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Keywords :Arabidopsis thaliana - Soluble phenolic compounds -Lignin -Mutant - Secondary cell wall - Biotic and abiotic stresses - Xylans

Doctoral school affiliation : ED145 "Sciences du Végétal" Université Paris-Sud

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
Richard Sibout

Research Scientist

Philippe Le Bris
Technician INRA

Yin Wang
PhD Student
from 01/09/11 to 31/08/14

Aline Voxeur
Ingénieur de recherche (projet ANR NoStressWall)
from 1/8/13 to 31/3/15

Lise Jouanin
Senior scientist CNRS

Sébastien Antelme
Technician INRA " Brachypodium "

Marie Séverine Ho Yue Kuang
PhD Student
départments BV and CEPIA
from 01/10 to 30/09/14


Objectives :

Plant biomass is mainly made up of polymers that constitute the skeleton of plant tissues. In most cases, these polymers are energy-rich linked sugars that form the major structural components in plant cell walls, particularly in the thick secondary cell walls which characterize certain tissues. In addition to polysaccharides other major cell wall polymers – lignins - limit access to cell wall sugars and negatively affects human utilization of biomass (livestock feed, paper manufacturing and lignocellulosic biofuel production). Lignin biosynthesis, transport and deposition are highly controlled in space (at the tissue level) and time because these molecules have mechanical and physical properties important for vessels integrity (figure 1), hardness of secondary tissues in dicots (figure 2) and pathogen resistance. Because of their significant economic impact and central role in higher plant development, lignins are one of the most intensively studied subjects in plant biochemistry. The team secondary cell wall (PARSE) has a long history in deciphering the lignin pathway in Arabidopsis. Our activity focused on important steps of lignin biosynthesis as well as interaction of this polymer with cell wall polysaccharides. In the context of the need of renewable energy and raw material for industry, the team developped genetic resources for Brachypodium, a new model system for biofuel genomics.
Figure 1: Vascular bundle in Brachypodium
(Photo: JC Palauqui)


Scientific questions:
1-How lignin is synthesized and deposited in the plant cell of dicots and grasses?
Despite the biosynthetic pathway of monolignol is now well described in dicots, it is not completely known in grasses. Moreover, issues still remained to be answered (storage, transport into apoplasm, polymerisation, subcompartimentation, regulation).
2-How genetic modification of the lignin pathway may impact biomass quality and saccharification efficiency ?
Lignin remains a barrier for several human utilisation of the biomass. Depending of the strategy, genetic modifications of lignification may dramatically impact biomass production and quality.
  Macintosh HD:Users:richard:Desktop:cells fiber.pdf
    Figure 2: Schematic representation of secondary tissues in dicots


figure 3.tif  
Arabidopsis thaliana (type I cell wall ) and Brachypodium distachyon (type II cell wall) are the two main plant models in our lab. We work with T-DNA and chemically induced mutants. To answer the scientific questions cited above we focus our research activities on the three following axis:
1/ Deciphering biological funtions of gene paralogs involved in monolignol biosynthesis because these genes belong to multigenic families in most cases.
2/ Biochemical characterisation of laccases and peroxidases activities (figure 3).
3/ Determination of “trans” factors impacting cell wall deposition in different tissues of stems.
  Figure 3 : Peroxidases and laccases allow polymerization of monolignols by oxidation.    


Main Results :

The team isolated or participated to the study of several mutants affected in the monolignol biosynthetic pathway both in Arabidopsis and Brachypodium (for instance for the cinnamyl alcohol dehydrogenase, CAD et caffeoyl acid O-methyl transferase,  COMT genes). Protein deficiency often results in modification of lignin content and quality but also in changes in soluble phenolic compounds, plant development or resistance to pathogenes. One of the most recent results is the demonstration of the role of laccases in lignin polymerisation in planta and that overexpression of small RNAs targeting laccases may impact lignin content. We also recently identified glycosyl hydrolases responsible for monolignol aglycone content in Arabisopsis.

Last, we produced a collection of natural accessions and a chemically-induced mutant collection (figure 4) which allow the identification of mutations in genes of interest with the help of the TILLING platform at URGV ( We also select plants with modified biomass content to isolate new alleles. Outcome of these works are possible thanks to the technical platforms at IJPB and to many collaborations specially with APSYNTH and BCR teams.


    Figure 4: Phenotypes observed in the Brachypodium mutant collection


Selected Publications :

Dobrovolskaya, O., Pont, C., Sibout, R., Martinek, P., Badaeva, E., Murat, F., Chosson, A., Watanabe, N., Prat, E., Gautier, N., Gautier, V., Poncet, C., Orlov, Y., Krasnikov, A., Berges, H.Salina, E., Laikova, L. and Salse, J. (2014) FRIZZY PANICLE drives supernumerary spikelets in bread wheat (T. aestivum L.). Plant Physiol. Nov 14. pii: pp.114.250043 (PubMed)

Voxeur, A., Wang, Y. and Sibout, R. (2014) Lignification: different mechanisms for a versatile polymer. Curr Opin Plant Biol, 23C, 83-90 (PubMed)

Girin, T., David, L.C., Chardin, C., Sibout, R., Krapp, A., Ferrario-Mery, S. and Daniel-Vedele, F. (2014) Brachypodium: a promising hub between model species and cereals. J Exp Bot, 65:, 5683-5696 (PubMed)

Marriott, P.E., Sibout, R., Lapierre, C., Fangel, J.U., Willats, W.G., Hofte, H., Gomez, L.D. and McQueen-Mason, S.J. (2014) Range of cell-wall alterations enhance saccharification in Brachypodium distachyon mutants. Proc Natl Acad Sci USA: 111, 14601-14606 (abstract)

Timpano, H., Sibout, R., Devaux, M.-F., Alvarado, C., Looten, R., Falourd, X., Pontoire, B., Martin, M., Legée, F., Cézard, L., Lapierre, C., Badel, E., Citerne, S., Vernhettes, S., Höfte, H., Guillon, F. and Gonneau, M. (2014) Brachypodium Cell Wall Mutant with Enhanced Saccharification Potential Despite Increased Lignin Content. BioEnergy Research: 1-15 (pdf)

Catalan, P., Chalhoub, B., Chochois, V., Garvin, D.F., Hasterok, R., Manzaneda, A.J., Mur, L.A., Pecchioni, N., Rasmussen, S.K., Vogel, J.P., and Voxeur, A. (2014). Update on the genomics and basic biology of Brachypodium: International Brachypodium Initiative (IBI). Trends in plant science 19: 414-8 (PubMed)

Petrik, D.L., Karlen, S.D., Cass, C.L., Padmakshan, D., Lu, F., Liu, S., Le Bris, P., Antelme, S., Santoro, N., Wilkerson, C.G., Sibout, R., Lapierre, C., Ralph, J., and Sedbrook, J.C. (2014). p-Coumaroyl-CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway in Brachypodium distachyon. Plant J 77, 713-726 (pubMed)

Dalmais M, Antelme S, Ho-Yue-Kuang S, Wang Y, Darracq O, Bouvier d’Yvoire M, Cézard L, Légée F, Blondet E, Oria N, Troadec C, Brunaud V, Jouanin L, Höfte H, Bendahmane A, Lapierre C, Sibout R(2013). A TILLING Platform for Functional Genomics in Brachypodium distachyon. Plos One. 8: e65503.

Wang Y, Chantreau M, Sibout R,Hawkins S (2013). Plant cell wall lignification and monolignol metabolism. Front Plant Sci. 4 : 220.

Sibout, R., and Hofte, H. (2012). Plant cell biology: the ABC of monolignol transport. Curr Biol 22, R533-535.

Berthet, S., Thévenin, J., Baratiny, D., Demont-Caulet, N., Debeaujon, I., Bidzinski, P., Leplé, J.C., Huis, R., Hawkins, S., Gomez, L.D., Lapierre, C., Jouanin, L. (2012) Role of plant laccases in lignin polymerization. In Lignins, biosynthesis, biodegradation and bioengineering. In Advances in Botanical Research 61, Jouanin L and Lapierre C, eds (Elsevier Ltd), pp 145-172.

Bouvier d'Yvoire, M., Bouchabke-Coussa, O., Voorend, W., Antelme, S., Cezard, L., Legee, F., Lebris, P., Legay, S., Whitehead, C., McQueen-Mason, S.J., Gomez, L.D., Jouanin, L., Lapierre, C., and Sibout, R. (2012). Disrupting the cinnamyl alcohol dehydrogenase 1 gene (BdCAD1) leads to altered lignification and improved saccharification in Brachypodium distachyon. Plant J. DOI: 10.1111/tpj.12053

Chapelle, A., Morreel, K., Vanholme, R., Le-Bris, P., Morin, H., Lapierre, C., Boerjan, W., Jouanin, L., and Demont-Caulet, N. (2012). Impact of the Absence of Stem-Specific beta-Glucosidases on Lignin and Monolignols. Plant physiology 160, 1204-1217.

Chavigneau, H., Delaunay, S., Goué, N., Coutial, A., Jouanin, L., Reymond, M., Méchin, V., Barrière, Y. (2012) QTL for floral stem lignin and degradability in three recombinant imbred line (RIL) progenies of Arabidopsis thaliana and search foe candidate genes in cell wall biosynthesis and degradability. Open J of Genetics 2: 7-30.   

Denancé, N., Ranocha, P., Oria, N., Barlet, X., Rivière, M.-P., Yadeta, K.-A., Hoffmann, L., Perreau, F., Clément, .G, Maia-Grondard, A., van der Berg G.C.M., Savetti, B., Fournier, S., Aubert, Y., Pelletier, S., Thomma, B., Molina, A., Jouanin, L., Marco, Y., Goffner, D. (2012) Arabidopsis wat1 (wall are thin-1)-mediated resistance to the bacterial vascular pathogen, Ralstonia solanacearum, is accompagnied by cross-regulation of salicylic and tryptophan metabolism. Plant J, DOI: 10.1111/tpj.12027

Harrington, M.J., Mutwil, M., Barrière, Y., and Sibout, R. (2012). Chapter 3 - Molecular Biology of Lignification in Grasses. In Advances in Botanical Research, Jouanin  and Lapierre, eds (Academic Press), pp. 77-112.

Berthet, S., Demont-Caulet, N., Pollet, B., Bidzinski, P., Cezard, L., Le Bris, P., Borrega, N., Herve, J., Blondet, E., Balzergue, S., Lapierre, C., and Jouanin, L. (2011b). Disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of Arabidopsis thaliana stems. The Plant Cell 23, 1124-1137.

Berthet, S., Demont-Caulet, N., Le-Bris, P., Hervé, J., Cézard, L., Pollet, B., Jouanin, L., Lapierre, C. (2011) Lignin-specific laccases, new targets for the engineering of lignification. Proceedings of the 16th ISWFPC, June 8-10. Tianjin, China. Beijing, China: China Light Industry Press: 1096-1101.

Thévenin, J., Pollet, B., Letarnec, B., Saulnier, L., Gissot, L., Maia-Grondard, A., Lapierre, C., and Jouanin, L. (2011). The simultaneous repression of CCR and CAD, two enzymes of the lignin biosynthetic pathway, results in sterility and dwarfism in Arabidopsis thaliana. Molecular Plant 4, 70-82.

Lebrun, J.D., Demont-Caulet, N., Cheviron, N., Laval, K., Trinsoutrot-Gattin, I., and Mougin, C. (2011). Secretion profiles of fungi as potential tools for metal ecotoxicity assessment: a study of enzymatic system in Trametes versicolor. Chemosphere 82, 340-345.

Rkljacic et al. (2011). Brachypodium as a model for the grasses: Today and the future. Plant Physiol 157: 3

Demont-Caulet, N., Lapierre, C., Jouanin, L., Baumberger, S., and Mechin, V. (2010). Arabidopsis peroxidase-catalyzed copolymerization of coniferyl and sinapyl alcohols: kinetics of an endwise process. Phytochemistry 71, 1673-1683.

Lu, F., Marita, J.M., Lapierre, C., Jouanin, L., Morreel, K., Boerjan, W., Ralph, J. (2010) Sequencing around 5-hydroxyconiferyl alcohol-derived units in caffeic acid O-methyl transferase-deficient poplar lignins. Plant Physiol 153 : 569-579.

Sanchez-Rodriguez C, Rubio-Somoza I, Sibout R, Persson S (2010) Phytohormones and the cell wall in Arabidopsis during seedling growth. . Trends Plant Sci. 2010 May;15(5):291-301.

I nternational Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010 Feb 11;463(7282):763-8.

Quentin M, Allasia V, Pegard A, Allais F, Ducrot P-H, Favery B, Levis C, Martinet S, Masur C, Ponchet M, Roby D, Schlaich N, Jouanin L, Keller H (2009) Imbalanced lignin biosynthesis promotes the sexual reproduction of homothallic oomycete pathogens. PloS Pathogens 5 : 1-9. (PubMed)

Minic Z, Jamet E, San-Clemente H, Peleltier S, Renou J-P, Rihouey C, Okinyo D, Proux C, Lerouge P, Jouanin L (2009) Transcriptomic analysis of Arabidopsis developing stems : a close-up on cell wall genes. BMC Plant Biology, Jan 16;9(1):6.(PubMed)

Ralph J, Kim H, Lu F, Grabber J, Leplé JC, Berrio-Sierra J,(Meyers et al., 2008) Mir Derikvand M, Jouanin L, Boerjan W, Lapierre C (2008) Identification and origin of a thioacidolysis marker compound for ferulic acid incorporation into angiosperm lignins (and a pseudo-marker compound for cinnamoyol-CoA reductase deficiency). Plant J 53 : 368-379. (PubMed)

Mir Derikvand M, Berrio-Sierra J, Ruel K, Pollet B, Do C-T, Thévenin J, Buffard D, Jouanin L, Lapierre C (2008) Redirection of the phenylpropanoid pathway to feroloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase. Planta 227 : 943-956.(PubMed)

Chavez Montes RA, Ranocha P, Martinez Y, Minic Z, Jouanin L, Marquis M, Saulnier L, Fulton LM, Cobbett CS, Bitton F, Renu JP, Jauneau A, goffner D (2008) Cell wall modifications in Arabidopsis plants with alterned alpha-L- arabinofuranosidae activity. Plant Physiol 147 : 63-77. (PubMed)

Eudes A, Mouille G, Thevenin J, Minic Z, Jouanin L (2008) Purification, cloning and functional characterization of an endogenous beta-glucosidase in Arabidopsis thaliana. Plant Cell Physiol 49 : 1331-1341. (PubMed)

Quentin M, Allasia V, Pegard A, Allais F, Ducrot P-H, Favery B, Levis C, Martinet S, Masur C, Ponchet M, Roby D, Schlaich N, Jouanin L, Keller H (2009) Imbalanced lignin biosynthesis promotes the sexual reproduction of homothallic oomycete pathogens. PloS Pathogens 5 : 1-9. (PubMed)

Minic Z, Jamet E, San-Clemente H, Peleltier S, Renou J-P, Rihouey C, Okinyo D, Proux C, Lerouge P, Jouanin L (2009) Transcriptomic analysis of Arabidopsis developing stems : a close-up on cell wall genes. BMC Plant Biology, Jan 16;9(1):6.(PubMed)

Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., and Zhu, J.K. (2008). Criteria for Annotation of Plant MicroRNAs. Plant Cell.2008 Dec;20(12):3186-90..(PubMed)

Do C-T, Pollet B, Thévenin J, Sibout R, Denoue D, Barrière Y, Lapierre C, Jouanin L.(2007) Both caffeoyl CoA enzyme 3-O-methyltransferase and caffeic acid O-methyltransferase I are involved in redundant functions for lignins, flavonoids and sinapoyl malate biosynthesis in Arabidopsis. Planta, 226, 1117-29 (PubMed)

Minic Z, Jamet E, Négroni L, der Garabedian, Zivy M, Jouanin L (2006) A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases.. J Exp Bot 58 : 2503-2512. (PubMed)

Eudes A, Pollet B, Sibout R, Do C-T, Séguin A, Lapierre C, Jouanin L (2006) Evidence for a role of AtCAD1 in lignification of elongating stems of Arabidopsis thaliana. Planta 225, 23-39. (PubMed)

Minic Z, Jouanin L (2006) Plant glycoside hydrolases in cell wall polysaccharide degradation. Plant Physiol Biochem 44, 435-449. (PubMed)

Minic Z, Do C-T, Rihouey C, Morin H, Lerouge P, Jouanin L (2006) Purification, functional characterization, cloning, and identification of mutants of a seed specific arabinan hydrolase in Arabidopsis. J Exp Bot 57, 2339-2351. (PubMed)

Barrière Y, Denoue D, Briand M, Simon M, Jouanin L, Durand-Tardif M (2006) Genetic variations of cell wall digestibility related traits in floral stems of Arabidopsis thaliana accessions as a basis for the improvement of the feeding value in maize and forage plants. Theor Appl Genet 113, 163-175. (PubMed)

Pineau C, Freydier A, Ranocha P, Jauneau A, Turner S, Lemonnier G, Renou J-P, Tarkowski P, Sandberg G, Jouanin L, Sundberg B, Boudet A-M, Goffner D, Pichon M (2005) hca, an Arabidopsis mutant exhibiting unusual cambial activity and altered vascular patterning. Plant J. 44, 271-289 (PubMed)

Barrière Y, Laperche A, Barrot L, Aurel G, Briand M, Jouanin L (2005) QTL analysis of lignification and cell wall digestibility in the Bay0 x Shahdara RIL progeny of Arabidopsis thaliana as a model system for forage plant. Plant Sci 168: 1235-1245.

Sibout R, Eudes A, Mouille G, Pollet B, Lapierre C, Jouanin L, Séguin A (2005). Cinnamyl alcohol dehydrogense C and D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17: 2059-2076. (PubMed)

Minic Z, Rihouey C, Do CT, Lerouge P, Jouanin L (2004) Purification and characterization of enzymes exhibiting beta-D-xylosidase activities in stem tissues of Arabidopsis thaliana. Plant Physiol. 135: 867-78 (PubMed)

Lapierre C, Pilate G, Pollet B, Mila I, Leplé J-C, Jouanin L, Kim H, Ralph J (2004) Signatures of cinnamyl alcohol dehydrogenases deficiency in poplar lignins. Phytochemistry 65 : 313-321. (PubMed)

Goujon T, Sibout R, Pollet B, Maba B, Nussaume L, Bechtold N, Lu F, Ralph J, Mila I, Barrière Y, Lapierre C, Jouanin, L (2003) A new Arabidopsis thaliana mutant deficient in the expression of O-methyltransferase 1: Impact on lignins and on sinapoyl esters. Plant Mol Biol 51 : 973-989. (PubMed)

Goujon T, Minic Z, El Amrani A, Lerouxel O, Aletti E, Lapiere C, Joseleau J-P, Jouanin L (2003) A novel higher plant (Arabidopsis thaliana) beta-xylosidase gene, is involved in secondary cell wall metabolism and plant development. Plant J 33 : 677-690. (PubMed)

Goujon T, Ferret V, Mila I, Pollet B, Ruel K, Burlat V, Joseleau J-P, Barrière Y, Lapierre C, Jouanin L (2003) Down-regulation of AtCCR1 gene in Arabidopsis thaliana : effects on phenotype, lignins and cell degradability. Planta 217 : 218-228. (PubMed)

Sibout R, Eudes A, Pollet B, Goujon T, Mila I, Granier F, Séguin A, Lapierre C, Jouanin L (2003) Expression pattern of two paralogues encoding cinnamyl alcohol dehydrogenase in Arabidopsis thaliana: Isolation and characterization of the corresponding mutants. Plant Physiol 132 : 848-860. (PubMed)

Goujon T, Sibout R, Eudes A, Jouanin L (2003) Genes involved in the biosynthesis of lignin precursors in Arabidopsis thaliana. Plant Physiol Biochem 41: 677-687.

Pilate G, Guiney E, Petit-Conil M, Lapierre C, Leplé J-C, Pollet B, Mila I, Halpin C, Jouanin L, Boerjan W, Schuch W, Cornu D (2002) Field performance of transgenic trees with altered lignin metabolism. Nature Biotech 20, 607-612. (PubMed)

Ruel K, Montiel MD, Goujon T, Jouanin L, Burlat V, Joseleau JP (2002) Interaction between lignin deposition and polysaccharide matrices during the assembly of the plant cell wall. Plant Biol 51, 2-8.

Sibout R, Baucher M, Gatineau M, Van Doorsselaere J, Mila I, Pollet B, Maba B, Pilate G, Lapierre C, Boerjan W, Jouanin L (2002) Expression of a poplar cDNA encoding a ferulate-5-hydroxylase increases S lignin deposition in Arabidopsis thaliana. Plant Physiol Biochem, 40, 1087-1096

Ralph J, Lapierre C, Marita J, Kim H, Fachuang L, Hatfield R, Ralph S, Chapple C, Franke R, Hemm M, Mackay J, Yahiaoui N, Boudet A, Pean M, Pilate G, Boerjan W, Jouanin L (2001) Elucidation of new structures in lignins of CAD- and COMT-deficient plants by NMR. PhytoChemistry 57, 99-1003. (PubMed)

Jouanin L, Goujon T, de Nadaï V, Martin MT, Mila I, Vallet C, Pollet B, Yoshinaga A, Chabbert B,Petit-Conil M, Lapierre C (2000) Lignification in transgenic poplars with extremely reduced caffeic acid O-methyltransferase. Plant Physiol 123 : 1363-1374. (PubMed)


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