Publications by authors named "Sylvain Prigent"

21 Publications

  • Page 1 of 1

Overproduction of ascorbic acid impairs pollen fertility in tomato.

J Exp Bot 2021 04;72(8):3091-3107

Université de Bordeaux, INRAE, UMR 1332 BFP, 33882 Villenave d'Ornon, France.

Ascorbate is a major antioxidant buffer in plants. Several approaches have been used to increase the ascorbate content of fruits and vegetables. Here, we combined forward genetics with mapping-by-sequencing approaches using an ethyl methanesulfonate (EMS)-mutagenized Micro-Tom population to identify putative regulators underlying a high-ascorbate phenotype in tomato fruits. Among the ascorbate-enriched mutants, the family with the highest fruit ascorbate level (P17C5, up to 5-fold wild-type level) had strongly impaired flower development and produced seedless fruit. Genetic characterization was performed by outcrossing P17C5 with cv. M82. We identified the mutation responsible for the ascorbate-enriched trait in a cis-acting upstream open reading frame (uORF) involved in the downstream regulation of GDP-l-galactose phosphorylase (GGP). Using a specific CRISPR strategy, we generated uORF-GGP1 mutants and confirmed the ascorbate-enriched phenotype. We further investigated the impact of the ascorbate-enriched trait in tomato plants by phenotyping the original P17C5 EMS mutant, the population of outcrossed P17C5 × M82 plants, and the CRISPR-mutated line. These studies revealed that high ascorbate content is linked to impaired floral organ architecture, particularly anther and pollen development, leading to male sterility. RNA-seq analysis suggested that uORF-GGP1 acts as a regulator of ascorbate synthesis that maintains redox homeostasis to allow appropriate plant development.
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http://dx.doi.org/10.1093/jxb/erab040DOI Listing
April 2021

Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis.

Plant Cell Environ 2021 May 25;44(5):1504-1521. Epub 2021 Jan 25.

Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine-Bordeaux, INRAE, Univ., Villenave d'Ornon, France.

In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins showed similar variation for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several increasing metabolites or proteins in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding.
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http://dx.doi.org/10.1111/pce.13993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248070PMC
May 2021

Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth.

J Nutr 2020 09;150(9):2268-2277

INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France.

Background: Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance.

Objective: We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material.

Methods: Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints.

Results: In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80).

Conclusions: These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.
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http://dx.doi.org/10.1093/jn/nxaa206DOI Listing
September 2020

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species.

J Exp Bot 2020 10;71(19):5823-5836

UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France.

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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http://dx.doi.org/10.1093/jxb/eraa302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540837PMC
October 2020

Polyphenol Profiles of Just Pruned Grapevine Canes from Wild Accessions and Cultivars.

J Agric Food Chem 2020 Nov 22;68(47):13397-13407. Epub 2020 Apr 22.

Université de Bordeaux, Unité de Recherche Oenologie, EA 4577, USC 1366 Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut des Sciences de la Vigne et du Vin (ISVV), 33882 Villenave d'Ornon France.

Grapevine canes are an abundant byproduct of the wine industry. The stilbene contents of cultivars have been largely studied, but little is known about the stilbene contents of wild accessions. Moreover, there have only been few studies on the quantification of other phenolic compounds in just pruned grapevine canes. In our study, we investigated the polyphenol profile of 51 genotypes belonging to 15 spp. A total of 36 polyphenols (20 stilbenes, 6 flavanols, 7 flavonols, and 3 phenolic acids) were analyzed by high-performance liquid chromatography coupled with a triple quadrupole mass spectrometer. Our results suggest that some wild accessions could be of interest in terms of the concentration of bioactive polyphenols and that flavanols contribute significantly to the antioxidant activity of grapevine cane extracts. To the best of our knowledge, this is the most exhaustive study of the polyphenolic composition of grapevine canes of wild spp.
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http://dx.doi.org/10.1021/acs.jafc.9b08099DOI Listing
November 2020

Metabolomics to Exploit the Primed Immune System of Tomato Fruit.

Metabolites 2020 Mar 6;10(3). Epub 2020 Mar 6.

UMR BFP, University Bordeaux, INRAE, 33882 Villenave d'Ornon, France.

Tomato is a major crop suffering substantial yield losses from diseases, as fruit decay at a postharvest level can claim up to 50% of the total production worldwide. Due to the environmental risks of fungicides, there is an increasing interest in exploiting plant immunity through priming, which is an adaptive strategy that improves plant defensive capacity by stimulating induced mechanisms. Broad-spectrum defence priming can be triggered by the compound ß-aminobutyric acid (BABA). In tomato plants, BABA induces resistance against various fungal and bacterial pathogens and different methods of application result in durable protection. Here, we demonstrate that the treatment of tomato plants with BABA resulted in a durable induced resistance in tomato fruit against , and . Targeted and untargeted metabolomics were used to investigate the metabolic regulations that underpin the priming of tomato fruit against pathogenic microbes that present different infection strategies. Metabolomic analyses revealed major changes after BABA treatment and after inoculation. Remarkably, primed responses seemed specific to the type of infection, rather than showing a common fingerprint of BABA-induced priming. Furthermore, top-down modelling from the detected metabolic markers allowed for the accurate prediction of the measured resistance to fruit pathogens and demonstrated that soluble sugars are essential to predict resistance to fruit pathogens. Altogether, our results demonstrate that metabolomics is particularly insightful for a better understanding of defence priming in fruit. Further experiments are underway in order to identify key metabolites that mediate broad-spectrum BABA-induced priming in tomato fruit.
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http://dx.doi.org/10.3390/metabo10030096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143431PMC
March 2020

Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling.

Front Plant Sci 2019 11;10:1201. Epub 2019 Oct 11.

UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d'Ornon, France.

Central metabolism is the engine of plant biomass, supplying fruit growth with building blocks, energy, and biochemical cofactors. Among metabolic cornerstones, nicotinamide adenine dinucleotide (NAD) is particularly pivotal for electron transfer through reduction-oxidation (redox) reactions, thus participating in a myriad of biochemical processes. Besides redox functions, NAD is now assumed to act as an integral regulator of signaling cascades involved in growth and environmental responses. However, the regulation of NAD metabolism and signaling during fruit development remains poorly studied and understood. Here, we benefit from RNAseq and proteomic data obtained from nine growth stages of tomato fruit (var. Moneymaker) to dissect mRNA and protein profiles that link to NAD metabolism, including biosynthesis, recycling, utilization, and putative transport. As expected for a cofactor synthesis pathway, protein profiles failed to detect enzymes involved in NAD synthesis or utilization, except for nicotinic acid phosphoribosyltransferase (NaPT) and nicotinamidase (NIC), which suggested that most NAD metabolic enzymes were poorly represented quantitatively. Further investigations on transcript data unveiled differential expression patterns during fruit development. Interestingly, among specific NAD metabolism-related genes, early biosynthetic genes were transcriptionally induced in very young fruits, in association with NAD kinase, while later stages of fruit growth rather showed an accumulation of transcripts involved in later stages of synthesis and in NAD recycling, which agreed with augmented NAD(P) levels. In addition, a more global overview of 119 mRNA and 78 protein significant markers for NAD(P)-dependent enzymes revealed differential patterns during tomato growth that evidenced clear regulations of primary metabolism, notably with respect to mitochondrial functions. Overall, we propose that NAD metabolism and signaling are very dynamic in the developing tomato fruit and that its differential regulation is certainly critical to fuel central metabolism linking to growth mechanisms.
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http://dx.doi.org/10.3389/fpls.2019.01201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798084PMC
October 2019

Genome-scale model of Rhodotorula toruloides metabolism.

Biotechnol Bioeng 2019 12 22;116(12):3396-3408. Epub 2019 Sep 22.

Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

The basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model (GEM) of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 852 genes, 2,731 reactions, and 2,277 metabolites, while lipid metabolism is described using the SLIMEr formalism allowing direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose, and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid, triacylglycerols, and carotenoids identified genes-some of which have previously been engineered to successfully increase production. This renders rtho-GEM valuable for future studies to improve the production of other oleochemicals of industrial relevance including value-added fatty acids and carotenoids, in addition to facilitate system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid-accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of the lipid production machinery in R. toruloides.
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http://dx.doi.org/10.1002/bit.27162DOI Listing
December 2019

Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi.

mSystems 2019 Mar-Apr;4(2). Epub 2019 Apr 16.

Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

Filamentous fungi possess great potential as sources of medicinal bioactive compounds, such as antibiotics, but efficient production is hampered by a limited understanding of how their metabolism is regulated. We investigated the metabolism of six secondary metabolite-producing fungi of the genus during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. A coexpression analysis revealed that expression of biosynthetic genes correlates with expression of genes associated with pathways responsible for the generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for the supply of precursors for secondary metabolism and suggest that the regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying fungal species that are optimized for the production of specific secondary metabolites and in designing metabolic engineering strategies to develop high-yielding fungal cell factories for production of secondary metabolites. Secondary metabolites are a major source of pharmaceuticals, especially antibiotics. However, the development of efficient processes of production of secondary metabolites has proved troublesome due to a limited understanding of the metabolic regulations governing secondary metabolism. By analyzing the conservation in gene expression across secondary metabolite-producing fungal species, we identified a metabolic signature that links primary and secondary metabolism and that demonstrates that fungal metabolism is tailored for the efficient production of secondary metabolites. The insight that we provide can be used to develop high-yielding fungal cell factories that are optimized for the production of specific secondary metabolites of pharmaceutical interest.
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http://dx.doi.org/10.1128/mSystems.00012-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469955PMC
April 2019

Modeling Protein Destiny in Developing Fruit.

Plant Physiol 2019 07 23;180(3):1709-1724. Epub 2019 Apr 23.

Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France

Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato () fruit. Quantitative data were collected for transcripts and proteins during fruit development. Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance. Furthermore, protein and transcript abundance were poorly correlated, and the coefficient of correlation decreased during fruit development and ripening, with transcript levels decreasing more than protein levels. A mathematical model with one ordinary differential equation was used to estimate translation ( ) and degradation ( ) rate constants for almost 2,400 detected transcript-protein pairs and was satisfactorily fitted for >1,000 pairs. The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d. The constants were validated and inspected for biological relevance. Proteins involved in protein synthesis had higher and values, indicating that the protein machinery is particularly flexible. Our model also predicts that protein concentration is more strongly affected by the rate of translation than that of degradation.
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http://dx.doi.org/10.1104/pp.19.00086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752906PMC
July 2019

Force Transmission between Three Tissues Controls Bipolar Planar Polarity Establishment and Morphogenesis.

Curr Biol 2019 04 28;29(8):1360-1368.e4. Epub 2019 Mar 28.

CNRS, Univ Rennes, IGDR (Institut de Génétique et Développement de Rennes) - UMR6290, 2 Avenue du Professeur Léon Bernard, 35000 Rennes, France. Electronic address:

How tissues from different developmental origins interact to achieve coordinated morphogenesis at the level of a whole organism is a fundamental question in developmental biology. While biochemical signaling pathways controlling morphogenesis have been extensively studied [1-3], morphogenesis of epithelial tissues can also be directed by mechanotransduction pathways physically linking two tissues [4-8]. C. elegans embryonic elongation requires the coordination of three tissues: muscles, the dorsal and ventral epidermis, and the lateral epidermis. Elongation starts by cell-shape changes driven by actomyosin contractions in the lateral epidermis [9, 10]. At mid-elongation, muscles become connected to the apical surface of the dorsal and ventral epidermis by molecular tendons formed by muscle integrins, extracellular matrix, and C. elegans hemidesmosomes (CeHDs). The mechanical signal generated by the onset of muscle contractions in the antero-posterior axis from mid-elongation is translated into a biochemical pathway controlling the maturation of CeHDs in the dorsal and ventral epidermis [11]. Consistently, mutations affecting muscle contractions or molecular tendons lead to a mid-elongation arrest [12]. Here, we found that the mechanical force generated by muscle contractions and relayed by molecular tendons is transmitted by adherens junctions to lateral epidermal cells, where it establishes a newly identified bipolar planar polarity of the apical PAR module. The planar polarized PAR module is then required for actin planar organization, thus contributing to the determination of the orientation of cell-shape changes and the elongation axis of the whole embryo. This mechanotransduction pathway is therefore essential to coordinate the morphogenesis of three embryonic tissues.
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http://dx.doi.org/10.1016/j.cub.2019.02.059DOI Listing
April 2019

Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism.

Biotechnol Bioeng 2018 10 25;115(10):2604-2612. Epub 2018 Jul 25.

Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden.

Modeling of metabolism at the genome-scale has proved to be an efficient method for explaining the phenotypic traits observed in living organisms. Further, it can be used as a means of predicting the effect of genetic modifications for example, development of microbial cell factories. With the increasing amount of genome sequencing data available, there exists a need to accurately and efficiently generate such genome-scale metabolic models (GEMs) of nonmodel organisms, for which data is sparse. In this study, we present an automatic reconstruction approach applied to 24 Penicillium species, which have potential for production of pharmaceutical secondary metabolites or use in the manufacturing of food products, such as cheeses. The models were based on the MetaCyc database and a previously published Penicillium GEM and gave rise to comprehensive genome-scale metabolic descriptions. The models proved that while central carbon metabolism is highly conserved, secondary metabolic pathways represent the main diversity among species. The automatic reconstruction approach presented in this study can be applied to generate GEMs of other understudied organisms, and the developed GEMs are a useful resource for the study of Penicillium metabolism, for example, for the scope of developing novel cell factories.
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http://dx.doi.org/10.1002/bit.26739DOI Listing
October 2018

A targeted 3D EM and correlative microscopy method using SEM array tomography.

Development 2018 06 21;145(12). Epub 2018 Jun 21.

University of Rennes 1, UMS Biosit, MRic, 35043 Rennes, France

Using electron microscopy to localize rare cellular events or structures in complex tissue is challenging. Correlative light and electron microscopy procedures have been developed to link fluorescent protein expression with ultrastructural resolution. Here, we present an optimized scanning electron microscopy (SEM) workflow for volumetric array tomography for asymmetric samples and model organisms (, , ). We modified a diamond knife to simplify serial section array acquisition with minimal artifacts. After array acquisition, the arrays were transferred to a glass coverslip or silicon wafer support. Using light microscopy, the arrays were screened rapidly for initial recognition of global anatomical features (organs or body traits). Then, using SEM, an in-depth study of the cells and/or organs of interest was performed. Our manual and automatic data acquisition strategies make 3D data acquisition and correlation simpler and more precise than alternative methods. This method can be used to address questions in cell and developmental biology that require the efficient identification of a labeled cell or organelle.
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http://dx.doi.org/10.1242/dev.160879DOI Listing
June 2018

Nature-Based Tourism Elicits a Phenotypic Shift in the Coping Abilities of Fish.

Front Physiol 2018 5;9:13. Epub 2018 Feb 5.

Graduate Program in Ecology, University of Brasília, Distrito Federal, Brazil.

Nature-based tourism is gaining extensive popularity, increasing the intensity and frequency of human-wildlife contacts. As a consequence, behavioral and physiological alterations were observed in most exposed animals. However, while the majority of these studies investigated the effects of punctual exposure to tourists, the consequences of constant exposition to humans in the wild remains overlooked. This is an important gap considering the exponential interest for recreational outdoor activities. To infer long-term effects of intensive tourism, we capitalized on , a short-lived sedentary Tetra fish who spends its life close to humans, on which it feeds on dead skin. Hence, those fish are constantly exposed to tourists throughout their lifecycle. Here we provide an integrated picture of the whole phenomenon by investigating, for the first time, the expression of genes involved in stress response and neurogenesis, as well as behavioral and hormonal responses of animals consistently exposed to tourists. Gene expression of the mineralocorticoid (and cortisol) receptor () and the neurogenic differentiation factor () were significantly higher in fish sampled in the touristic zone compared to those sampled in the control zone. Additionally, after a simulated stress in artificial and controlled conditions, those fish previously exposed to visitors produced more cortisol and presented increased behavioral signs of stress compared to their non-exposed conspecifics. Overall, nature-based tourism appeared to shift selection pressures, favoring a sensitive phenotype that does not thrive under natural conditions. The ecological implications of this change in coping style remain, nevertheless, an open question.
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http://dx.doi.org/10.3389/fphys.2018.00013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807742PMC
February 2018

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.

Nat Microbiol 2017 Apr 3;2:17044. Epub 2017 Apr 3.

Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.

Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.
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http://dx.doi.org/10.1038/nmicrobiol.2017.44DOI Listing
April 2017

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.

PLoS Comput Biol 2017 01 27;13(1):e1005276. Epub 2017 Jan 27.

Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France.

Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.
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http://dx.doi.org/10.1371/journal.pcbi.1005276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302834PMC
January 2017

Neurite analyzer: An original Fiji plugin for quantification of neuritogenesis in two-dimensional images.

J Neurosci Methods 2016 09 20;271:86-91. Epub 2016 Jul 20.

Transcription, Environment and Cancer Group, Institute of Research in Environmental and Occupational Health (IRSET), INSERM, Rennes, France. Electronic address:

Background: In life sciences, there is a growing need for new informatics tools designed to provide automated solutions in order to analyze big amounts of images obtained from high-throughput imaging systems. Among the most widely used assays in neurotoxicity, endocrinology and brain diseases, the neurite outgrowth assay is popular.

New Method: Cell-to-cell quantification of the main morphological features of neurite outgrowth assays remains very challenging. Here, we provide a new pipeline developed on Fiji software for analysis of series of two-dimensional images. It allows the automated analysis of most of these features.

Results: We tested the accuracy and usefulness of the software by confirming the effects of estradiol and hypoxia on in vitro neuronal differentiation, previously published by different authors with manual analysis methods. With this new method, we highlighted original interesting data.

Comparison With Existing Method(s): The innovation brought by this plugin lies in the fact that it can process multiple images at the same time, in order to obtain: the number of nuclei, the number of neurites, the length of neurites, the number of neurites junctions, the number of neurites branches, the length of each branch, the position of the branch in the image, the angle of each branch, but also the area of each cell and the number of neurites per cell.

Conclusions: This plugin is easy to use, highly sensitive, and allows the experimenter to acquire ready-to-use data coming from a vast amount of images.
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http://dx.doi.org/10.1016/j.jneumeth.2016.07.011DOI Listing
September 2016

Unlocking the potential of fungi: the QuantFung project.

Fungal Biol Biotechnol 2015 16;2. Epub 2015 Sep 16.

Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1186/s40694-015-0016-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611658PMC
September 2015

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.

Plant J 2014 Oct 27;80(2):367-81. Epub 2014 Aug 27.

Université de Rennes 1, IRISA UMR 6074, Campus de Beaulieu, 35042, Rennes, France; CNRS, IRISA UMR 6074, Campus de Beaulieu, 35042, Rennes, France; Centre Rennes-Bretagne-Atlantique, Projet Dyliss, INRIA, Campus de Beaulieu, 35042, Rennes Cedex, France.

Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post-genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome-scale metabolic network for E. siliculosus, EctoGEM (http://ectogem.irisa.fr). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co-factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.
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http://dx.doi.org/10.1111/tpj.12627DOI Listing
October 2014

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.

OMICS 2011 Dec 2;15(12):883-92. Epub 2011 Dec 2.

UPMC Univ Paris 6 , UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.

Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.
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http://dx.doi.org/10.1089/omi.2011.0089DOI Listing
December 2011

Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network.

Mol Reprod Dev 2010 Mar;77(3):257-64

UPMC univ Paris 06, UMR 7150 Mer et santé, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique, Roscoff, France.

The large and rapid increase in the rate of protein synthesis following fertilization of the sea urchin egg has long been a paradigm of translational control, an important component of the regulation of gene expression in cells. This translational up-regulation is linked to physiological changes that occur upon fertilization and is necessary for entry into first cell division cycle. Accumulated knowledge on cap-dependent initiation of translation makes it suited and timely to start integrating the data into a system view of biological functions. Using a programming environment for system biology coupled with model validation (named Biocham), we have built an integrative model for cap-dependent initiation of translation. The model is described by abstract rules. It contains 51 reactions involved in 74 molecular complexes. The model proved to be coherent with existing knowledge by using queries based on computational tree logic (CTL) as well as Boolean simulations. The model could simulate the change in translation occurring at fertilization in the sea urchin model. It could also be coupled with an existing model designed for cell-cycle control. Therefore, the cap-dependent translation initiation model can be considered a first step towards the eukaryotic translation regulation network.
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http://dx.doi.org/10.1002/mrd.21142DOI Listing
March 2010
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