = partial deletion of the β-galactosidase lacZ gene (removing N-terminal aa 11–41), allowing α-complementation; required for blue/white selection on X-Gal plates using LacZ α subunit.
- λ– or LAM– = λ lysogen deletion; approximate map location: 17.40; information from CGSC
- lamR or malT1 or malT1(LamR) = mutation in malT1 conferring λ resistance [1]
- leuB = Mutation in leuB, disrupting leucine biosynthesis.
- Δlon = Mutation of the Lon protease
- malA = Mutation abolishing mannitol metabolism.
- 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 = Mutation in methionine biosynthesis enzyme MetB; methionine auxotroph
- metC = Mutation in methionine biosynthesis enzyme MetC; methionine auxotroph
- mrr = Mutation eliminating restriction of DNA methylated at the sequence CmAG or GmAC
- mtlA = Mutation in mannitol permease MtlA; cannot metabolize 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.
- proAB = mutation in proline biosynthesis enzymes; proline auxotroph, unless (as often) complemented by proAB+ on F plasmid
- recA1 = For reduced occurrence of unwanted recombination in cloned DNA; cells UV sensitive, deficient in DNA repair
- recA13 = as for recA1, but DNA constructs 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 = cannot metabolize rhamnose
- 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]
- sbcBC = ExoI activity abolished; usually present in recBC strains; recombination proficient, stablizes inverted repeats
- sr1 = cannot metabolize sorbitol
- supE = glnV
- supF = tyrT
- thi = thiamine auxotroph
- thyA = thymidine auxotroph
- 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 F 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
Antibiotic resistance nomenclature based on ASM AAC conventions
- AmpR = ampicillin resistance, usually by β-lactamase TEM (class A): bla. Older: ApR
- AprR = apramycin resistance, usually by aminoglycoside N3-acetyltransferase (AAC(3′)-IV): aacC4.
- BleR = bleomycin/phleomycin/Zeocin resistance, usually by bleomycin-binding protein: ble.
- ChlR = chloramphenicol resistance, usually by chloramphenicol O-acetyltransferase A-1: cat. Older: CmR or CamR.
- EryR = erythromycin resistance, usually by macrolide 2'-phosphotransferase I (MPH(2′)-I): mphA.
- GenR = gentamicin resistance, usually by aminoglycoside-N3-acetyltransferase (AAC(3′)-I): aacC1. Older: GmR
- KanR = kanamycin resistance, usually by aminoglycoside 3′-phosphotransferase type I (APH(3′)-I): aphA1, nptI; or type II (aph(3′)-II): aphA2, nptII, neo. Older: KmR
- SptR = spectinomycin resistance, usually by aminoglycoside (3″)9-O-adenylyltransferase:aadA1.
- StrR = streptomycin resistance, usually by SptR gene aadA1 or by genomic rpsL mutation. Older: SmR
- TetR = tetracycline resistance, usually by a tetracycline efflux antiporter:tetA. Older: TcR
- TmpR = trimethoprim resistance, usually by dihydrofolate reductase type II (DHFR): dhfr.