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Transposon-Host Interactions and Plant Biodiversity

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Keywords :Transposable elements - Retrotransposons - Biodiversity - Stress - Allopolyploidy - Nicotiana tabacum - Solanaceae

Doctoral school affiliation :

Contacts :

Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

tél : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19

	Group leader Marie-Angèle Grandbastien Senior Scientist INRA
	Julien Daniel Technician
	Howard Laten Professor (Loyola University, Chicago, USA) from 13/01/12 to 31/08/12

	Corinne Mhiri Engineer INRA Transposable elements and allopolyploidy
	Quynh Trang Bui Post-doc 1/03/2009 ->31/05/2012

Summary :

Retrotransposons are mobile genetic entities that amplify in the genome by an RNA intermediate (Figure 1). They account for almost 42% of the human genome and for more than 80% of some plant genomes, and thus are the largest component of the genetic material of most eukaryotes. Their biological role is largely unknown. Their activity, although controlled by the plant and the element itself, can have a major impact on the host genome, as they can induce either structural alterations or regulate neighbouring gene expression. Our research activities focus on the impact of TEs on host genomes, from the control of their activity, in particular in response to stress, up to their molecular evolution and their functional and evolutive impact. Our historical model is the tobacco Tnt1 retrotransposon (Figure 2) but our studies have extended to other elements and other Solanaceous species (tomato, pepper). In the last four years, our major research topics have included TE involment in genome changes generated by allopolyploidy and projects aimed at using TE insertion polymorphisms to evaluate the genetic diversity of Solanaeae. We also recently developped projects on TE impact on gene expression.

Main Results :

Tnt1 expression is induced by stress (Figure 3). This regulation correlates with the presence of several motifs in the retrotransposon U3 promoter region that are also found to regulate plant defense genes (Figure 2). In addition, in several Solanaceae species, Tnt1 elements evolve by modulating these regulatory sequences (Figure 4), possibly reflecting evolutionary adaptation to their host or to its environmental history. More recently, we developped insertion polymorphisms analysis (SSAP or Sequence Specific Amplified Polymorphisms, Figure 5) to study the transpositional activation of Tnt1 and other elements (Figure 5). We showed that factors of microbial origin are able to activate Tnt1 transposition. We also showed that the tobacco allotetraploid genome results from a turnover of retrotransposon sequences, in likely correlation with the species formation, and that Tnt1 transposition was activated in synthetic tobacco hybrids. These results suugest that the retrotransposon content of a plant species is influenced by the host evolutionary history, with periods of rapid turnovers influenced by allopolyploidy events. We have also shown that retrotransposon insertion polymorphisms are useful to evaluate genetic diversity and interspecific relationships in germplasm collectons of tomato, pepper and related species.
Our current research projects focus on the mechanisms involved in the activation of retrotransposons during allopolyploidy and on the evolutionary consequences of these phenomenons in allotetraploid sections of variable ages in the genus Nicotiana. In addition, we are studying the influence of transposable elements on the modulation of tomato and tobacco gene expression, and in particular the impact of chimaeric transcripts between transposable elements and cellular genes.

Selected Publications :

Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186: 135–147.

Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien M-A (2010). Impact of transposable elements in organization and functioning of allopolyploid genomes. New Phytol 186: 37–45

Tam SM, Lefèbvre V, Palloix A, Sage-Palloix A-M, Mhiri C and Grandbastien M-A (2009). LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor Appl Genet 119: 973-989

Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien M-A, Ainouche ML (2009). Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184: 1003-1015.

Grandbastien M.-A. (2008) Retrotransposons of plants, "Encyclopedia of Virology, Third Edition, 5 vols", Eds B.W.J. Mahy and M.H.V. Van Regenmortel, Elsevier, Oxford (UK) pp428-436

Ainouche ML, Fortune PM, Salmon, Parisod C, Grandbastien, M-A, Fukunaga K, Ricou M and Misset M-T (2009). Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae). Biol. Invasions 11: 1159-1173.

Manetti M-E, Rossi M, Nakabashi M, Grandbastien M-A and Van Sluys M-A (2009). The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species. Mol. Genet. Genomics 281: 261-271 (PubMed)

Grandbastien M-A (2008) Retrotransposons of plants, In "Encyclopedia of Virology, Third Edition, 5 vols", Editors B.W.J. Mahy and M.H.V. Van Regenmortel, Elsevier, Oxford (UK), pp 428-436

Le QH, Melayah D, Bonnivard E, Petit M and Grandbastien M-A (2007). Distribution dynamics of the Tnt1 retrotransposon in tobacco. Mol Gen Genet 278, 639-651 (PubMed)

Lim KY, Kovarik A, Matyasek R, Chase MW, Clarkson JJ, Grandbastien M-A, Leitch AR (2007) Near complete genome turnover in five million years of plant evolution. New Phytol 175, 756–763 (PubMed)

Petit M, Lim KY, Julio E, Poncet C, Dorlhac De Borne F, Kovarik A, Leitch AR, Grandbastien M-A and Mhiri C (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Gen Genet 278, 1-15 (PubMed)

Dadejová M, Lim YK, Soucková-Skalická K, Matyásek R, Grandbastien M-A, Leitch AR and Kovarík A (2007) Transcription activity of rRNA genes correlates with their tendency towards intergenomic homogenisation in Nicotiana allotetraploids. New Phytol 174, 658-668 (PubMed)

Tam SM, Causse M, Garchery C, Burck H, Mhiri C and Grandbastien M-A (2007) The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species. J Evolution Biol 20,1056-1072 (PubMed)

Tam SM, Mhiri C and Grandbastien M-A (2006) Transposable elements and the analysis of plant biodiversity. In "Functional Plant Genomics", JF Morot-Gaudry, P Lea and JF Briat Eds, Sciences Publishers, Enfield, NH, USA, chapter 26, pp 529-558

Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce S, Grandbastien M-A (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110, 819–831 (PubMed)

Grandbastien M-A, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa A-PP, Le QH, Melayah D, Petit M, Poncet C, Tam S-M, Van Sluys M-A, Mhiri C (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 110, 229-241 (PubMed)

Melayah D, Lim KY, Bonnivard E, Chalhoub B, Dorlhac de Borne F, Mhiri C, Leitch AR, Grandbastien M-A (2004) Distribution of the Tnt1 retrotransposon family in the amphidiploid tobacco and its wild Nicotiana relatives. Biol J Linn Soc 82, 639-649

Pourtau N, Lauga B, Grandbastien M-A, Goulas P and Salvado J-C (2004) The promoter of the Tnt1A retrotransposon: a biomarker to monitor ozone but not formaldehyde and benzene pollution. Water Air Soil Poll 159, 115-124

Mhiri C, Grandbastien M.-A. (2004) Eléments transposables et analyse de la biodiversité végétale. Dans "La génomique en biologie végétale", Editeurs JF Morot-Gaudry et JF Briat, INRA Editions, pp 377-402

Pourtau N, Lauga B, Audéon C, Grandbastien M-A, Goulas P and Salvado J-C (2003) The promoter of the Tnt1A retrotransposon is activated by ozone air pollution in tomato, but not in its natural host tobacco. Plant Sci 165, 983-992

Araujo P.G., Casacuberta J.M., Costa A.P.P., Hashimoto R.Y., Grandbastien M.-A. and Van Sluys M.-A. (2001). Retrolyc1 subfamilies defined by different U3 regulatory regions in the Lycopersicon genus. Mol. Gen. Genom. 266:35-41 (PubMed)

Beguiristain T., Grandbastien M.-A., Puigdomenech P. and Casacuberta P. (2001). Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol. 127: 212-221 (PubMed)

Leprince A.S., Grandbastien M.-A. and Meyer C. (2001). Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion. Plant Mol. Biol. 47: 533-541 (PubMed)

Melayah D., Bonnivard E., Chalhoub B., Audéon C. and Grandbastien M.-A. (2001). The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant J. 28: 159-168 (PubMed)

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