Publications by authors named "Corinne Rancurel"

25 Publications

  • Page 1 of 1

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes.

Genes (Basel) 2020 11 13;11(11). Epub 2020 Nov 13.

INRAE, Plant Health and Environment, University Côte d'Azur, CNRS, ISA, F-06903 Sophia-Antipolis CEDEX, France.

Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of , one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.
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http://dx.doi.org/10.3390/genes11111347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696266PMC
November 2020

Transcriptomic and Ultrastructural Signatures of K-Induced Aggregation in Zoospores.

Microorganisms 2020 Jul 7;8(7). Epub 2020 Jul 7.

Université Côte d'Azur, INRAE, CNRS, ISA, 06903 Sophia Antipolis, France.

Most pathogenic oomycetes of the genus spread in water films as flagellated zoospores. Zoospores perceive and produce signals attracting other zoospores, resulting in autoaggregation in vitro or biofilm formation on plant surface. The mechanisms underlying intercellular communication and consequent attraction, adhesion and aggregation are largely unknown. In the perception of a K gradient induces coordinated motion and aggregation. To define cellular and molecular events associated with oomycete aggregation, we combined transcriptomic and ultrastructural analyses. Results indicate involvement of electroception in K sensing. They establish that the transcriptome repertoire required for swimming and aggregation is already fully functional at zoospore release. At the time points analyzed, aggregates are mainly constituted of zoospores. They produce vesicular and fibrillary material discharged at cell-to-cell contacts. Consistently, the signature of transcriptome dynamics during transition to aggregates is an upregulation of genes potentially related to vesicular trafficking. Moreover, transcriptomic and functional analyses show a strong enhancement of carbonic anhydrase activity, indicating that pH homeostasis may contribute to aggregation by acting on both zoospore movement and adhesion. This study poses the molecular and cellular bases of aggregative behavior within oomycetes and expands the current knowledge of ion perception-mediated dissemination of propagules in the rhizosphere.
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http://dx.doi.org/10.3390/microorganisms8071012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409359PMC
July 2020

Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen .

Front Genet 2020 5;11:557. Epub 2020 Jun 5.

INRAE, UCA, CNRS, ISA Sophia Antipolis, Biot, France.

Satellite DNA is a class of repetitive sequences that are organized in long arrays of tandemly repeated units in most eukaryotes. Long considered as selfish DNA, satellite sequences are now proposed to contribute to genome integrity. Despite their potential impact on the architecture and evolution of the genome, satellite DNAs have not been investigated in oomycetes due to the paucity of genomic data and the difficulty of assembling highly conserved satellite arrays. Yet gaining knowledge on the structure and evolution of genomes of oomycete pathogens is crucial to understanding the mechanisms underlying adaptation to their environment and to proposing efficient disease control strategies. A assembly of the genome of , an important oomycete plant pathogen, led to the identification of several families of tandemly repeated sequences varying in size, copy number, and sequence conservation. Among them, two abundant families, designated as and , displayed typical features of satellite DNA and were collectively designated as . These two satellite families differ by their length, sequence, organization, genomic environment, and evolutionary dynamics. , but not , presented homologs among oomycetes. This observation, as well as the characterization of transcripts of families, suggested that these satellite DNA families likely play a conserved role within this important group of pathogens.
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http://dx.doi.org/10.3389/fgene.2020.00557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290008PMC
June 2020

Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes.

iScience 2019 Nov 24;21:587-602. Epub 2019 Oct 24.

Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK; Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.

Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.
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http://dx.doi.org/10.1016/j.isci.2019.10.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889759PMC
November 2019

SATQPCR: Website for statistical analysis of real-time quantitative PCR data.

Mol Cell Probes 2019 08 5;46:101418. Epub 2019 Jul 5.

INRA/CNRS/UCA ISA, 06903, 400 route des Chappes, BP167, Sophia Antipolis, France. Electronic address:

SATQPCR is a web tool providing statistical analysis of real-time quantitative PCR data including all MIQE rules (gene efficiency, selection of reference genes and normalization with them). Our application is a quick tool that provides to the biologist, graphs as well as statistical tables summarizing their results with the chosen methods (t-test or ANOVA with Tukey test). The application is available at http://satqpcr.sophia.inra.fr with a demo dataset. Source code can be found at https://framagit.org/. SUPPLEMENTARY INFORMATION: Tutorials at http://satqpcr.sophia.inra.fr/cgi/help.cgi.
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http://dx.doi.org/10.1016/j.mcp.2019.07.001DOI Listing
August 2019

In Vitro Acquisition of Specific Small Interfering RNAs Inhibits the Expression of Some Target Genes in the Plant Ectoparasite .

Int J Mol Sci 2019 Jul 3;20(13). Epub 2019 Jul 3.

SVQV, INRA, Université de Strasbourg, 68000 Colmar, France.

is an important plant parasitic nematode that induces direct damages and specifically transmits the , which is particularly harmful for grapevines. Genomic resources of this nematode species are still limited and no functional gene validation technology is available. RNA interference (RNAi) is a powerful technology to study gene function and here we describe the application of RNAi on several genes in . Soaking the nematodes for 48 h in a suspension containing specific small interfering RNAs resulted in a partial inhibition of the accumulation of some targeted mRNA. However, low reproducible silencing efficiency was observed which could arise from silencing pathway deficiencies. Indeed, essential accustomed proteins for these pathways were not found in the proteome predicted from transcriptomic data. The most reproducible silencing effect was obtained when targeting the gene potentially involved in endo-exocytosis of synaptic molecules. This represents the first report of gene silencing in a nematode belonging to the family.
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http://dx.doi.org/10.3390/ijms20133266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651894PMC
July 2019

Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexually reproducing species.

BMC Genomics 2018 May 3;19(1):321. Epub 2018 May 3.

Université Côte d'Azur, INRA, ISA, Sophia Antipolis, France.

Background: The renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are mediated by DNA methylation, stable chromatin modifications and non-coding RNA-associated gene silencing involving specific proteins called epigenetic factors. Multiple organisms, ranging from plants to yeast and mammals, have been used as model systems to study epigenetics. The interactions between parasites and their hosts are models of choice to study these mechanisms because the selective pressures are strong and the evolution is fast. The asexually reproducing root-knot nematodes (RKN) offer different advantages to study the processes and mechanisms involved in epigenetic regulation. RKN genomes sequencing and annotation have identified numerous genes, however, which of those are involved in the adaption to an environment and potentially relevant to the evolution of plant-parasitism is yet to be discovered.

Results: Here, we used a functional comparative annotation strategy combining orthology data, mining of curated genomics as well as protein domain databases and phylogenetic reconstructions. Overall, we show that (i) neither RKN, nor the model nematode Caenorhabditis elegans possess any DNA methyltransferases (DNMT) (ii) RKN do not possess the complete machinery for DNA methylation on the 6th position of adenine (6mA) (iii) histone (de)acetylation and (de)methylation pathways are conserved between C. elegans and RKN, and the corresponding genes are amplified in asexually reproducing RKN (iv) some specific non-coding RNA families found in plant-parasitic nematodes are dissimilar from those in C. elegans. In the asexually reproducing RKN Meloidogyne incognita, expression data from various developmental stages supported the putative role of these proteins in epigenetic regulations.

Conclusions: Our results refine previous predictions on the epigenetic machinery of model species and constitute the most comprehensive description of epigenetic factors relevant to the plant-parasitic lifestyle and/or asexual mode of reproduction of RKN. Providing an atlas of epigenetic factors in RKN is an informative resource that will enable researchers to explore their potential role in adaptation of these parasites to their environment.
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http://dx.doi.org/10.1186/s12864-018-4686-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934874PMC
May 2018

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.

Genes (Basel) 2017 Oct 23;8(10). Epub 2017 Oct 23.

Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, and , representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from and , respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.
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http://dx.doi.org/10.3390/genes8100287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664137PMC
October 2017

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.

Genes (Basel) 2017 Sep 29;8(10). Epub 2017 Sep 29.

INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.
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http://dx.doi.org/10.3390/genes8100248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664098PMC
September 2017

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

PLoS Genet 2017 06 8;13(6):e1006777. Epub 2017 Jun 8.

INRA, Université Côte d'Azur, CNRS, ISA, France.

Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.
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http://dx.doi.org/10.1371/journal.pgen.1006777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465968PMC
June 2017

Tomato root microbiota and Phytophthora parasitica-associated disease.

Microbiome 2017 05 16;5(1):56. Epub 2017 May 16.

Université Côte d'Azur, INRA, CNRS, ISA, Sophia Antipolis, France.

Background: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica.

Results: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P. parasitica biofilm. Colonization of the host root surface by the oomycete was associated with a shift in microbial community involving a Bacteroidetes/Proteobacteria transition and Flavobacteriaceae as the most abundant family. Identification of members of the P. parasitica-associated microbiota interfering with biology and oomycete infection was carried out by screening for bacteria able to (i) grow on a P. parasitica extract-based medium (ii), exhibit in vitro probiotic or antibiotic activity towards the oomycete (iii), have an impact on the oomycete infection cycle in a tripartite interaction S. lycopersicum-P. parasitica-bacteria. One Pseudomonas phylotype was found to exacerbate disease symptoms in tomato plants. The lack of significant gene expression response of P. parasitica effectors to Pseudomonas suggested that the increase in plant susceptibility was not associated with an increase in virulence. Our results reveal that Pseudomonas spp. establishes commensal interactions with the oomycete. Bacteria preferentially colonize the surface of the biofilm rather than the roots, so that they can infect plant cells without any apparent infection of P. parasitica.

Conclusions: The presence of the pathogenic oomycete P. parasitica in the tomato rhizosphere leads to a shift in the rhizospheric microbiota composition. It contributes to the habitat extension of Pseudomonas species mediated through a physical association between the oomycete and the bacteria.
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http://dx.doi.org/10.1186/s40168-017-0273-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434524PMC
May 2017

Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks.

Front Plant Sci 2016 7;7:794. Epub 2016 Jun 7.

Biochimie and Physiologie Moléculaire des Plantes, UMR 5004 Centre National de la Recherche Scientifique/386 Institut National de la Recherche Agronomique/SupAgro Montpellier/Université de Montpellier, Campus SupAgro-Institut National de la Recherche Agronomique Montpellier, France.

Root hairs are involved in water and nutrient uptake, and thereby in plant autotrophy. In legumes, they also play a crucial role in establishment of rhizobial symbiosis. To obtain a holistic view of Medicago truncatula genes expressed in root hairs and of their regulation during the first hours of the engagement in rhizobial symbiotic interaction, a high throughput RNA sequencing on isolated root hairs from roots challenged or not with lipochitooligosaccharides Nod factors (NF) for 4 or 20 h was carried out. This provided a repertoire of genes displaying expression in root hairs, responding or not to NF, and specific or not to legumes. In analyzing the transcriptome dataset, special attention was paid to pumps, transporters, or channels active at the plasma membrane, to other proteins likely to play a role in nutrient ion uptake, NF electrical and calcium signaling, control of the redox status or the dynamic reprogramming of root hair transcriptome induced by NF treatment, and to the identification of papilionoid legume-specific genes expressed in root hairs. About 10% of the root hair expressed genes were significantly up- or down-regulated by NF treatment, suggesting their involvement in remodeling plant functions to allow establishment of the symbiotic relationship. For instance, NF-induced changes in expression of genes encoding plasma membrane transport systems or disease response proteins indicate that root hairs reduce their involvement in nutrient ion absorption and adapt their immune system in order to engage in the symbiotic interaction. It also appears that the redox status of root hair cells is tuned in response to NF perception. In addition, 1176 genes that could be considered as "papilionoid legume-specific" were identified in the M. truncatula root hair transcriptome, from which 141 were found to possess an ortholog in every of the six legume genomes that we considered, suggesting their involvement in essential functions specific to legumes. This transcriptome provides a valuable resource to investigate root hair biology in legumes and the roles that these cells play in rhizobial symbiosis establishment. These results could also contribute to the long-term objective of transferring this symbiotic capacity to non-legume plants.
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http://dx.doi.org/10.3389/fpls.2016.00794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894911PMC
July 2016

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Genome Biol 2016 Jun 10;17(1):124. Epub 2016 Jun 10.

USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA.

Background: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes.

Results: We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative 'effector islands' in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking.

Conclusions: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.
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http://dx.doi.org/10.1186/s13059-016-0985-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901422PMC
June 2016

Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome.

PLoS One 2014 31;9(12):e115022. Epub 2014 Dec 31.

Institute Sophia Agrobiotech, INRA/CNRS/UNS, University Nice Sophia Antipolis, Sophia Antipolis, France.

Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115022PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281257PMC
September 2015

The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.

Genome Biol Evol 2014 Aug 13;6(9):2181-94. Epub 2014 Aug 13.

Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, United Kingdom

Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, "specific" have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes.
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http://dx.doi.org/10.1093/gbe/evu171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202313PMC
August 2014

A hierarchical classification of polysaccharide lyases for glycogenomics.

Biochem J 2010 Dec;432(3):437-44

Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France.

Carbohydrate-active enzymes face huge substrate diversity in a highly selective manner using only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. In the present paper, a classification of polysaccharide lyases (the enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is shown thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (http://www.cazy.org).
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http://dx.doi.org/10.1042/BJ20101185DOI Listing
December 2010

Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation.

J Virol 2009 Oct 29;83(20):10719-36. Epub 2009 Jul 29.

Architecture et Fonction des Macromolécules Biologiques, Case 932, Campus de Luminy, 13288 Marseille Cedex 9, France.

It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called "overprinting." To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.
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http://dx.doi.org/10.1128/JVI.00595-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753099PMC
October 2009

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.

Nucleic Acids Res 2009 Jan 5;37(Database issue):D233-8. Epub 2008 Oct 5.

Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France.

The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.
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http://dx.doi.org/10.1093/nar/gkn663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686590PMC
January 2009

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

PLoS Genet 2008 May 30;4(5):e1000087. Epub 2008 May 30.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA.

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.
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http://dx.doi.org/10.1371/journal.pgen.1000087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386152PMC
May 2008

FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.

Fungal Genet Biol 2008 May 26;45(5):638-45. Epub 2008 Jan 26.

UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 Avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France.

The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.
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http://dx.doi.org/10.1016/j.fgb.2008.01.004DOI Listing
May 2008

Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins.

Protein Eng Des Sel 2006 Dec 2;19(12):555-62. Epub 2006 Nov 2.

Architecture et Fonction des Macromolécules Biologiques, UMR6098 CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France.

Family GH13, also known as the alpha-amylase family, is the largest sequence-based family of glycoside hydrolases and groups together a number of different enzyme activities and substrate specificities acting on alpha-glycosidic bonds. This polyspecificity results in the fact that the simple membership of this family cannot be used for the prediction of gene function based on sequence alone. In order to establish robust groups that show an improved correlation between sequence and enzymatic specificity, we have performed a large-scale analysis of 1691 family GH13 sequences by combining clustering, similarity search and phylogenetic methods. About 80% of the sequences could be reliably classified into 35 subfamilies. Most subfamilies appear monofunctional (i.e. contain enzymes with the same substrate and the same product). The close examination of the other, apparently polyspecific, subfamilies revealed that they actually group together enzymes with strongly related (or even sometimes virtually identical) activities. Overall our subfamily assignment allows to set the limits for genomic function prediction on this large family of biologically and industrially important enzymes.
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http://dx.doi.org/10.1093/protein/gzl044DOI Listing
December 2006

VaZyMolO: a tool to define and classify modularity in viral proteins.

J Gen Virol 2005 Mar;86(Pt 3):743-749

Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, ESIL, 163 Avenue de Luminy, Case 925, F-13288 Marseille Cedex 9, France.

Viral structural genomic projects aim at unveiling the function of unknown viral proteins by employing high-throughput approaches to determine their 3D structure and to identify their function through fold-homology studies. The 'viral enzyme module localization' (VaZyMolO) tool has been developed, which aims at defining viral protein modules that might be expressed in a soluble and functionally active form, thereby identifying candidates for crystallization studies. VaZyMolO includes 114 complete viral genome sequences of both negative- and positive-sense, single-stranded RNA viruses available from NCBI. In VaZyMolO, a module is defined as a structural and/or functional unit. Modules were first identified by homology search and then validated by the convergence of results from sequence composition analysis, motif search, transmembrane region search and domain definitions, as found in the literature. The public interface of VaZyMolO, which is accessible from http://www.vazymolo.org, allows comparison of a query sequence to all VaZyMolO modules of known function.
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http://dx.doi.org/10.1099/vir.0.80590-0DOI Listing
March 2005

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world.

Proc Natl Acad Sci U S A 2004 Mar 8;101(11):3792-6. Epub 2004 Mar 8.

Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098 Centre National de la Recherche Scientifique and Universités Aix-Marseille I et II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-A resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide/oligonucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication/transcription machinery.
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http://dx.doi.org/10.1073/pnas.0307877101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC374323PMC
March 2004

Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein.

Acta Crystallogr D Biol Crystallogr 2003 Sep 19;59(Pt 9):1628-31. Epub 2003 Aug 19.

Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités Aix-Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France.

The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive-stranded RNA virus (SARS-CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS-CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5 kbp in length, the largest of the known RNA viruses, and encode 20-30 mature proteins. The functions of many of these polypeptides, including the Nsp9-Nsp10 replicase-cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8 A resolution and belong to space group P6(1/5)22, with unit-cell parameters a = b = 89.7, c = 136.7 A. With two molecules in the asymmetric unit, the solvent content is 60% (V(M) = 3.1 A(3) Da(-1)).
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http://dx.doi.org/10.1107/s0907444903016779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161644PMC
September 2003

Synthesis, Structure, and Magnetism of Mono- and Binuclear Manganese(II) Compounds of Nitronyl Nitroxide Substituted Phosphine Oxides.

Inorg Chem 1999 Oct;38(21):4753-4758

Laboratoire des Sciences Moléculaires, Institut de Chimie de la Matière Condensée de Bordeaux, UPR CNRS No. 9048, F-33608 Pessac, France, Groupe Matériaux Moléculaires, UMR CNRS No. 6511, Université Rennes 1, F-35042 Rennes, France, and Centre de Physique Moléculaire Optique et Hertzienne, UMR CNRS Université Bordeaux 1, 351, cours de la Libération, F-33405 Talence, France.

Complexes of manganese(II)-containing aminoxyl radical substituted phosphine oxide ligands are reported. The compounds [(o-nitronyl nitroxide-phenyl)diphenylphosphine oxide]bis(hexafluoroacetylacetonato)manganese(II), 3, and bis{[(p-nitronyl nitroxide-phenyl) diphenylphosphine oxide]bis(hexafluoroacetylacetonato)manganese(II)}, 4, prepared by addition of the free radical phosphine oxides to Mn(hfac)(2), were structurally characterized. Complex 3 is mononuclear, containing an O,O-chelating ortho-substituted radical phosphine oxide ligand, while in 4 the para-substituted ligands bridge two Mn(hfac)(2) units to yield a binuclear molecular rectangle. The magnetic behavior of both systems is dominated by a strong antiferromagnetic Mn(II)-aminoxyl interaction (J = -213 (3), -218 (4) cm(-)(1) with H = -JS(Mn).S(rad)) to give effective S = 2 ground state units. The S = 3 excited state is populated at high temperatures. At low temperatures a decrease in chi(M)T in both complexes is attributable primarily to inter- or intramolecular antiferromagnetic interactions rather than zero-field splitting (ZFS) of the S = 2 ground state. For the bimetallic compound, the magnetic data indicate that ligand-mediated interactions between the Mn(II) spin carriers are weak. The powder EPR spectra of both systems have been recorded and successfully simulated, giving a ZFS parameter D = 0.112 cm(-)(1). Crystals of 3 are triclinic, space group P&onemacr; with a = 10.6672(19) Å, b = 13.270(6) Å, c = 15.363(3) Å, alpha = 93.84(2) degrees, beta = 108.054(16) degrees, gamma = 105.69(3) degrees, and Z = 2. Crystals of 4 are monoclinic, space group P2(1)/a with a = 12.463(6) Å, b = 19.315(3) Å, c = 17.084(9) Å, alpha = 90 degrees, beta = 98.49(2) degrees, gamma = 90 degrees, and Z = 2.
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http://dx.doi.org/10.1021/ic990527gDOI Listing
October 1999
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