- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Reviewers Acknowledgment
- Submit a Manuscript
- Subscription Information
- Table of Contents
International Journal of Plant Genomics
Volume 2012 (2012), Article ID 874743, 17 pages
doi:10.1155/2012/874743
Evolutionary History of LTR Retrotransposon Chromodomains in Plants
1Laboratory of Molecular Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
2Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
3Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
4Department of Biological Sciences, University at Albany, Life Sciences Building 2061, 1400 Washington Avenue, Albany, NY 12222, USA
Received 15 September 2011; Revised 27 January 2012; Accepted 12 February 2012
Academic Editor: Jim Leebens-Mack
Copyright © 2012 Anton Novikov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Linked References
- R. Paro and D. S. Hogness, “The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila,” Proceedings of the National Academy of Sciences of the United States of America, vol. 88, no. 1, pp. 263–267, 1991. View at Publisher · View at Google Scholar · View at Scopus
- E. V. Koonin, S. Zhou, and J. C. Lucchesi, “The chromo superfamily: new members, duplication of the chrome domain and possible role in delivering transcription regulators to chromatin,” Nucleic Acids Research, vol. 23, no. 21, pp. 4229–4233, 1995. View at Scopus
- A. Brehm, K. R. Tufteland, R. Aasland, and P. B. Becker, “The many colours of chromodomains,” BioEssays, vol. 26, no. 2, pp. 133–140, 2004. View at Publisher · View at Google Scholar · View at Scopus
- F. Aasland and A. F. Stewart, “The chrome shadow domain, a second chrome domain in heterochromatin-binding protein 1, HP1,” Nucleic Acids Research, vol. 23, no. 16, pp. 3168–3173, 1995. View at Scopus
- L. J. Ball, N. V. Murzina, R. W. Broadhurst et al., “Structure of the chromatin binding (chromo) domain from mouse modifier protein 1,” EMBO Journal, vol. 16, no. 9, pp. 2473–2481, 1997. View at Publisher · View at Google Scholar · View at Scopus
- S. A. Jacobs, S. D. Taverna, Y. Zhang et al., “Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3,” EMBO Journal, vol. 20, no. 18, pp. 5232–5241, 2001. View at Publisher · View at Google Scholar · View at Scopus
- S. A. Jacobs and S. Khorasanizadeh, “Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail,” Science, vol. 295, no. 5562, pp. 2080–2083, 2002. View at Publisher · View at Google Scholar · View at Scopus
- S. V. Brasher, B. O. Smith, R. H. Fogh et al., “The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer,” EMBO Journal, vol. 19, no. 7, pp. 1587–1597, 2000. View at Scopus
- A. J. Bannister, P. Zegerman, J. F. Partridge et al., “Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain,” Nature, vol. 410, no. 6824, pp. 120–124, 2001. View at Publisher · View at Google Scholar · View at Scopus
- M. Lachner, D. O'Carroll, S. Rea, K. Mechtler, and T. Jenuwein, “Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins,” Nature, vol. 410, no. 6824, pp. 116–120, 2001. View at Publisher · View at Google Scholar · View at Scopus
- J. Nakayama, J. C. Rice, B. D. Strahl, C. D. Allis, and S. I. S. Grewal, “Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly,” Science, vol. 292, no. 5514, pp. 110–113, 2001. View at Publisher · View at Google Scholar · View at Scopus
- H. S. Malik and T. H. Eickbush, “Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons,” Journal of Virology, vol. 73, no. 6, pp. 5186–5190, 1999. View at Scopus
- B. Gorinšek, F. Gubenšek, and D. Kordiš, “Evolutionary genomics of chromoviruses in eukaryotes,” Molecular Biology and Evolution, vol. 21, no. 5, pp. 781–798, 2004. View at Publisher · View at Google Scholar
- I. Marín and C. Lloréns, “Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data,” Molecular Biology and Evolution, vol. 17, no. 7, pp. 1040–1049, 2000. View at Scopus
- X. Gao, Y. Hou, H. Ebina, H. L. Levin, and D. F. Voytas, “Chromodomains direct integration of retrotransposons to heterochromatin,” Genome Research, vol. 18, no. 3, pp. 359–369, 2008. View at Publisher · View at Google Scholar · View at Scopus
- O. Novikova, V. Mayorov, G. Smyshlyaev et al., “Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta),” Plant Journal, vol. 56, no. 4, pp. 562–574, 2008. View at Publisher · View at Google Scholar · View at Scopus
- O. Novikova, “Chromodomains and LTR retrotransposons in plants,” Communitative and Integrative Biology, vol. 2, no. 2, pp. 158–162, 2009. View at Scopus
- O. Novikova, G. Smyshlyaev, and A. Blinov, “Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants,” BMC Genomics, vol. 11, no. 1, article 231, 2010. View at Publisher · View at Google Scholar · View at Scopus
- H. Nakayashiki, T. Awa, Y. Tosa, and S. Mayama, “The C-terminal chromodomain-like module in the integrase domain is crucial for high transposition efficiency of the retrotransposon MAGGY,” FEBS Letters, vol. 579, no. 2, pp. 488–492, 2005. View at Publisher · View at Google Scholar · View at Scopus
- A. Hizi and H. L. Levin, “The integrase of the long terminal repeat-retrotransposon Tf1 has a chromodomain that modulates integrase activities,” Journal of Biological Chemistry, vol. 280, no. 47, pp. 39086–39094, 2005. View at Publisher · View at Google Scholar · View at Scopus
- T. Wicker, F. Sabot, A. Hua-Van et al., “A unified classification system for eukaryotic transposable elements,” Nature Reviews Genetics, vol. 8, no. 12, pp. 973–982, 2007. View at Publisher · View at Google Scholar · View at Scopus
- P. Sanmiguel and J. L. Bennetzen, “Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons,” Annals of Botany, vol. 82, pp. 37–44, 1998. View at Publisher · View at Google Scholar · View at Scopus
- W. N. Stewart and G. W. Rothwell, Paleobotany and the Evolution of Plants, Cambridge University Press, New York, NY, USA, 1993.
- M. Parniske, B. B. H. Wulff, G. Bonnema, C. M. Thomas, D. A. Jones, and J. D. G. Jones, “Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1,” Molecular Plant-Microbe Interactions, vol. 12, no. 2, pp. 93–102, 1999. View at Scopus
- K. J. Dej, T. Gerasimova, V. G. Corces, and J. D. Boeke, “A hotspot for the Drosophila gypsy retroelement in the ovo locus,” Nucleic Acids Research, vol. 26, no. 17, pp. 4019–4024, 1998. View at Scopus
- H. M. Temin, “Origin of retroviruses from cellular moveable genetic elements,” Cell, vol. 21, no. 3, pp. 599–600, 1980. View at Scopus
- D. Kuykendall, J. Shao, and K. Trimmer, “A nest of LTR retrotransposons adjacent the disease resistance-priming gene NPR1 in Beta vulgaris L. U.S. Hybrid H20,” International Journal of Plant Genomics, vol. 2009, Article ID 576742, 2009. View at Publisher · View at Google Scholar · View at Scopus
- B. Piegu, R. Guyot, N. Picault et al., “Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice,” Genome Research, vol. 16, no. 10, pp. 1262–1269, 2006. View at Publisher · View at Google Scholar · View at Scopus
- G. Caetano-Anollés, “Evolution of genome size in the grasses,” Crop Science, vol. 45, no. 5, pp. 1809–1816, 2005. View at Publisher · View at Google Scholar · View at Scopus
- C. Vitte and O. Panaud, “LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model,” Cytogenetic and Genome Research, vol. 110, no. 1-4, pp. 91–107, 2005. View at Publisher · View at Google Scholar · View at Scopus
- K. Tajul-Arifin, R. Teasdale, T. Ravasi et al., “Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome,” Genome Research, vol. 13, no. 6 B, pp. 1416–1429, 2003. View at Publisher · View at Google Scholar · View at Scopus
- P. R. Nielsen, D. Nietlispach, H. R. Mott et al., “Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9,” Nature, vol. 416, no. 6876, pp. 103–107, 2002. View at Publisher · View at Google Scholar · View at Scopus
- J. F. Flanagan, L. Z. Mi, M. Chruszcz et al., “Double chromodomains cooperate to recognize the methylated histone H3 tail,” Nature, vol. 438, no. 7071, pp. 1181–1185, 2005. View at Publisher · View at Google Scholar · View at Scopus
- Y. Xiong and T. H. Eickbush, “Origin and evolution of retroelements based upon their reverse transcriptase sequences,” EMBO Journal, vol. 9, no. 10, pp. 3353–3362, 1990. View at Scopus
- S. Boissinot and A. V. Furano, “Adaptive evolution in LINE-1 retrotransposons,” Molecular Biology and Evolution, vol. 18, no. 12, pp. 2186–2194, 2001. View at Scopus
- R. S. Baucom, J. C. Estill, C. Chaparro et al., “Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome,” PLoS Genetics, vol. 5, no. 11, Article ID e1000732, 2009. View at Publisher · View at Google Scholar · View at Scopus
- S. J. Wood, “Prolines and amyloidogenicity in fragments of the alzheimer's peptide β/A4,” Biochemistry, vol. 34, no. 3, pp. 724–730, 1995.
- P. Y. Chou and G. D. Fasman, “β-Turns in proteins,” Journal of Molecular Biology, vol. 115, no. 2, pp. 135–175, 1977. View at Scopus
- A. Roy, A. Kucukural, and Y. Zhang, “I-TASSER: a unified platform for automated protein structure and function prediction,” Nature protocols, vol. 5, no. 4, pp. 725–738, 2010. View at Scopus
- J. L. Bowman, S. K. Floyd, and K. Sakakibara, “Green genes-comparative genomics of the green branch of life,” Cell, vol. 129, no. 2, pp. 229–234, 2007. View at Publisher · View at Google Scholar · View at Scopus
- M. L. Berbee and J. W. Taylor, “Fungal molecular evolution: gene trees and geologic time,” in The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research, D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, Eds., vol. 7 of Systematics and Evolution, part B, pp. 229–246, Springer, New York, NY, USA, 2001.
- S. B. Hedges, “The origin and evolution of model organisms,” Nature Reviews Genetics, vol. 3, no. 11, pp. 838–849, 2002. View at Publisher · View at Google Scholar · View at Scopus
- H. S. Malik, “Ribonuclease H evolution in retrotransposable elements,” Cytogenetic and Genome Research, vol. 110, no. 1-4, pp. 392–401, 2005. View at Publisher · View at Google Scholar · View at Scopus
- H. S. Malik and T. H. Eickbush, “Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons,” Journal of Virology, vol. 73, no. 6, pp. 5186–5190, 1999. View at Scopus
- C. Llorens, M. A. Fares, and A. Moya, “Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis,” BMC Evolutionary Biology, vol. 8, no. 1, article 276, 2008. View at Publisher · View at Google Scholar · View at Scopus
- P. Dimitri and N. Junakovic, “Revising the selfish DNA hypothesis: new evidence on accumulation of transposable elements in heterochromatin,” Trends in Genetics, vol. 15, no. 4, pp. 123–124, 1999. View at Publisher · View at Google Scholar · View at Scopus
- J. Fuchs, G. Jovtchev, and I. Schubert, “The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms,” Chromosome Research, vol. 16, no. 6, pp. 891–898, 2008. View at Publisher · View at Google Scholar · View at Scopus
- T. Yamada, W. Fischle, T. Sugiyama, C. D. Allis, and S. I. S. Grewal, “The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast,” Molecular Cell, vol. 20, no. 2, pp. 173–185, 2005. View at Publisher · View at Google Scholar · View at Scopus
- A. H. F. M. Peters, S. Kubicek, K. Mechtler et al., “Partitioning and plasticity of repressive histone methylation states in mammalian chromatin,” Molecular Cell, vol. 12, no. 6, pp. 1577–1589, 2003. View at Publisher · View at Google Scholar · View at Scopus
- J. C. Rice, S. D. Briggs, B. Ueberheide et al., “Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains,” Molecular Cell, vol. 12, no. 6, pp. 1591–1598, 2003. View at Publisher · View at Google Scholar · View at Scopus
- C. Liu, F. Lu, X. Cui, and X. Cao, “Histone methylation in higher plants,” Annual Review of Plant Biology, vol. 61, pp. 395–420, 2010. View at Publisher · View at Google Scholar · View at Scopus
- A. M. Lindroth, D. Shultis, Z. Jasencakova et al., “Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMENTHYLASE3,” EMBO Journal, vol. 23, no. 21, pp. 4286–4296, 2004. View at Publisher · View at Google Scholar · View at Scopus
- J. Fuchs, D. Demidov, A. Houben, and I. Schubert, “Chromosomal histone modification patterns—from conservation to diversity,” Trends in Plant Science, vol. 11, no. 4, pp. 199–208, 2006. View at Publisher · View at Google Scholar · View at Scopus
- J. Shi and R. K. Dawe, “Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27,” Genetics, vol. 173, no. 3, pp. 1571–1583, 2006. View at Publisher · View at Google Scholar · View at Scopus
- M. Carchilan, M. Delgado, T. Ribeiro et al., “Transcriptionally active heterochromatin in rye B chromosomes,” Plant Cell, vol. 19, no. 6, pp. 1738–1749, 2007. View at Publisher · View at Google Scholar · View at Scopus
- S. Marschner, K. Kumke, and A. Houben, “B chromosomes of B. dichromosomatica show a reduced level of euchromatic histone H3 methylation marks,” Chromosome Research, vol. 15, no. 2, pp. 215–222, 2007. View at Publisher · View at Google Scholar · View at Scopus
- J. Fuchs and I. Schubert, “Chromosomal distribution and functional interpretation of epigenetic histone marks in plants,” in Plant Cytogenetics, Vol. 1: Genome Structure and Chromosome Function, H. Bass and J. A. Birchler, Eds., Springer, New York, NY, USA, 2011.
- M. K. Dhar, J. Fuchs, and A. Houben, “Distribution of Eu- and heterochromatin in plantagoovata,” Cytogenetic and Genome Research, vol. 125, no. 3, pp. 235–240, 2009. View at Publisher · View at Google Scholar · View at Scopus
- S. Spiker, “An evolutionary comparison of plant histones,” Biochimica et Biophysica Acta, vol. 400, no. 2, pp. 461–467, 1975. View at Scopus
- Z. Yang and J. R. Bielawski, “Statistical methods for detecting molecular adaptation,” Trends in Ecology and Evolution, vol. 15, no. 12, pp. 496–503, 2000. View at Publisher · View at Google Scholar · View at Scopus
- C. F. Qi, F. Bonhomme, A. Buckler-White et al., “Molecular phylogeny of Fv1,” Mammalian Genome, vol. 9, no. 12, pp. 1049–1055, 1998. View at Publisher · View at Google Scholar · View at Scopus
- H. S. Malik and S. Henikoff, “Positive selection of iris, a retroviral envelope-derived host gene in Drosophila melonogaster,” PLoS Genetics, vol. 1, no. 4, pp. 0429–0443, 2005. View at Publisher · View at Google Scholar · View at Scopus
- D. Vermaak, S. Henikoff, and H. S. Malik, “Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila,” PLoS Genetics, vol. 1, no. 1, pp. 0096–0108, 2005. View at Publisher · View at Google Scholar · View at Scopus
- C. Biémont, “Are transposable elements simply silenced or are they under house arrest?” Trends in Genetics, vol. 25, no. 8, pp. 333–334, 2009. View at Publisher · View at Google Scholar · View at Scopus
- J. A. Banks, T. Nishiyama, M. Hasebe et al., “The Selaginella genome identifies genetic changes associated with the evolution of vascular plants,” Science, vol. 332, no. 6032, pp. 960–963, 2011. View at Publisher · View at Google Scholar
- J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Scopus
- S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, “New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0,” Systematic Biology, vol. 59, no. 3, pp. 307–321, 2010. View at Publisher · View at Google Scholar · View at Scopus
- K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar
- M. Anisimova and O. Gascuel, “Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative,” Systematic Biology, vol. 55, no. 4, pp. 539–552, 2006. View at Publisher · View at Google Scholar · View at Scopus
- S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003. View at Publisher · View at Google Scholar · View at Scopus
- R. Wernersson and A. G. Pedersen, “RevTrans: multiple alignment of coding DNA from aligned amino acid sequences,” Nucleic Acids Research, vol. 31, no. 13, pp. 3537–3539, 2003. View at Publisher · View at Google Scholar · View at Scopus
- Z. Yang, “Maximum-likelihood models for combined analyses of multiple sequence data,” Journal of Molecular Evolution, vol. 42, no. 5, pp. 587–596, 1996. View at Publisher · View at Google Scholar · View at Scopus
- Z. Yang, “PAML: a program package for phylogenetic analysis by maximum likelihood,” Computer Applications in the Biosciences, vol. 13, no. 5, pp. 555–556, 1997. View at Scopus
- Z. Yang, “PAML 4: phylogenetic analysis by maximum likelihood,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1586–1591, 2007. View at Publisher · View at Google Scholar · View at Scopus
- J. Zhang, R. Nielsen, and Z. Yang, “Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level,” Molecular Biology and Evolution, vol. 22, no. 12, pp. 2472–2479, 2005. View at Publisher · View at Google Scholar · View at Scopus
- Z. Yang, W. S. W. Wong, and R. Nielsen, “Bayes empirical Bayes inference of amino acid sites under positive selection,” Molecular Biology and Evolution, vol. 22, no. 4, pp. 1107–1118, 2005. View at Publisher · View at Google Scholar · View at Scopus
- J. P. Bielawski and Z. Yang, “A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution,” Journal of Molecular Evolution, vol. 59, no. 1, pp. 121–132, 2004. View at Scopus
- Z. Yang and R. Nielsent, “Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages,” Molecular Biology and Evolution, vol. 19, no. 6, pp. 908–917, 2002. View at Scopus
- M. Anisimova and Z. Yang, “Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites,” Molecular Biology and Evolution, vol. 24, no. 5, pp. 1219–1228, 2007. View at Publisher · View at Google Scholar · View at Scopus