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{{Short description|Type of mobile genetic element}}
In biology, a '''gene cassette''' is a type of [[mobile genetic element]] that contains a gene and a [[Site-specific recombination|recombination]] site. Each cassette usually contains a single gene and tends to be very small, containing approximately 500–1,000 [[base pair]]s. They may exist incorporated into an [[integron]] or freely as circular DNA.<ref name=":0">{{cite journal|pmid=7783631|year=1995|last1=Hall|first1=RM|last2=Collis|first2=CM|title=Mobile gene cassettes and integrons: Capture and spread of genes by site-specific recombination|volume=15|issue=4|pages=593–600|journal=Molecular Microbiology|doi=10.1111/j.1365-2958.1995.tb02368.x |doi-access=free}}</ref> Gene cassettes can move around within an organism's genome or be transferred to another organism in the environment via [[horizontal gene transfer]]. These cassettes often carry [[antibiotic resistance]] [[gene]]s. An example would be the ''[[Kanamycin A#KanMX marker|kanMX]]'' cassette which confers [[kanamycin]] (an [[antibiotic]]) resistance upon [[bacteria]].

== Integrons ==
{{Main article|Integron}}
Integrons are genetic structures in [[bacteria]] which express and are capable of acquiring and exchanging gene cassettes. The integron consists of a [[promoter (biology)|promoter]], an attachment site, and an [[integrase]] gene that encodes a [[Site-specific recombination|site-specific]] [[recombinase]]<ref name="pmid24367362">{{cite journal | author=Rapa RA, Labbate M | title=The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg | journal= [[Frontiers in Microbiology]] | volume=4 | year=2013 | page=385 | doi=10.3389/fmicb.2013.00385 | pmc=3856429 | pmid=24367362 | doi-access=free }}</ref> There are three classes of integrons described.<ref name=":0" /> The mobile units that insert into integrons are gene cassettes.<ref name="pmid24367362" /> For cassettes that carry a single gene without a promoter, the entire series of cassettes is [[transcription (genetics)|transcribed]] from an adjacent promoter within the integron.<ref>{{Cite journal|last1=Collis|first1=C. M.|last2=Hall|first2=R. M.|date=1995-01-01|title=Expression of antibiotic resistance genes in the integrated cassettes of integrons|journal=Antimicrobial Agents and Chemotherapy|volume=39|issue=1|pages=155–162|issn=0066-4804|pmc=162502|pmid=7695299|doi=10.1128/aac.39.1.155}}</ref> The gene cassettes are speculated to be inserted and excised via a circular intermediate.<ref>{{Cite journal|last1=Collis|first1=Christina M.|last2=Hall|first2=Ruth M.|date=1992-10-01|title=Gene cassettes from the insert region of integrons are excised as covalently closed circles|journal=Molecular Microbiology|language=en|volume=6|issue=19|pages=2875–2885|doi=10.1111/j.1365-2958.1992.tb01467.x|pmid=1331702 |s2cid=24986780 |issn=1365-2958}}</ref> This would involve recombination between short sequences found at their termini and known as 59 base elements (59-be)—which may not be 59 bases long. The 59-be are a diverse family of sequences that function as recognition sites for the site-specific integrase (enzyme responsible for integrating the gene cassette into an integron) that occur downstream from the gene coding sequence.<ref>{{Cite journal|last1=Hall|first1=R. M.|last2=Brookes|first2=D. E.|last3=Stokes|first3=H. W.|date=1991-08-01|title=Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point|journal=Molecular Microbiology|volume=5|issue=8|pages=1941–1959|issn=0950-382X|pmid=1662753|doi=10.1111/j.1365-2958.1991.tb00817.x|s2cid=23447071 }}</ref>

=== Diversity and prevalence ===
The ability of genetic elements like gene cassettes to excise and insert into genomes results in highly similar gene regions appearing in distantly related organisms. The three classes of integrons are similar in structure and are identified by where the insertions occur and what systems they coincide with. Class 1 integrons are seen in a diverse group of bacterial genomes and likely are all descendant from one common ancestor. The prevalence of the integron has shaped bacterial evolution by allowing rapid transfer of genes that are novel to an organism, such as antibiotic resistance genes.<ref>{{Cite journal|last=Gillings|first=Michael|date=Jan 2017|title=Class 1 Integrons as Invasive Species|journal=Current Opinion in Microbiology|volume=38|pages=10–15|doi=10.1016/j.mib.2017.03.002|pmid=28414952}}</ref>

== Genetic engineering ==
In [[genetic engineering]], a gene cassette is a manipulable fragment of DNA carrying, and capable of expressing, one or more genes of interest between one or more sets of [[restriction site]]s. It can be transferred from one DNA sequence (usually on a [[Plasmid#Vectors|vector]]) to another by 'cutting' the fragment out using [[restriction enzyme]]s and 'pasting' it back into the new context. The vectors containing the gene of interest typically also carry an antibiotic resistance gene called a [[selectable marker]] to easily identify cells that have successfully integrated the vector into their genome.

To introduce a vector into a target cell, a state of [[Natural competence|competence]] must be inferred on the cell. This state is induced in the lab by incubating cells with calcium chloride before a brief heat shock, or by [[electroporation]]. This makes the cells more susceptible to the plasmid that is being inserted. Once the plasmid has been added, the cells are grown in the presence of an antibiotic to confirm the uptake and expression of the new genetic elements.

The usage of CRISPR/Cas9 systems has shown success in inserting genes into eukaryotic genomes.<ref>[https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr Broad Institute]</ref> While CRISPR modification is still in its infancy, there is significant evidence for usage in combination with other techniques to produce high throughput (HTP) genome editing systems.<ref>{{Cite journal|last1=Aida|first1=Tomomi|last2=Nakade|first2=Shota|last3=Sakuma|first3=Tetsushi|last4=Izu|first4=Yayoi|last5=Oishi|first5=Ayu|last6=Mochida|first6=Keiji|last7=Ishikubo|first7=Harumi|last8=Usami|first8=Takako|last9=Aizawa|first9=Hidenori|date=2016-01-01|title=Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ|journal=BMC Genomics|volume=17|issue=1|page=979|doi=10.1186/s12864-016-3331-9|issn=1471-2164|pmc=5126809|pmid=27894274 |doi-access=free }}</ref> Genetic engineering of bacteria for production of a variety of industrial products, including biofuels and specialty chemicals/nutraceuticals is a major area of research.<ref>{{Cite journal|last1=Chakraborty|first1=Debkumar|last2=Gupta|first2=Gaganjot|last3=Kaur|first3=Baljinder|date=2016-12-01|title=Metabolic engineering of E. coli top 10 for production of vanillin through FA catabolic pathway and bioprocess optimization using RSM|journal=Protein Expression and Purification|volume=128|pages=123–133|doi=10.1016/j.pep.2016.08.015|pmid=27591788}}</ref>

== Horizontal gene transfer ==
{{Main article|Horizontal gene transfer}}
Horizontal gene transfer (HGT) is the transfer of genetic elements between cells other than parental inheritance. HGT is responsible for much of the spread of antibiotic resistance among bacteria.<ref>{{Cite journal|last1=Gyles|first1=C.|last2=Boerlin|first2=P.|date=2014-03-01|title=Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease|journal=Veterinary Pathology|volume=51|issue=2|pages=328–340|doi=10.1177/0300985813511131|issn=1544-2217|pmid=24318976|s2cid=206510894 |doi-access=free}}</ref> Gene cassettes containing antibiotic resistance genes, or other virulence factors such as exotoxins, can be transferred from cell to cell via phage, [[Transduction (genetics)|transduction]], taken up from the environment, [[Transformation (genetics)|transformation]],<ref>{{Cite journal|last1=Domingues|first1=Sara|last2=Harms|first2=Klaus|last3=Fricke|first3=W. Florian|last4=Johnsen|first4=Pål J.|last5=Silva|first5=Gabriela J. da|last6=Nielsen|first6=Kaare Magne|date=2012-08-02|title=Natural Transformation Facilitates Transfer of Transposons, Integrons and Gene Cassettes between Bacterial Species|journal=PLOS Pathogens|volume=8|issue=8|article-number=e1002837|doi=10.1371/journal.ppat.1002837|issn=1553-7374|pmc=3410848|pmid=22876180 |doi-access=free }}</ref> or by bacterial conjugation.<ref>{{Cite journal|last=Sun|first=J| date = 1 Aug 2010|title=Original Article: Characterization of Two Novel Gene Cassettes, Dfra27 and Aada16, in a Non-O1, Non-O139 Vibrio Cholerae Isolate from China.|journal=Clinical Microbiology and Infection|volume=16|issue=8|pages=1125–1129|doi=10.1111/j.1469-0691.2009.03060.x|pmid=19906273|doi-access=free}}</ref> The ability to transfer gene cassettes between organisms has played a large role in the evolution of prokaryotes. Many commensal organisms, such as ''E. coli'', regularly harbor one or more gene cassettes that convey antibiotic resistance.<ref>{{Cite journal|last1=Kheiri|first1=Roohollah|last2=Akhtari|first2=Leili|date=2016-01-01|title=Antimicrobial resistance and integron gene cassette arrays in commensal Escherichia coli from human and animal sources in IRI|journal=Gut Pathogens|volume=8|issue=1|page=40|doi=10.1186/s13099-016-0123-3|issn=1757-4749|pmc=5006490|pmid=27582900 |doi-access=free }}</ref> Horizontal transfer of genetic elements from non-pathogenic commensals to unrelated species results in highly virulent pathogens that can carry [[multiple antibiotic resistance]] genes. The increasing prevalence of resistance creates challenging questions for researchers and physicians.

==See also==
* [[Expression cassette]]

==References==
<references />
* {{cite journal | last1 = Stokes | first1 = H.W. | display-authors = etal | date = Nov 1997 | title = Structure and function of 59-base element recombination sites associated with mobile gene cassettes | pmid = 9427403 | journal = Mol Microbiol | volume = 26 | issue = 4| pages = 731–45 | doi=10.1046/j.1365-2958.1997.6091980.x| doi-access = free }}
* {{cite journal | last1 = Partridge | first1 = S | last2 = Tsafnat | first2 = G | last3 = Coiera | first3 = E | last4 = Iredell | first4 = J | year = 2009 | title = Gene cassettes and cassette arrays in mobile resistance integrons | journal = FEMS Microbiology Reviews | volume = 33 | issue = 4| pages = 757–784 | doi=10.1111/j.1574-6976.2009.00175.x| pmid = 19416365 | doi-access = }}

==External links==
* [https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr Broad Institute]
* [http://cariboubio.com Caribou Biosciences]
* [https://www.ginkgobioworks.com Ginkgo Bioworks]

[[Category:Genetics]]

Gene cassette - История изменений

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