Alain Lecharny
Scientific Career
| 1973 | CNRS, Research Assistant, Phytotron laboratory,Gif-sur-Yvette, France. |
| 1981 | PhD thesis |
| 1982 | Post-Doctoral Research Fellow, Freiburg University i.Br. Germany Grant from the Foundation von Humboldt |
| 1986 | CNRS, Senior Research Scientist, Plant Biotechnology Research Institute, UMR8618, Paris XI University, Orsay, France |
| 1999 | CNRS, Director of Research IBP UMR8618, Paris XI University, Orsay, France  andURGV UMR INRA1165-CNRS8114-UEVE, Evry, France |
| 2010 | URGV UMR INRA1165-UEVE, Evry, France Director of ERL 8196 CNRS “Bioinformatique et Génomique Végétale” |
Publications
Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis.
BMC Evol Biol. 2008 Oct 24;8(1):291. PMID: 18950478
Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, Moreau H, Kreis M, Lecharny A.
Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
Laboratoire de Biologie Cellulaire, Institut J. P. Bourgin, INRA, 78026 Versailles Cedex, France
Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, CNRS–Université Pierre et Marie Curie, BP44, 66651 Banyuls sur Mer Cedex, France
ABSTRACT: BACKGROUND: The Wuschel related homeobox (WOX) family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG) using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. RESULTS: The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. CONCLUSION: Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most likely by preventing premature differentiation. The future use of Ostreococcus tauri and Physcomitrella patens as biological models should allow us to obtain a better insight into the functional importance of WOX13 OG genes.
Unique genes in plants: specificities and conserved features throughout evolution.
BMC Evol Biol. 2008 Oct 10;8:280. PMID: 18847470
Armisén D, Lecharny A, Aubourg S.
URGV , UMR INRA 1165 - CNRS 8114 - Université d'Evry Val d'Essonne, 2 rue Gaston Crémieux, CP 5708, F-91057 Evry Cedex, France. armisen@evry.inra.fr
BACKGROUND: Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and species-specific unique genes. RESULTS: We identified the unique genes within both A. thaliana and O. sativa genomes and classified them according to the number of homologs in the alternative species: none (U{1:0}), one (U{1:1}) or several (U{1:m}). Regardless of the species, all the genes in these groups present some conserved characteristics, such as small average protein size and abnormal intron number. In order to understand the origin and function of unique genes, we further characterized the U{1:1} gene pairs. The possible involvement of sequence convergence in the creation of U{1:1} pairs was discarded due to the frequent conservation of intron positions. Furthermore, an orthology relationship between the two members of each U{1:1} pair was strongly supported by a high conservation in the protein sizes and transcription levels. Within the promoter of the unique conserved genes, we found a number of TATA and TELO boxes that specifically differed from their mean number in the whole genome. Many unique genes have been conserved as unique through evolution from the green alga Ostreococcus lucimarinus to higher plants. Plant unique genes may also have homologs in bacteria and we showed a link between the targeting towards plastids of proteins encoded by plant nuclear unique genes and their homology with a bacterial protein. CONCLUSION: Many of the A. thaliana and O. sativa unique genes are conserved in plants for which the ancestor diverged at least 725 million years ago (MYA). Half of these genes are also present in other eukaryotic and/or prokaryotic species. Thus, our results indicate that (i) a strong negative selection pressure has conserved a number of genes as unique in genomes throughout evolution, (ii) most unique genes are subjected to a low divergence rate, (iii) they have some features observed in housekeeping genes but for most of them there is no functional annotation and (iv) they may have an ancient origin involving a possible gene transfer from ancestral chloroplasts or bacteria to the plant nucleus.
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.
Nucleic Acids Res. 2008 Jan;36(Database issue):D986-90. Epub 2007 Oct 16. PMID: 17940091
Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Sébastien Aubourg, Alain Lecharny, Jean-Pierre Renou, Brunaud V.
URGV - UMR INRA 1165-CNRS 8114-UEVE, Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Versailles, France,
Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, Paris
Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS, Orsay, France.
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150-500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions. All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100. CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.
BMC Genomics. 2007 Nov 2;8(1):401 PMID: 17980019
Sébastien Aubourg, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Alain Lecharny,
Jean-Pierre Renou
ABSTRACT: BACKGROUND: Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models.
RESULTS:
The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS.
CONCLUSIONS:
This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs.
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007 PMID: 17721507
Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain,
Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico,
Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin,
Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier & Patrick Wincker
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Formation of the Arabidopsis pentatricopeptide repeat family
Plant Physiol. 2006 Jul;141(3):825-39. PMID: 16825340
Rivals E, Bruyere C, Toffano-Nioche C, Lecharny A (2006):
Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5506, Université de Montpellier II, 34392 Montpellier cedex 5, France.
In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.
L'organisation des génomes végétaux révélée par leur annotation.
Biofutur, Vol 25/265 - 2006 - pp.33-37
Aubourg S., Delseny M. and Lecharny A. (2006)
Depuis une dizaine d'années, la communauté internationale des génomistes a considérablement investi dans la caractérisation d'une sélection de génomes végétaux modèles. Les connaissances déduites des séquences génomiques servent maintenant de socle à la compréhension de l'organisation et de l'évolution des génomes, à l'obtention de données fonctionnelles et à leur analyse intégrative.
Biofutur,(Subscribers Only)
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6. PMID: 15608279
Aubourg S, Brunaud V, Bruyere C, Cock M, Cooke R, Cottet A, Couloux A, Dehais P, Deleage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C,
Geourjon C, Grienenberger JM, Houlne G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J,
Risler JL, Riviere S, Rombauts S, Rouze P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C,
Tognolli M, Caboche M and Lecharny A (2005)
URGV (INRA/CNRS/UEVE) Evry, France
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
Plant Cell. 2004 Aug;16(8):2089-103. Epub 2004 Jul 21. PMID: 15269332
Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I.
URGV, INRA, CNRS, Université d'Evry Val d'Essone
The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
Un modèle statistique pour l'intégration de l'ADN-T dans le génome d'Arabidopsis thaliana. In « La fluidité des génomes et ses conséquences »
Ed. Commission du Génie Biomoléculaire. (2004)
Lecharny A.
DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes
Plant Biotechnol J. 2004 Sep;2(5):401-15. PMID: 17168887
Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M and Lecharny A (2004)
Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Université de Paris-Sud-ERS/CNRS Orsay, France.
The model genome of Arabidopsis thaliana contains a DEAD-box RNA helicase family (RH) of 58 members, i.e. almost twice as many as in the animal or yeast genomes. Transcript profiling using real-time quantitative polymerase chain reaction (PCR) has been obtained for 20 AtRHs from nine different organs. Two AtRHs exhibited plant-specific profiles associated with photosynthetic and sink organs. The other 18 AtRHs had the same transcript profile, and the levels of transcription of these 'housekeeping'AtRHs were under strict quantitative control over a large range of values. Transcript levels may be very different between the most recently duplicated genes. The master regulatory element in the definition of the transcript level is the simultaneous presence of a TATA-box and an intron in the 5' untranslated region (UTR). There is a positive and highly significant correlation between the size of the 5' UTR intron and the transcription level, as long as a characteristic TATA-box is present. Our work on the housekeeping AtRHs suggests a scenario for the evolution of duplicated genes, leading to both highly and poorly transcribed genes in the same terminal branch of the phylogenetic tree. The general evolutionary drive of the AtRH family, after duplication of a highly transcribed ancestral AtRH, was towards an alteration of the transcriptional activity of the divergent duplicates through successive events of suppression of the TATA-box and/or the 5' UTR intron.
FLAGdb++, a database for the functional analysis of the Arabidopsis genome.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D347-50. PMID: 14681431
Samson F, Brunaud V, Duchene S, De Oliveira Y, Caboche M, Lecharny A and Aubourg S (2004)
URGV, UMR INRA 1165, CNRS 8114, Université d'Evry, Evry, France.
FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. FLAGdb++ displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results. A selected subset of the available information is linked to a locus represented on an easy-to-interpret and memorable graphical display. Data are curated, processed and formatted before their integration into FLAGdb++. FLAGdb++ contains different options for easy back and forth navigation through many loci selected at the start of a session. It includes an original two-component visualization of the data, a genome-wide and a local view, which are permanently linked and display complementary information. Density curves along the chromosomes may be displayed in parallel for suggesting correlations between different structural and functional data. FLAGdb++ is fully accessible here.
Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure.
J Struct Funct Genomics. 2003;3(1-4):111-6. PMID: 12836690
Lecharny A., Boudet N., Gy I., Aubourg S. and Kreis M. (2003)
Institut de Biotechnologie des Plantes, Unité Mixte de Recherche-Centre National de la Recherche Scientifique 8618, Université de Paris-Sud, Bât. 630, F-91405 Orsay Cedex, France. lecharny@ibp.u-psud.fr
Gene duplication is considered to be a source of genetic information for the creation of new functions. The Arabidopsis thaliana genome sequence revealed that a majority of plant genes belong to gene families. Regarding the problem of genes involved in the genesis of novel organs or functions during evolution, the reconstitution of the evolutionary history of gene families is of critical importance. A comparison of the intron/exon gene structure may provide clues for the understanding of the evolutionary mechanisms underlying the genesis of gene families. An extensive study of A. thaliana genome showed that families of duplicated genes may be organized according to the number and/or density of intron and the diversity in gene structure. In this paper, we propose a genomic classification of several A. thaliana gene families based on introns in an evolutionary perspective.
Journal of Structural and Functional Genomics, n°3, p 111-116. - NCBI
T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.
EMBO Rep. 2002 Dec;3(12):1152-7. Epub 2002 Nov 21. PMID: 12446565
Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A.
URGV, UMR en Génomique Végétale, INRA/CNRS/Université Evry-Val d'Essonne, France.
A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2–3 base pairs long, that preferentially includes a G close to the right end of the T-DNA.
Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana.
Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29. PMID: 12207221
Aubourg S, Lecharny A, Bohlmann J.
URGV, INRA, FRE-CNRS, Evry , France.
A family of 40 terpenoid synthase genes ( AtTPS) was discovered by genome sequence analysis in Arabidopsis thaliana. This is the largest and most diverse group of TPS genes currently known for any species. AtTPS genes cluster into five phylogenetic subfamilies of the plant TPS superfamily. Surprisingly, thirty AtTPS closely resemble, in all aspects of gene architecture, sequence relatedness and phylogenetic placement, the genes for plant monoterpene synthases, sesquiterpene synthases or diterpene synthases of secondary metabolism. Rapid evolution of these AtTPS resulted from repeated gene duplication and sequence divergence with minor changes in gene architecture. In contrast, only two AtTPS genes have known functions in basic (primary) metabolism, namely gibberellin biosynthesis. This striking difference in rates of gene diversification in primary and secondary metabolism is relevant for an understanding of the evolution of terpenoid natural product diversity. Eight AtTPS genes are interrupted and are likely to be inactive pseudogenes. The localization of AtTPS genes on all five chromosomes reflects the dynamics of the Arabidopsis genome; however, several AtTPS genes are clustered and organized in tandem repeats. Furthermore, some AtTPS genes are localized with prenyltransferase genes ( AtGGPPS, geranylgeranyl diphosphate synthase) in contiguous genomic clusters encoding consecutive steps in terpenoid biosynthesis. The clustered organization may have implications for TPS gene evolution and the evolution of pathway segments for the synthesis of terpenoid natural products. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.
Nucleic Acids Res. 2002 Jan 1;30(1):94-7. PMID: 11752264
Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A.
URGV, INRA, FRE CNRS, 2, rue Gaston Crémieux, F-91000 Evry, France.
A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented database, FLAGdb/FST (http://genoplante-info.infobiogen.fr). The main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested. FSTs are anchored to the genome sequences of A.thaliana and positions of both predicted genes and FSTs are shown graphically on sequences. Requests to locate the genomic position of a query sequence are made using BLAST programs. The response delivered by FLAGdb/FST is a graphical representation of the putative FSTs and of predicted genes in a 20 kb region.
Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis and Drosophila.
Genome Res. 2001 Dec;11(12):2101-14. PMID: 11731501
Boudet N., Aubourg S., Toffano-Nioche C., Kreis M. and Lecharny A. (2001)
Institut de Biotechnologie des Plantes, Unité Mixte de Recherche-Centre National Recherche Scientifique 8618, Université de Paris-Sud, Bât. 630, F-91405 Orsay Cedex, France.
The DEAD box RNA helicase (RH) proteins are homologs involved in diverse cellular functions in all of the organisms from prokaryotes to eukaryotes. Nevertheless, there is a lack of conservation in the splicing pattern in the 53 Arabidopsis thaliana (AtRHs), the 32 Caenorhabditis elegans (CeRHs) and the 29 Drosophila melanogaster (DmRHs) genes. Of the 153 different observed intron positions, 4 are conserved between AtRHs, CeRHs, and DmRHs, and one position is also found in RHs from yeast and human. Of the 27 different AtRH structures with introns, 20 have at least one predicted ancient intron in the regions coding for the catalytic domain. In all of the organisms examined, we found at least one gene with most of its intron predicted to be ancient. In A. thaliana, the large diversity in RH structures suggests that duplications of the ancestral RH were followed by a high number of intron deletions and additions. The very high bias toward phase 0 introns is in favor of intron addition, preferentially in phase 0. Results from this comparative study of the same gene family in a plant and in two animals are discussed in terms of the general mechanisms of gene family evolution.
Improved PCR-walking for large-scale isolation of plant T-DNA borders.
Biotechniques. 2001 Mar;30(3):496-8, 502, 504. PMID: 11252785
Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L.
INRA, Evry, France.
Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.
Plant Mol Biol. 2000 Mar;42(5):703-17. PMID: 10809443
185 Tavares R., Aubourg S., Lecharny A and Kreis M. (2000)
Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Université de Paris-Sud, Orsay France.
The Arabidopsis Genome Initiative has released up to now more than 80% of the genome sequence of Arabidopsis thaliana. About 70% of the identified genes have at least one paralogue. In order to understand the biological function of individual genes, it is essential to study the structure, expression and organization of the entire multigene family. A systematic analysis of multigene families, made possible by the amount of genomic sequence data available, provides important clues for the understanding of genome evolution and plasticity. In this paper, four multigene families of A. thaliana are characterized, namely LCAD, HD-GL2, LGT and MYST. Members of HD-GL2 and LCAD have already been reported in plants. The LGT genes specify proteins containing motifs of glycosyl transferase. No plant genes similar to the LGT genes have been reported to date. The novel MYST family, most likely plant-specific, encodes proteins with no identified function. Sequencing and in silico analysis led to the characterization of 29 novel genes belonging to these four gene families. The organization, structure and evolution of all the members of the four families are discussed, as well as their chromosome location. Expression data of some of the paralogues of each family are also presented.
In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants.
Plant Mol Biol. 2000 Mar;42(4):603-13. PMID: 10809006
Aubourg S., Boudet N., Kreis M. and Lecharny A. (2000)
Institut de Biotechnologie des Plantes, UMR CNRS 8618, Laboratoire de Biologie du Développement des Plantes, Université de Paris-Sud, Orsay, France.
In the sequences released by the Arabidopsis Genome Initiative (AGI), we discovered a new and unexpectedly large family of orphan genes (127 genes by 01.08.99), named AtPCMP. The distribution of the AtPCMP genes on the five chromosomes suggests that the genome of Arabidopsis thaliana contains more than 200 genes of this family (1% of the whole genome). The deduced AtPCMP proteins are characterized by a surprising combinatorial organization of sequence motifs. The amino-terminal domain is made of a succession of three conserved motifs which generate an important diversity. These proteins are classified into three subfamilies based on the length and nature of their carboxy-terminal domain constituted by 1-6 motifs. All the motifs characterized have an important level of conservation in both sequence and spacing. A specific signature of this large family is defined. The presence of ESTs in databases and the detection of clones in A. thaliana cDNA libraries indicate that most of the genes of this family are expressed. The absence of similar sequences outside the plant kingdom strongly suggests that this unusually large orphan family is unique to plants. Features, the genesis, the potential function and the evolution of this plant combinatorial and modular protein family are discussed.
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.
Nature. 1999 Dec 16;402(6763):769-77. PMID: 10617198
Lecharny A., Aubourg S. [List pp.]
GSF-Forschungszentrum f. Umwelt u. Gesundheit, Munich Information Center for Protein Sequences am Max-Planck-Institut f. Biochemie, Germany.
The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
The arabinose kinase, ARA1, gene of Arabidopsis is a novel member of the galactose kinase gene family
Plant Mol Biol. 1999 Mar;39(5):1003-12. PMID: 10344205
Sherson S, Gy I, Medd J, Schmidt R, Dean C, Kreis M, Lecharny A, Cobbett C, (1999):
Department of Genetics, University of Melbourne, Parkville, Australia.
The arabinose-sensitive ara1-1 mutant of Arabidopsis is deficient in arabinose kinase activity. A candidate for the ARA1 gene. ISA1, has been previously identified through the Arabidopsis genome sequencing initiative. Here we demonstrate that (1) the ARA1 gene coincides with ISA1 in a positional cloning strategy; (2) there are mutations in the ISA1 gene in both the ara1-1 mutant and an intragenic suppressor mutant; and (3) the ara1-1 and suppressor mutant phenotypes can be complemented by the expression of the ISA1 cDNA in transgenic plants. Together these observations confirm that ISA1 is the ARA1 gene. ARA1 is a member of the galactose kinase family of genes and represents a new substrate specificity among this and other families of sugar kinases. A second gene with similarities to members of the galactose kinase gene family has been identified in the EST database. A 1.8 kb cDNA contained an open reading-frame predicted to encode a 496 amino acid polypeptide. The GAL1 cDNA was expressed in a galK mutant of Escherichia coli and in vitro assays of extracts of the strain expressing GAL1 confirmed that the cDNA encodes a galactose kinase activity. Both GAL1 and ARA1 cross-hybridise at low stringency to other sequences suggesting the presence of additional members of the galactose kinase gene family.
Structure and expression of three src2 homologues and a novel subfamily of flavoprotein monooxygenase genes revealed by the analysis of a 25 kb fragment from Arabidopsis thaliana chromosome IV.
Gene. 1999 Apr 16;230(2):197-205. PMID: 10216258
Aubourg S., Picaud A., Kreis M. and Lecharny A. (1999)
Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, ERS/CNRS 569, F-91405, Orsay Cedex, France.
Biological and computer-assisted analyses of a 25kb fragment from Arabidopsis thaliana chromosome IV led to the characterization of two multigene families and three novel orphan genes, not previously described. The first gene family named AtMO1-4 encodes monooxygenases, related to the prokaryotic salicylate hydroxylases. The second gene family contains three members, two on the analysed 25kb fragment and one on chromosome I. The latter three genes lack introns and are homologous to the previously studied Glycine max src2 gene which is overexpressed at low temperature. Gene expression and primary structure of the deduced proteins are described and compared. Three genes of unknown function, showing tissue specific expressions, are characterized on the 25kb fragment. Full length or partial cognate cDNAs have been sequenced for all the genes studied.
The DEAD box RNA helicase family in Arabidopsis thaliana.
Nucleic Acids Res. 1999 January 15; 27(2): 628–636. PMID: 9862990
Aubourg S., Kreis M. and Lecharny A.
Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud-ERS/CNRS 569, F-91405 Orsay Cedex, France.
The numerous genomic sequences and ESTs released by the Arabidopsis thaliana Genome Initiative (AGI) have allowed a systematic and functional study of the DEAD box RNA helicase family. Sequencing and in silico analysis led to the characterization of 28 novel A. thaliana DEAD box RNA helicases forming a family of 32 members, named AtRH. Fourteen AtRH genes with an unexpected heterogeneous mosaic structure are described and compared bringing new information about the genesis of the gene family. The mapping of the AtRH genes shows their repartition on the five chromosomes without clustering and therefore AtRH s have been estimated to 60 genes per A.thaliana haploid genome. Sequence comparisons revealed a very conserved catalytic central domain flanked or not by four classes of extensions in the N- and/or C- extremities. The global amino acid composition of the extensions are tentatively correlated to specific functions such as targeting, protein interaction or RNA binding. The expression of the 32 AtRH genes has been recorded in different tissues. Separate patterns of expression and alternative polyadenylation sites have been shown. Based on the integration of all this information, we propose a classification of the AtRH proteins into subfamilies with associated functions.
Structure and expression of an asparaginyl-tRNA Synthetase gene adjacent to a new gene of 15 exons, from the chromosome IV of Arabidopsis thaliana.
Biochim Biophys Acta. 1998 Jul 9;1398(3):225-31. PMID: 9655910
Aubourg S., Chéron A., Kreis M. and Lecharny A. (1998)
Institut de Biotechnologie des Plantes, ERS/CNRS 569, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, F-91405 Orsay Cedex, France.
The gene AtNS1 coding for an asparaginyl-tRNA synthetase and located on chromosome IV of Arabidopsis thaliana has been characterized. AtNS1 is the first asparaginyl-tRNA synthetase gene described in higher plants. The genomic environment of AtNS1 has been studied, as well as a partial cDNA of a second homologous asparaginyl-tRNA synthetase gene, AtNS2. Both AtNS1 and AtNS2 exhibit the highest similarity with prokaryotic homologues. A large novel gene of 15 exons, named AtG2484-1, is located adjacent to AtNS1. AtG2484-1 shows features rarely described in plants including large exons and one 3' non-coding exon. PCR and Northern analyses were carried out to obtain information about the expression of these genes in various A. thaliana tissues.
Analysis of a 14 kb fragment containing a putative cell wall protein gene and a candidate for the ARA1, arabinose kinase gene.
Gene. 1998 Mar 16;209(1-2):201-10. PMID: 9524266
Gy I., Aubourg S., Sherson S., Cobbett C.S., Chéron A., Kreis M. and Lecharny A. (1998)
Institut de Biotechnologie des Plantes, Laboratoire de Biologie du Développement des Plantes, Bâtiment 630, Université de Paris-Sud, CNRS-ERS 569, F-91405, Orsay, Cedex, France.
An Arabidopsis thaliana genomic DNA fragment of 14kb has been characterized in the framework of the E.S.S.A. programme. Computational and molecular approaches identified three novel gene sequences coding, respectively, for a protein of unknown function, a putative membrane-anchored cell wall protein and an arabinose kinase gene corresponding to the locus ARA1. The latter two genes named AtSEB1 and AtISA1 have been characterized in detail. They are very different in their organization, codon usage and level of expression. Homologues of AtSEB1 and AtISA1 have been identified. Sequence comparisons showed that the former genes contained a long 5' extension coding for an N-terminal domain probably specifying subcellular localization. Cloning and sequencing of the cognate cDNA for the AtISA1 homologue in A. thaliana, named GAL1, indicate that it encodes for a galactokinase-like protein. Our results highlight the integrative outcome of a systematic sequencing project in which links between biochemically and genetically characterized mutants, ESTs and genomic sequence data are generated.
Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana.
Nature, n°391, p 485-488. 1998 PMID: 9461215
Lecharny A., Aubourg S.
The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.
Structure, organization and putative function of the genes identified within a 23.9 kb fragment from Arabidopsis thaliana chromosome IV.
Gene. 1997 Oct 15;199(1-2):241-53. PMID: 9358062
Aubourg S., Takvorian A., Chéron A., Kreis M. and Lecharny A. (1997)
Laboratoire de Biologie du Développement des Plantes, Institut de Biotechnologie des Plantes, ERS/CNRS 569, Université de Paris-Sud, Orsay, France.
In the framework of the complete genome sequencing programme of the crucifer Arabidopsis thaliana, a 23.9-kb fragment from the long arm of chromosome IV has been analysed. This paper presents a methodological approach, integrating computerized predictions, database screening, the sequencing of cognate cDNAs and a PCR-based detection of expression that allows the accumulation of an important amount of information from an anonymous sequence. This work revealed the organization of novel genes and the vestige of a copia-like retrotransposon. The gene AtRH1 encodes the first member of a new subfamily of the plant DEAD box RNA helicases. A recurrent and complete search of dbEST has been used to evaluate the number of different RNA helicases expressed in A. thaliana. On the 18 discriminated members of the family, only a small number seems to be expressed at a relatively high level. The putative gene AtTS1 encodes a novel terpene synthase in A. thaliana, and the genes G14587-5 and G14587-6 encode unknown proteins. This study illustrates most of the situations that could be encountered during the analysis of an anonymous sequence from A. thaliana.
Characterization of two members of the Arabidopsis thaliana gene family, Atßfruct3 and Atßfruct4, coding for vacuolar invertases.
Gene. 1997 Sep 15;197(1-2):239-51. PMID: 9332372
Haouazine-Takvorian N, Tymowska-Lalanne Z, Takvorian A, Tregear J, Lejeune B, Lecharny A, Kreis M:
Université de Paris-Sud, IBP, URA/CNRS 1128, Orsay, France.
We have isolated and characterized two Arabidopsis thaliana cDNAs and their cognate genes, At beta fruct3 and At beta fruct4, encoding vacuolar forms of invertase. Our sequencing results showed that the gene At beta fruct3 is located downstream of the 3-ketoacyl-acyl carrier protein synthase III gene (AtKasIII). At beta fruct3 and 4 are functional and organized into seven exons and six introns with an identical organization. The At beta fruct3 and At beta fruct4 genes encode, respectively, polypeptides of 648 and 664 residues that contain all the characteristic hallmarks of vacuolar invertases. A. thaliana is the first plant of which both cell-wall (At beta fruct1 and At beta fruct2) and vacuolar (At beta fruct3 and At beta fruct4) genes are characterized. The same number of exons and introns is seen in the genes At beta fruct1, At beta fruct3 and At beta fruct4 as well as in all other invertase genes described to date. However, the position of the third intron is different in At beta fruct3 and At beta fruct4. At beta fruct2 shows a different organization. A neighbour-joining distance tree shows that the A. thaliana vacuolar invertases described here are, as expected, more closely related to vacuolar invertases from other plant species (e.g., carrot) than to the A. thaliana cell-wall invertases. The evolution of plant invertase genes from a common ancestral gene is discussed. Our results demonstrate that in A. thaliana, at least two genes encoding vacuolar invertases are expressed during the development of the plant. Southern blot hybridization experiments suggest the presence of one copy of, respectively, At beta fruct3 and At beta fruct4 per haploid genome, and Northern blot analysis demonstrates that vacuolar invertase genes are highly expressed in stems, roots, flowers and at very low levels in mature leaves.
Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs.
The Plant J. 9: 101-124 (1996).PMID: 8580968
Cooke R. RM, Laudié M., Grellet F., Delseny M., Morris P-C., Guerrier D., Giraudat J., Quigley F., Clabault G., Li Y-F., Mache R., Krivitzky M., Jean-Jacques-Gy I., Kreis M.,
Lecharny A., Parmentier Y., Marbach J., Fleck J., Clément B., Philips G., Hervé C., Bardet C., Tremousaygue D., Lescure B., Lacomme C., Roby D., Jourjon M-F., Chabrier P., Charpenteau J-L., Deprez T., Amselem J.., Chiapello H., Höfte H.:
Laboratoire de Physiologie et Biologie Moléculaires Végétal es, URA565 du CNRS, Université de Perpignan, France. cooke@univ-perp.fr
Nearly 7000 Arabidopsis thaliana-expressed sequence tags (ESTs) from 10 cDNA libraries have been sequenced, of which almost 5000 non-redundant tags have been submitted to the EMBL data bank. The quality of the cDNA libraries used is analysed. Similarity searches in international protein data banks have allowed the detection of significant similarities to a wide range of proteins from many organisms. Alignment with ESTs from the rice systematic sequencing project has allowed the detection of amino acid motifs which are conserved between the two organisms, thus identifying tags to genes encoding highly conserved proteins. These genes are candidates for a common framework in genome mapping projects in different plants.
Arabidopsis Gene and cDNA encoding cell-wall invertase.
Plant Physiol. 1994 Feb;104(2):809-10. PMID: 8159800
Schwebel-Dugué N., EMN, Krivitzky M., Jean-Jacques I., Williams J.H.H., Thomas M., Lecharny A.:
Biologie du Développement des Plantes, Bâtiment 430, UA-Centre National de la Recherche Scientifique 1128, Université de Paris-Sud, Orsay, France.
Sucrose synthase in developing maize leaves. Regulation of activity by protein level during the import to export transition
Plant Physiol. 1990 Oct;94(2):516-523. PMID: 16667743
Nguen-Quoc B, Krivitzky M, Huber SC, Lecharny A.:
Laboratoire de Structure et Métabolisme des Plantes, CNRS (URA 1128), Université de Paris-Sud, Bât. 430, 91405 Orsay Cédex, France.
The maize (Zea mays) leaf is a valuable system to study the sucrose import to sucrose export transition at the cellular level. Rapidly growing and fully heterotrophic cells in the basal part of the young leaf showed a high sucrose synthase (SS) activity. Leaf SS has been purified to homogeneity. By comparison with purified kernel SS isozymes, the leaf SS has been identified as SS(2). SS(1) protein and SS(2) protein were clearly separated by electrophoresis and the two monomers differed in size by 6 kilodaltons. Nevertheless, kinetic parameters of both enzymes were very similar. Immunodetection of SS protein showed that in young heterotrophic tissues SS(2) was a major protein accounting for 3% of the total protein. Concurrent with greening, SS activity decreased and the change of activity was explained by regulation of the protein level. In mature green tissues, which are synthetizing sucrose as evidenced by the presence of sucrose phosphate synthase activity, SS activity was almost completely absent. Results suggested that down regulation of SS(2) enzyme protein level was an early event in the transition from import to export status of the leaf.
Genetic variability in carbon fixation, sucrose-P-synthase and ADP glucose pyrophosphorylase in maize plants of differing growth rate
Plant Physiol. 1989 Feb;89(2):416-420. PMID: 16666558
Rocher JP, Lecharny A, Reyss A, Joussaume M.:
Laboratoire “Structure et Métabolisme des Plantes,” associé au CNRS (UA 1128), Bât. 430, Université de Paris-Sud, 91405 Orsay, France.
The net photosynthetic rate and the activities of ribulose 1,5 bisphosphate carboxylase (RubisCo), phosphoenolpyruvate carboxylase, sucrose-P-synthase, and ADP glucose-pyrophosphorylase, key enzymes of the leaf carbohydrate metabolism were compared in eight maize (Zea mays L.) genotypes presenting large differences in growth rate. The sucrose-P-synthase activity varied in the ratio 1 to 3 from the less active to the more active genotype and this variation was highly correlated with those in growth rate. ADP glucose pyrophosphorylase activity was not significantly different from one genotype to another whatever the basis for expression, leaf area, or soluble protein. The photosynthetic rate varied with similar amplitude (1:1) to the RubisCo activity or RubisCo quantity but the correlation with growth rate was highly significant for photosynthesis and nonsignificant for RubisCo or phosphoenolpyruvate carboxylase. So, in our series of genotypes the sucrose synthesis capacities as expressed by sucrose phosphate synthase activity seem to have a good predicting value for mean growth rate at a young stage.
Stem extension rate in light-grown plants. Effects of photo- and thermoperiodic treatments on the endogenous circadian rhythm in Chenopodium rubrum.
Plant Physiol. 1985 Nov;79(3):625-629. PMID: 16664462
Lecharny A, Schwall M, Wagner E:
Institut de Physiologie Végétale, CNRS, 91190 Gif-sur-Yvette, France.
Low temperature pulses have two effects on the circadian rhythm exhibited by stem extension rate of green Chenopodium rubrum plants. First, low temperature pulses have the same effect on the phasing of the rhythm as a dark period interrupting continuous light. Second, low temperature pulses stimulate stem extension rate during the 10 hours immediately following the end of the pulse. A difference in temperature between soil and air increases this effect. In any case, it is the change in temperature which is essential and not a specific temperature. Effects of light and temperature on phasing and amplitude of the rhythm explain why the maximal stem growth is observed under normal photo-thermoperiodic conditions, i.e. a high temperature during the photoperiod and a low temperature during the dark period.
Phytochrome and green plants.
Lecharny A:
Physiologie Végétale, 23: 963-982 (1985).
Circadian rhyhmicity in energy metabolism: a prerequisite for the cooperation between the organelles of eukariotic cells.
Wagner E, BS, Schwall M, Lecharny A, Bergfeld R, Kossmann I, Bonzon M & Greppin H.:
Endocyt.C.Res. 1: 81-93 (1984).
Photostimulation of hydroxypyruvate reductase activity in peroxisomes of Pharbitis nil seedlings. 2: Photoreceptors in bluelight.
Tchang F, Lecharny A, Mazliak P:
Plant and Cell Physiology 25: 1039-1043 (1984).
Photostimulation of hydroxypyruvate reductase activity in peroxisomes of Pharbitis nil seedlings. 1: Action spectrum.
Tchang F, Lecharny A, Mazliak P:
Plant and Cell Physiology 25: 1033-1037 (1984).
Dependence of the stomatal index on the environmental factors during stomatal differentiation in leaves of Vigna sinensis L.
Schoch PG, Jacques R, Lecharny A , Sibi M .:
Journal of Exp. Bot. 35: 1405-1409 (1984).
Stem extension rate in light-grown plants. Evidence for an endogenous circadian rhythm in Chenopodium rubrum.
Lecharny A, Wagner E:
Physiologia Plantarum 60: 437-443 (1984).
Oleic acid metabolism: a biochemical marker to study photoregulation of epicotyl elongation in Vigna unguiculata.
de March G, Trémolières A, Lecharny A.:
Physiologia Plantarum 60: 401-408 (1984).
Photoinhibition of internode elongation rate in light-grown Vigna sinensis L. Control by light quality.
Lecharny A, Jacques R:
Plant, Cell and Environment 5: 31-36 (1982).
The effect of monochromatic light on trans-hexadecenoic acid and chlorophyll accumulation in etiolated leaves of Vigna sinensis L.
Guët C, Trémolières A, Lecharny A.:
Photochem.Photobiol. 35: 283-284 (1982).
Photocontrôle de l'allongelent des tiges principales de plantes cultivées en alternance de lumière et d'obscurité.
Lecharny A:
Organe de photoréception, cinétique des vitesses d'allongement et action du phytochrome., pp. 116. Université P. et M. Curie, Paris 6., Paris (1981).
Photomodulation of growth and specific changes in fatty acid amounts in internodes of green Vigna sinensis L.
Lecharny A, Trémolières A, Jacques R.:
Planta 152: 487-490 (1981).
Circadian endogenous growth rhythm in tomato.
Assaad I LA, Millet B.:
Plant Physiol. 67: 113 (1981).
Light inhibition of internode elongation in green plants. A kinetic study with Vigna sinensis L.
Lecharny A, Jacques R:
Planta 149: 384-388 (1980).
Phytochrome and internode elongation in Chenopodium polyspermum L. The light fluence rate during the day and the end-of-day effect.
Lecharny A, Jacques R:
Planta 146: 575-578 (1979).
Phytochrome and internode elongation in Chenopodium polyspermum L. Sites of photoperception.
Lecharny A:
Planta 145: 405-409 (1979).
Two phytochrome-dependent processes in Anagallis arvensis L.: flowering and stem elongation.
Imhoff C, Lecharny A, Jacques R, Brulfert J.:
Plant, Cell and environment 146: 575-578 (1979).
Phytochrome et indice stomatique des feuilles de Vigna sinensis L.
Schoch PG LA, Jacques R, Zinsou C.:
C.R.Acad.Sc.Paris 285: 877-879 (1977).
Influence de l'éclairement et de la température sur l'indice stomatique des feuilles du Vigna sinensis L.
Schoch P.G., Lecharny A, Zinsou C.:
C.R.Acad.Sc.Paris 285: 673-675 (1977).
Phytochrome et croissance des tiges; variations de l'effet de la lumière en fonction du temps et du lieu de photoréception.
Lecharny A JR:
Physiol.Vég. 12: 721-738 (1974).
Effet de la lumière sur la croissance des tiges; ses variations au cours d'un cycle photopériodique de 24 heures. Rôle du phytochrome et influence du lieu de photoperception.
Lecharny A:
Physiologie Végétale, pp. 44. Université de Paris VI, Paris (1973).
La croissance du Chenopodium polyspermum L.: mise en évidence de différentes phases de sensibilité à la lumière par l'intermédiaire du phytochrome, au cours de la période d'obscurité.
Lecharny A:
Physiologie végétale approfondie, pp. 26. Université de Paris VI, Paris (1972).
Phytochrome et variations de sensibilité aux éclairements de faible énergie.
Lecharny A Jacques R:
C.R. Acad.Sc. Paris 275 D: 2227-2230 (1972).
Proceedings:
Phytochrome and internode elongation in Chenopodium polyspermum L. The light fluence rate during the day and the end-of-day effect. in "Photoreceptors and plant development"
Lecharny A, Jacques. 1980.
De Greef J ed. Antwerpen University Press. 571-575.
Correlation between oleic acid content and cell elongation in Vigna radiata and Vigna sinensis. in "Biochemistry and metabolism of plant lipids".
Dubacq JP, Goldberg R, de March G, Prat R, Tremolières A, Lecharny A. 1982.
Kuiper PJC & Wintermans JFGM ed. Elsevier Biomedical Press, Amsterdam. 467-470.
Light regulation of lipid metabolism and peroxisomal activity in sunflower and Phabitis nil cotyledons. in "Biochemistry and metabolism of plant lipids".
Tchang F, Oursel A, Lecharny A, Connan A, Robert D, Tremolières A, Mazliak P. 1982.
Kuiper PJC & Wintermans JFGM ed. Elsevier Biomedical Press, Amsterdam. 483-486.
Relationships between source leaf photosynthesis, export and grain filling in maize.
Prioul JL, Reyss A, Schwebel-Dugue N, Lecharny A. 1990.
in Current Research in Photosynthesis, Vol IV, 871-874.
Sucrose cleavage in relation to import and metabolism of sugars in sink organs.
Ho LC, Lecharny A, Willenbrink J. 1990.
in Recent Advances in Phloem Transport and Assimilate Compartmentation. Bonnemain JL, Delrot S, Dainty J, Lucas WJ ed.
Sucrose synthase B-fructosidase and sucrose metabolism in leaves.
Lecharny A., Nguyen-Quoc B. 1991.
In Plant Sciences today. Ed. INRA, 107-108.
Characterisation of immunological differences between two sucrose synthase enzymes of maize.
Nguyen-Quoc B., Krivitsky M., Huber S.C., Lecharny A., 1991.
In Plant Sciences today. Ed. INRA, 132.
Plant protein phosphorylation in signal transduction and the control of development: Cloning and characterization of protein kinase genes from Arabidopsis and Petunia.
Tregear JW, Decroocq-Ferrant V, Thomas M, Bianchi M, Le Guen L, Lessard P, Lecharny A, Kreis M. 1995.
In: Protein Phosphorylation in Plants, eds PR Shewry, NG Halford and R Hooley, pp. 279-295.
Comparative genomics of a DEAD box RNA helicase gene family in Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster.
Boudet N, Aubourg S, Kreis M and Lecharny A.
JOBIM, 2002.
Sélection de motifs candidates pour la regulation des genes chez Arabidopsis thaliana sur des critères topologiques.
Bernard V., Brunaud V., Serizet C., Martin-Magniette M.-L., Caboche M., Aubourg S. and Lecharny A.
5-7 juillet 2006, Journées Ouvertes Biologie Informatique et Mathématiques (JOBIM'2006). Bordeaux, France. Actes Session 1, 17-28.
Chapters in Books
L’organisation des génomes végétaux révélée par leur annotation.
Aubourg S., Delseny M. and Lecharny A. (2006)
Depuis une dizaine d’années, la communauté internationale des génomistes a considérablement investi dans la caractérisation d’une sélection de génomes végétaux modèles. Les connaissances déduites des séquences génomiques servent maintenant de socle à la compréhension de l’organisation et de l’évolution des génomes, à l’obtention de données fonctionnelles et à leur analyse intégrative.
Biofutur, n°265, p 33-37.
Un modèle statistique pour l’intégration de l’ADN-T dans le génome d’Arabidopsis thaliana. In « La fluidité des génomes et ses conséquences »,
Lecharny A.
Ed. Commission du Génie Biomoléculaire. (2004)
Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. In Genome Evolution, Gene and Genome Duplications and the Origin of Novel Gene Functions
Lecharny A, Boudet N, Gy I, Aubourg S, M Kreis:
pp 111-116. A. Meyer and Y. Van de Peer eds. Kluwer Academic Publishers. 2003.
Vulgarisation papers (in french)
Lumière et croissance des tiges.
Jacques R, Lecharny A. 1975.
Lux 81, 26.
Photomorphogenèse du Chenopodium polyspermum L. in Etudes de Biologie Végétale.
Jacques R, Lecharny A. 1976.
Hommage au Professeur P.Chouard , R.Jacques ed. Paris.
La photomorphogenèse végétale : analyse des effets physiologiques de la lumière, au laboratoire et en milieu naturel.
Jacques R, Lecharny A, Schoch PG. 1980.
Bulletin de la Société d'Ecophysiologie. 5, 111-147.
Le point sur le séquençage du génome nucléaire d'Arabidopsis thaliana.
Lecharny A, Kreis M. 1996.
La Lettre de l'Association des Sélectionneurs Français, 47 :65-69.
Un modèle statistique pour l’intégration de l’ADN-T dans le génome d’Arabidopsis thaliana. In « La fluidité des génomes et ses conséquences »
Lecharny A.
Ed. Commission du Génie Biomoléculaire. (2004)
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