1887
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

Transposable Elements

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Buy this Microbiology Spectrum Article
Price Non-Member $15.00
  • Author: Peter W. Atkinson1
  • Editors: Mick Chandler2, Nancy Craig3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521; 2: Université Paul Sabatier, Toulouse, France; 3: Johns Hopkins University, Baltimore, MD
  • Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
  • Received 18 September 2014 Accepted 20 February 2015 Published 02 July 2015
  • Peter Atkinson, peter.atkinson@ucr.edu
image of <span class="jp-italic">hAT</span> Transposable Elements
    Preview this microbiology spectrum article:
    Zoom in
    Zoomout

    Transposable Elements, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/3/4/MDNA3-0054-2014-1.gif /docserver/preview/fulltext/microbiolspec/3/4/MDNA3-0054-2014-2.gif
  • Abstract:

    transposons are ancient in their origin and they are widespread across eukaryote kingdoms. They can be present in large numbers in many genomes. However, only a few active forms of these elements have so far been discovered indicating that, like all transposable elements, there is selective pressure to inactivate them. Nonetheless, there have been sufficient numbers of active elements and their transposases characterized that permit an analysis of their structure and function. This review analyzes these and provides a comparison with the several domesticated genes discovered in eukaryote genomes. Active transposons have also been developed as genetic tools and understanding how these may be optimally utilized in new hosts will depend, in part, on understanding the basis of their function in genomes.

  • Citation: Atkinson P. 2015. Transposable Elements. Microbiol Spectrum 3(4):MDNA3-0054-2014. doi:10.1128/microbiolspec.MDNA3-0054-2014.

Key Concept Ranking

Basic Amino Acids
0.51859224
Acidic Amino Acids
0.5175274
Aromatic Amino Acids
0.50562745
Transcription Start Site
0.43287247
0.51859224

References

1. Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Ann Rev Genet 41:331–368. [PubMed][CrossRef]
2. Oliver KR, McComb JA, Greene WK. 2013. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 5:1886–1901. [PubMed][CrossRef]
3. Mack AM, Crawford NM. 2001. The Arabidopsis TAG1 transposase has an N-terminal zinc finger DNA binding domain that recognizes distinct subterminal motifs. Plant Cell 13:2319–2331. [PubMed][CrossRef]
4. Kunze R, Starlinger P. 1989. The putative transposase of transposable element Ac from Zea mays L. interacts with subterminal sequences of Ac. Embo J 8:3177–3185. [PubMed]
5. Kahlon AS, Hice RH, O'Brochta DA, Atkinson PW. 2011. DNA binding activities of the Herves transposase from the mosquito Anopheles gambiae. Mobile DNA 2:9. [PubMed][CrossRef]
6. Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss A-L, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F. 2014. Structural basis for transposon end recognition by Hermes, an octameric hAT DNA transposase from Musca domestica. Cell 158:353–367. [PubMed][CrossRef]
7. Coen ES, Robbins TP, Almeida J, Hudson A, Carpenter R. 1989. Consequences and mechanisms of transposition in Antirrhinum majus, p 413–436. In Berg D, Howe M (ed), Mobile DNA. American Society for Microbiology, Washington DC.
8. Atkinson PW, Warren WD, O'Brochta DA. 1993. The hobo transposable element of Drosophila can be cross-mobilized in houseflies and excises like the Ac element of maize. Proc Natl Acad Sci USA 83:9693–9697. [PubMed][CrossRef]
9. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, Craig NL. 2004. Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432:995–1001. [PubMed][CrossRef]
10. Hickman AB, Chandler M, Dyda F. 2010. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45:50–69. [PubMed][CrossRef]
11. Yuan YW, Wessler SR. 2011. The catalytic domain of all eukaryotic cut-and-paste transposon superfamilies. Proc Natl Acad Sci USA 108:7884–7889. [PubMed][CrossRef]
12. Rubin E, Lithwick G, Levy AA. 2001. Structure and evolution of the hAT transposon superfamily. Genetics 158:949–957. [PubMed]
13. Kempken F, Windhofer F. 2001. The hAT family: a versatile transposon group common to plants. fungi, animals, and man. Chromosoma 110:1–9. [PubMed][CrossRef]
14. Du C, Hoffman A, He L, Caronna J, Dooner HK. 2011. The complete Ac/Ds transposon family of maize. BMC Genomics 12:588. [PubMed][CrossRef]
15. Lazarow K, Doll M-L, Kunze R. 2013. Molecular biology of maize Ac/Ds elements: an overview, p 59–82. In Peterson T (ed), Plant Transposable Elements: Methods and Protocols, vol. 1057. Springer, New York, NY. [PubMed][CrossRef]
16. Federoff NV. 1989. Maize transposable elements, p 375–411. In Berg DE, Howe MM (ed), Mobile DNA. ASM Press, Washington DC.
17. Kunze R, Weil CF. 2002. The hAT and CACTA superfamilies of plant transposons, p 565–610. In Craig NL, Craigie R, Gellert M, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington DC. [CrossRef]
18. McClintock B. 1947. Cytogenetic studies of maize and Neurospora. Carnegie Institution of Washington Year Book 46:146–152.
19. McClintock B. 1948. Mutable loci in maize. Carnegie Institution of Washington Year Book 47:155–169.
20. McGinnis W, Shermoen AW, Beckendorf SK. 1983. A transposable element inserted just 5′ to a Drosophila glue protein gene alters gene expression and chromatin structure. Cell 34:75–84. [PubMed][CrossRef]
21. Arensburger P, Hice RH, Zhou L, Smith RC, Tom AC, Wright JA, Knapp JA, O'Brochta DA, Craig NL, Atkinson PW. 2011. Phylogenetic and functional characterization of the hAT transposon superfamily. Genetics 188:45–57. [PubMed][CrossRef]
22. Rossato DO, Ludwig A, Depra M, Loreto ELS, Ruiz A, Valenta VLS. 2014. BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila. Genome Biol Evol 6:352–365. [PubMed][CrossRef]
23. Zhang HH, Shen YH, Xu HE, Liang HY, Han MJ, Zhang Z. 2013. A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature repeat transposable elements (MITEs) and horizontal transfer. Insect Mol Biol 22:584–596. [PubMed][CrossRef]
24. Christoff A-P, Lerto ELS, Sepel LMN. 2012. Evolutionary history of the Tip100 transposon in the genus Ipomoea. Genet Mol Biol 35:460–465. [PubMed][CrossRef]
25. Warren WD, Atkinson PW, Obrochta DA. 1994. The Hermes transposable element from the house fly, Musca domestica, is a short inverted repeat-type element of the hobo, Ac, and Tam3 (hAT) element family. Genet Res 64:87–97. [PubMed][CrossRef]
26. Pascual L, Periquet G. 1991. Distribution of hobo transposable elements in natural populations of Drosophila melanogaster. Mol Biol Evol 8:282–296. [PubMed]
27. Simmons GM. 1992. Horizontal transfer of hobo transposable elements within the Drosophila melanogaster species complex - evidence from DNA sequencing. Mol Biol Evol 9:1050–1060. [PubMed]
28. Ortiz MD, Loreto ELS. 2009. Characterization of new hAT transposable elements in 12 Drosophila genomes. Genetica 135:67–75. [PubMed][CrossRef]
29. Ladeveze V, Chaminade N, Lemeunier F, Periquet G, Aulard S. 2012. General survey of hAT transposon superfamily with highlight on hobo element in Drosophila. Genetica 140:375–392. [PubMed][CrossRef]
30. Pace JKI, Gilbert C, Clark MS, Feschotte C. 2008. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A 105:17023–17028. [PubMed][CrossRef]
31. Habu Y, Histomi Y, Iida S. 1998. Molecular characterization of the mutable flaked allele for flower variegation in the common morning glory. Plant J 16:371–376. [PubMed][CrossRef]
32. Mota NR, Ludwig A, da Silva Valente VL, Loreto ELS. 2010. harrow: new Drosophila hAT transposons involved in horizontal transfer. Insect Mol Biol 19:217–228. [PubMed][CrossRef]
33. Depra M, Panzera Y, Ludwig A, Valenta VLS, Loreto ELS. 2010. hosimary: a new hAT transposon group involved in horizontal transfer. Mol Genet Genomics 283:451–459. [PubMed][CrossRef]
34. Zou S, Du X, Yuan J, Jiang X. 2010. Cloning of goldfish hAT transposon Tgf2 and its structure. Hereditas 32:1–6.
35. Jiang XY, Du XD, Tian YM, Shen RJ, Sun CF, Zou SM. 2012. Goldfish transposase Tgf2 presumably from recent horizontal transfer is active. FASEB J 26:2743–2752. [PubMed][CrossRef]
36. Koga A, Shimada A, Shima A, Sakaizumi M, Tachida H, Hori H. 2000. Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element. Genetics 155:273–281. [PubMed]
37. Gilbert C, Hernandez SS, Flores-Benabib J, Smith EN, Feschotte C. 2012. Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol 29:503–515. [PubMed][CrossRef]
38. Ray DA, Pagan HJT, Thompson ML, Stevens RD. 2006. Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol 24:632–639. [PubMed][CrossRef]
39. Novick P, Smith J, Ray D, Boissinot S. 2010. Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449:85–94. [PubMed][CrossRef]
40. Baker B, Schell J, Lorz H, Fedoroff N. 1986. Transposition of the maize controlling element Activator in tobacco. Proc Natl Acad Sci U S A 83:4844–4848. [PubMed][CrossRef]
41. Laufs J, Wirtz U, Kammann M, Matzeit V, Schaefer S, Schell J, Czernilofsky AP, Baker B, Gronenborn B. 1990. Wheat dwarf virus Ac/Ds vectors: expression and excision of transposable elements introduced into various cereals by a viral replicon. Proc Natl Acad Sci U S A 87:7752–7756. [PubMed][CrossRef]
42. Izawa T, Miyazaki C, Yamamoto M, Terada R, Iida S, Shimamoto K. 1991. Introduction and transposition of the maize transposable element Ac in rice (Oryza sativa L). Mol Gen Genet 227:391–396. [PubMed][CrossRef]
43. Chuck G, Robbins T, Nijjar C, Ralston E, Courtney-Gutterson N, Dooner HK. 1993. Tagging and cloning of a petunia flower color gene with the maize transposable element activator. Plant Cell 5:371–378. [PubMed][CrossRef]
44. Finnegan EJ, Lawrence GJ, Dennis ES, Ellis JG. 1993. Behaviour of modified Ac elements in flax callus and regenerated plants. Plant Mol Biol 22:625–633. [PubMed][CrossRef]
45. McElroy D, Louwerse JD, McElroy SM, Lemaux PG. 1997. Development of a simple transient assay for Ac/Ds activity in cells of intact barley tissue. Plant J 11:157–165. [PubMed][CrossRef]
46. Yoder JI. 1990. Rapid proliferation of the maize transposable element Activator in transgenic tomato. Plant Cell 2:723–730. [PubMed][CrossRef]
47. Yang CH, Ellis JG, Michelmore RW. 1993. Infrequent transposition of Ac in lettuce, Lactuca sativa. Plant Mol Biol 22:793–805. [PubMed][CrossRef]
48. Lisson R, Hellert J, Ringleb M, Machens F, Kraus J, Hehl R. 2010. Alternative splicing of the maize Ac transposase transcript in transgenic sugar beet (Beta vulgaris L.). Plant Mol Biol 74:19–32. [PubMed][CrossRef]
49. Babwah V, Waddell S. 2002. Trans-activation of the maize transposable element, Ds, in Brassica napus. Theor Appl Genet 104:1141–1149. [PubMed][CrossRef]
50. Qu S, Jeon JS, Ouwerkekr PBF, Bellizzi M, Leach J, Ronald P, Wang GL. 2009. Construction and application of efficient Ac-Ds transposon tagging vectors in rice. J Integr Plant Biol 51:982–992. [PubMed][CrossRef]
51. Lazarow K, Du M-L, Weimer R, Kunze R. 2012. A hyperactive transposase of the maize transposable element Activator (Ac). Genetics 191:747–756. [PubMed][CrossRef]
52. Blackman RK, Macy M, Koehler D, Grimaila R, Gelbart WM. 1989. Identification of a fully functional hobo transposable element and its use for germ line transformation of Drosophila. EMBO J 8:211–217. [PubMed]
53. Rubin GM, Spradling AC. 1982. Genetic transformation of Drosophila with transposable element vectors. Science 218:348–353. [PubMed][CrossRef]
54. Gangadhrana S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL. 2010. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo. Proc Natl Acad Sci U S A 107:21966–21972. [PubMed][CrossRef]
55. Li X, Ewis HE, Hice RH, Malani N, Parker N, Zhou L, Feshotte C, Bushman FD, Atkinson PW, Craig NL. 2013. A resurrected mammalian hAT transposable element and closely related insect element are highly active in human cell culture. Proc Natl Acad Sci U S A 110:E478–E487. [PubMed][CrossRef]
56. Woodward LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. 2012. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. PLoS One 7:e42666. [PubMed][CrossRef]
57. Hori H., Suzuki M., Inagaki H., Oshima T., Koga A. 1998. An active Ac-like transposable element in teleost fish. J Mar Biotechnol 6:206–207. [PubMed]
58. Kawakami K, Noda T. 2004. Transposition of the Tol2 element, an Ac-like element from the Japanese Medaka fish Oryzias latipes, in mouse embryonic stem cells. Genetics 166:895–899. [PubMed][CrossRef]
59. Asakawa K, Suster ML, Mizusawa K, Nagayoshi S, Kotani T, Urasaki A, Kishimoto Y, Kawakami K. 2008. Genetic dissection of neural circits by Tol2 transposon-mediated Gal4 gene and enhancer tranpping in zebrafish. Proc Natl Acad Sci U S A 105:1255–1260. [PubMed][CrossRef]
60. Asakawa K, Kawakami K. 2009. The Tol2-mediated Gal4-UAS method for gene and enhancer trapping in zebrafish. Methods 49:275–281. [PubMed][CrossRef]
61. Urasaki A, Mito T, Noji S, Ueda R, Kawakami K. 2008. Transposition of the vertebrate Tol2 transposable element in Drosophila melanogaster. Gene 425:64–68. [PubMed][CrossRef]
62. Hamlet MR, Yergeau DA, Kuliyev E, Takeda M, Taira M, Kawakami M, Mead PE. 2006. Tol2 transposon-mediated transgenesis in Xenopus tropicalis. Genesis 44:438–445. [PubMed][CrossRef]
63. Kawakami K, Takeda H, Kawakami N, Kobayashi M, Mishina M. 2004. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Developmental Cell 7:133–144. [PubMed][CrossRef]
64. Scott EK, Mason L, Arrenberg AB, Ziv L, Goose NJ, Xiao T, Chi NC, K. A, Kawakami K, Baier H. 2007. Taregting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat Methods 4:332–326. [PubMed]
65. Kawakami K, Abe G, Asada T, K. A, Fukada R, Ito A, Lal P, Mouri N, Muto A, Suster ML, Takakubo A, Wada H, Yoshida M. 2010. zTrap: zebrafish gene trap and enhancer trap database. BMC Dev Biol 10:105. [PubMed]
66. Macdonald J, Taylor L, Sherman A, Kawakami K, Takahashi Y, Sang HM, McGrew MJ. 2012. Efficient gene modification and germ-line transmission of primordial germ cells using piggyBac and Tol2 transposons. Proc Natl Acad Sci U S A 109:E1466–E1472. [PubMed][CrossRef]
67. Mayasari NI, Mukougawa K, Shigeoka T, Kawaichi M, Ishida Y. 2012. Mixture of differentially tagged Tol2 transposons accelerates conditional disruption of a broad spectrum of genes in mouse embryonic stem cells. Nucleic Acids Res 20:e97. [PubMed][CrossRef]
68. Freeman S, Chrysostomou E, Kawakami K, Takahashi Y, Daudet N. 2012. Tol2-mediated gene transfer and in ovo electroporation of the optic placode: a powerful and versatile approach for invetifatin embryonic development and regeneration of the chicken inner-ear. Methods Mol Biol 916:127–139. [PubMed][CrossRef]
69. Yergeau DA, Kelley CM, Kuliyev E, Zhu H, Sater AK, Wells DE, Mead PE. 2010. Remobilization of Tol2 transposons in Xenopus tropicalis. BMC Dev Biol 10:11. [PubMed][CrossRef]
70. Lane MA, Kimber M, Khokha MK. 2013. Breeding based remobilization of Tol2 transposon in Xenopus tropicalis. PLoS ONE 8:e76807. [PubMed][CrossRef]
71. Meir YJ, Weirauch MT, Yang HS, Chung PC, Yu RK, Wu SC. 2011. Genome-wide target profiling of piggyBac and Tol2 in HEK392: pros and cons for gene discovery and gene therapy. BMC Biotechnol 11:28. [PubMed][CrossRef]
72. Huang X, Guo H, Tammana S, Jung YC, E. M, Bassi P, Cao Q, Tu ZJ, Kim YC, Ekker SC, Wu X, Wang SM, Zhou X. 2010. Gene transfer efficiency and genome-wide integration profiling of Sleeping Beauty, Tol2, and piggyBac transposons in human primary T cells. Mol Ther 18:1803–1813. [PubMed][CrossRef]
73. Backfisch B, Kozin VV, Kirchmaier S, Tessmar-Raible K, Raible F. 2014. Tools for gene-regulatory analyses in th marine annelid Platynereis dumerilii. PLoS ONE 9:e93076. [PubMed][CrossRef]
74. Coen ES, Carpenter R, Martin C. 1986. Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus. Cell 47:285–296. [PubMed][CrossRef]
75. Weil CF, Kunze R. 2000. Transposition of maize Ac/Ds transposable elements in the yeast Saccharomyces cerevisiae. Nat Genet 26:187–190. [PubMed][CrossRef]
76. Calvi BR, Hong TJ, Findley SD, Gelbart WM. 1991. Evidence for a common evolutionary origin of inverted terminal repeat transposons in Drosophila and plants: hobo, Activator and Tam3. Cell 66:465–471. [PubMed][CrossRef]
77. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F. 2005. Molecular architecture of a eukaryotic transposase. Nat Struct Mol Biol 12:715–721. [PubMed][CrossRef]
78. Warren WD, Atkinson PW, O'Brochta DA. 1994. The Hermes transposable element from the housefly, Musca domestica, is a short inverted repeat-type element of the hobo, Ac, and Tam3 (hAT) element family. Genet Res 64:87–97. [PubMed][CrossRef]
79. Sarkar A, Coates CJ, Whyard S, Willhoeft U, Atkinson PW, O'Brochta DA. 1997. The Hermes element from Musca domestica can transpose in four families of cylorrhaphan flies. Genetica 99:15–29. [PubMed][CrossRef]
80. Subramanian RA, Cathcart LA, Krafsur ES, Atkinson PW, O’Brochta DA. 2009. Hermes transposon distribution in Musca domestica. J. Hered. 100:473–480. [PubMed][CrossRef]
81. Sarkar A, Yardley K, Atkinson PW, James AA, O'Brochta DA. 1997. Transposition of the Hermes element in embryos of the vector mosquito, Aedes aegypti. Insect Biochem Mol Biol 27:359–363. [PubMed][CrossRef]
82. Pinkerton AC, O'Brochta DA, Atkinson PW. 1996. Mobility of hAT transposable elements in the Old World American bollworm, Helicoverpa armigera. Insect Mol Biol 5:223–227. [PubMed][CrossRef]
83. Zhao Y, Eggleston P. 1998. Stable transformation of an Anopheles gambiae cell line mediated by the Hermes mobile genetic element. Insect Biochem Mol Biol 28:213–219. [CrossRef]
84. Lehane MJ, Atkinson PW, O'Brochta DA. 2000. Hermes-mediated genetic transformation of the stable fly, Stomoxys calcitrans.Insect Mol Biol 9:531–538. [PubMed][CrossRef]
85. Michel K, Stamenova A, Pinkerton AC, Franz G, Robinson AS, Gariou-Papalexiou A, Zacharopoulou A, O'Brochta DA, Atkinson PW. 2001. Hermes-mediated germ-line transformation of the Mediterranean fruit fly, Ceratitis capitata. Insect Mol Biol 10:155–162. [PubMed][CrossRef]
86. O'Brochta DA, Warren WD, Saville KJ, Atkinson PW. 1996. Hermes, a functional non-drosophilid gene vector from Musca domestica. Genetics 142:907–914. [PubMed]
87. Marcus JM, Ramos DM, Monteiro A. 2004. Germline transformation of the butterfly Bicyclus anynana. Proc Biol Sci 271(Suppl 5):S263–S265. [PubMed][CrossRef]
88. Pinkerton AC, Michel K, O'Brochta DA, Atkinson, PW. 2000. Green fluorescent protein as a genetic marker in transgenic Aedes aegypti. Insect Mol. Biol. 9:1–10. [PubMed][CrossRef]
89. Jasinskiene N, Coates CJ, Benedict MQ, Cornel AJ, Salazar-Rafferty C, James AA, Collins FH. 1998. Stable, transposon-mediated transformation of the yellow fever mosquito, Aedes aegypti, using the Hermes element from the house fly. Proc Natl Acad Sci U S A 95:3743–3747. [PubMed][CrossRef]
90. Evertts AG, Plymire C, Craig NL, Levin HL. 2007. The Hermes transposon of Musca domestica is an efficient tool for the mutagenesis of Schizosaccharomyces pombe. Genetics 177:2519–2523. [PubMed][CrossRef]
91. Park JM, Evertts AG, Levin HL. 2009. The Hermes transposon of Musca domestica and its use as a mutagen of Schizosaccharomyces pombe. Methods 49:243–247. [PubMed][CrossRef]
92. Guo Y, Park JM, Cui B, Humes E, Gangadhrana S, Hung S, FitzGerald PC, Hoe KL, Grewak SI, Craig NL, Levin HL. 2013. Integration profiling if gene function with dense maps of transposon integration. Genetics 195:599–609. [PubMed][CrossRef]
93. Urasaki A, Morvan G, Kawakami K. 2006. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetive sequence in the subterminal region essential for transposition. Genetics 174:639–649. [PubMed][CrossRef]
94. Coupland G, Plum C, Chatterjee S, Post A, Starlinger P. 1989. Sequences near the termini are required for transposition of the maize transposon Ac in transgenic tobacco plants. Proc Natl Acad Sci U S A 86:9385–9388. [PubMed][CrossRef]
95. Kim YJ, Hice RH, O'Brochta DA, Atkinson PW. 2011. DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster. Genetica 139:985–987. [PubMed][CrossRef]
96. Liu D, Mack A, Wang R, Galli M, Belk J, Ketpura NI, Crawford NM. 2001. Functional dissection of the cis-acting sequences of the Arabidopsis transposable element Tag1 reveals dissimilar subterminal sequence and minimal spacing requirements for transposition. Genetics 157:817–830. [PubMed]
97. Feldmar S, Kunze R. 1991. The ORFa protein, the putative transposase of maize transposable element Ac, has a basic DNA binding domain. EMBO J 10:4003–4010. [PubMed]
98. Calvi BR, Hong TJ, Findley SD, Gelbart WM. 1991. Evidence for a common evolutionary origin of inverted repeat transposons in Drosophila and plants: hobo, Activator, and Tam3. Cell 66:465–471. [PubMed][CrossRef]
99. Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C. 2011. T-Coffee: a web server for the mutiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res 39:W13–W17. [PubMed][CrossRef]
100. Davies DR, Goryshin IY, Reznikoff WS, Rayment I. 2000. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289:77–85. [PubMed][CrossRef]
101. Aravind L. 2000. The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposase. Trends Bicohem Sci 25:421–423. [CrossRef]
102. Feldmar S., Kunze R. 1991. The ORFa protein, the putative transposase of maize transposable element Ac, has a basic DNA binding domain. EMBO J 10:4003–4010. [PubMed]
103. Becker HA, Kunze R. 1997. Maize Activator transposase has a bipartite DNA binding domain that recognizes subterminal sequences and the terminal inverted repeats. Mol Gen Genet 254:219–230. [CrossRef]
104. Kunze R, Behrens U, Courage-Franzkowiak U, Feldmar S, Kuhn S, Lutticke R. 1993. Dominant transposition-deficient mutants of maize Activator (Ac) transposase. Proc Natl Acad Sci U S A 90:7094–7098. [PubMed][CrossRef]
105. Sundaraajan P, Atkinson PW, O'Brochta DA. 1999. Transposable element interactions in insects: Crossmobilization of hobo and Hermes. Insect Mol Biol 8:359–368. [CrossRef]
106. Essers L, Adophs RH, Kunze R. 2000. A highly conserved domain of the maize activator tranposases in involved in dimerization. Plant Cell 12:211–224. [PubMed][CrossRef]
107. Michel K, O'Brochta DA, Atkinson PW. 2003. The C-terminus of the Hermes transposase contains a protein multimerization domain. Insect Biochem Mol Biol 33:959–970. [PubMed][CrossRef]
108. Volff JN. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28:913–922. [PubMed][CrossRef]
109. Sinzelle L, Izsvak Z, Ivics Z. 2009. Molecular domestication of transposable elements: From detrimental parasites to useful host genes. Cell Mol Life Sci 66:1073–1093. [PubMed][CrossRef]
110. Bundock P, Hooykaas P. 2005. An Arabidopsis hAT-like transposase is essential for plant developmement. Nature 436:282–284. [PubMed][CrossRef]
111. Knip M, Hiemstra S, Sietsma A, Castelein M, de Pater S, Hooykaas P. 2013. DAYSLEEPER: a nuclear and vesicular-localized protein that is expressed in proliferating tissues. BMS Plant Biology 13:211. [PubMed][CrossRef]
112. Muehlbauer GJ, Bhau BS, Syed NH, Cho S, Marshall D, Patetron S, Buisine N, Chalhoub B, Flavell AJ. 2006. A hAT superfamily transposase recruited by the cereal grass genome. Mol Gen Genomics 275:553–563. [PubMed][CrossRef]
113. Chesney MA, Kidd ARI, Kimble J. 2006. gon-14 functions with class B and class C synthetic multivulva genes to control larval growth in Caenorhabdidtis elegans. Genetics 172:915–928. [PubMed][CrossRef]
114. Hirose F, Ohshima N, Shiraki M, Inoue YH, Taguchi O, Nishi Y, NMatsukage A, Yamaguchi M. 2001. Ectopic expression of DREF induces DNA synthesis, apoptosis, and unusual morphogenesis in the Drosophila eye imaginal disc: Possible interactions with Polycomb and trithorax group proteins. Mol Cell Biol 21:7231–7242. [PubMed][CrossRef]
115. Gale MJ, Blakely CM, Hopkins DA, Melville MW, Wambach M, Romano PR, Katze MG. 1998. Regulatio of interferon-induced protein kinase PKR: modulation of P58IPK inhibitory function by a novel protein, P52rIPK. Mol Cell Biol 18:859–871. [PubMed]
116. Smit AFA. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9:657–663. [PubMed][CrossRef]
117. Tipney HJ, Hinsley TA, Brass A, Metcalf K, Donnai D, Tassabehji M. 2004. Isolation and characerization of GTF2IRD2, a novel fusion gene and member of the TFII-I family of transcription factors, deleted in Williams-Beuren syndrome. Eur J Hum Genet 12:551–560. [PubMed][CrossRef]
118. Robertson HM. 2002. Evolution of DNA transposons in eukaryotes, p 1093–1110. In Craig NL, Cragie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington DC. [CrossRef]
119. Yamashita D, Sano Y, Adachi Y, Okamoto Y, Osadai H, Takahashi T, Yamaguchi T, Osumi T, Hirose F. 2007. hDREF regulates cell proliferation and expression of ribosomal protein genes. Mol Cell Biol 27:2003–2013. [PubMed][CrossRef]
120. Matsukage A, Hirose F, Yoo MA, Yamaguchi M. 2008. The DRE/DREF transcriptional regulatory system: a master key for cell proliferation. Biochim Biophys Acta 1779:81–89. [PubMed][CrossRef]
121. Chen T, Li M, Ding Y, Zhang LS, Xi Y, Pan WJ, Tao DL, Wang JY, Li L. 2009. Identification of zinc-finger BED domain-containing 3 (Zbed3) as a novel axin-interacting protein that activates Wnt/beta-catenin signaling. J Biol Chem 284:6683–6689. [PubMed][CrossRef]
122. Hayward A, Ghazal A, Andersson G, Andersson L, Jern P. 2013. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. PLoS ONE 8:e59940. [PubMed][CrossRef]
123. Saghizadeh M, Gribanova Y, Akhmedov NB, Farber DB. 2011. ZBED4, a cone and Muller cell protein in human retina, has a different cellular expression in mouse. Mol Vis 17:2011–2018. [PubMed]
124. Andersson L, Andersson G, Hjalm G, Jiang L, Lindblad-Toh K, Lindroth AM, Markljung E, Nystrom AM, Rubin CJ, Sundstrom E. 2010. ZBED6. The birth of a new transcription factor in the common ancestor of placental mammals. Transcription 1:144–148. [PubMed][CrossRef]
125. Markljung E, Jiang L, Jaffe JD, Mikkelson TS, Wallerman O, Larhammar M, Zhang X, Wang L, Saenz-Vash V, Gnirke A, Lindroth AM, Barres R, J. Y, Stromberg S, De S, Ponten F, Lander ES, Carr SA, Zierath JR, Kullander K, Wadelius C, Lindblad-Toh K, Andersson G, Hjalm G, Andersson L. 2009. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 7:e100256. [PubMed][CrossRef]
126. Knip M, de Pater S, Hooykaas PJ. 2012. The SLEEPER genes: a transposon-derived angiosperm-specific gene family. BMC Plant Biol 12:192. [PubMed][CrossRef]
microbiolspec.MDNA3-0054-2014.citations
cm/3/4
content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0054-2014
Loading

Citations loading...

Loading

Article metrics loading...

/content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0054-2014
2015-07-02
2017-09-22

Abstract:

transposons are ancient in their origin and they are widespread across eukaryote kingdoms. They can be present in large numbers in many genomes. However, only a few active forms of these elements have so far been discovered indicating that, like all transposable elements, there is selective pressure to inactivate them. Nonetheless, there have been sufficient numbers of active elements and their transposases characterized that permit an analysis of their structure and function. This review analyzes these and provides a comparison with the several domesticated genes discovered in eukaryote genomes. Active transposons have also been developed as genetic tools and understanding how these may be optimally utilized in new hosts will depend, in part, on understanding the basis of their function in genomes.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

The mechanism of element excision. The chemical mechanism of element excision is shown based on studies undertaken with the element and transposase ( 9 ). The initial nick occurs on the nontransferred strand of the transposon that leads to the formation of an intermediate structure in which a hairpin loop is formed at the end of the flanking DNA with this second nick exposing the 3′OH of the terminal nucleotide on the transferred strand of the transposon. Therefore, it can undertake strand transfer to the target DNA molecule. doi:10.1128/microbiolspec.MDNA3-0054-2014.f1

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Conserved amino acids across hAT transposases. The four functional domains of hAT transposases are shown with conserved amino acids between 22 hAT transposases shown below. The DDE catalytic triad is shown in red and, based on the cocrystal structure of the Hermes transposase bound with the 16-mer L terminal inverted repeat (TIR), amino acids involved in DNA binding of the TIR, which are moderately conserved across the hAT transposases, are shown in blue. The relative positions of other amino acids that bind to the Hermes L TIR but are not conserved across the hAT transposases are shown by black bars. The position of the DNA binding cleft in the Hermes transposase is show by the blue bar located at the N-end of the insertion domain. Yellow-highlighted amino acids are very highly conserved across these transposases. The locations of the three conserved regions identified in the HFLI hobo transposase are shown underneath. doi:10.1128/microbiolspec.MDNA3-0054-2014.f2

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3a
FIGURE 3a

Comparison of hAT transposase sequences. (A) Consensus alignment of 22 hAT transposases. The alignment was obtained using the program M-Coffee, which uses multiple sequence alignment programs. The location of each sequence within its transposase is shown by the amino acid numbers. The location of the DDE motif is shown above the alignments, conserved resides are shown below the alignments along with the locations of the domains and the six conserved blocks originally identified by Rubin et al. ( 12 ). Amino acids identified as being critical for Hermes transposase activity and/or DNA binding from the Hermes transpososome cocrystal by Hickman et al. ( 6 ) are shown in red as are identical amino acids present in the same locations in the other transposases. The C and H amino acids proposed to constitute the BED domain are shown in blue. Accession numbers are: Tol2 (BAA87039), Tgf2 (AFC96942), Herves (AAS21248), Tam3 (CAA38906), Ac (CAA29005), nDart1 (BAI39457), TCUP (ABC59221.1), Hobo (A39652), Homer (AAD03082), Hermes (AAB60236), TcBuster (ABF20545), AeBuster1 (ABF20543), Tag1 (AAC25101), Restless (CAA93759), Tol1 (BAF64515), Crypt1 (AF283502), BuT2 (AF368884), and IpTip100 (BAA36225). (B) Relative location of the conserved regions identified in Fig. 3A on the Hermes transposase and terminal inverted repeat tetramer ( 6 ). doi:10.1128/microbiolspec.MDNA3-0054-2014.f3a

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3b
FIGURE 3b

Comparison of hAT transposase sequences. (A) Consensus alignment of 22 hAT transposases. The alignment was obtained using the program M-Coffee, which uses multiple sequence alignment programs. The location of each sequence within its transposase is shown by the amino acid numbers. The location of the DDE motif is shown above the alignments, conserved resides are shown below the alignments along with the locations of the domains and the six conserved blocks originally identified by Rubin et al. ( 12 ). Amino acids identified as being critical for Hermes transposase activity and/or DNA binding from the Hermes transpososome cocrystal by Hickman et al. ( 6 ) are shown in red as are identical amino acids present in the same locations in the other transposases. The C and H amino acids proposed to constitute the BED domain are shown in blue. Accession numbers are: Tol2 (BAA87039), Tgf2 (AFC96942), Herves (AAS21248), Tam3 (CAA38906), Ac (CAA29005), nDart1 (BAI39457), TCUP (ABC59221.1), Hobo (A39652), Homer (AAD03082), Hermes (AAB60236), TcBuster (ABF20545), AeBuster1 (ABF20543), Tag1 (AAC25101), Restless (CAA93759), Tol1 (BAF64515), Crypt1 (AF283502), BuT2 (AF368884), and IpTip100 (BAA36225). (B) Relative location of the conserved regions identified in Fig. 3A on the Hermes transposase and terminal inverted repeat tetramer ( 6 ). doi:10.1128/microbiolspec.MDNA3-0054-2014.f3b

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4a
FIGURE 4a

The organization of subterminal direct repeats in 17 active transposon from the and families and five transposons from the family. The relative positions of these repeats in the 300 bp at each end of the transposon is shown together with the sequences of these repeats that are located under the name of each transposon. Asterisks denote where biochemical studies using purified transposase have confirmed binding to these repeats. The orientation of the repeats on the top or bottom strand of the transposon is depicted by the position of the filled circle above or below the transposon ends. In some cases, the direct repeats overlap with the terminal inverted repeats. doi:10.1128/microbiolspec.MDNA3-0054-2014.f4a

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4b
FIGURE 4b

The organization of subterminal direct repeats in 17 active transposon from the and families and five transposons from the family. The relative positions of these repeats in the 300 bp at each end of the transposon is shown together with the sequences of these repeats that are located under the name of each transposon. Asterisks denote where biochemical studies using purified transposase have confirmed binding to these repeats. The orientation of the repeats on the top or bottom strand of the transposon is depicted by the position of the filled circle above or below the transposon ends. In some cases, the direct repeats overlap with the terminal inverted repeats. doi:10.1128/microbiolspec.MDNA3-0054-2014.f4b

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Alignment of the left terminal inverted repeats (TIRs) of the 17 active transposons from the and families and the five from the family. (A) Alignment showing the conservation of A2 and G5 amongst these transposons with a lower degree of conservation of C11 when the TIRs exceed 10 bp in length. (B) The weblogo generated from the first 8 bp of each of the TIRs in (A) with the amino acids that interact with these in the Hermes transpoase shown below ( 6 ). These are grouped according to their location in the DNA binding domain (DNA), the first catalytic domain (CAT 1), the insertion domain (INS), or the second catalytic domain (CAT 2) of the transposase. *Denotes that the interaction with the TIR is with the main chain of the amino acid. Amino acids in red interact with the nontransferred strand, those in black with the transferred strand. The nontransferred strand is shown in the weblogo. doi:10.1128/microbiolspec.MDNA3-0054-2014.f5

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6a
FIGURE 6a

Amino acid sequence comparison of domesticated hAT transposases. (A) Consensus alignment of 11 domesticated genes derived from hAT transposases and the Hermes transposase. The location of each sequence within its transposase is shown by the amino acid numbers. The location of conserved resides are shown below the alignments along with the locations of the domains. Amino acids identified as being critical for Hermes transposase activity and/or DNA binding from the Hermes transpososome cocrystal by Hickman et al. ( 6 ) are shown in red as are identical amino acids present in the same locations in the other proteins. The C and H amino acids proposed to constitute the BED domain are shown in blue. Accession numbers are: ZBED1 (AAH15030), ZBED4 (NP_055653), ZBED5 (Q49AG3), ZBED6 (NP_001167579), DAYSLEEPER (Q9M2N5), KIAA0543_ZnF862 (060290), P52rIPK (O43422), DREF (BAA24727), GON-14a (CCD71205), GTF21RD2 (AAP14955), and b-Gary (CAJ32531). (B) Conserved key amino acids in domesticated genes derived from hAT transposases and the Hermes transposase. The amino acids are listed along the top of the table. Underneath is a diagram showing the domain they reside in. Black boxes indicate that the amino acid is present in this location in the domesticated gene. Gray boxes denote an amino acid is present that is chemically similar to the amino acid listed at the top of the table and this is shown in the box. Empty boxes indicate no conservation. The number of these amino acids missing from each protein is listed in the final column. The number missing at each location is listed in the final row. doi:10.1128/microbiolspec.MDNA3-0054-2014.f6a

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6b
FIGURE 6b

Amino acid sequence comparison of domesticated hAT transposases. (A) Consensus alignment of 11 domesticated genes derived from hAT transposases and the Hermes transposase. The location of each sequence within its transposase is shown by the amino acid numbers. The location of conserved resides are shown below the alignments along with the locations of the domains. Amino acids identified as being critical for Hermes transposase activity and/or DNA binding from the Hermes transpososome cocrystal by Hickman et al. ( 6 ) are shown in red as are identical amino acids present in the same locations in the other proteins. The C and H amino acids proposed to constitute the BED domain are shown in blue. Accession numbers are: ZBED1 (AAH15030), ZBED4 (NP_055653), ZBED5 (Q49AG3), ZBED6 (NP_001167579), DAYSLEEPER (Q9M2N5), KIAA0543_ZnF862 (060290), P52rIPK (O43422), DREF (BAA24727), GON-14a (CCD71205), GTF21RD2 (AAP14955), and b-Gary (CAJ32531). (B) Conserved key amino acids in domesticated genes derived from hAT transposases and the Hermes transposase. The amino acids are listed along the top of the table. Underneath is a diagram showing the domain they reside in. Black boxes indicate that the amino acid is present in this location in the domesticated gene. Gray boxes denote an amino acid is present that is chemically similar to the amino acid listed at the top of the table and this is shown in the box. Empty boxes indicate no conservation. The number of these amino acids missing from each protein is listed in the final column. The number missing at each location is listed in the final row. doi:10.1128/microbiolspec.MDNA3-0054-2014.f6b

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0054-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

Supplemental Material

No supplementary material available for this content.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error