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(A) Transposable elements are flanked by inverted tandem repeats (TIRs). (B) Transposases cleave the transposable element at the TIRs. The free transposable element inserts into another part of the genome.

The mobilome is the entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes[1], prokaryotes[2], and viruses[3]. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elements in eukaryotes, and plasmids and prophages being the major types in prokaryotes.[4] Virophages contribute to the viral mobilome.[5]

Mobilome in eukaryotes

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Transposable elements are elements that can move about or propagate within the genome, and are the major constituents of the eukaryotic mobilome.[4] Transposable elements can be regarded as genetic parasites because they exploit the host cell's transcription and translation mechanisms to extract and insert themselves in different parts of the genome, regardless of the phenotypic effect on the host.[6]

Eukaryotic transposable elements were first discovered in maize (Zea mays) in which kernels showed a dotted color pattern.[7] Barbara McClintock described the maize Ac/Ds system in which the Ac locus promotes the excision of the Ds locus from the genome, and excised Ds elements can mutate genes responsible for pigment production by inserting into their coding regions.[8]

Other examples of transposable elements include: yeast (Saccharomyces cerevisiae) Ty elements, a retrotransposon which encodes a reverse transcriptase to convert its mRNA transcript into DNA which can then insert into other parts of the genome;[9][10] and fruit fly (Drosophila melanogaster) P-elements, which randomly inserts into the genome to cause mutations in germ line cells, but not in somatic cells.[11]

Mobilome in prokaryotes

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Bacterial conjugation. (1) Production of pilus. (2) Pilus connects two bacteria. (3) One strand of plasmid DNA moves into the recipient. (4) Both bacteria contain identical plasmids.

Plasmids were discovered in the 1940s as genetic materials outside of bacterial chromosomes.[12] Prophages are genomes of bacteriophages (a type of virus) that are inserted into bacterial chromosomes; prophages can then be spread to other bacteria through the lytic cycle and lysogenic cycle of viral replication.[13]

While transposable elements are also found in prokaryotic genomes[14], the most common mobile genetic elements in the prokaryotic genome are plasmids and prophages.[4]

Plasmids and prophages can move between genomesn through bacterial conjugation, allowing horizontal gene transfer.[15] Plasmids often carry genes that are responsible for bacterial antibiotic resistance; as these plasmids replicate and pass from one genome to another, the whole bacterial population can quickly adapt to the antibiotic.[16][17] Prophages can loop out of bacterial chromosomes to produce bacteriophages that go on to infect other bacteria with the prophages; this allows prophages to propagate quickly among the bacterial population, to the harm of the bacterial host.[13]


Mobilome in viruses

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Discovered in 2008 in a strain of Acanthamoeba castellanii mimivirus[18], virophages are an element of the virus mobilome.[5] Virophages are viruses that replicate only when host cells are co-infected with helper viruses.[19] Following co-infection, helper viruses exploit the host cell's transcription/translation machinery to produce their own machinery; virophages replicate through the machinery of either the host cell or the viruses.[19] The replication of virophages can negatively impact the replication of helper viruses.[18][20]

Sputnik[18][21] and mavirus[22] are examples of virophages.

References

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  1. ^ Hurst, Gregory D. D.; Werren, John H. (2001-08). "The role of selfish genetic elements in eukaryotic evolution". Nature Reviews Genetics. 2 (8): 597–606. doi:10.1038/35084545. ISSN 1471-0064. {{cite journal}}: Check date values in: |date= (help)
  2. ^ Toussaint, Ariane; Merlin, Christophe (2002-01-01). "Mobile Elements as a Combination of Functional Modules". Plasmid. 47 (1): 26–35. doi:10.1006/plas.2001.1552. ISSN 0147-619X.
  3. ^ Miller, David Wayne; Miller, Lois K. (1982-10). "A virus mutant with an insertion of a copia -like transposable element". Nature. 299 (5883): 562–564. doi:10.1038/299562a0. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
  4. ^ a b c Siefert, Janet L. (2009), Gogarten, Maria Boekels; Gogarten, Johann Peter; Olendzenski, Lorraine C. (eds.), "Defining the Mobilome", Horizontal Gene Transfer: Genomes in Flux, Methods in Molecular Biology, Humana Press, pp. 13–27, doi:10.1007/978-1-60327-853-9_2, ISBN 9781603278539, retrieved 2019-10-08
  5. ^ a b Bekliz, Meriem; Colson, Philippe; La Scola, Bernard (2016/11). "The Expanding Family of Virophages". Viruses. 8 (11): 317. doi:10.3390/v8110317. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  6. ^ Wallau, Gabriel Luz; Ortiz, Mauro Freitas; Loreto, Elgion Lucio Silva (2012). "Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives". Genome Biology and Evolution. 4 (8): 801–811. doi:10.1093/gbe/evs055. ISSN 1759-6653.
  7. ^ Coe, Edward H. (2001-11). "The origins of maize genetics". Nature Reviews Genetics. 2 (11): 898–905. doi:10.1038/35098524. ISSN 1471-0064. {{cite journal}}: Check date values in: |date= (help)
  8. ^ McClintock, Barbara (1950-06-01). "The origin and behavior of mutable loci in maize". Proceedings of the National Academy of Sciences. 36 (6): 344–355. doi:10.1073/pnas.36.6.344. ISSN 0027-8424. PMID 15430309.
  9. ^ Mellor, Jane; Malim, Michael H.; Gull, Keith; Tuite, Mick F.; McCready, Shirley; Dibbayawan, Teresa; Kingsman, Susan M.; Kingsman, Alan J. (1985-12). "Reverse transcriptase activity and Ty RNA are associated with virus-like particles in yeast". Nature. 318 (6046): 583–586. doi:10.1038/318583a0. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
  10. ^ Garfinkel, David J.; Boeke, Jef D.; Fink, Gerald R. (1985-09-01). "Ty element transposition: Reverse transcriptase and virus-like particles". Cell. 42 (2): 507–517. doi:10.1016/0092-8674(85)90108-4. ISSN 0092-8674.
  11. ^ Laski, Frank A.; Rio, Donald C.; Rubin, Gerald M. (1986-01-17). "Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing". Cell. 44 (1): 7–19. doi:10.1016/0092-8674(86)90480-0. ISSN 0092-8674.
  12. ^ Sonneborn, T M (1950-4). "The cytoplasm in heredity". Heredity. 4 (1): 11–36. doi:10.1038/hdy.1950.2. ISSN 0018-067X. {{cite journal}}: Check date values in: |date= (help)
  13. ^ a b Bertani, G. (1953-01-01). "Lysogenic Versus Lytic Cycle of Phage Multiplication". Cold Spring Harbor Symposia on Quantitative Biology. 18: 65–70. doi:10.1101/SQB.1953.018.01.014. ISSN 0091-7451. PMID 13168970.
  14. ^ Campbell, A.; Berg, D.; Botstein, D.; Lederberg, E. M.; Novick, R. P.; Starlinger, P.; Szybalski, W. (1979-03-01). "Nomenclature of transposable elements in prokaryotes". Gene. 5 (3): 197–206. doi:10.1016/0378-1119(79)90078-7. ISSN 0378-1119.
  15. ^ Juhas, Mario (2015-01-02). "Horizontal gene transfer in human pathogens". Critical Reviews in Microbiology. 41 (1): 101–108. doi:10.3109/1040841X.2013.804031. ISSN 1040-841X.
  16. ^ Harrison, Ellie; Brockhurst, Michael A. (2012-06-01). "Plasmid-mediated horizontal gene transfer is a coevolutionary process". Trends in Microbiology. 20 (6): 262–267. doi:10.1016/j.tim.2012.04.003. ISSN 0966-842X.
  17. ^ Gillings, Michael R. (2013). "Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome". Frontiers in Microbiology. 4. doi:10.3389/fmicb.2013.00004. ISSN 1664-302X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  18. ^ a b c La Scola, Bernard; Desnues, Christelle; Pagnier, Isabelle; Robert, Catherine; Barrassi, Lina; Fournous, Ghislain; Merchat, Michèle; Suzan-Monti, Marie; Forterre, Patrick; Koonin, Eugene; Raoult, Didier (2008-09). "The virophage as a unique parasite of the giant mimivirus". Nature. 455 (7209): 100–104. doi:10.1038/nature07218. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
  19. ^ a b Claverie, Jean-Michel; Abergel, Chantal (2009). "Mimivirus and its Virophage". Annual Review of Genetics. 43 (1): 49–66. doi:10.1146/annurev-genet-102108-134255. PMID 19653859.
  20. ^ Duponchel, Sarah; Fischer, Matthias G. (2019-03-21). "Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses". PLOS Pathogens. 15 (3): e1007592. doi:10.1371/journal.ppat.1007592. ISSN 1553-7374. PMC 6428243. PMID 30897185.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  21. ^ Sun, Siyang; Scola, Bernard La; Bowman, Valorie D.; Ryan, Christopher M.; Whitelegge, Julian P.; Raoult, Didier; Rossmann, Michael G. (2010-01-15). "Structural Studies of the Sputnik Virophage". Journal of Virology. 84 (2): 894–897. doi:10.1128/JVI.01957-09. ISSN 0022-538X. PMID 19889775.
  22. ^ Fischer, Matthias G.; Hackl, Thomas (2016-12). "Host genome integration and giant virus-induced reactivation of the virophage mavirus". Nature. 540 (7632): 288–291. doi:10.1038/nature20593. ISSN 1476-4687. {{cite journal}}: Check date values in: |date= (help)
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