Editing Escherichia coli (section)

==Model organism in life science research==
{{main|Escherichia coli in molecular biology}}
[[File:Escherichia-coli-bacterium(1).tif|thumb|300px|''Escherichia coli'' bacterium, 2021, Illustration by David S. Goodsell, RCSB Protein Data Bank<br>This painting shows a cross-section through an ''Escherichia coli'' cell. The characteristic two-membrane cell wall of gram-negative bacteria is shown in green, with many lipopolysaccharide chains extending from the surface and a network of cross-linked peptidoglycan strands between the membranes. The genome of the cell forms a loosely-defined "nucleoid", shown here in yellow, and interacts with many DNA-binding proteins, shown in tan and orange. Large soluble molecules, such as ribosomes (colored in reddish purple), mostly occupy the space around the nucleoid.]]

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]].<ref name="lee1996">{{cite journal | vauthors = Lee SY | title = High cell-density culture of ''Escherichia coli'' | journal = Trends in Biotechnology | volume = 14 | issue = 3 | pages = 98–105 | date = March 1996 | pmid = 8867291 | doi = 10.1016/0167-7799(96)80930-9 }}</ref> The work of [[Stanley Norman Cohen]] and [[Herbert Boyer]] in ''E. coli'', using [[plasmid]]s and [[restriction enzyme]]s to create [[recombinant DNA]], became a foundation of biotechnology.<ref name="birth">{{cite journal | vauthors = Russo E | s2cid = 4357773 | title = The birth of biotechnology | journal = Nature | volume = 421 | issue = 6921 | pages = 456–57 | date = January 2003 | pmid = 12540923 | doi = 10.1038/nj6921-456a | bibcode = 2003Natur.421..456R | doi-access = free }}</ref>

''E. coli'' is a very versatile host for the production of [[heterologous]] [[protein]]s,<ref name="Cornelis" /> and various [[Protein expression (biotechnology)|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]].<ref>{{cite web |url=http://www.littletree.com.au/dna.htm |title=Recombinant DNA Technology in the Synthesis of Human Insulin |access-date=30 November 2007 |vauthors = Tof I |year=1994 |publisher=Little Tree Pty. Ltd.}}</ref>

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 [[periplasmic space]] or in the cytoplasm of mutants rendered sufficiently oxidizing to allow disulphide-bonds to form,<ref name="pmid10570136">{{cite journal | vauthors = Bessette PH, Aslund F, Beckwith J, Georgiou G | title = Efficient folding of proteins with multiple disulfide bonds in the ''Escherichia coli'' cytoplasm | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 24 | pages = 13703–08 | date = November 1999 | pmid = 10570136 | pmc = 24128 | doi = 10.1073/pnas.96.24.13703 | bibcode = 1999PNAS...9613703B | doi-access = free }}</ref> 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''.<ref>{{cite journal | vauthors = Ihssen J, Kowarik M, Dilettoso S, Tanner C, Wacker M, Thöny-Meyer L | title = Production of glycoprotein vaccines in ''Escherichia coli'' | journal = Microbial Cell Factories | volume = 9 | issue = 61 | pages = 61 | date = August 2010 | pmid = 20701771 | pmc = 2927510 | doi = 10.1186/1475-2859-9-61 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Wacker M, Linton D, Hitchen PG, Nita-Lazar M, Haslam SM, North SJ, Panico M, Morris HR, Dell A, Wren BW, Aebi M | display-authors = 6 | title = N-linked glycosylation in ''Campylobacter jejuni'' and its functional transfer into ''E. coli'' | journal = Science | volume = 298 | issue = 5599 | pages = 1790–93 | date = November 2002 | pmid = 12459590 | doi = 10.1126/science.298.5599.1790 | bibcode = 2002Sci...298.1790W }}</ref><ref>{{cite journal | vauthors = Huang CJ, Lin H, Yang X | s2cid = 15584320 | title = Industrial production of recombinant therapeutics in ''Escherichia coli'' and its recent advancements | journal = Journal of Industrial Microbiology & Biotechnology | volume = 39 | issue = 3 | pages = 383–99 | date = March 2012 | pmid = 22252444 | doi = 10.1007/s10295-011-1082-9 | doi-access = free }}</ref>

Modified ''E. coli'' cells have been used in [[vaccine]] development, [[bioremediation]], production of [[biofuels]],<ref>{{cite web | vauthors = Summers R | date = 24 April 2013 | url = https://www.newscientist.com/article/dn23431-bacteria-churn-out-first-ever-petrollike-biofuel.html | title = Bacteria churn out first ever petrol-like biofuel | work = New Scientist | access-date = 27 April 2013 }}</ref> lighting, and production of immobilised [[enzyme]]s.<ref name="Cornelis">{{cite journal | vauthors = Cornelis P | title = Expressing genes in different Escherichia coli compartments | journal = Current Opinion in Biotechnology | volume = 11 | issue = 5 | pages = 450–54 | date = October 2000 | pmid = 11024362 | doi = 10.1016/S0958-1669(00)00131-2 }}</ref><ref>{{cite news |url=http://news.discovery.com/tech/alternative-power-sources/bacteria-powered-light-bulb-is-electricity-free-130815.htm |title=Bacteria-Powered Light Bulb Is Electricity-Free |date=15 August 2013 |author=Halverson, Nic |access-date=22 October 2013 |archive-date=25 May 2016 |archive-url=https://web.archive.org/web/20160525132633/http://news.discovery.com/tech/alternative-power-sources/bacteria-powered-light-bulb-is-electricity-free-130815.htm |url-status=dead}}</ref>

Strain K-12 is a mutant form of ''E. coli'' that over-expresses the enzyme [[Alkaline phosphatase]] (ALP).<ref name=":1">{{Cite book|title=Fundamental Laboratory Approaches for Biochemistry and Biotechnology |vauthors = Ninfa AJ, Ballou DP |publisher=Wiley |year=2009 |isbn=978-0470087664|pages=230}}</ref> 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 [[Receptor (biochemistry)|constitutive activity]]. This particular mutant form is used to isolate and purify the aforementioned enzyme.<ref name=":1" />

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.<ref>{{cite journal |vauthors = Cui Y, Zhou P, Peng J, Peng M, Zhou Y, Lin Y, Liu L |title = Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in ''Escherichia coli'' |journal = Brazilian Journal of Medical and Biological Research = Revista Brasileira de Pesquisas Medicas e Biologicas | volume = 41 | issue = 5 | pages = 380–388 | date = May 2008 | pmid = 18545812 | doi = 10.1590/s0100-879x2008000500006 | doi-access = free }}</ref> 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===
[[File:Escherichia coli with phages.jpg|thumb| [[Scanning helium ion microscope|Helium ion microscopy]] image showing [[T4 phage]] infecting ''E. coli''. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 μm wide.<ref>{{cite journal | vauthors = Leppänen M, Sundberg LR, Laanto E, de Freitas Almeida GM, Papponen P, Maasilta IJ | title = Imaging Bacterial Colonies and Phage-Bacterium Interaction at Sub-Nanometer Resolution Using Helium-Ion Microscopy | journal = Advanced Biosystems | volume = 1 | issue = 8 | pages = e1700070 | date = August 2017 | pmid = 32646179 | doi = 10.1002/adbi.201700070 | s2cid = 90960276 | url = http://urn.fi/URN:NBN:fi:jyu-202006043941 }}</ref>]]''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 laboratory strains lose their ability to form [[biofilm]]s.<ref>{{cite journal | vauthors = Fux CA, Shirtliff M, Stoodley P, Costerton JW | title = Can laboratory reference strains mirror "real-world" pathogenesis? | journal = Trends in Microbiology | volume = 13 | issue = 2 | pages = 58–63 | date = February 2005 | pmid = 15680764 | doi = 10.1016/j.tim.2004.11.001 | s2cid = 8765887 | url = https://scholarworks.montana.edu/xmlui/handle/1/13365 }}</ref><ref>{{cite journal | vauthors = Vidal O, Longin R, Prigent-Combaret C, Dorel C, Hooreman M, Lejeune P | title = 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 | journal = Journal of Bacteriology | volume = 180 | issue = 9 | pages = 2442–49 | date = May 1998 | pmid = 9573197 | pmc = 107187 | doi =  10.1128/JB.180.9.2442-2449.1998}}</ref> These features protect wild-type strains from [[antibody|antibodies]] and other chemical attacks, but require a large expenditure of energy and material resources. ''E. coli'' is often used as a representative microorganism in the research of novel water treatment and sterilisation methods, including [[photocatalysis]]. By standard [[Bacteriological water analysis#Plate count|plate count methods]], following sequential dilutions, and growth on agar gel plates, the concentration of viable organisms or CFUs (Colony Forming Units), in a known volume of treated water can be evaluated, allowing the comparative assessment of materials performance.<ref>{{cite journal | vauthors = Hanaor D, Michelazzi M, Chenu J, Leonelli C, Sorrell CC | title = The effects of firing conditions on the properties of electrophoretically deposited titanium dioxide films on graphite substrates. | journal = Journal of the European Ceramic Society | date = December 2011 | volume = 31 | issue = 15 | pages = 2877–85 | doi = 10.1016/j.jeurceramsoc.2011.07.007 | arxiv = 1303.2757 | s2cid = 93406448 }}</ref>

In 1946, [[Joshua Lederberg]] and [[Edward Tatum]] first described the phenomenon known as [[bacterial conjugation]] using ''E. coli'' as a model bacterium,<ref>{{cite journal | vauthors = Lederberg J, Tatum EL | s2cid = 1826960 | title = Gene recombination in ''Escherichia coli'' | journal = Nature | volume = 158 | issue = 4016 | pages = 558 | date = October 1946 | pmid = 21001945 | doi = 10.1038/158558a0 | url = http://profiles.nlm.nih.gov/BB/G/A/S/Z/_/bbgasz.pdf | bibcode = 1946Natur.158..558L }} Source: [http://profiles.nlm.nih.gov/BB/G/A/S/Z/ National Library of Medicine – The Joshua Lederberg Papers]</ref> and it remains the primary model to study conjugation.<ref>{{cite book|title=Biological Activity of Crystal|pages=169}}</ref> ''E. coli'' was an integral part of the first experiments to understand [[bacteriophage|phage]] genetics,<ref>{{cite journal | vauthors = Susman M | title = The Cold Spring Harbor Phage Course (1945–1970): a 50th anniversary remembrance | journal = Genetics | volume = 139 | issue = 3 | pages = 1101–06 | date = March 1995 | doi = 10.1093/genetics/139.3.1101 | pmid = 7768426 | pmc = 1206443 | url = https://www.cshl.edu/History/phagecourse.html | archive-url = https://web.archive.org/web/20060916155323/https://www.cshl.edu/History/phagecourse.html | url-status = dead | archive-date = 16 September 2006 }}</ref> and early researchers, such as [[Seymour Benzer]], used ''E. coli'' and phage T4 to understand the topography of gene structure.<ref name="pmid16590840">{{cite journal | vauthors = Benzer S | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47 | issue = 3 | pages = 403–15 | date = March 1961 | pmid = 16590840 | pmc = 221592 | doi = 10.1073/pnas.47.3.403 | bibcode = 1961PNAS...47..403B | title = On the Topography of the Genetic Fine Structure | doi-access = free }}</ref> Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.<ref>{{cite web |title=Facts about ''E.Coli'' |url=http://eol.org/pages/972688/details |publisher=Encyclopedia of Life |access-date=27 November 2013}}</ref>

''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.<ref name="Blattner_1997" />

==== MDS42 ====
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''",<ref>{{cite web |url=http://www.scarabgenomics.com/ |title=Scarab Genomics LLC. Company web site.}}</ref> where 15% of the genome of the parental strain (''E. coli'' K-12 MG1655) were removed to aid in molecular biology efficiency, removing [[IS elements]], [[pseudogene]]s and [[phages]], resulting in better maintenance of plasmid-encoded toxic genes, which are often inactivated by transposons.<ref>{{cite journal |vauthors = Umenhoffer K, Fehér T, Balikó G, Ayaydin F, Pósfai J, Blattner FR, Pósfai G |title = Reduced evolvability of ''Escherichia coli'' MDS42, an IS-less cellular chassis for molecular and synthetic biology applications | journal = Microbial Cell Factories | volume = 9 | pages = 38 | date = May 2010 | pmid = 20492662 | pmc = 2891674 | doi = 10.1186/1475-2859-9-38 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Pósfai G, Plunkett G, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR | s2cid = 43287314 | display-authors = 6 | title = Emergent properties of reduced-genome Escherichia coli | journal = Science | volume = 312 | issue = 5776 | pages = 1044–46 | date = May 2006 | pmid = 16645050 | doi = 10.1126/science.1126439 | bibcode = 2006Sci...312.1044P }}</ref><ref>{{cite journal | vauthors = Kolisnychenko V, Plunkett G, Herring CD, Fehér T, Pósfai J, Blattner FR, Pósfai G | title = Engineering a reduced Escherichia coli genome | journal = Genome Research | volume = 12 | issue = 4 | pages = 640–47 | date = April 2002 | pmid = 11932248 | pmc = 187512 | doi = 10.1101/gr.217202 }}</ref> Biochemistry and replication machinery were not altered.

By evaluating the possible combination of [[Nanotechnology|nanotechnologies]] with [[landscape ecology]], complex habitat landscapes can be generated with details at the nanoscale.<ref name="pmid17090676">{{cite journal | vauthors = Keymer JE, Galajda P, Muldoon C, Park S, Austin RH | title = Bacterial metapopulations in nanofabricated landscapes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 46 | pages = 17290–95 | date = November 2006 | pmid = 17090676 | pmc = 1635019 | doi = 10.1073/pnas.0607971103 | bibcode = 2006PNAS..10317290K | doi-access = free }}</ref> 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.

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.<ref>{{cite journal | vauthors = Tirumalai MR, Karouia F, Tran Q, Stepanov VG, Bruce RJ, Ott M, Pierson DL, Fox GE| title = The adaptation of ''Escherichia coli'' cells grown in simulated microgravity for an extended period is both phenotypic and genomic.| journal = npj Microgravity | volume =3 |issue= 15| date = May 2017 | page = 15| pmid = 28649637 | pmc = 5460176 | doi = 10.1038/s41526-017-0020-1}}</ref><ref>{{cite journal | vauthors = Tirumalai MR, Karouia F, Tran Q, Stepanov VG, Bruce RJ, Ott M, Pierson DL, Fox GE| title = Evaluation of acquired antibiotic resistance in ''Escherichia coli'' exposed to long-term low-shear modeled microgravity and background antibiotic exposure| journal = mBio | volume =10 |issue= e02637-18| date = January 2019 | pmid = 30647159 | pmc = 6336426  | doi = 10.1128/mBio.02637-18}}</ref>