Escherichia coli

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"E. coli" redirects here. For the protozoan parasite, see Entamoeba coli.
This article is about Escherichia coli as a species. For E. coli in medicine, see Pathogenic Escherichia coli. For E. coli in molecular biology, see Escherichia coli (molecular biology).
Escherichia coli
EscherichiaColi NIAID.jpg
Scientific classification
Domain: Bacteria
Kingdom: Eubacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: coli
Binomial name
Escherichia coli
(Migula 1895)
Castellani and Chalmers 1919
Synonyms

Bacillus coli communis Escherich 1885

Escherichia coli (/ˌɛʃɨˈrɪkiə ˈkl/;[1] commonly abbreviated E. coli) is a Gram-negative, facultatively anaerobic, rod-shaped bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).[2] Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination.[3][4] The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2,[5] and preventing colonization of the intestine with pathogenic bacteria.[6][7]

E. coli and other facultative anaerobes constitute about 0.1% of gut flora,[8] and fecal–oral transmission is the major route through which pathogenic strains of the bacterium cause disease. Cells are able to survive outside the body for a limited amount of time, which makes them ideal indicator organisms to test environmental samples for fecal contamination.[9][10] There is, however, a growing body of research that has examined environmentally persistent E. coli which can survive for extended periods outside of the host.[11]

The bacterium can be grown easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is the most widely studied prokaryotic model organism, and an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA. Under favourable conditions it takes only 20 minutes to reproduce.[12]

Biology and biochemistry[edit]

Model of successive binary fission in E. coli

E. coli is Gram-negative (bacteria which do not retain Crystal violet dye), facultative anaerobic(that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent) and non-sporulating.[13] Cells are typically rod-shaped, and are about 2.0 micrometers (μm) long and 0.25–1.0 μm in diameter, with a cell volume of 0.6–0.7 μm3.[14][15] It can live on a wide variety of substrates. E. coli uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate and carbon dioxide. Since many pathways in mixed-acid fermentation produce hydrogen gas, these pathways require the levels of hydrogen to be low, as is the case when E. coli lives together with hydrogen-consuming organisms, such as methanogens or sulphate-reducing bacteria.[16]

Optimal growth of E. coli occurs at 37 °C (98.6 °F) but some laboratory strains can multiply at temperatures of up to 49 °C (120 °F).[17] Growth can be driven by aerobic or anaerobic respiration, using a large variety of redox pairs, including the oxidation of pyruvic acid, formic acid, hydrogen and amino acids, and the reduction of substrates such as oxygen, nitrate, fumarate, dimethyl sulfoxide and trimethylamine N-oxide.[18]

Strains that possess flagella are motile. The flagella have a peritrichous arrangement.[19]

E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation, transduction or transformation, which allows genetic material to spread horizontally through an existing population. This process led to the spread of the gene encoding shiga toxin from Shigella to E. coli O157:H7, carried by a bacteriophage.[20]

Diversity[edit]

Escherichia coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of a large number of isolates of E. coli and related bacteria shows that a taxonomic reclassification would be desirable. However, this has not been done, largely due to its medical importance[21] and E. coli remains one of the most diverse bacterial species: only 20% of the genome is common to all strains.[22]

In fact, from the evolutionary point of view, the members of genus Shigella (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) should be classified as E. coli strains, a phenomenon termed taxa in disguise.[23] Similarly, other strains of E. coli (e.g. the K-12 strain commonly used in recombinant DNA work) are sufficiently different that they would merit reclassification.

A strain is a sub-group within the species that has unique characteristics that distinguish it from other strains. These differences are often detectable only at the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain pathogenic capacity, the ability to use a unique carbon source, the ability to take upon a particular ecological niche or the ability to resist antimicrobial agents. Different strains of E. coli are often host-specific, making it possible to determine the source of fecal contamination in environmental samples.[9][10] For example, knowing which E. coli strains are present in a water sample allows researchers to make assumptions about whether the contamination originated from a human, another mammal or a bird.

Serotypes[edit]

A common subdivision system of E. coli, but not based on evolutionary relatedness, is by serotype, which is based on major surface antigens (O antigen: part of lipopolysaccharide layer; H: flagellin; K antigen: capsule), e.g. O157:H7).[24] It is however common to cite only the serogroup, i.e. the O-antigen. At present about 190 serogroups are known.[25] The common laboratory strain has a mutation that prevents the formation of an O-antigen and is thus non-typeable.

Genome plasticity[edit]

Like all lifeforms, new strains of E. coli evolve through the natural biological processes of mutation, gene duplication and horizontal gene transfer, in particular 18% of the genome of the laboratory strain MG1655 was horizontally acquired since the divergence from Salmonella.[26] In microbiology, all strains of E. coli derive from E. coli K-12 or E. coli B strains. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is unpleasant in healthy adults and is often lethal to children in the developing world.[27] More virulent strains, such as O157:H7 cause serious illness or death in the elderly, the very young or the immunocompromised.[6][27]

Neotype strain[edit]

E. coli is the type species of the genus (Escherichia) and in turn Escherichia is the type genus of the family Enterobacteriaceae, where it should be noted that the family name does not stem from the genus Enterobacter + "i" (sic.) + "aceae", but from "enterobacterium" + "aceae" (enterobacterium being not a genus, but an alternative trivial name to enteric bacterium).[28][29][30]

The original strain described by Escherich is believed to be lost, consequently a new type strain (neotype) was chosen as a representative: the neotype strain is ATCC 11775,[31] also known as NCTC 9001,[32] which is pathogenic to chickens and has an O1:K1:H7 serotype.[33] However, in most studies either O157:H7 or K-12 MG1655 or K-12 W3110 are used as a representative E.coli.

Phylogeny of Escherichia coli strains[edit]

A large number of strains belonging to this species have been isolated and characterised. In addition to serotype (vide supra), they can be classified according to their phylogeny, i.e. the inferred evolutionary history, as shown below where the species is divided into six groups.[22][34]

The link between phylogenetic distance ("relatedness") and pathology is small, e.g. the O157:H7 serotype strains, which form a clade ("an exclusive group")—group E below—are all enterohaemorragic strains (EHEC), but not all EHEC strains are closely related. In fact, four different species of Shigella are nested among E. coli strains (vide supra), while Escherichia albertii and Escherichia fergusonii are outside of this group. All commonly used research strains of E. coli belong to group A and are derived mainly from Clifton's K-12 strain (λ⁺ F⁺; O16) and to a lesser degree from d'Herelle's Bacillus coli strain (B strain)(O7).



Salmonella enterica




E. albertii




E. fergusonii




Group B2

E. coli SE15 (O150:H5. Commensal)



E. coli E2348/69 (O127:H6. Enteropathogenic)




Group D

E. coli UMN026 (O17:K52:H18. Extracellular pathogenic)




E. coli (O19:H34. Extracellular pathogenic)



E. coli (O7:K1. Extracellular pathogenic)





group E


E. coli EDL933 (O157:H7 EHEC)



E. coli Sakai (O157:H7 EHEC)





E. coli EC4115 (O157:H7 EHEC)



E. coli TW14359 (O157:H7 EHEC)





Shigella


Shigella dysenteriae




Shigella sonnei




Shigella flexneri







Group B1


E. coli E24377A (O139:H28. Enterotoxigenic)






E. coli E110019




E. coli 11368 (O26:H11. EHEC)



E. coli 11128 (O111:H-. EHEC)







E. coli IAI1 O8 (Commensal)



E. coli 53638 (EIEC)





E. coli SE11 (O152:H28. Commensal)



E. coli B7A









E. coli 12009 (O103:H2. EHEC)



E. coli GOS1 (O104:H4 EAHEC) German 2011 outbreak




E. coli E22





E. coli Olso O103



E. coli 55989 (O128:H2. Enteroaggressive)







Group A


E. coli ATCC8739 (O146. Crook's E.coli used in phage work in the 1950s)




K-12 strain derivatives

E. coli K-12 W3110 (O16. λ⁻ F⁻ "wild type" molecular biology strain)



E. coli K-12 DH10b (O16. high electrocompetency molecular biology strain)



E. coli K-12 DH1 (O16. high chemical competency molecular biology strain)



E. coli K-12 MG1655 (O16. λ⁻ F⁻ "wild type" molecular biology strain)



E. coli BW2952 (O16. competent molecular biology strain)





E. coli 101-1 (O? H?. EAEC)


B strain derivatives

E. coli B REL606 (O7. high competency molecular biology strain)



E. coli BL21-DE3 (O7. expression molecular biology strain with T7 polymerase for pET system)














Genomics[edit]

The first complete DNA sequence of an E. coli genome (laboratory strain K-12 derivative MG1655) was published in 1997. It was found to be a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes. Despite having been the subject of intensive genetic analysis for approximately 40 years, a large number of these genes were previously unknown. The coding density was found to be very high, with a mean distance between genes of only 118 base pairs. The genome was observed to contain a significant number of transposable genetic elements, repeat elements, cryptic prophages, and bacteriophage remnants.[35]

Today, over 60 complete genomic sequences of Escherichia and Shigella species are available. Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences present in every one of the isolates, while approximately 80% of each genome can vary among isolates.[22] Each individual genome contains between 4,000 and 5,500 genes, but the total number of different genes among all of the sequenced E. coli strains (the pan-genome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the E. coli pangenome originated in other species and arrived through the process of horizontal gene transfer.[36]

Proteomics[edit]

Proteome[edit]

Several studies have investigated the proteome of E. coli. By 2006, 1,627 (38%) of the 4,237 open reading frames (ORFs) had been identified experimentally.[37]

Interactome[edit]

The interactome of E. coli has been studied by affinity purification and mass spectrometry (AP/MS) and by analyzing the binary interactions among its proteins.

Protein complexes. A 2006 study purified 4,339 proteins from cultures of strain K-12 and found interacting partners for 2,667 proteins, many of which had unknown functions at the time.[38] A 2009 study found 5,993 interactions between proteins of the same E. coli strain though this data showed little overlap with that of the 2006 publication.[39]

Binary interactions. Rajagopala et al. (2014) have carried out systematic yeast two-hybrid screens with most E. coli proteins and found a total of 2,234 protein-protein interactions.[40] This study also integrated genetic interactions and protein structures and mapped 458 interactions within 227 protein complexes.

Normal microbiota[edit]

E. coli normally colonizes an infant's gastrointestinal tract within 40 hours of birth, arriving with food or water or with the individuals handling the child. In the bowel, it adheres to the mucus of the large intestine. It is the primary facultative anaerobe of the human gastrointestinal tract.[41] (Facultative anaerobes are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire genetic elements encoding for virulence factors, they remain benign commensals.[42]

Therapeutic use[edit]

Nonpathogenic Escherichia coli strain Nissle 1917 also known as Mutaflor and Escherichia coli O83:K24:H31 (known as Colinfant[43]) are used as a probiotic agents in medicine, mainly for the treatment of various gastroenterological diseases,[44] including inflammatory bowel disease.[45]

Role in disease[edit]

Virulent strains of E. coli can cause gastroenteritis, urinary tract infections, and neonatal meningitis. In rarer cases, virulent strains are also responsible for hemolytic-uremic syndrome, peritonitis, mastitis, septicemia and Gram-negative pneumonia.[41]

UPEC (uropathogenic E. coli) is one of the main causes of urinary tract infections.[46] It is part of the normal flora in the gut and can be introduced in many ways. In particular for females, the direction of wiping after defecation (wiping back to front) can lead to fecal contamination of the urogenital orifices. Anal intercourse can also introduce this bacteria into the male urethra, and in switching from anal to vaginal intercourse the male can also introduce UPEC to the female urogenital system.[46] For more information, see the databases at the end of the article or UPEC pathogenicity.

In May 2011, one E. coli strain, Escherichia coli O104:H4, has been the subject of a bacterial outbreak that began in Germany. Certain strains of E. coli are a major cause of foodborne illness. The outbreak started when several people in Germany were infected with enterohemorrhagic E. coli (EHEC) bacteria, leading to hemolytic-uremic syndrome (HUS), a medical emergency that requires urgent treatment. The outbreak did not only concern Germany, but 11 other countries, including regions in North America.[47] On 30 June 2011 the German Bundesinstitut für Risikobewertung (BfR) (Federal Institute for Risk Assessment, a federal, fully legal entity under public law of the Federal Republic of Germany, an institute within the German Federal Ministry of Food, Agriculture and Consumer Protection) announced that seeds of fenugreek from Egypt were likely the cause of the EHEC outbreak.[48]

Model organism in life science research[edit]

Role in biotechnology[edit]

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.[49] 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.[50]

E. coli is a very versatile host for the production of heterologous proteins,[51] and various protein expression systems have been developed which allow the production of recombinant proteins in E. coli. Researchers can introduce genes into the microbes using plasmids which permit high level expression of protein, and such protein may be mass-produced in industrial fermentation processes. One of the first useful applications of recombinant DNA technology was the manipulation of E. coli to produce human insulin.[52]

Many proteins previously thought difficult or impossible to be expressed in E. coli in folded form have also been successfully expressed in E. coli. For example, proteins with multiple disulphide bonds may be produced in the periplasmic space or in the cytoplasm of mutants rendered sufficiently oxidizing to allow disulphide-bonds to form,[53] while proteins requiring post-translational modification such as glycosylation for stability or function have been expressed using the N-linked glycosylation system of Campylobacter jejuni engineered into E. coli.[54][55][56]

Modified E. coli cells have been used in vaccine development, bioremediation, production of biofuels;[57] lighting, and production of immobilised enzymes.[51][58]

Model organism[edit]

E. coli is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. E. coli K12) 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.[59][60] 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,[61] and it remains the primary model to study conjugation.[62] E. coli was an integral part of the first experiments to understand phage genetics,[63] and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.[64] Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.[65]

E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997.[35]

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.[66] In this experiment, one population of E. coli unexpectedly evolved the ability to aerobically metabolize citrate, which 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.

By evaluating the possible combination of nanotechnologies with landscape ecology, complex habitat landscapes can be generated with details at the nanoscale.[67] On such synthetic ecosystems, evolutionary experiments with E. coli have been performed to study the spatial biophysics of adaptation in an island biogeography on-chip.

Studies are also being performed attempting to program E. coli to solve complicated mathematics problems, such as the Hamiltonian path problem.[68]

History[edit]

The genera Escherichia and Salmonella diverged around 102 million years ago (credibility interval: 57–176 mya), which coincides with the divergence of their hosts: the former being found in mammals and the latter in birds and reptiles.[69] This was followed by a split of the escherichian ancestor into five species (E. albertii, E. coli, E. fergusonii, E. hermannii and E. vulneris.) The last E. coli ancestor split between 20 and 30 million years ago.[70]

In 1885, a German pediatrician, Theodor Escherich, discovered this organism in the feces of healthy individuals and called it Bacterium coli commune due to the fact 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[71]).[72] Bacterium coli was the type species of the now invalid genus Bacterium when it was revealed that the former type species ("Bacterium triloculare") was missing.[73] Following a revision of Bacterium it was reclassified as Bacillus coli by Migula in 1895[74] and later reclassified in the newly created genus Escherichia, named after its original discoverer.[75]

The genus belongs in a group of bacteria informally known as "coliforms", and is a member of the Enterobacteriaceae family ("the enterics") of the Gammaproteobacteria.[28]

See also[edit]

References[edit]

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External links[edit]

E. coli databases[edit]

  • Bacteriome E. coli interaction database
  • coliBASE (subset of the comparative genomics database xBASE)
  • EcoSal Continually updated Web resource based on the classic ASM Press publication Escherichia coli and Salmonella: Cellular and Molecular Biology
  • ECODAB The structure of the O-antigens that form the basis of the serological classification of E. coli
  • Coli Genetic Stock Center Strains and genetic information on E. coli K-12
  • EcoCyc – literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways
  • PortEco (formerly EcoliHub) – NIH-funded comprehensive data resource for E. coli K-12 and its phage, plasmids, and mobile genetic elements
  • EcoliWiki is the community annotation component of PortEco
  • RegulonDB RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell E. coli K-12.
  • Uropathogenic Escherichia coli (UPEC)

General databases with E. coli-related information[edit]

  • 5S rRNA Database Information on nucleotide sequences of 5S rRNAs and their genes
  • ACLAME A CLAssification of Mobile genetic Elements
  • AlignACE Matrices that search for additional binding sites in the E. coli genomic sequence
  • ArrayExpress Database of functional genomics experiments
  • ASAP Comprehensive genome information for several enteric bacteria with community annotation
  • BioGPS Gene portal hub
  • BRENDA Comprehensive Enzyme Information System
  • BSGI Bacterial Structural Genomics Initiative
  • CATH Protein Structure Classification
  • CBS Genome Atlas
  • CDD Conserved Domain Database
  • CIBEX Center for Information Biology Gene Expression Database
  • COGs