Escherichia coli
Escherichia coli | |
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Scientific classification | |
Domain: | Bacteria |
Phylum: | Pseudomonadota |
Class: | Gammaproteobacteria |
Order: | Enterobacterales |
Family: | Enterobacteriaceae |
Genus: | Escherichia |
Species: | E. coli
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Binomial name | |
Escherichia coli | |
Synonyms | |
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Escherichia coli (
E. coli and other
The bacterium can be
Biology and biochemistry
Clinical data | |
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License data | |
ATC code |
Type and morphology
E. coli is a gram-negative,
E. coli stains gram-negative because its cell wall is composed of a thin
The flagella which allow the bacteria to swim have a peritrichous arrangement.[22] It also attaches and effaces to the microvilli of the intestines via an adhesion molecule known as intimin.[23]
Metabolism
E. coli can live on a wide variety of substrates and uses
In addition, E. coli's metabolism can be rewired to solely use
E. coli has three native glycolytic pathways:
Catabolite repression
When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as
Culture growth
Optimum growth of E. coli occurs at 37 °C (99 °F), but some laboratory strains can multiply at temperatures up to 49 °C (120 °F).
Cell cycle
The bacterial cell cycle is divided into three stages. The B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA. The D period refers to the stage between the conclusion of DNA replication and the end of cell division.[30] The doubling rate of E. coli is higher when more nutrients are available. However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the previous round of replication has completed, resulting in multiple replication forks along the DNA and overlapping cell cycles.[31]
The number of replication forks in fast growing E. coli typically follows 2n (n = 1, 2 or 3). This only happens if
Although E. coli reproduces by binary fission the two supposedly identical cells produced by cell division are functionally asymmetric with the old pole cell acting as an aging parent that repeatedly produces rejuvenated offspring.[34] When exposed to an elevated stress level, damage accumulation in an old E. coli lineage may surpass its immortality threshold so that it arrests division and becomes mortal.[35] Cellular aging is a general process, affecting prokaryotes and eukaryotes alike.[35]
Genetic adaptation
E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation or transduction, which allows genetic material to spread horizontally through an existing population. The process of transduction, which uses the bacterial virus called a bacteriophage,[36] is where the spread of the gene encoding for the Shiga toxin from the Shigella bacteria to E. coli helped produce E. coli O157:H7, the Shiga toxin-producing strain of E. coli.
Diversity
E. coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of many 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,[37] and E. coli remains one of the most diverse bacterial species: only 20% of the genes in a typical E. coli genome is shared among all strains.[38]
In fact, from the more constructive point of view, the members of genus Shigella (S. dysenteriae, S. flexneri, S. boydii, and S. sonnei) should be classified as E. coli strains, a phenomenon termed
A
Serotypes
A common subdivision system of E. coli, but not based on evolutionary relatedness, is by serotype, which is based on major surface
Genome plasticity and evolution
Like all lifeforms, new strains of E. coli
The genera
The
In the microbial world, a relationship of predation can be established similar to that observed in the animal world. Considered, it has been seen that E. coli is the prey of multiple generalist predators, such as Myxococcus xanthus. In this predator-prey relationship, a parallel evolution of both species is observed through genomic and phenotypic modifications, in the case of E. coli the modifications are modified in two aspects involved in their virulence such as mucoid production (excessive production of exoplasmic acid alginate ) and the suppression of the OmpT gene, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, following a co-evolutionary model demonstrated by the Red Queen hypothesis.[48]
Neotype strain
E. coli is the type species of the genus (Escherichia) and in turn Escherichia is the type genus of the family Enterobacteriaceae, where 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).[49][50][51]
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 U5/41T,
Phylogeny of E. coli strains
This section's OR extension of Sims & Kim 2011, which is outdated anyways and should be replaced by Meier-Kolthoff et al. 2014 (fig 6).. . Please help update this article to reflect recent events or newly available information. (January 2021) |
Many strains belonging to this species have been isolated and characterised. In addition to serotype (vide supra), they can be classified according to their
The link between phylogenetic distance ("relatedness") and pathology is small,
There have been multiple proposals to revise the taxonomy to match phylogeny.[52] However, all these proposals need to face the fact that Shigella remains a widely used name in medicine and find ways to reduce any confusion that can stem from renaming.[61]
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Genomics
The first complete
More than three hundred complete genomic sequences of Escherichia and Shigella species are known. The genome sequence of the type strain of E. coli was added to this collection before 2014.
Gene nomenclature
Genes in E. coli are usually named in accordance with the uniform nomenclature proposed by Demerec et al.[64] Gene names are 3-letter acronyms that derive from their function (when known) or mutant phenotype and are italicized. When multiple genes have the same acronym, the different genes are designated by a capital later that follows the acronym and is also italicized. For instance, recA is named after its role in homologous recombination plus the letter A. Functionally related genes are named recB, recC, recD etc. The proteins are named by uppercase acronyms, e.g. RecA, RecB, etc. When the genome of E. coli strain K-12 substr. MG1655 was sequenced, all known or predicted protein-coding genes were numbered (more or less) in their order on the genome and abbreviated by b numbers, such as b2819 (= recD). The "b" names were created after Fred Blattner, who led the genome sequence effort.[62] Another numbering system was introduced with the sequence of another E. coli K-12 substrain, W3110, which was sequenced in Japan and hence uses numbers starting by JW... (Japanese W3110), e.g. JW2787 (= recD).[65] Hence, recD = b2819 = JW2787. Note, however, that most databases have their own numbering system, e.g. the EcoGene database[66] uses EG10826 for recD. Finally, ECK numbers are specifically used for alleles in the MG1655 strain of E. coli K-12.[66] Complete lists of genes and their synonyms can be obtained from databases such as EcoGene or Uniprot.
Proteomics
Proteome
The genome sequence of E. coli predicts 4288 protein-coding genes, of which 38 percent initially had no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.[62]
Several studies have experimentally investigated the
Post-translational modifications (PTMs)
Although much fewer bacterial proteins seem to have post-translational modifications (PTMs) compared to eukaryotic proteins, a substantial number of proteins are modified in E. coli. For instance, Potel et al. (2018) found 227 phosphoproteins of which 173 were phosphorylated on histidine. Interestingly, the majority of phosphorylated amino acids were serine (1,220 sites) with only 246 sites on histidine and 501 phosphorylated threonines and 162 tyrosines.[69]
Interactome
The
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.[70] A 2009 study found 5,993 interactions between proteins of the same E. coli strain, though these data showed little overlap with those of the 2006 publication.[71]
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.
Normal microbiota
E. coli belongs to a group of bacteria informally known as
Therapeutic use
Due to the low cost and speed with which it can be grown and modified in laboratory settings, E. coli is a popular expression platform for the production of
Role in disease
Most E. coli strains do not cause disease, naturally living in the gut,
Some strains of E. coli, for example O157:H7, can produce
Uropathogenic E. coli (UPEC) is one of the main causes of urinary tract infections.[87] It is part of the normal microbiota 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 bacterium into the male urethra, and in switching from anal to vaginal intercourse, the male can also introduce UPEC to the female urogenital system.
In May 2011, one E. coli strain,
Some studies have demonstrated an absence of E. coli in the gut flora of subjects with the metabolic disorder Phenylketonuria. It is hypothesized that the absence of these normal bacterium impairs the production of the key vitamins B2 (riboflavin) and K2 (menaquinone) – vitamins which are implicated in many physiological roles in humans such as cellular and bone metabolism – and so contributes to the disorder.[91]
Carbapenem-resistant E. coli (carbapenemase-producing E. coli) that are resistant to the
Incubation period
The time between ingesting the STEC bacteria and feeling sick is called the "incubation period". The incubation period is usually 3–4 days after the exposure, but may be as short as 1 day or as long as 10 days. The symptoms often begin slowly with mild belly pain or non-bloody diarrhea that worsens over several days. HUS, if it occurs, develops an average 7 days after the first symptoms, when the diarrhea is improving.[93]
Diagnosis
Diagnosis of infectious diarrhea and identification of antimicrobial resistance is performed using a
Current
Treatment
The mainstay of treatment is the assessment of
Prevention
ETEC is the type of E. coli that most vaccine development efforts are focused on.
Other proven prevention methods for E. coli transmission include handwashing and improved sanitation and drinking water, as transmission occurs through fecal contamination of food and water supplies. Additionally, thoroughly cooking meat and avoiding consumption of raw, unpasteurized beverages, such as juices and milk are other proven methods for preventing E. coli. Lastly, cross-contamination of utensils and work spaces should be avoided when preparing food.[99]
Model organism in life science research
Because of its long history of laboratory culture and ease of manipulation, E. coli plays an important role in modern biological engineering and industrial microbiology.[101] 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.[102]
E. coli is a very versatile host for the production of
Many proteins previously thought difficult or impossible to be expressed in E. coli in folded form have been successfully expressed in E. coli. For example, proteins with multiple disulphide bonds may be produced in the
Modified E. coli cells have been used in
Strain K-12 is a mutant form of E. coli that over-expresses the enzyme Alkaline phosphatase (ALP).[111] The mutation arises due to a defect in the gene that constantly codes for the enzyme. A gene that is producing a product without any inhibition is said to have constitutive activity. This particular mutant form is used to isolate and purify the aforementioned enzyme.[111]
Strain OP50 of Escherichia coli is used for maintenance of Caenorhabditis elegans cultures.
Strain JM109 is a mutant form of E. coli that is recA and endA deficient. The strain can be utilized for blue/white screening when the cells carry the fertility factor episome.[112] Lack of recA decreases the possibility of unwanted restriction of the DNA of interest and lack of endA inhibit plasmid DNA decomposition. Thus, JM109 is useful for cloning and expression systems.
Model organism
E. coli is frequently used as a model organism in
In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium,[116] and it remains the primary model to study conjugation.[117] E. coli was an integral part of the first experiments to understand phage genetics,[118] and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.[119] Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.[120]
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.[62]
From 2002 to 2010, a team at the Hungarian Academy of Science created a strain of Escherichia coli called MDS42, which is now sold by Scarab Genomics of Madison, WI under the name of "Clean Genome E. coli", Biochemistry and replication machinery were not altered.
By evaluating the possible combination of
In other studies, non-pathogenic E. coli has been used as a model microorganism towards understanding the effects of simulated microgravity (on Earth) on the same.[126][127]
Uses in biological computing
Since 1961, scientists proposed the idea of genetic circuits used for computational tasks. Collaboration between biologists and computing scientists has allowed designing digital logic gates on the metabolism of E. coli. As Lac operon is a two-stage process, genetic regulation in the bacteria is used to realize computing functions. The process is controlled at the transcription stage of DNA into messenger RNA.[128]
Studies are being performed attempting to program E. coli to solve complicated mathematics problems, such as the Hamiltonian path problem.[129]
A computer to control protein production of E. coli within
In July 2017, separate experiments with E. coli published on Nature showed the potential of using living cells for computing tasks and storing information.[133] A team formed with collaborators of the Biodesign Institute at Arizona State University and Harvard's Wyss Institute for Biologically Inspired Engineering developed a biological computer inside E. coli that responded to a dozen inputs. The team called the computer "ribocomputer", as it was composed of ribonucleic acid.[134][135] Meanwhile, Harvard researchers probed that is possible to store information in bacteria after successfully archiving images and movies in the DNA of living E. coli cells.[136][137] In 2021, a team led by biophysicist Sangram Bagh realized a study with E. coli to solve 2 × 2 maze problems to probe the principle for distributed computing among cells.[138][139]
History
In 1885, the German-Austrian pediatrician Theodor Escherich discovered this organism in the feces of healthy individuals. He called it Bacterium coli commune because it is found in the colon. 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).[98][140][141]
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.[142] Following a revision of Bacterium, it was reclassified as Bacillus coli by Migula in 1895[143] and later reclassified in the newly created genus Escherichia, named after its original discoverer, by Aldo Castellani and Albert John Chalmers.[144]
In 1996, an outbreak of E. coli food poisoning occurred in Wishaw, Scotland, killing 21 people.[145][146] This death toll was exceeded in 2011, when the 2011 Germany E. coli O104:H4 outbreak, linked to organic fenugreek sprouts, killed 53 people.
Uses
E. coli has several practical uses besides its use as a vector for genetic experiments and processes. For example, E. coli can be used to generate synthetic propane and recombinant human growth hormone.[147][148]
See also
- BolA-like protein family
- Carbon monoxide-releasing molecules
- Contamination control
- Dam dcm strain
- Eijkman test
- Fecal coliform
- International Code of Nomenclature of Bacteria
- List of strains of Escherichia coli
- Mannan oligosaccharide-based nutritional supplements
- Overflow metabolism
- T4 rII system
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