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Genotypes, Phenotypes and Markers

DEFINITIONS of Genotype, Phenotype and Marker for e. Coli

What is a Genotype?

A genotype is a list of mutant genes in an organism. In addition to mutations of the genome, other genetic elements such as prophage or plasmids can also be included. They are listed in brackets. The most popular prophages are DE3 (a λ derivative with the T7 RNA polymerase cloned in) and φ80dlacΔM15, which carries the half of the beta-galactosidase required for blue/white screening in plasmids like pUC19. The F plasmid also usually has a genotype because most F plasmids have E. coli chromosomal DNA in them. These are referred to as F’ (F prime).

It is assumed that any of the genes that are not mentioned in the genotype are wild type. A strain may have an unknown mutation. For example, JM109 is a lon mutant. The genotype of JM109 usually does not mention lon because it is not well known that it is there. It was discovered during the study of a different gene.1 Conversely, a mutation in a genotype does not always mean that the mutation is really there. At times, it has been deduced that the mutation is there based on the genotype from the properties of the parental strain. For example, almost every genotype claims that the HB101 is a proline auxotroph,2 but it has since been determined that it is not.3

What is a Phenotype?

A phenotype is a property that is genetically determined, but the mutated gene is unknown. For example, a strain that is resistant to phage T1 is referred to as T1R. The resistance could be due to an insertion sequence in the T1 receptor that is coded by the tonA gene (also known as the fhuA gene). If it is, the strain is referred to as tonA (or fhuA). If the tonA gene is found to be wild type, then another mutation must be causing the T1 resistance. Therefore, since it is still unknown, T1R is used to describe the strain. Another instance in which the phenotype is included is when the genotype does not clearly represent the trait. For example, the genotype rpsL indicates that the strain is resistant to streptomycin. StrR is used to indicate resistance to streptomycin instead as it clearly indicates the trait.

What is a Marker?

A marker is any mutation that distinguishes (“marks”) a strain. A marker can be a gene mutation or a phenotype. The presence of a prophage or of plasmids is not usually referred to as a “marker.”

Most likely, the strain that you are working with contains the mutations that you desire: recA, endA, lacΔM15, rpsL and tonA. However, it is important to remember that E. coli laboratory strains have been mutagenized, mixed up and transduced for years.4 As a result, the probability that the strain has all of the mutations in the genotype and only those mutations varies greatly. This is why trying different strain backgrounds is recommended when experiments are not working as expected.

Guide to E. coli Markers

References

1.
Robert Bebee. 1998. PhD. Thesis George Washington University. [dissertation].
2.
Boyer HW, Roulland-dussoix D. 1969. A complementation analysis of the restriction and modification of DNA in Escherichia coli. Journal of Molecular Biology. 41(3):459-472. https://doi.org/10.1016/0022-2836(69)90288-5
3.
Serebrijski I, Reyes O, Leblon G. 1995. Corrected gene assignments of Escherichia coli pro- mutations.. 177(24):7261-7264. https://doi.org/10.1128/jb.177.24.7261-7264.1995
4.
Berlyn, M.K.B. 1996. Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., Vol. 2, pp. 1715-1902. ASM Press.

Genotypes of Selected E. coli Strains

  • BL21 E. coli B F– ompT gal [E. coli B is naturally dcm and lon] hsdSB
  • BL21(DE3) E. coli B F– ompT gal [E. coli B is naturally dcm and lon] hsdSB with DE3, a λ prophage carrying the T7 RNA polymerase gene and lacIQ
  • C600 F– [e14– (McrF–) or e14+ (McrF+)] thr-1 leuB6 thi-1 lacY1 glnV44 rfbD1 fhuA21
  • CJ236 F Δ(HindIII)::cat (Tra+ Pil+ CamR )/ ung-1 relA1 dut-1 thi-1 spoT1 mcrA
  • GC5 F´ endA1 hsdR17 (rK–mK+) glnV44 thi-1 recA1 gyrA (Nalr) relA1 Δ(lacIZYA-argF)U169 (φ80dlacΔ(lacZ)M15 fhuA
  • GM48 F– thr leu thi lacY galK galT ara fhuA tsx dam dcm glnV44
  • HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13
  • JM83 F– ara Δ(lac-proAB) rpsL (Strr)[φ80 dlacΔ(lacZ)M15] thi
  • JM101 F´traD36 proA+B+ lacIq Δ(lacZ)M15/ Δ(lac-proAB) glnV thi
  • JM103 F´ traD36 lacIqΔ(lacZ)M15 proA+B+/endA1 glnV sbcBC thi-1 rpsL (Strr) Δ(lac-pro) (P1) (rK–mK+ rP1+ mP1+)
  • JM105 F´ traD36 lacIqΔ(lacZ)M15 proA+B+/thi rpsL (Strr) endA sbcB15 sbcC hsdR4 (rK–mK+) Δ(lac-proAB)
  • JM107 F´ traD36 lacIq Δ(lacZ)M15 proA+B+/e14–(McrA–) Δ(lac-proAB) thi gyrA96 (Nalr) endA1 hsdR17 (rK– mK+) relA1 glnV44
  • JM109 F´traD36 proA+B+ lacIq Δ(lacZ)M15/ Δ(lac-proAB) glnV44 e14- gyrA96 recA1 relA1 endA1 thi hsdR17
  • JM110 F´ traD36 lacIqΔ(lacZ)M15 proA+B+IrpsL (Strr) thr leu thi lacY galK galT ara fhuA dam dcm glnV44 Δ(lac-proAB)
  • K802 F– e14- (McrA-) lacY1 or Δ(lac)6 glnV44 galK2 galT22 rfbD1 metB1 mcrB1 hsdR2 (rK–mK+)
  • LE392 F– e14– (McrA–) hsdR514 (rK–mK+) glnV44 supF58 lacY1 or Δ(lacIZY)6 galK2 galT22 metB1 trpR55
  • MC1061 F– araD139 Δ(ara-leu)7696 galE15 galK16 Δ(lac)X74 rpsL (Strr) hsdR2 (rK–mK+) mcrA mcrB1
  • MM294 F– endA1 hsdR17 (rK–mK+) glnV44 thi-1 relA1 rfbD1 spoT1
  • NM477 C600 Δ(hsdMS-mcrB)5 (rK–mK+ McrBC–)
  • NM522 F´proA+B+ lacIq Δ(lacZ)M15/ Δ(lac-proAB) glnV thi-1 Δ(hsdS-mcrB)5
  • NM554 MC1061 recA13
  • NM621 F– hsdR (rK–mK+) mcrA mcrB glnV44 recD1009
  • RR1 HB101 RecA+
  • χ1776 F– fhuA53 dapD8 minA1 glnV44 Δ(gal-uvrB)40 minB2 rfb-2 gyrA25 (Nalr) thyA142 oms-2 metC65 oms-1 (tte-1) Δ(bioH-asd)29 cycB2 cycA1 hsdR2 (rK– mK+) mcrB1

References

1.
Oct. 31, 2005. E. coli Strain Genotypes New England Biolabs . [Internet]. Available from: http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/ecoli_genotypes.asp
2.
Wertman KF, Wyman AR, Botstein D. 1986. Host/vector interactions which affect the viability of recombinant phage lambda clones. Gene. 49(2):253-262. https://doi.org/10.1016/0378-1119(86)90286-6
3.
Yanisch-Perron C, Vieira J, Messing J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Gene. 33(1):103-119. https://doi.org/10.1016/0378-1119(85)90120-9
4.
Sambrook, J, Fritsch, E.F, Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual 2nd ed.. Cold Spring Harbor Laboratory Press: Cold Spring Harbor.
5.
Huynh, T.V. et al. 1985. DNA Cloning Vol. 1, (pp. 56–110). IRL Press Limited: Oxford, England.
6.
Raleigh E, Murray N, Revel H, Blumenthal R, Westaway D, Reith A, Rigby P, Elhai J, Hanahan D. 1988. McrA and McrB restriction phenotypes of someE.colistrains and implications for gene cloning. Nucl Acids Res. 16(4):1563-1575. https://doi.org/10.1093/nar/16.4.1563
7.
Woodcock D, Crowther P, Doherty J, Jefferson S, DeCruz E, Noyer-Weidner M, Smith S, Michael M, Graham M. 1989. Quantitative evaluation ofEscherichia colihost strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucl Acids Res. 17(9):3469-3478. https://doi.org/10.1093/nar/17.9.3469
8.
Raleigh, E.A, Lech, K, Brent, R. 1989. Current Protocols in Molecular Biology p. 1.4. Publishing Associates and Wiley Interscience New York.
9.
Berlyn, M.K.B. 1996. Escherichia coli and Salmonella: cellular and molecular biology 2nd ed. Vol. 2 pp. 1715–1902. ASM Press.
10.
Miller, J.H. 1972. Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press : Cold Spring Harbor.
11.
Whittaker PA, Campbell AJ, Southern EM, Murray NE. 1988. Enhanced recovery and restriction mapping of DNA fragments cloned in a new ? vector. Nucl Acids Res. 16(14):6725-6736. https://doi.org/10.1093/nar/16.14.6725
12.
Murray NE, Brammar WJ, Murray K. 1977. Lambdoid phages that simplify the recovery of in vitro recombinants. Molec. Gen. Genet.. 150(1): https://doi.org/10.1007/bf02425325
13.
Palmer B, Marinus M. 1994. The dam and dcm strains of Escherichia coli ? a review. Gene. 143(1):1-12. https://doi.org/10.1016/0378-1119(94)90597-5
14.
Boyer HW, Roulland-dussoix D. 1969. A complementation analysis of the restriction and modification of DNA in Escherichia coli. Journal of Molecular Biology. 41(3):459-472. https://doi.org/10.1016/0022-2836(69)90288-5
15.
Silhavy,, T.J. et al.. 1984. Experiments with Gene Fusions (pp. xi–xii). Cold Spring Harbor Laboratory: Cold Spring Harbor.
16.
Bullock, W.O. et al. 1987. XL1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection. BioTechniques 5 376–378.
17.
Maurizi MR, Trisler P, Gottesman S. 1985. Insertional mutagenesis of the lon gene in Escherichia coli: lon is dispensable.. 164(3):1124-1135. https://doi.org/10.1128/jb.164.3.1124-1135.1985
18.
Studier, F.W. et al. 1990. Methods in Enzymology Vol. 185 pp. 60–89 Academic Press San Diego.
19.
Kelleher JE, Raleigh EA. 1991. A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides.. 173(16):5220-5223. https://doi.org/10.1128/jb.173.16.5220-5223.1991
20.
Woodcock D, Crowther P, Doherty J, Jefferson S, DeCruz E, Noyer-Weidner M, Smith S, Michael M, Graham M. 1989. Quantitative evaluation ofEscherichia colihost strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucl Acids Res. 17(9):3469-3478. https://doi.org/10.1093/nar/17.9.3469
21.
Palmer B, Marinus M. 1994. The dam and dcm strains of Escherichia coli ? a review. Gene. 143(1):1-12. https://doi.org/10.1016/0378-1119(94)90597-5
22.
Yanisch-Perron C, Vieira J, Messing J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Gene. 33(1):103-119. https://doi.org/10.1016/0378-1119(85)90120-9
23.
Messing, J. 1979. Recombinant DNA Technical Bulletin (NIH) 2 43–48 https://www.biodiversitylibrary.org/item/248045#page/1/mode/1up.
24.
Gough JA, Murray NE, Brenner S. 1983. Sequence diversity among related genes for recognition of specific targets in DNA molecules. Journal of Molecular Biology. 166(1):1-19. https://doi.org/10.1016/s0022-2836(83)80047-3
25.
Baker TA, Grossman AD, Gross CA. 1984. A gene regulating the heat shock response in Escherichia coli also affects proteolysis.. Proceedings of the National Academy of Sciences. 81(21):6779-6783. https://doi.org/10.1073/pnas.81.21.6779
26.
Grossman AD, Burgess RR, Walter W, Gross CA. 1983. Mutations in the Lon gene of E. coli K12 phenotypically suppress a mutation in the sigma subunit of RNA polymerase. Cell. 32(1):151-159. https://doi.org/10.1016/0092-8674(83)90505-6
27.
Chung CH, Goldberg AL. 1981. The product of the lon (capR) gene in Escherichia coli is the ATP-dependent protease, protease La.. Proceedings of the National Academy of Sciences. 78(8):4931-4935. https://doi.org/10.1073/pnas.78.8.4931
28.
Straus DB, Walter WA, Gross CA. 1988. Escherichia coli heat shock gene mutants are defective in proteolysis.. Genes & Development. 2(12b):1851-1858. https://doi.org/10.1101/gad.2.12b.1851
29.
Kowit J, Goldberg A. 1977. Intermediate steps in the degradation of a specific abnormal protein in Escherichia coli. Journal of Biological Chemistry. 252(23):8350-8357. https://doi.org/10.1016/s0021-9258(19)75226-0
30.
Silber KR, Sauer RT. 1994. Deletion of the prc (tsp) gene provides evidence for additional tail-specific proteolytic activity in Escherichia coli K-12. Molec. Gen. Genet.. 242(2):237-240. https://doi.org/10.1007/bf00391018
31.
ELISH ME, PIERCE JR, EARHART CF. 1988. Biochemical Analysis of Spontaneous fepA Mutants of Escherichia coli. Microbiology. 134(5):1355-1364. https://doi.org/10.1099/00221287-134-5-1355
32.
Kunkel, T.A. et al. 1987. Methods in Enzymology Vol. 154 pp. 367-382. Academic Press San Diego.
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