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Mobilome

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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 genomes 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 GD, Werren JH (August 2001). "The role of selfish genetic elements in eukaryotic evolution". Nature Reviews. Genetics. 2 (8): 597–606. doi:10.1038/35084545. PMID 11483984. S2CID 2715605.
  2. ^ Toussaint A, Merlin C (January 2002). "Mobile elements as a combination of functional modules". Plasmid. 47 (1): 26–35. doi:10.1006/plas.2001.1552. PMID 11798283.
  3. ^ Miller DW, Miller LK (October 1982). "A virus mutant with an insertion of a copia-like transposable element". Nature. 299 (5883): 562–4. Bibcode:1982Natur.299..562M. doi:10.1038/299562a0. PMID 6289125. S2CID 4275018.
  4. ^ a b c Siefert JL (2009). "Defining the Mobilome". In Gogarten MB, Gogarten JP, Olendzenski LC (eds.). Horizontal Gene Transfer: Genomes in Flux. Methods in Molecular Biology. Vol. 532. Humana Press. pp. 13–27. doi:10.1007/978-1-60327-853-9_2. ISBN 9781603278539. PMID 19271177.
  5. ^ a b Bekliz M, Colson P, La Scola B (November 2016). "The Expanding Family of Virophages". Viruses. 8 (11): 317. doi:10.3390/v8110317. PMC 5127031. PMID 27886075.
  6. ^ Wallau GL, Ortiz MF, Loreto EL (2012). "Horizontal transposon transfer in eukarya: detection, bias, and perspectives". Genome Biology and Evolution. 4 (8): 689–99. doi:10.1093/gbe/evs055. PMC 3516303. PMID 22798449.
  7. ^ Coe EH (November 2001). "The origins of maize genetics". Nature Reviews. Genetics. 2 (11): 898–905. doi:10.1038/35098524. PMID 11715045. S2CID 5498836.
  8. ^ McClintock B (June 1950). "The origin and behavior of mutable loci in maize". Proceedings of the National Academy of Sciences of the United States of America. 36 (6): 344–55. Bibcode:1950PNAS...36..344M. doi:10.1073/pnas.36.6.344. PMC 1063197. PMID 15430309.
  9. ^ Mellor J, Malim MH, Gull K, Tuite MF, McCready S, Dibbayawan T, et al. (December 1985). "Reverse transcriptase activity and Ty RNA are associated with virus-like particles in yeast". Nature. 318 (6046): 583–6. Bibcode:1985Natur.318..583M. doi:10.1038/318583a0. PMID 2415827. S2CID 4314282.
  10. ^ Garfinkel DJ, Boeke JD, Fink GR (September 1985). "Ty element transposition: reverse transcriptase and virus-like particles". Cell. 42 (2): 507–17. doi:10.1016/0092-8674(85)90108-4. PMID 2411424. S2CID 35750065.
  11. ^ Laski FA, Rio DC, Rubin GM (January 1986). "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. PMID 3000622. S2CID 18364777.
  12. ^ Sonneborn TM (April 1950). "The cytoplasm in heredity". Heredity. 4 (1): 11–36. doi:10.1038/hdy.1950.2. PMID 15415003.
  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. PMID 13168970.
  14. ^ Campbell A, Berg DE, Botstein D, Lederberg EM, Novick RP, Starlinger P, Szybalski W (March 1979). "Nomenclature of transposable elements in prokaryotes". Gene. 5 (3): 197–206. doi:10.1016/0378-1119(79)90078-7. PMID 467979.
  15. ^ Juhas M (February 2015). "Horizontal gene transfer in human pathogens" (PDF). Critical Reviews in Microbiology. 41 (1): 101–8. doi:10.3109/1040841X.2013.804031. PMID 23862575. S2CID 5193869.
  16. ^ Harrison E, Brockhurst MA (June 2012). "Plasmid-mediated horizontal gene transfer is a coevolutionary process" (PDF). Trends in Microbiology. 20 (6): 262–7. doi:10.1016/j.tim.2012.04.003. PMID 22564249.
  17. ^ Gillings MR (2013). "Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome". Frontiers in Microbiology. 4: 4. doi:10.3389/fmicb.2013.00004. PMC 3560386. PMID 23386843.
  18. ^ a b c La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, et al. (September 2008). "The virophage as a unique parasite of the giant mimivirus". Nature. 455 (7209): 100–4. Bibcode:2008Natur.455..100L. doi:10.1038/nature07218. PMID 18690211. S2CID 4422249.
  19. ^ a b Claverie JM, Abergel C (2009). "Mimivirus and its virophage". Annual Review of Genetics. 43 (1): 49–66. doi:10.1146/annurev-genet-102108-134255. PMID 19653859.
  20. ^ Duponchel S, Fischer MG (March 2019). "Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses". PLOS Pathogens. 15 (3): e1007592. doi:10.1371/journal.ppat.1007592. PMC 6428243. PMID 30897185.
  21. ^ Sun S, La Scola B, Bowman VD, Ryan CM, Whitelegge JP, Raoult D, Rossmann MG (January 2010). "Structural studies of the Sputnik virophage". Journal of Virology. 84 (2): 894–7. doi:10.1128/JVI.01957-09. PMC 2798384. PMID 19889775.
  22. ^ Fischer MG, Hackl T (December 2016). "Host genome integration and giant virus-induced reactivation of the virophage mavirus" (PDF). Nature. 540 (7632): 288–291. Bibcode:2016Natur.540..288F. doi:10.1038/nature20593. PMID 27929021. S2CID 4458402.
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