Skip to main content
SpringerLink
Log in
Book cover

Transposable Elements and Genome Evolution pp 15–25Cite as

Is the evolution of transposable elements modular?

  • Chapter

Part of the book series: Georgia Genetics Review 1 ((GEGR,volume 1))

Abstract

The evolution of transposable element structures can be analyzed in populations and species and by comparing the functional domains in the main classes of elements. We begin with a synthesis of what we know about the evolution of the mariner elements in the Drosophilidae family in terms of populations and species. We suggest that internal deletion does not occur at random, but appears to frequently occur between short internal repeats. We compared the functional domains of the DNA and/or amino acid sequences to detect similarities between the main classes of elements. This included the gag, reverse transcriptase, and envelope genes of retrotransposons and retroviruses, and the integrases of retrotransposons and retroviruses, and transposases of class II elements. We find that each domain can have its own evolutionary history. Thus, the evolution of transposable elements can be seen to be modular.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Altschul, S.F., T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller & D.J. Lipman, 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  • Auge-Gouillou, C., Y. Bigot, N. Pollet, M.H. Hamelin, M. Meunier-Rotival & G. Periquet, 1995. Human and other mammalian genomes contain transposons of the mariner family. FEBS Lett. 368: 541–546.

    Article  PubMed  CAS  Google Scholar 

  • Bailey, T.L. & C. Elkan, 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers, pp. 28–36 in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, California.

    Google Scholar 

  • Bigot, Y., C. Augé-Gouillou & G. Periquet, 1996. Computer analyses reveal a hobo-like element in the nematode Caenorhabditis elegans, which presents a conserved transposase domain common with the Tc1-mariner transposon family. Gene 174: 265–271.

    Article  PubMed  CAS  Google Scholar 

  • Black, D.M., M.S. Jackson, M.G. Kidwell & G.A. Dover, 1987. KP elements repress hybrid dysgenesis in Drosophila melanogaster. EMBOJ. 6:4125.

    PubMed  CAS  Google Scholar 

  • Brunet, F., F. Godin, C. Bazin & P. Capy, 1999. Phylogenetic analysis of Mos1-like transposable elements in the Drosophilidae. J. Mol. Evol. 49: 760–768.

    Article  PubMed  CAS  Google Scholar 

  • Brunet, F., F. Godin, C. Bazin, J.R. David & P. Capy, 1996. The mariner transposable element in natural populations of Drosophila teissieri. J. Mol. Evol. 42: 669–675.

    Article  PubMed  CAS  Google Scholar 

  • Calvi, B.R., T.J. Hong, S.D. Findley & W.M. Gelbart, 1991. Evidence for a common evolutionary origin of inverted repeat transposons in Drosophila and plants: hobo, Activator, and Tam3. Cell 66: 465–471.

    Article  PubMed  CAS  Google Scholar 

  • Capy, P., C. Bazin, D. Higuet & T. Langin, 1997a. Dynamic and Evolution of Transposable Elements. R.G. Landes Company, Austin, Texas, USA.

    Google Scholar 

  • Capy, P., C. Bazin, D. Higuet & T. Langin, 1997b. Evolution and Impact of Transposable Elements. Kluwer Academic Publishers, Dordrecht.

    Google Scholar 

  • Capy, P., T. Langin, Y. Bigot, F. Brunet, M.J. Daboussi, G. Periquet, J.R. David & D.L. Hartl, 1994. Horizontal transmission versus ancient origin: mariner in the witness box. Genetica 93: 161–170.

    Article  PubMed  CAS  Google Scholar 

  • Capy, P., T. Langin, D. Higuet, P. Maurer & C. Bazin, 1997c. Does the integrase of LTR-retrotransposons and most of the trans-posases of class II elements share a common ancestor? Genetica 100: 63–72.

    Article  PubMed  CAS  Google Scholar 

  • Capy, P., R. Vitalis, T. Langin, D. Higuet & C. Bazin, 1996. Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? J. Mol. Evol. 42: 359–369.

    Article  PubMed  CAS  Google Scholar 

  • Chaboissier, M.C., A. Bucheton & D.J. Finnegan, 1998. Copy number control of a transposable element, the I factor, a LINE-like element in Drosophila. Proc. Natl. Acad. Sci. USA 95: 11781–11785.

    Article  PubMed  CAS  Google Scholar 

  • Covey, S.N., 1986. Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus. Nucleic Acids Res. 14: 623–633.

    Article  PubMed  CAS  Google Scholar 

  • Craven, R.C., A.E.L.-d. Pree, R.A.W. JR & J.W. Wills, 1995. Genetic analysis of the Major Homology Region for the Rous Sarcoma Virus gag protein. J. Virol. 69: 4213–4227.

    PubMed  CAS  Google Scholar 

  • Dayhoff, M.O., R.M. Schwartz & B.C. Orcutt, 1978. A model of evolutionary change in proteins, pp. 345–352 in Atlas of Protein Sequence and Structure, edited by M. O. Dayhoff. Natl. Biomed. Res. Found., Washington, DC.

    Google Scholar 

  • Doak, T.G., F.P. Doerder, C.L. Jahn & G. Herrick, 1994. A proposed superfamily of transposase-related genes: new members in transposon-like elements of cilliated protozoa and a common ‘D35E’ motif. Proc. Natl. Acad. Sci. USA 91: 942–946.

    Article  PubMed  CAS  Google Scholar 

  • Doolittle, W.F. & C. Sapienza, 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603.

    Article  PubMed  CAS  Google Scholar 

  • Fayet, O., P. Ramond, P. Polard, M.F. Frère & M. Chandler, 1990. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol. Microbiol. 4: 1771–1777.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J., 1993. PHYLIP (Phylogeny Inference Package). Version 3.5.C University of Washington, Seattle.

    Google Scholar 

  • Feng, Q., J.V. Moran, H.J. Kazazian & J.D. Boeke, 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905–916.

    Article  PubMed  CAS  Google Scholar 

  • Finnegan, D.J., 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103–107.

    Article  PubMed  CAS  Google Scholar 

  • Gaboriaud, C., V. Bissery, T. Benchetrit & J.P. Mornon, 1987. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. Febs Lett 224: 149–155.

    Article  PubMed  CAS  Google Scholar 

  • Garcia-Fernàndez, J., G. Marfany, J. Bagunà & E. Salò, 1993. Infiltration of mariner elements. Nature 364: 109–110.

    Article  PubMed  Google Scholar 

  • George, D.G., L.T. Hunt & W.C. Barker, 1988. Current methods in sequence comparison and analysis, pp. 127–149 in Macromolecular Sequencing and Synthesis, edited by D. H. Schlesinger. A.R. Liss, New York.

    Google Scholar 

  • Gilbert, D.G., 1998. SeqPup: a biosequence editor. Version 0.8c. Distributed by the author at seqpup@bio.indiana.edu.

    Google Scholar 

  • Grenier, E., M. Abadon, F. Brunet, P. Capy & P. Abad, 1999. A mariner-like transposable element in the entomopathogenic nematode Heterorhabdis bacteriophora, horizontal trasmission versus ancient origin. J. Mol. Evol. 48: 328–336.

    Article  PubMed  CAS  Google Scholar 

  • Jacobson, J.W., M.M. Medhora & D.L. Haiti, 1986. Molecular structure of a somatically unstable element in Drosophila. Proc. Natl. Acad. Sci. USA 83: 8684–8688.

    Article  PubMed  CAS  Google Scholar 

  • Jarvik, T. & K.G. Lark, 1998. Characterization of Soymarl, a mariner element in soybean. Genetics 149: 1569–1574.

    PubMed  CAS  Google Scholar 

  • Jensen, S., M.P. Gassama & T. Heidmann, 1999. Taming of transposable elements by homology-dependent gene silencing. Nat. Genet. 21:209–212.

    Article  PubMed  CAS  Google Scholar 

  • Jordan, I.K. & J.F. McDonald, 1999a. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome [letter]. Mol. Biol. Evol. 16: 419–422.

    Article  PubMed  CAS  Google Scholar 

  • Jordan, I.K. & J.F. McDonald, 1999b. Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements. Genetica 107: 3–13.

    Article  PubMed  CAS  Google Scholar 

  • Labrador, M. & A. Fontdevila, 1994. High transposition rates of Osvaldo, a new Drosophila buzzatii retrotransposon. Mol. Gen. Genet. 245: 661–674.

    Article  PubMed  CAS  Google Scholar 

  • Laten, H.M., A. Majumdar & E.A. Gaucher, 1998. SIRE-1, a copia/Ty1 retroelement from soybean, encodes a retroviral envelope-like protein. Proc. Natl. Acad. Sci. USA 95: 6897–6902.

    Article  PubMed  CAS  Google Scholar 

  • Lemesle-Varloot, L., B. Henrissat, C. Gaboriaud, V. Bissery, A. Morgat & J.P. Mornon, 1990. Hydrophobie cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72: 555–574.

    Article  PubMed  CAS  Google Scholar 

  • Lerat, E. & P. Capy, 1999. Retrotransposons and retroviruses: analysis of the envelope gene. Mol. Biol. Evol. 16: 1198–1207.

    Article  PubMed  CAS  Google Scholar 

  • Luan, D.D., M.H. Korman, J.L. Jakubczak & T.H. Eickbush, 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal traget site: a mechanism for non-LTR retrotransposition. Cell 72: 595–605.

    Article  PubMed  CAS  Google Scholar 

  • Mammano, F., A. Öhagen, S. Höglund & H. Göttlinger, 1994. Role of the Major Homology Region of Human Immunodeficiency Virus type 1 in virion morphogenesis. J. Virol. 68: 4927–4936.

    PubMed  CAS  Google Scholar 

  • Maruyama, K. & D.L. Hartl, 1991. Evolution of the transposable element mariner in Drosophila species. Genetics 128: 319–329.

    PubMed  CAS  Google Scholar 

  • McClure, M., 1993. Evolutionary history of reverse transcriptase, pp. 425–444 in Reverse transcriptase, edited by M. Skalka, and S. P. Goff. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.

    Google Scholar 

  • McClure, M.A., 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol. Biol. Evol. 8: 835–856.

    PubMed  CAS  Google Scholar 

  • Morgan, G.T., 1995. Identification in the human genome of mobile elements spread by DNA-mediated transposition. J. Mol. Biol. 17: 1–5.

    Article  Google Scholar 

  • Okazaki, S., H. Ishikawa & H. Fujiwara, 1995. Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori. Mol. Cell. Biol. 15: 4545–4552.

    PubMed  CAS  Google Scholar 

  • Oosumi, T., W.R. Belknap & B. Garlick, 1995. Mariner transposons in humans. Nature 378: 672–672.

    Article  PubMed  CAS  Google Scholar 

  • Orgel, L.E. & F.H.C. Crick, 1980. Selfish DNA: the ultimate parasite. Nature 284: 604–607.

    Article  PubMed  CAS  Google Scholar 

  • Pardue, M.-L., O.N. Danilevskaya, K.L. Traverse & K. Lowen-haupt, 1997. Evolutionary links between telomeres and transposable elements. Genetica 100: 73–84.

    Article  PubMed  CAS  Google Scholar 

  • Petrov, D.A., E.R. Lozovskaya & D.L. Hartl, 1996. High intrinsic rate of DNA loss in Drosophila. Nature 384: 346–349.

    Article  PubMed  CAS  Google Scholar 

  • Reiter, L.T., T. Murakami, T. Koeuth, L. Pentao, D.M. Muzny, R.A. Gibbs & J.R. Lupski, 1996. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nature Genet. 12: 288–297.

    Article  PubMed  CAS  Google Scholar 

  • Robertson, H.M., 1997. Multiple mariner transposons in flatworms and hydras are related to those of insects. J. Heredity 88: 195–201.

    Article  CAS  Google Scholar 

  • Robertson, H.M. & E.G. MacLeod, 1993. Five major subfamilies of mariner transposable elements in insects, including the Mediterranean fruit fly, and related arthropods. Insect Mol. Biol. 2: 125–139.

    Article  PubMed  CAS  Google Scholar 

  • Robertson, H.M. & R. Martos, 1997. Molecular evolution of the second ancient human mariner transposon, Hsmar2, illustrates patterns of neutral evolution in the human genome lineage. Gene 205: 219–228.

    Article  PubMed  CAS  Google Scholar 

  • Robertson, H.M. & K.L. Zumpano, 1997. Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome. Gene 205: 203–217.

    Article  PubMed  CAS  Google Scholar 

  • Robertson, H.M., Z.L. Zumpano, A.R. Lohe & D.L. Hartl, 1996. Reconstruction of the ancient mariners of humans. Nature Genet. 12: 360–361.

    Article  PubMed  CAS  Google Scholar 

  • Rubin, E. & A.A. Levy, 1997. Abortive gap repair: underlying mechanism for Ds element formation. Mol. Cell Biol. 17: 6294–6302.

    PubMed  CAS  Google Scholar 

  • Sedensky, M.M., S.J. Hudson, B. Everson & P.G. Morgan, 1994. Identification of a mariner-like, repetitive sequence in C. elegans. Nucleic Acids Res. 22: 1719–1723.

    Article  CAS  Google Scholar 

  • Streck, R.D., J.E. MacGaffey & S.K. Beckendorf, 1986. The structure of hobo transposable elements and their insertion. EMBO J. 5: 3615–3623.

    PubMed  CAS  Google Scholar 

  • Strimmer, K. & A. vonHaeseler, 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13: 964–969.

    Article  CAS  Google Scholar 

  • Swofford, D.L., 1993. Phylogenetic analysis using parsimony. Version 3.1.1. Smithsonian Institution Washington DC.

    Google Scholar 

  • Swofford, D.L., G.J. Olsen, P.J. Waddel & D.M. Hillis, 1996. Phylogenetic inference, pp. 407–514 in Molecular Systematics, edited by D. M. Hillis, Moritz and Mable. Sinauer.

    Google Scholar 

  • Wiley, L.J., L.G. Riley, N.C. Sangster & A.S. Weiss, 1997. mle-1, a mariner-like transposable element in the nematode Trichostrongylus colubriformis. Gene 188: 235–237.

    Article  PubMed  CAS  Google Scholar 

  • Xiong, Y. & T.H. Eickbush, 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353–3362.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratoire Populations, Génétique et Evolution, Centre National de la Recherche Scientifique, 91198, Gif/Yvette Cedex, France

    Emmanuelle Lerat, Frédéric Brunet, Claude Bazin & Pierre Capy

Authors
  1. Emmanuelle Lerat
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Frédéric Brunet
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Claude Bazin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pierre Capy
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

John F. McDonald

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Lerat, E., Brunet, F., Bazin, C., Capy, P. (2000). Is the evolution of transposable elements modular?. In: McDonald, J.F. (eds) Transposable Elements and Genome Evolution. Georgia Genetics Review 1, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4156-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-4156-7_3

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5812-4

  • Online ISBN: 978-94-011-4156-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation