Genetic Markers

A genotype indicates the genetic state of the DNA in an organism. It is a theoretical construct describing a genetic situation that explains the observed properties (phenotype, see below) of a strain. E. coli genotypes list only genes that are defective (1). If a gene is not mentioned, then it is not known to be mutated*†. Prophages and plasmids that were present in the original K-12 strain (F, l, e14, rac) are normally listed only if absent. However, we have not listed l except when it is present, and we have listed F and its variants in all cases. Parentheses or brackets surround a prophage or plasmid when listed. Genes are given three-letter, lower-case, italicized names (e.g. dam) that are intended to be mnemonics suggesting the function of the gene (here DNA adenine methylase). If the same function is affected by several genes, the different genes are distinguished with uppercase italic letters (e.g. recA, recB, recC, recD all affect recombination). Proper notation omits superscript + or - in a genotype, but these are sometimes used redundantly for clarity, as with F'lac-proA+B+. Deletion mutations are noted as Δ, followed by the names of deleted genes in parentheses, [e.g. Δ(lac-pro)]. All genes between the named genes are also deleted. Specific mutations are given allele numbers that are usually italic arabic numerals (e.g hsdR17) and may be characterized as am=amber (UAG) mutation or ts=inactive at high temperature, as appropriate. Some common alleles [e.g. Δ(lac-pro)X111] break the rules. If two strains' genotypes list a gene with the same allele number, they should carry exactly the same mutation.

The phenotype of a strain is an observable behavior, e.g. Lac- fails to grow on lactose as a sole carbon source. Phenotypes are capitalized and in Roman type, and the letters are always followed by superscript + or - (or sometimes r, resistant, or s, sensitive). Although phenotypes do not, strictly speaking, belong in a genotype, they are sometimes included following the genotype designation when the former is not obvious from the latter [e.g. rpsL104 (Str)-gene name from ribosomal protein, small subunit, S12, confers resistance to streptomycin].

Some common genes of interest are described below ; a catalogue of genetically defined genes can be found in reference 2 and on the very useful Internet site maintained by the E. coli Genetic Stock Center (CGSC) at Yale University. Additional information from CGSC can be obtained from curator Mary Berlyn by e-mail

The designation R(...) means Rearrangement by analogy with IN(...) for INversion (4). Thus, "R(xxx::Tn10--TetS)" signifies the former presence of a Tn10 insertion. For insertions of wild-type Tn10, the rearrangement was presumably Tn10 promoted, since 99% of TetS derivatives of Tn10-containing strains have acquired transposon-promoted rearrangements (5, 6, 7) that spare one or both IS10 elements.

* Most E. coli laboratory strains have been heavily mutagenized over forty years of study, and different lines may carry different, so far undiscovered, mutations that may or may not affect your situation. For this reason, it is sometimes useful to try more than one line, or strain background, in your experiments.

E. coli B and its derivatives are naturally Lon- and Dcm-. We have listed this in brackets even though it is the wild type state for these strains.


  1. Demerec et al. (1966) Genetics 54, 61-76. PMID: 5961488
  2. Berlyn, M.K.B. (1996) in F. C. Niedhardt et al. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, (2nd ed.), Vol. 2, (pp. 1715-1902). ASM Press. PMID: 9729611
  3. Raleigh, E.A. et al. (1991) J. Bacteriol. 173, 2707-2709. PMID: 2013582
  4. Hill, C. W. and B. W. Harnish. (1981) Inversions between ribosomal RNA genes of Escherichia coli. Proc Natl Acad Sci U S A. 78:7069-72. PMID: 6273909
  5. Kleckner, N., K. Reichardt and D. Botstein. (1979) Inversions and deletions of the Salmonella chromosome generated by the translocatable tetracycline resistance element Tn10. J. Mol. Biol. 127:89-115. PMID: 370414
  6. Raleigh, E. A. and N. Kleckner. (1984) Multiple IS10 rearrangements in Escherichia coli. J. Mol. Biol. 173:437-61. PMID: 6323719
  7. Simons, R. W., F. Houman and N. Kleckner. (1987) Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 53:85-96 PMID: 3596251
dam Endogenous adenine methylation at GATC sequences abolished. dam strains have a high recombination frequency, express DNA repair functions constitutively, and are poorly transformed by Dam-modified plasmids. Used for making DNA susceptible to cleavage by some restriction enzymes (e.g., BclI).
dcm Endogenous cytosine methylation at CCWGG sequences abolished. Used for making DNA susceptible to cleavage by some restriction enzymes (e.g. AvaII).
dnaJ One of several "chaperonins" is inactive. This defect has been shown to stabilize certain mutant proteins expressed in E. coli.
dut  dUTPase activity abolished. In combination with ung, allows incorporation of uracil into DNA. Some procedures for oligonucleotide mutagenesis use this.
endA Activity of nonspecific Endonuclease I abolished. DNA preparations are thought to be of higher quality when prepared from endA strains.
e14 An excisable prophage-like element, present in K-12 but missing from many derivatives. e14 carries the mcrA gene among others, so e14- strains are McrA-.
F A low-copy number self-transmissible plasmid. F' factors carry portions of the E. coli chromosome, most notably the lac operon and proAB on F' lac-proA+B+.
fhuA An iron uptake receptor is mutated. This mutation confers resistance to phage T1 (ferric hydroxamate uptake). Former name is tonA.
gal The ability to metabolize galactose is abolished.
glnV See supE.
gyrA A point mutation in DNA gyrase, subunit A. This mutation confers resistance to the antibiotic nalidixic acid.
hflA Results in high frequency lysogenization by l.
DNA that does not contain methylation of certain sequences is recognized as foreign by EcoKI or EcoBI and restricted (degraded). These enzymes recognize different sequences and are encoded by different alleles of hsdRMS. hsdR mutations abolish restriction but not protective methylation (r-m+), while hsdS mutations abolish both (r-m-). DNA made in the latter will be restricted when introduced into a wild-type strain. See E. coli K12.
lacIq The lac repressor is overproduced, turning off expression from Plac more completely.
lacZ β-galactosidase activity is abolished.
lacZ::T7gene 1 The phage T7 RNA polymerase (= gene 1) is inserted into the lacZ gene.

Lactose permease activity abolished.

D(lac) = deletion; there are four common deletions involving lac:

D(lacZ)M15 expresses a fragment that complements the lac alpha-fragment encoded by many vectors. These vectors will yield blue color on X-Gal only if the host carries DM15.

DU169, DX111, and DX74 all delete the entire lac operon from the chromosome, in addition to varying amounts of flanking DNA. DX111 deletes proAB as well, so that the cell requires proline for growth on minimal medium, unless it also carries F'lac proA+B+.

lon Activity of a protease responsible for degrading aberrant proteins abolished. Some eukaryotic proteins are stabilized in lon strains. E. coli B naturally lacks Lon.
lysY The lysozyme gene from the T7 bacteriophage is mutated. The mutation K128Y eliminates lysozyme activity, but the mutant protein still binds to and inhibits T7 RNA polymerase.
malB The malB region encompasses the genes malEFG and malK lamB malM. D(malB) deletes most or all of this region and eliminates expression of Maltose Binding Protein (MalE).
A restriction system that requires methyl mcrBC cytosine is abolished. DNA containing methylcytosine in some sequences is restricted by Mcr+. dcm-modified DNA is not restricted by Mcr+. Δ(mcrC-mrr) deletes six genes: mcrC-mcrB-hsdS-hsdM-hsdR-mrr; mcrA is lost with e14. See E. coli K12.
mrr A restriction system requiring cytosine or adenine methylation abolished; however, dam- , dcm-or EcoKI-modified DNA is not restricted by Mrr+. The methylcytosine-dependent activity is also known as McrF (3). See E. coli K12.
mtl The ability to metabolize the sugar alcohol mannitol is abolished.
ompT Activity of outer membrane protease (protease VII) is abolished.
phoA Activity of alkaline phosphatase is abolished.
Prc See tsp.
recA Homologous recombination abolished; particularly desirable when working with sequences containing direct repeats >50 bp.
Exonuclease and recombination activity of Exonuclease V abolished. Homologous recombination is much reduced in recB recC strains that are not also sbcB or sbcA. Stability of inverted repeat sequences is enhanced in recB recC strains, especially if they are also sbcB sbcC. Plasmid replication may be aberrant. 
recD Exonuclease activity of ExoV abolished, but recombination activity elevated. Inverted repeat sequences in l can be propagated in recD strains. Plasmid replication is aberrant.
recF Plasmid-by-plasmid homologous recombination abolished.
recJ Plasmid-by-plasmid homologous recombination abolished.
relA1 Lacks ppGpp synthesis during the stringent response to amino acid starvation; activity of ATP:GTP 3´-pyrophosphotransferase (EC2.7.6.5 ) is abolished.
rfbD Lacks functional TDP-rhamnose synthetase, and thus does not synthesize the cell surface O-antigen.
rpoH (also known as htpR) Lack of this heat-shock transcription factor abolishes expression of some stress-induced protease activities in addition to lon. Some cloned proteins are more stable in rpoHam supCts strains at high temperature.
sbcB Exo I activity abolished. Strains carrying recB recC and sbcB are usually also sbcC. These quadruple mutant strains are recombination-proficient and propagate inverted repeats in l, but plasmid replication is aberrant.
sbcC Usually found with recB recC sbcB. However, strains carrying sbcC alone are recombination-proficient and stably propagate inverted repeats both in l and in plasmids.
sulA Mutations in this gene inhibit cell division, allowing cells to recover from DNA damage in a lon mutant background (suppressor of Lon).
supC(ts) A thermosensitive tyrosine-inserting ochre (UAA) and amber (UAG) suppressor tRNA. Nonsense mutations in the same strain are suppressed only at low temperatures. Now called tyrT.
supE A glutamine-inserting amber (UAG) suppressor tRNA; required for growth of some phage vectors. Now called glnV.
supF A tyrosine-inserting amber (UAG) suppressor tRNA; required for lytic growth of S7 or S100 λ phage, such as λgt11. Now called tyrT.
thi-1 The ability to synthesize thiamine is abolished (vitamin B1).

traD The self-transmissibility of the F factor is severely reduced.
tsp A periplasmic protease that may degrade secreted or cytoplasmically overexpressed proteins after lysis is abolished. Now called prc.
tsx Confers resistance to bacteriophage T6.
tyrT See supC, supF.
ung Uracil N-glycosylase activity abolished. Uracil incorporated into DNA is removed by Ung+, leaving baseless site. See dut.
xyl The ability to metabolize the sugar xylose is abolished.
(P1) The cell carries a P1 prophage. Such strains express the P1 restriction system.
(P2) The cell carries a P2 prophage. This allows selection against Red+ Gam+ l (Spi- selection).
(f80) The cell carries the lambdoid prophage f80. A defective f80 prophage carrying the lac M15 deletion is present in some strains.
(Mu) Mu prophage; Mud means the phage is defective.