Insertion sequence: Difference between revisions
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'''Insertion element''' (also known as an '''IS''', an '''insertion sequence element''', or an '''IS element''') is a short [[DNA]] sequence that acts as a simple [[transposon|transposable element]]. Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 [[base pair|bp]] in length) and only code for proteins implicated in the [[Transposable element|transposition]] activity (they are thus different from other [[transposons]], which also carry accessory genes such as [[antimicrobial resistance|antibiotic resistance]] genes). |
'''Insertion element''' (also known as an '''IS''', an '''insertion sequence element''', or an '''IS element''') is a short [[DNA]] sequence that acts as a simple [[transposon|transposable element]]. Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 [[base pair|bp]] in length) and only code for proteins implicated in the [[Transposable element|transposition]] activity (they are thus different from other [[transposons]], which also carry accessory genes such as [[antimicrobial resistance|antibiotic resistance]] genes). |
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A particular insertion sequence may be named according to the form IS''n'', where ''n'' is a [[natural number|number]] (e.g. IS''1'', IS''2'', IS''3'', IS''10'', IS''50'', IS''911'', IS''26'' etc.); this is not the only naming scheme used, however. |
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== Composition == |
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These proteins are usually the [[transposase]] which catalyses the enzymatic reaction allowing the IS to move, and also one regulatory protein which either stimulates or inhibits the transposition activity. The coding region in an insertion sequence is usually flanked by [[inverted repeat]]s. For example, the well-known IS''911'' (1250 bp) is flanked by two 36bp inverted repeat extremities and the coding region has two genes partially overlapping ''orfA'' and ''orfAB'', coding the transposase (OrfAB) and a regulatory protein (OrfA). |
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[[Image:Composite transposon.svg|thumbnail|Diagram illustrating the role of insertion sequences ("IS") in a composite transposon]] |
[[Image:Composite transposon.svg|thumbnail|Diagram illustrating the role of insertion sequences ("IS") in a composite transposon]] |
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A complex transposon does not rely on flanking insertion sequences for resolvase. The resolvase is part of the tns genome and cuts at flanking inverted repeats. |
A complex transposon does not rely on flanking insertion sequences for resolvase. The resolvase is part of the tns genome and cuts at flanking inverted repeats. |
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== Evolutionary role == |
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| ⚫ | Transposition frequency of IS elements is dependent of multiple parameters, including culture growth phase, medium composition, oxygen tension, growth scale, and structural conformation of target sites (e.g.: curvature, presence of certain motifs, DNA composition).<ref name=Oliveira>{{cite journal | vauthors = Goncalves GA, Oliveira PH, Gomes AG, Prather KL, Lewis LA, Parzeres DM, Monteiro GA | title = Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters | journal = Appl Microbiol Biotechnol | volume = 98 | issue = 15 | pages = 6609–6619 | date = 2014 | doi = 10.1007/s00253-014-5695-6 | pmid = 24769900 | url = http://dspace.mit.edu/bitstream/1721.1/104375/1/253_2014_Article_5695.pdf | hdl = 1721.1/104375 | s2cid = 9826684 | hdl-access = free }}</ref> Recombination between genomic IS sites can enable bacteria to adapt to new environments, making IS elements an important mechanism for evolution in bacteria.<ref>{{cite journal | vauthors = Cerisy T, Souterre T, Torres-Romero I, Boutard M, Dubois I, Patrouix J, Labadie K, Berrabah W, Salanoubat M, Doring V, Tolonen AC | title = Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics | journal = Appl Environ Microbiol | volume = 83 | issue = 11 | pages = e00289-17 | date = 2017 | doi = 10.1128/AEM.00289-17 | pmid = 28363966 | pmc = 5440714 | hdl = 1721.1/104375 | s2cid = 4705511 | hdl-access = free }}</ref> |
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Although insertion sequences are usually discussed in the context of [[prokaryote|prokaryotic]] [[genome]]s, certain [[eukaryote|eukaryotic]] DNA sequences belonging to the family of Tc1/''mariner'' transposable elements may be considered to be insertion sequences.<ref>{{Cite journal|last1=Mahillon|first1=Jacques|last2=Chandler|first2=Michael|date=2020-12-26|title=Insertion Sequences|journal=Microbiology and Molecular Biology Reviews|language=en|volume=62|issue=3|pages=725–774|doi=10.1128/MMBR.62.3.725-774.1998|issn=1092-2172|pmc=98933|pmid=9729608}}</ref> |
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| ⚫ | Transposition frequency of IS elements is dependent of multiple parameters, including culture growth phase, medium composition, oxygen tension, growth scale, and structural conformation of target sites (e.g.: curvature, presence of certain motifs, DNA composition).<ref name=Oliveira>{{cite journal | vauthors = Goncalves GA, Oliveira PH, Gomes AG, Prather KL, Lewis LA, Parzeres DM, Monteiro GA | title = Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters | journal = Appl Microbiol Biotechnol | volume = 98 | issue = 15 | pages = 6609–6619 | date = 2014 | doi = 10.1007/s00253-014-5695-6 | pmid = 24769900 | url = http://dspace.mit.edu/bitstream/1721.1/104375/1/253_2014_Article_5695.pdf | hdl = 1721.1/104375 | s2cid = 9826684 | hdl-access = free }}</ref> Recombination between genomic IS sites can enable bacteria to adapt to new environments, making IS elements an important mechanism for evolution in bacteria.<ref>{{cite journal | vauthors = Cerisy T, Souterre T, Torres-Romero I, Boutard M, Dubois I, Patrouix J, Labadie K, Berrabah W, Salanoubat M, Doring V, Tolonen AC | title = Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics | journal = Appl Environ Microbiol | volume = 83 | issue = 11 | pages = e00289-17 | date = 2017 | doi = 10.1128/AEM.00289-17 | pmid = 28363966 | pmc = 5440714 | bibcode = 2017ApEnM..83E.289C | hdl = 1721.1/104375 | s2cid = 4705511 | hdl-access = free }}</ref> |
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==See also== |
==See also== |
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Latest revision as of 13:01, 15 December 2024
Insertion element (also known as an IS, an insertion sequence element, or an IS element) is a short DNA sequence that acts as a simple transposable element. Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 bp in length) and only code for proteins implicated in the transposition activity (they are thus different from other transposons, which also carry accessory genes such as antibiotic resistance genes).
A particular insertion sequence may be named according to the form ISn, where n is a number (e.g. IS1, IS2, IS3, IS10, IS50, IS911, IS26 etc.); this is not the only naming scheme used, however.
Composition
[edit]These proteins are usually the transposase which catalyses the enzymatic reaction allowing the IS to move, and also one regulatory protein which either stimulates or inhibits the transposition activity. The coding region in an insertion sequence is usually flanked by inverted repeats. For example, the well-known IS911 (1250 bp) is flanked by two 36bp inverted repeat extremities and the coding region has two genes partially overlapping orfA and orfAB, coding the transposase (OrfAB) and a regulatory protein (OrfA).
In addition to occurring autonomously, insertion sequences may also occur as parts of composite transposons. In a composite transposon, two insertion sequences flank one or more accessory genes, such as an antibiotic resistance gene (e.g. Tn10, Tn5). Nevertheless, there exist another sort of transposons, called unit transposons, that do not carry insertion sequences at their extremities (e.g. Tn7).
A complex transposon does not rely on flanking insertion sequences for resolvase. The resolvase is part of the tns genome and cuts at flanking inverted repeats.
Evolutionary role
[edit]Although insertion sequences are usually discussed in the context of prokaryotic genomes, certain eukaryotic DNA sequences belonging to the family of Tc1/mariner transposable elements may be considered to be insertion sequences.[1]
Transposition frequency of IS elements is dependent of multiple parameters, including culture growth phase, medium composition, oxygen tension, growth scale, and structural conformation of target sites (e.g.: curvature, presence of certain motifs, DNA composition).[2] Recombination between genomic IS sites can enable bacteria to adapt to new environments, making IS elements an important mechanism for evolution in bacteria.[3]
See also
[edit]References
[edit]- ^ Mahillon, Jacques; Chandler, Michael (2020-12-26). "Insertion Sequences". Microbiology and Molecular Biology Reviews. 62 (3): 725–774. doi:10.1128/MMBR.62.3.725-774.1998. ISSN 1092-2172. PMC 98933. PMID 9729608.
- ^ Goncalves GA, Oliveira PH, Gomes AG, Prather KL, Lewis LA, Parzeres DM, Monteiro GA (2014). "Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters" (PDF). Appl Microbiol Biotechnol. 98 (15): 6609–6619. doi:10.1007/s00253-014-5695-6. hdl:1721.1/104375. PMID 24769900. S2CID 9826684.
- ^ Cerisy T, Souterre T, Torres-Romero I, Boutard M, Dubois I, Patrouix J, Labadie K, Berrabah W, Salanoubat M, Doring V, Tolonen AC (2017). "Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics". Appl Environ Microbiol. 83 (11): e00289-17. Bibcode:2017ApEnM..83E.289C. doi:10.1128/AEM.00289-17. hdl:1721.1/104375. PMC 5440714. PMID 28363966. S2CID 4705511.
- Campbell, Neil A. and Reece, Jane B. (2002). Biology (6th ed.), pp. 345–346. San Francisco: Benjamin Cummings. ISBN 0-8053-6624-5.
- Mahillon Jacques, Chandler Michael (2020). "Insertion sequences". Microbiology and Molecular Biology Reviews. 62 (3): 725–774. doi:10.1128/MMBR.62.3.725-774.1998. PMC 98933. PMID 9729608.
- Prescott, Lansing M.; Harley, John P.; and Klein, Donald A. (2002). Microbiology (5th ed.), pp. 298–299. New York: McGraw-Hill. ISBN 0-07-232041-9.
- Shuler, Michael L. and Kargi, Fikret (2002). Bioprocess Engineering: Basic Concepts (2nd ed.), p. 220. Upper Saddle River, NJ: Prentice Hall PTR. ISBN 0-13-081908-5.
