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Escherichia coli

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General information about Escherichia coli.

Contents

General Information

  • Escherichia coli is a rod-shaped bacterium. Each bacterium measures approximately 0.5 μm in width by 2 μm in length. E. coli is a Gram-negative bacterium. E. coli cells stain Gram negative because they have a thin cell wall with only 1 to 2 layers of peptidoglycan. E. coli is a facultative anaerobe, which means it does not require oxygen, but grows better in the presence of oxygen.

Taxonomy

E. coli is a member of the:

  • Bacteria;
    • Proteobacteria;
      • Gammaproteobacteria;
        • Enterobacteriales;
          • Enterobacteriaceae;
            • Escherichia.

Major subgroups

E. coli strains fall into five major taxonomic lineages (A, B1, B2, D, and E; ) [3]. In addition, species in the genus Shigella group within the E. coli groupings and different Shigella species have different E. coli groups as their closest relatives. E. coli K-12 strains are in subgroup A. Different methods for producing phylogenies provide different insights into the evolution of E. coli as a group[4][5].

NCBI Taxonomy

E. coli at NCBI taxonomy encompasses a large number of strains with different taxonomy IDs.

As of January 2010, the groupings in the NCBI taxonomy do not reflect the major groupings of E. coli and Shigella strains.

Laboratory E. coli strains

For more on why we study nonpathogenic laboratory E. coli, see E. coli as a model organism

See Category:Strain:E. coli and Category:Strains
Major E. coli lab strains used for basic research are mostly derived from E. coli K-12 and E. coli B.

E. coli K-12

Note that correct usage is K-12, not K12. E. coli K-12 is not serotype K. Escherichia coli K-12 was isolated in the fall of 1922 from the stool sample of a diptheria patient in Palo Atlo, California. The use of E. coli K-12 as a model organism for research was by sheer luck as E.L. Tatum received a culture of K-12 along with other species of bacteria for his biochemical genetic research. E. coli K-12 is prototrophic, easy to cultivate and its short generation time makes it easy to study in large populations.

E. coli B

E.coli B is the clonal descendant of a Bacillus coli strain from the Istitut Pasteur in Paris used by d'Herelle in his early studies of bacteriophages .Daegelen [6] examined the literature to derive what is known about the geneology of E. coli B strains. Current E. coli B strains are derived from the E. coli used in the phage studies of the Luria, Delbruck, and Hershey groups associated with the Cold Spring Harbor Phage community. Strain E.coli B is the common host for phages T1-T7 which led to the widspread use of B along with E. coli K-12.

E. coli C

Lieb et al. [7] describe differences between E. coli C, B, and K-12 in their study of hybrids between different E. coli strains.


E. coli W

E. coli Crookes

Morphology

E.coli negatively stained with Ammonium Molybdate and analyzed by EM (electron microscopy). Image courtesy of Christos Savva (Microscopy & Imaging Center) and Thomas Wood (Dept. of Chemical Engineering) at Texas A&M University.


cryo-EM picture of E.coli (dark blobs are hexagonal ice crystals). Image courtesy of Christos Savva (Microscopy & Imaging Center) and Ry Young (Dept. of Bio/Bio) at Texas A&M University.

Types

E. coli types are based on major surface antigens[8]

  • O-antigen: the O antigen is part of the lipopolysaccharide. O antigens were originally defined by reaction with antisera from rabbits immunized with boiled bacteria. Hundreds of O groups have been identified.
  • H-antigen: H antigen is flagellin
  • K-antigens: K antigens were named for capsule (Kapsel in German). Sera subdivide K antigens into L, B, and A groups. At the molecular level, there are two major kinds of K antigens
    • polysaccharide K antigens
    • protein K antigens, mostly fimbriae
  • R-antigen:

Strains O antigen H antigen K antigen Notes

K-12

O16 (mutant)

K-12 is phenotypically rough
Note that K-12 does NOT refer to an antigenic type, and should be hyphenated
Complementation using WG1 shows that the parent of laboratory K-12 strains was of type O16 PMID:7512872[9]

B

C


Chemical Composition

From Neidhardt[10] based on B/r.

Component %total dry weight Amount (fg/cell) Mol. wt Molecules/cell N. of kinds

Protein

55.0

156

4 x 104

2,350,000

1,850

RNA

20.5

58

23S rRNA

31.0

1.0 x 106

18,700

1

16S rRNA

15.5

5.0 x 105

18,700

1

5S rRNA

1.2

3.9 x 104

18,700

1

tRNA

8.2

2.5 x 104

198,000

60

mRNA

2.3

1 x 106

1,380

600

DNA

3.1

8.8

2.5 x 109

2.1

1

Lipid

9.1

25.9

705

22,000,000

Lipopolysaccharide

3.4

9.7

4,070

1,430,000

Peptidoglycan

2.5

7.1

(904)n

1

1

Glycogen

2.5

7.1

1 x 106

4,300

1

Polyamines

0.4

1.1

Putrescine

0.83

88

5,600,000

1

Spermidine

0.27

145

1,100,000

1

Metabolites, cofactors, ions

3.5

9.9

800+

Metal Content

Metal Growth medium Intracellular conc. Conc. in medium Method Reference Notes

Mg12

LB

PMID:11397910[11]

Mg12

Minimal

PMID:11397910[11]

K19

LB

PMID:11397910[11]

K19

Minimal

PMID:11397910[11]

Ca20

LB

PMID:11397910[11]

Ca20

Minimal

PMID:11397910[11]

V23

LB

PMID:11397910[11]

V23

Minimal

PMID:11397910[11]

Cr24

LB

PMID:11397910[11]

Cr24

Minimal

PMID:11397910[11]

Co27

Minimal

PMID:11397910[11]

Ni28

LB

PMID:11397910[11]

Mn25

LB

PMID:11397910[11]

Ni28

Minimal

PMID:11397910[11]

Cu29

LB

PMID:11397910[11]

Fe26

LB

PMID:11397910[11]

Cu29

Minimal

PMID:11397910[11]

Fe26

Minimal

PMID:11397910[11]

Zn30

LB

PMID:11397910[11]

Co27

LB

PMID:11397910[11]

Zn30

Minimal

PMID:11397910[11]

Mn25

Minimal

PMID:11397910[11]

Se34

LB

PMID:11397910[11]

Se34

Minimal

PMID:11397910[11]

Mo42

LB

PMID:11397910[11]

Mo42

Minimal

PMID:11397910[11]

Mg12

GGM minimal

24.2 mg liter-1

ICP-AES

PMID:19377097[12]

Ca20

GGM minimal

2.83 mg liter-1

ICP-AES

PMID:19377097[12]

Mo42

GGM minimal

0.068 mg liter-1

ICP-AES

PMID:19377097[12]

Co27

GGM minimal

0.018 mg liter-1

ICP-AES

PMID:19377097[12]

Cu29

GGM minimal

0.033 mg liter-1

ICP-AES

PMID:19377097[12]

Fe26

GGM minimal

0.886 mg liter-1

ICP-AES

PMID:19377097[12]

Zn30

GGM minimal

0.340 mg liter-1

ICP-AES

PMID:19377097[12]


Pangenome

The pangenome is the nonredundant set of all genes found in all strains of a bacterial species. Based on analysis of 61 E. coli genomes, Lukjancenko et al.[13] identified 15,741 gene families in the E. coli pangenome.

Educational Resources

Other E. coli Sequencing Projects

There are roughly 200 completed or ongoing sequencing projects for strains of E. coli. While this list continues to grow, some are listed here on EcoliWiki and NCBI has a complete list.

See also

References

See Help:References for how to manage references in EcoliWiki.

  1. Cummings, JH & Macfarlane, GT () Role of intestinal bacteria in nutrient metabolism. JPEN J Parenter Enteral Nutr 21 357-65 PubMed EcoliWiki page
  2. Kindberg, C et al. (1987) Menaquinone production and utilization in germ-free rats after inoculation with specific organisms. J. Nutr. 117 1032-5 PubMed EcoliWiki page
  3. Touchon, M et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5 e1000344 PubMed EcoliWiki page
  4. Zhang, Y & Lin, K (2012) A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. BMC Evol. Biol. 12 174 PubMed EcoliWiki page
  5. Sims, GE & Kim, SH (2011) Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Natl. Acad. Sci. U.S.A. 108 8329-34 PubMed EcoliWiki page
  6. Daegelen, P et al. (2009) Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). J. Mol. Biol. 394 634-43 PubMed EcoliWiki page
  7. LIEB, M et al. (1955) A study of hybrids between two strains of Escherichia coli. J. Bacteriol. 69 468-71 PubMed EcoliWiki page
  8. Orskov, I et al. (1977) Serology, chemistry, and genetics of O and K antigens of Escherichia coli. Bacteriol Rev 41 667-710 PubMed EcoliWiki page
  9. Liu, D & Reeves, PR (1994) Escherichia coli K12 regains its O antigen. Microbiology (Reading, Engl.) 140 ( Pt 1) 49-57 PubMed EcoliWiki page
  10. Neidhardt, FC et al. (1996) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 2nd ed. (ASM Press, Washington, DC)
  11. 11.00 11.01 11.02 11.03 11.04 11.05 11.06 11.07 11.08 11.09 11.10 11.11 11.12 11.13 11.14 11.15 11.16 11.17 11.18 11.19 11.20 11.21 11.22 11.23 11.24 11.25 Outten, CE & O'Halloran, TV (2001) Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis. Science 292 2488-92 PubMed EcoliWiki page
  12. 12.0 12.1 12.2 12.3 12.4 12.5 12.6 Graham, AI et al. (2009) Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins. J. Biol. Chem. 284 18377-89 PubMed EcoliWiki page
  13. Lukjancenko, O et al. (2010) Comparison of 61 sequenced Escherichia coli genomes. Microb. Ecol. 60 708-20 PubMed EcoliWiki page