Escherichia coli in molecular biology
Escherichia coli (/ /; commonly abbreviated E. coli) is a Gram-negative gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms). The descendants of two isolates, K-12 and B strain, are used routinely in molecular biology as both a tool and a model organism.
Escherichia coli is one of the most diverse bacterial species, with several pathogenic strains with different symptoms and with only 20% of the genome common to all strains. Furthermore, from the evolutionary point of view, the members of genus Shigella (dysenteriae, flexneri, boydii, sonnei) are actually E. coli strains "in disguise" (i.e. E. coli is paraphyletic to the genus).
In 1885, Theodor Escherich, a German pediatrician, first discovered this species in the feces of healthy individuals and called it Bacterium coli commune because it is found in the colon and early classifications of Prokaryotes placed these in a handful of genera based on their shape and motility (at that time Ernst Haeckel's classification of Bacteria in the kingdom Monera was in place).
Due to its ease of culture and fast doubling, it was used in the early microbiology experiments; however, bacteria were considered primitive and pre-cellular and received little attention before 1944, when Avery, Macleod and McCarty demonstrated that DNA was the genetic material using Salmonella typhimurium, following which Escherichia coli was used for linkage mapping studies.
Four of the many E. coli strains (K-12, B, C, and W) are thought of as model organism strains. These are classified in Risk Group 1 in biosafety guidelines.
A strain was isolated from a stool sample of a patient convalescent from diphtheria and was labelled K-12 (not an antigen) in 1922 at Stanford University. This isolate was used in 1940s by Charles E. Clifton to study nitrogen metabolism, who deposited it in ATCC (strain ATCC 10798) and lent it to Edward Tatum for his tryptophan biosynthesis experiments, despite its idiosyncrasies due to the F+ λ+ phenotype. In the course of the passages it lost its O antigen and in 1953 was cured first of its lambda phage (strain W1485 by UV by Joshua Lederberg and colleagues) and then in 1985 of the F plasmid by acridine orange curing. Strains derived from MG1655 include DH1, parent of DH5α and in turn of DH10B (rebranded as TOP10 by Invitrogen). An alternative lineage from W1485 is that of W2637 (which contains an inversion rrnD-rrnE), which in turn resulted in W3110. Due to the lack of specific record-keeping, the "pedigree" of strains was not available and had to be inferred by consulting lab-book and records in order to set up the E. coli Genetic Stock Centre at Yale by Barbara Bachmann. The different strains have been derived through treating E. coli K-12 with agents such as nitrogen mustard, ultra-violet radiation, X-ray etc. An extensive list of Escherichia coli K-12 strain derivatives and their individual construction, genotypes, phenotypes, plasmids and phage information can be viewed at Ecoliwiki.
A second common laboratory strain is the B strain, whose history is less straightforward and the first naming of the strain as E. coli B was by Delbrück and Luria in 1942 in their study of bacteriophages T1 and T7. The original E. coli B strain, known then as Bacillus coli, originated from Félix d'Herelle from the Institut Pasteur in Paris around 1918 who studied bacteriophages, who claimed that it originated from Collection of the Institut Pasteur, but no strains of that period exist. The strain of d'Herelle was passed to Jules Bordet, Director of the Institut Pasteur du Brabant in Bruxelles and his student André Gratia. The former passed the strain to Ann Kuttner ("the Bact. coli obtained from Dr. Bordet") and in turn to Eugène Wollman (B. coli Bordet), whose son deposited it in 1963 (CIP 63.70) as "strain BAM" (B American), while André Gratia passed the strain to Martha Wollstein, a researcher at Rockefeller, who refers to the strain as "Brussels strain of Bacillus coli" in 1921, who in turn passed it to Jacques Bronfenbrenner (B. coli P.C.), who passed it to Delbrück and Luria. This strain gave rise to several other strains, such as REL606 and BL21.
E. coli C is morphologically distinct from other E. coli strains; it is more spherical in shape and has a distinct distribution of its nucleoid.
Role in biotechnology
Because of its long history of laboratory culture and ease of manipulation, E. coli also plays an important role in modern biological engineering and industrial microbiology. The work of Stanley Norman Cohen and Herbert Boyer in E. coli, using plasmids and restriction enzymes to create recombinant DNA, became a foundation of biotechnology.
Considered a very versatile host for the production of heterologous proteins, researchers can introduce genes into the microbes using plasmids, allowing for the mass production of proteins in industrial fermentation processes. Genetic systems have also been developed which allow the production of recombinant proteins using E. coli. One of the first useful applications of recombinant DNA technology was the manipulation of E. coli to produce human insulin. Modified E. coli have been used in vaccine development, bioremediation, and production of immobilised enzymes.
E. coli have been used successfully to produce proteins previously thought difficult or impossible in E. coli, such as those containing multiple disulfide bonds or those requiring post-translational modification for stability or function. The cellular environment of E. coli is normally too reducing for disulphide bonds to form, proteins with disulphide bonds therefore may be secreted to its periplasmic space, however, mutants in which the reduction of both thioredoxins and glutathione is impaired also allow disulphide bonded proteins to be produced in the cytoplasm of E. coli. It has also been used to produce proteins with various post-translational modifications, including glycoproteins by using the N-linked glycosylation system of Campylobacter jejuni engineered into E. coli. Efforts are currently under way to expand this technology to produce complex glycosylations.
E. coli is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. E. coli K-12) are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Many lab strains lose their ability to form biofilms. These features protect wild type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources.
In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium, and it remains a primary model to study conjugation. E. coli was an integral part of the first experiments to understand phage genetics, and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure. Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.
E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K-12 was published by Science in 1997.
Lenski's long-term evolution experiment
The long-term evolution experiments using E. coli, begun by Richard Lenski in 1988, have allowed direct observation of major evolutionary shifts in the laboratory. In this experiment, one population of E. coli unexpectedly evolved the ability to aerobically metabolize citrate. This capacity is extremely rare in E. coli. As the inability to grow aerobically is normally used as a diagnostic criterion with which to differentiate E. coli from other, closely related bacteria such as Salmonella, this innovation may mark a speciation event observed in the lab.
- Lukjancenko, O.; Wassenaar, T.M.; Ussery, D.W. (2010). "Comparison of 61 sequenced Escherichia coli genomes". Microb. Ecol. 60 (4): 708–720. doi:10.1007/s00248-010-9717-3. PMC 2974192. PMID 20623278.
- Lan, R.; Reeves, P.R. (2002). "Escherichia coli in disguise: molecular origins of Shigella". Microbes Infect. 4 (11): 1125–1132. doi:10.1016/S1286-4579(02)01637-4. PMID 12361912.
- Haeckel, Ernst (1867). Generelle Morphologie der Organismen. Reimer, Berlin. ISBN 978-1-144-00186-3.
- Escherich T (1885). "Die Darmbakterien des Neugeborenen und Säuglinge". Fortschr. Med. 3: 515–522.
- MIGULA (W.): Bacteriaceae (Stabchenbacterien). In: A. ENGLER and K. PRANTL (eds): Die Naturlichen Pfanzenfamilien, W. Engelmann, Leipzig, Teil I, Abteilung Ia, 1895, pp. 20–30.
- CASTELLANI (A.) and CHALMERS (A.J.): Manual of Tropical Medicine, 3rd ed., Williams Wood and Co., New York, 1919.
- Lederber, J. 2004 E. coli K-12. Microbiology today 31:116
- Daegelen, P.; Studier, F. W.; Lenski, R. E.; Cure, S.; Kim, J. F. (2009). "Tracing Ancestors and Relatives of Escherichia coli B, and the Derivation of B Strains REL606 and BL21(DE3)". Journal of Molecular Biology. 394 (4): 634–643. doi:10.1016/j.jmb.2009.09.022. PMID 19765591.
- Bachmann, B. J. (1972). "Pedigrees of some mutant strains of Escherichia coli K-12". Bacteriological Reviews. 36 (4): 525–557. doi:10.1128/mmbr.36.4.525-557.1972. PMC 408331. PMID 4568763.
- Tatum E. L.; Lederberg J. (1947). "Gene recombination in the bacterium Escherichia coli". J. Bacteriol. 53: 673–684. doi:10.1128/jb.53.6.673-684.1947.
- E. coli genotypes – OpenWetWare
- Meselson, M; Yuan, R (1968). "DNA restriction enzyme from E. Coli". Nature. 217 (5134): 1110–4. Bibcode:1968Natur.217.1110M. doi:10.1038/2171110a0. PMID 4868368.
- Delbrück M.; Luria S. E. (1942). "Interference between bacterial viruses: I. Interference between two bacterial viruses acting upon the same host, and the mechanism of virus growth". Arch. Biochem. 1: 111–141.
- D'Herelle F (1918). "Sur le rôle du microbe filtrant bactériophage dans la dysenterie bacillaire". Comptes Rendus Acad. Sci. 167: 970–972.
- d'Herelle, F. (1926). In Le bactériophage et son comportement. Monographies de l'Institut Pasteur, Masson et Cie, Libraires de l'Académie de Médecine, 120, Boulevard Saint Germain, Paris-VIe, France.
- Bordet J.; Ciuca M. (1920). "Le bactériophage de d'Herelle, sa production et son interprétation". Comptes Rendus Soc. Biol. 83: 1296–1298.
- Gratia A.; Jaumain D. (1921). "Dualité du principe lytique du colibacille et du staphylococque". Comptes Rendus Soc. Biol. 84: 882–884.
- Kuttner A. G. (1923). "Bacteriophage phenomena". J. Bacteriol. 8 (1): 49–101. doi:10.1128/jb.8.1.49-101.1923. PMC 379003. PMID 16558985.
- Wollman E (1925). "Recherches sur la bactériophagie (phénomène de Twort-d'Hérelle)". Ann. Inst. Pasteur. 39: 789–832.
- Wollstein M (1921). "Studies on the phenomenon of d'Herelle with Bacillus dysenteriae". J. Exp. Med. 34 (5): 467–476. doi:10.1084/jem.34.5.467. PMC 2128695. PMID 19868572.
- Lieb, M.; Weigle, J. J.; Kellenberger, E. (1955). "A study of hybrids between two strains of Escherichia coli". Journal of Bacteriology. 69 (4): 468–471. PMC 357561. PMID 14367303.
- Colin T Archer; Jihyun F Kim; Haeyoung Jeong; Jin H Park; Claudia E Vickers; Sang Y Lee; Lars K Nielsen (2011). "The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli". BMC Genomics. 12: 9. doi:10.1186/1471-2164-12-9. PMC 3032704. PMID 21208457.
- Lee SY (1996). "High cell-density culture of Escherichia coli". Trends Biotechnol. 14 (3): 98–105. doi:10.1016/0167-7799(96)80930-9. PMID 8867291.
- Russo E (January 2003). "The birth of biotechnology". Nature. 421 (6921): 456–7. Bibcode:2003Natur.421..456R. doi:10.1038/nj6921-456a. PMID 12540923.
- Cornelis P (2000). "Expressing genes in different Escherichia coli compartments". Current Opinion in Biotechnology. 11 (5): 450–4. doi:10.1016/S0958-1669(00)00131-2. PMID 11024362.
- Tof, Ilanit (1994). "Recombinant DNA Technology in the Synthesis of Human Insulin". Little Tree Pty. Ltd. Retrieved 2007-11-30.
- Paul H. Bessette; Fredrik Åslund; Jon Beckwith; George Georgiou (1999). "Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm". Proc. Natl. Acad. Sci. U.S.A. 96 (24): 13703–8. Bibcode:1999PNAS...9613703B. doi:10.1073/pnas.96.24.13703. PMC 24128. PMID 10570136.
- Ihssen J, Kowarik M, Dilettoso S, Tanner C, Wacker M, Thöny-Meyer L (2010). "Production of glycoprotein vaccines in Escherichia coli". Microbial Cell Factories. 9 (61): 494–7. doi:10.1186/1475-2859-9-61. PMC 2927510. PMID 20701771.
- Wacker M, Linton D, Hitchen PG, Nita-Lazar M, Haslam SM, North SJ, Panico M, Morris HR, Dell A, Wren BW, Aebi M (2002). "N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coli". Science. 298 (5599): 1790–1793. Bibcode:2002Sci...298.1790W. doi:10.1126/science.298.5599.1790. PMID 12459590.
- Valderrama-Rincon JD, Fisher AC, Merritt JH, Fan YY, Reading CA, Chhiba K, Heiss C, Azadi P, Aebi M, Delisa MP (2012). "An engineered eukaryotic protein glycosylation pathway in Escherichia coli". Nat Chem Biol. 8 (5): 434–6. doi:10.1038/nchembio.921. PMC 3449280. PMID 22446837.
- Huang CJ, Lin H, Yang X (2012). "Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements". J Ind Microbiol Biotechnol. 39 (3): 383–99. doi:10.1007/s10295-011-1082-9. PMID 22252444.
- "E. coli can solve math problems". The Deccan Chronicle. July 26, 2009. Retrieved July 26, 2009.
- Fux CA, Shirtliff M, Stoodley P, Costerton JW (2005). "Can laboratory reference strains mirror "real-world" pathogenesis?". Trends Microbiol. 13 (2): 58–63. doi:10.1016/j.tim.2004.11.001. PMID 15680764.
- Vidal O, Longin R, Prigent-Combaret C, Dorel C, Hooreman M, Lejeune P (1998). "Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression". J. Bacteriol. 180 (9): 2442–9. doi:10.1128/JB.180.9.2442-2449.1998. PMC 107187. PMID 9573197.
- Lederberg, Joshua; E.L. Tatum (October 19, 1946). "Gene recombination in E. coli" (PDF). Nature. 158 (4016): 558. Bibcode:1946Natur.158..558L. doi:10.1038/158558a0. PMID 21001945. Source: National Library of Medicine – The Joshua Lederberg Papers
- F Xavier Gomis-Rüth; Miquel Coll (December 2006). "Cut and move: protein machinery for DNA processing in bacterial conjugation". Current Opinion in Structural Biology. 16 (6): 744–752. doi:10.1016/j.sbi.2006.10.004. hdl:10261/104348. PMID 17079132.
- "The Phage Course – Origins". Cold Spring Harbor Laboratory. 2006. Archived from the original on September 16, 2006. Retrieved 2007-12-03.
- Benzer, Seymour (March 1961). "On the topography of the genetic fine structure". PNAS. 47 (3): 403–15. Bibcode:1961PNAS...47..403B. doi:10.1073/pnas.47.3.403. PMC 221592. PMID 16590840.
- Frederick R. Blattner; Guy Plunkett III; Craig Bloch; Nicole Perna; Valerie Burland; Monica Riley; Julio Collado-Vides; Jeremy Glasner; Christopher Rode; George Mayhew; Jason Gregor; Nelson Davis; Heather Kirkpatrick; Michael Goeden; Debra Rose; Bob Mau; Ying Shao (September 5, 1997). "The complete genome sequence of Escherichia coli K-12". Science. 277 (5331): 1453–1462. doi:10.1126/science.277.5331.1453. PMID 9278503.
- Bob Holmes (June 9, 2008). "Bacteria make major evolutionary shift in the lab". New Scientist. Archived from the original on August 28, 2008.