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Host-Retrotransposon Interactions
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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

Quynh Trang BUI
Research Scientist

 


Summary :


Retrotransposons are mobile genetic elements that amplify in the genome by an RNA intermediate. They represent the major component of plant genomes. 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 evolutionary impact. Our historical model is the tobacco Tnt1 retrotransposon (Figure 1) but our studies have extended to other elements. In the last years, our major research topics have included retrotransposon involment in genome changes generated by allopolyploidy in the genus Nicotiana. We also study the functional impact of the retrotransposon stress response, through the formation of cotranscripts that may modulate gene expression.


Main Results :


Tnt1 expression is induced by stress (Figure 2). This regulation correlates with the presence of several motifs in the retrotransposon U3 promoter region that are also found to regulate plant defense genes. In addition, Tnt1 elements evolve by modulating these regulatory sequences, reflecting the acquisition of new regulations. We developped insertion polymorphisms analysis (SSAP or Sequence Specific Amplified Polymorphism, Figure 5) to study the transpositional activation of Tnt1 and other elements (Figure 3). 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 is activated in synthetic tobacco hybrids. These results suggest that the retrotransposon content of a plant species is influenced by the host evolutionary history, with periods of rapid turnovers influenced by allopolyploidy events. Our current research projects have extended these studies to various other allotetraploid species of the genus Nicotiana.
In addition, we are studying the functional impact of retrotransposons on tobacco gene expression. We have shown that the LTRs of several retrotransposons can drive the production, in stress conditions, of chimeric cotranscripts with adjacent genes. By modulating the expression of these genes, retrotransposons could play a role in the global host response to various stimuli.


Selected Publications :


Galindo-González L, Mhiri C, Deyholos MK, Grandbastien M-A (2017) LTR-retrotransposons in plants: engines of evolution. Gene 626: 14-25 

Vives C, Charlot F, Mhiri C, Contreras B, Daniel J, Epert A, Voytas DF, Grandbastien M-A, Nogué F, Casacuberta JM (2016). Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon. New Phytol 212:759-769

Galindo-González L, Mhiri C, Grandbastien M-A, Deyholos MK (2016). Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. BMC Genomics 17:1002

McCarthy EW, Arnold SEJ, Chittka L, Le Comber SC, Verity R, Dodsworth S, Knapp S, Kelly LJ, Chase MW, Baldwin IT, Kovarik A, Mhiri C, Taylor L, Leitch AR (2015) The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae). Ann Bot 115: 1117–1131

Anca IA, Fromentin J, Bui QT, Mhiri C, Grandbastien M-A, Simon-Plas F (2014) Different tobacco retrotransposons are specifically modulated by the elicitor cryptogein and reactive oxygen species. J Plant Physiol 171: 1533–1540

Renny-Byfield S, Kovarik A, Kelly L, Macas J, Novak P, Chase M, Nichols RA, Pancholi M, Grandbastien M-A, Leitch A (2013) Diploidisation and genome size change in allopolyploids is associated with differential dynamics of low and high copy sequences. Plant J 74: 829-839

Matyasek R, Renny-Byfield S, Fulnecek J, Macas J, Grandbastien M-A, Nichols R, Leitch A, Kovarik A (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13: 722

Parisod C, Mhiri C, Lim KY, Clarkson JJ, Chase MW, Leitch AR, Grandbastien M-A (2012) Differential dynamics of transposable elements during long-term diploidization of Nicotiana section Repandae (Solanaceae) allopolyploid genomes. PLoS ONE 7: e50352

Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D, Grandbastien M-A, Charcosset A, Tenaillon MI (2012) Maize genetic diversity and association mapping using transposable element insertion polymorphisms. Theor Appl Genet 124: 1521-1537

Renny-Byfield S, Chester M, Kovařík A, Le Comber SC, Grandbastien M-A, Deloger M, Nichols R, Macas J, Novák P, Chase MW, Leitch AR (2011). Next generation sequencing reveals genome downsizing in allopolyploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Mol Biol Evol 28: 2843-2854

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

Tam SM, Lefèbvre V, Palloix A, Sage-Palloix A-M, Mhiri C, 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

Zerjal T, Joets J, Alix A, Grandbastien M-A, Tenaillon MI (2009) Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Mol Biol 71: 99-114

Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, Grandbastien M-A, Bowler C (2009) Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 10: 624

Ainouche ML, Fortune PM, Salmon, Parisod C, Grandbastien, M-A, Fukunaga K, Ricou M, 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, 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

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

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

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

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

Tam SM, Causse M, Garchery C, Burck H, Mhiri C, 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

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

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, 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

Pourtau N, Lauga B, Audéon C, Grandbastien M-A, Goulas P, 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 PG, Casacuberta JM, Costa APP, Hashimoto RY, Grandbastien M-A, Van Sluys M-A (2001) Retrolyc1 subfamilies defined by different U3 regulatory regions in the Lycopersicon genus. Mol Genet Genomics 266:35-41

Beguiristain T, Grandbastien M-A, Puigdomenech P, Casacuberta JM (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

Leprince AS, Grandbastien M-A, 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

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

Costa APP, Scortecci KC, Hashimoto RY, Araujo PG, Grandbastien M-A, Van Sluys M-A (1999) Retrolyc1-1, a member of the Tnt1 retrotransposon super-family in the Lycopersicon peruvianum genome. Genetica 107: 65-72

Mhiri C, De Wit PGJM, Grandbastien M-A (1999) Activation of the promoter of the Tnt1 retrotransposon in tomato after inoculation with the fungal pathogen Cladosporium fulvum. Mol Plant-Microbe Interact 12: 592-603

Vernhettes S, Grandbastien M-A, Casacuberta JM (1998) The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high plasticity of its regulatory sequences. Mol Biol Evol 15: 827-836

Vernhettes S, Grandbastien M-A, Casacuberta JM (1997) In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Mol Biol 35: 673-679

Mhiri C, Morel J-B, Vernhettes S, Casacuberta JM, Lucas H, Grandbastien M-A (1997) The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress. Plant Mol Biol 33: 257-266

Grappin P, Audéon C, Chupeau M-C, Grandbastien M-A (1996) Molecular and functional characterization of Slide, an Ac-like autonomous transposable element from tobacco. Mol Gen Genet 252: 386-397

Moreau-Mhiri C, Morel J-B, Audéon C, Ferault M, Grandbastien M-A, Lucas H (1996) Regulation of the tobacco Tnt1 retrotransposon in heterologous species following pathogen-related stress. Plant J 9: 409-419

Casacuberta JM, Vernhettes S, Grandbastien M-A (1995) Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J 14: 2670-2678

Lucas H, Feuerbach F, Kunert K, Grandbastien M-A, Caboche M (1995) RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J 14: 2364-2373

Pouteau S, Grandbastien M-A, Boccara M (1994) Microbial elicitors of plant defense responses activate transcription of a retrotransposon. Plant J 5: 535-542

Pauls PK, Kunert K, Huttner E, Grandbastien M-A (1994) Expression of the tobacco Tnt1 retrotransposon promoter in heterologous species. Plant Mol Biol 26: 393-402

Casacuberta JM, Grandbastien M-A (1993) Characterisation of LTR sequences involved in the protoplast specific expression of the tobacco Tnt1 retrotransposon. Nucleic Acids Res 21: 2087-2093

Pouteau S, Spielmann A, Meyer C, Grandbastien M-A, Caboche M (1991) Effects of Tnt1 tobacco retrotransposon insertion on target gene transcription. Mol Gen Genet 228: 233-239

Pouteau S, Huttner E, Grandbastien M-A, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10: 1911-1918

Grandbastien M-A, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated via plant cell genetics. Nature 337: 376-380

Grandbastien M-A, Missonier C, Goujaud J, Bourgin J-P, Deshayes A, Caboche M (1989) Cellular genetic study of a somatic instability in a tobacco mutant: in vitro isolation of valine-resistant spontaneous mutants. Theor Appl Genet 77: 482-488

Grandbastien M-A, Berry-Lowe S, Shirley BW, Meagher RB (1986) Two soybean ribulose-1,5-biphosphate carboxylase small subunit genes share extensive homology even in distant flanking sequences. Plant Mol Biol 7, 451-465

Grandbastien M-A, Bourgin J-P, Caboche M (1985) Valine-resistance, a potential marker in plant cell genetics. II. Optimization of UV mutagenesis and selection of valine-resistant colonies derived from tobacco mesophyll protoplasts. Genetics 109: 409-425

Marion-Poll A, Missonier C, Grandbastien M-A, Caboche M (1984) Growth inhibition of tobacco protoplast-deievd cells by methothrexate: relationships with nitrate assimilation. Plant Sci Letters 36: 169-176

 

Reviews, book chapters and edited books

Grandbastien M-A (2015) LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochim Biophys Acta, 1849:403-416

Parisod C, Salmon A, Ainouche M, Grandbastien M-A
(2014) Detecting epigenetic effects of transposable elements in plants. Methods Mol Biol. 1112, 211-217

Azman AS, Mhiri C, Grandbastien M-A and Tam, SM
(2014) Transposable elements and the detection of somaclonal variation in plant tissue culture: a review. Malays Appl Biol 43, 1-12

Grandbastien M-A, Casacuberta JM (2012) Editors, Plant Transposable Elements: Impact on Genome Structure and Function. Topics in Current Genetics, Springer, Vol 24, 330 pp

Bui QT, Grandbastien M-A (2012) LTR retrotransposons as Controlling Elements of genome response to stress?. In M-A Grandbastien & JM Casacuberta, eds, Plant Transposable Elements: Impact on Genome Structure and Function, Topics in Current Genetics, Springer, 24: 273-296

Kovarik A, Renny-Byfield S, Grandbastien M-A, Leitch AR (2012) Evolutionary implication of genome and karyotype restructuring hybrid in Nicotiana tabacum L. In PS Soltis, DE Soltis, eds, Polyploidy and genome evolution, Springer-Verlag Berlin Heildeberg, pp 209-224

Grandbastien M-A (2010) Plant transposable elements and plasticity of host genomes: the stress connection. In I Kovalchuk, O Kovalchuk, eds, Genome Instability and Transgenerational Effects, Nova Science Publishers Inc., pp  343-376

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

Grandbastien M-A (2008) Retrotransposons of plants, In BWJ Mahy and MHV Van Regenmortel, eds, Encyclopedia of Virology, Third Edition, 5 vols, Elsevier, Oxford (UK), pp 428-436

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

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

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

M-A Grandbastien (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3: 181-187

Grandbastien M-A, Lucas H, Mhiri C, Morel J-B, Vernhettes S, Casacuberta JM (1997) The expression of the tobacco Tnt1 retrotransposon is linked to the plant defense response. Genetica 100: 241-252

Casacuberta JM, Vernhettes S, Audéon C, Grandbastien M-A (1997) Quasispecies in retrotransposons : a role for sequence variability in Tnt1 evolution. Genetica 100: 109-117

Grandbastien M-A, Audeon C, Casacuberta JM, Grappin P, Lucas H, Moreau C, Pouteau S (1994) Functional analysis of the tobacco retrotransposon. Genetica 93: 181-189

Grandbastien M-A (1992) Retroelements in higher plants. Trends Genet 8: 103-108

 

  

 


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