Eric Maréchal

Cea Leti, Grenoble, Rhône-Alpes, France

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Publications (85)436.04 Total impact

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    ABSTRACT: Inorganic phosphate (Pi) is present in most soils at sub-optimal concentrations, strongly limiting plant development. Plants have the ability to sense and adapt to the surrounding ionic environment, and several genes involved in the response to Pi starvation have been identified. However, a global understanding of the regulatory mechanisms involved in this process is still elusive. Here, we have initiated a "chemical genetics" approach and isolated compounds that inhibit the response to Pi starvation in Arabidopsis thaliana. Molecules were screened for their ability to inhibit the expression of a Pi starvation marker gene (the high-affinity Pi transporter PHT1;4). A drug family named Phosphatin (Phosphate starvation inhibitor: PTN) was thus identified, whose members act as partial suppressors of Pi starvation responses. PTN addition also reduced various traits of Pi starvation such as phospholipid/glycolipid conversion, and the accumulation of starch and anthocyanins. A transcriptomic assay revealed a broad impact of PTN on the expression of many genes regulated by low Pi availability. Despite the reduced amount of Pi transporters and resulting reduced Pi uptake capacity, no reduction of Pi content was observed. In addition, PTN improved plant growth; this reveals that the developmental restrictions induced by Pi starvation are not a consequence of metabolic limitation, but also result from genetic regulation. This highlights the existence of signal transduction pathway(s) that limit plant development under the Pi starvation condition.
    Plant physiology. 09/2014;
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    ABSTRACT: The metabolic profiling of various microalga species and their genetic variants, grown under varied environmental conditions, has become critical to accelerate the exploration of phytoplankton biodiversity and biology. The accumulation of valuable metabolites, such as glycerolipids, is also sought in microalgae for biotechnological applications ranging from food, feed, medicine, cosmetics to bioenergy and green chemistry. In this report we describe the direct analysis of metabolites and glycerolipids in small cell populations of the green alga Chlamydomonas reinhardtii, using laser ablation electrospray ionization (LAESI) mass spectrometry (MS) coupled with ion mobility separation (IMS). These microorganisms are capable of redirecting energy storage pathways from starch to neutral lipids depending on environmental conditions and nutrient availability. Metabolite and lipid production was monitored in wild type (WT), and genetically modified C. reinhardtii strains with an impaired starch pathway. Lipids, such as triacylglycerols (TAG) and diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) were monitored over time under altered light conditions. More than 200 ions related to metabolites, e.g., arginine, cysteine, serine, palmitate, chlorophyll a, chlorophyll b, etc., were detected. The lipid profiles at different light intensities for strains with impaired starch pathway (Sta1 and Sta6) contained 26 glycerolipids, such as DGTS, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), as well as 33 TAG species. Results were obtained over a 72-hour time period in high and low light conditions for the WT species and the two mutants. Our results indicate that LAESI-IMS-MS can be utilized for the rapid analysis of increased TAG production at elevated light intensities. Compared to WT, the Sta6 strain showed 2.5-times higher lipid production at 72 hours under high light conditions. The results demonstrate our ability to rapidly observe numerous changes in metabolite and lipid levels in microalgae populations. These capabilities are expected to facilitate the exploration of genetically altered microalgae strains for biofuel production.
    The Analyst 09/2014; · 4.23 Impact Factor
  • Eric Maréchal, Olivier Bastien
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    ABSTRACT: In Angiosperms, the biosynthesis of galactolipids involves enzymes localized in the inner envelope membrane (IEM) of chloroplasts, including a phosphatidic acid phosphatase (PAP), dephosphorylating phosphatidic acid (PA) into diacylglycerol (DAG), and MGD1, transferring a galactose onto DAG thus generating monogalactosyldiacylglycerol (MGDG). It has been shown that PA and DAG could be synthesized in the plastid via the so-called 'prokaryotic' pathway or imported from the endoplasmic reticulum via the 'eukaryotic' pathway. In vitro studies support the existence of (1) a negative regulation of the plastid PAP by DAG and (2) an activation of MGD1 by PA. We developed a mathematical model of the IEM galactolipid biosynthesis pathway to understand the properties of the system ruled by the presence of these two regulatory motifs. We demonstrated that the design of the system implies that PA should accumulate to levels that are not observed experimentally, regardless of its prokaryotic or eukaryotic origin. PA should therefore be used for other syntheses, such as that of phosphatidylglycerol. Whereas a massive influx of eukaryotic PA appears unlikely, an influx of eukaryotic DAG in the IEM is supported by simulations. The model also implies that DAG cannot transiently accumulate and that PA mainly acts as a signal switching the whole system on. Eventually, this analysis highlights the fact that the PAP enzyme could easily become dispensable and that the design of the system, with the two regulatory motifs, could precede the loss of the PAP gene or activity in this pathway, a phenomenon that occurred independently in most clades of Angiosperms.
    Journal of Theoretical Biology 07/2014; · 2.35 Impact Factor
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    ABSTRACT: Thylakoid membranes, the universal structure where photosynthesis takes place in all oxygenic photosynthetic organisms from cyanobacteria to higher plants, have a unique lipid composition. They contain a high fraction of 2 uncharged glycolipids, the galactoglycerolipids mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively), and an anionic sulfolipid, sulfoquinovosediacylglycerol (SQDG). A remarkable feature of the evolution from cyanobacteria to higher plants is the conservation of MGDG, DGDG, SQDG, and phosphatidylglycerol (PG), the major phospholipid of thylakoids. Using neutron diffraction on reconstituted thylakoid lipid extracts, we observed that the thylakoid lipid mixture self-organizes as a regular stack of bilayers. This natural lipid mixture was shown to switch from hexagonal II toward lamellar phase on hydration. This transition and the observed phase coexistence are modulated by the fine-tuning of the lipid profile, in particular the MGDG/DGDG ratio, and by the hydration. Our analysis highlights the critical role of DGDG as a contributing component to the membrane stacking via hydrogen bonds between polar heads of adjacent bilayers. DGDG interactions balance the repulsive electrostatic contribution of the charged lipids PG and SQDG and allow the persistence of regularly stacked membranes at high hydration. In developmental contexts or in response to environmental variations, these properties can contribute to the highly dynamic flexibility of plastid structure.-Demé, B., Cataye, C., Block, M. A., Maréchal, E., Jouhet, J. Contribution of galactoglycerolipids to the 3-dimensional architecture of thylakoids.
    The FASEB Journal 04/2014; · 5.70 Impact Factor
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    ABSTRACT: Mono- and digalactosyldiacylglycerol (MGDG and DGDG) are the most abundant lipids of photosynthetic membranes (thylakoids). In Arabidopsis green tissues, MGD1 is the main enzyme synthesizing MGDG. This monotopic enzyme is embedded in the inner envelope membrane of chloroplasts. DGDG synthesis occurs in the outer envelope membrane. Although the suborganellar localization of MGD1 has been determined, it is still not known how the lipid/glycolipid composition influences its binding to the membrane. The existence of a topological relationship between MGD1 and "embryonic" thylakoids is also unknown. To investigate MGD1 membrane binding, we used a Langmuir membrane model allowing the tuning of both lipid composition and packing. Surprisingly, MGD1 presents a high affinity to MGDG, its product, which maintains the enzyme bound to the membrane. This positive feedback is consistent with the low level of diacylglycerol, the substrate of MGD1, in chloroplast membranes. By contrast, MGD1 is excluded from membranes highly enriched in, or made of, pure DGDG. DGDG therefore exerts a retrocontrol, which is effective on the overall synthesis of galactolipids. Previously identified activators, phosphatidic acid and phosphatidylglycerol, also play a role on MGD1 membrane binding via electrostatic interactions, compensating the exclusion triggered by DGDG. The opposite effects of MGDG and DGDG suggest a role of these lipids on the localization of MGD1 in specific domains. Consistently, MGDG induces the self-organization of MGD1 into elongated and reticulated nanostructures scaffolding the chloroplast membrane.-Sarkis, J., Rocha, J., Maniti, O., Jouhet, J., Vié, V., Block, M. A., Breton, C., Maréchal, E., Girard-Egrot, A. The influence of lipids on MGD1 membrane binding highlights novel mechanisms for galactolipid biosynthesis regulation in chloroplasts.
    The FASEB Journal 04/2014; · 5.70 Impact Factor
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    ABSTRACT: Photosynthetic membranes have a unique lipid composition that has been remarkably well conserved from cyanobacteria to chloroplasts. These membranes are characterized by a very high content in galactoglycerolipids, i.e., mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively). Galactoglycerolipids make up the bulk of the lipid matrix in which photosynthetic complexes are embedded. They are also known to fulfill specific functions, such as stabilizing photosystems, being a source of polyunsaturated fatty acids for various purposes and, in some eukaryotes, being exported to other subcellular compartments. The conservation of MGDG and DGDG suggests that selection pressures might have conserved the enzymes involved in their biosynthesis, but this does not appear to be the case. Important evolutionary transitions comprise primary endosymbiosis (from a symbiotic cyanobacterium to a primary chloroplast) and secondary endosymbiosis (from a symbiotic unicellular algal eukaryote to a secondary plastid). In this review, we compare biosynthetic pathways based on available molecular and biochemical data, highlighting enzymatic reactions that have been conserved and others that have diverged or been lost, as well as the emergence of parallel and alternative biosynthetic systems originating from other metabolic pathways. Questions for future research are highlighted.
    Progress in lipid research 03/2014; · 10.67 Impact Factor
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    ABSTRACT: A piperidinyl-benzimidazolidinone scaffold has been found in the structure of different inhibitors of membrane glycerolipid metabolism, acting on enzymes manipulating diacylglycerol or phosphatidic acid. Screening a focus library of piperidinyl-benzimidazolidinone analogs might therefore identify compounds acting against infectious parasites. We first evaluated the in vitro effects of (S)-2-(dibenzylamino)-3-phenylpropyl 4-(1,2-dihydro-2-oxobenzo[d]imidazol-3-yl)piperidine-1-carboxylate (compound 1) on Toxoplasma gondii and Plasmodium falciparum. In T. gondii, motility and apical complex integrity appeared unaffected, whereas cell division was inhibited at concentrations of compound 1 in the micromolar range. In P. falciparum, proliferation of erythrocytic stages was inhibited, without any delayed death phenotype. We then explored a library of 250 analogs in two steps. We selected 114 compounds with an IC50 cutoff of 2 μM on at least one species and determined in vitro selectivity indexes (SI), based on toxicity against K-562 human cells. We identified compounds with high gains in IC50 (in the 100 nM range) and SI (up to 1,000-2,000). Isobole analyses of two of the most active compounds against P. falciparum indicated that their interaction with artemisin was additive. We propose structure activity relationship (SAR) models, which will be useful for the design of probes to identify the compounds' target(s), and optimizations for mono- or combined-therapeutic strategies.
    Antimicrobial Agents and Chemotherapy 02/2014; · 4.57 Impact Factor
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    ABSTRACT: Probing molecules using perdeuteration (i.e deuteration in which all hydrogen atoms are replaced by deuterium) is extremely useful in a wide range of biophysical techniques. In the case of lipids, the synthesis of the biologically relevant unsaturated perdeuterated lipids is challenging and not usually pursued. In this work, perdeuterated phospholipids and sterols from the yeast Pichia pastoris grown in deuterated medium are extracted and analyzed as derivatives by gas chromatography and mass spectrometry respectively. When yeast cells are grown in a deuterated environment, the phospholipid homeostasis is maintained but the fatty acid unsaturation level is modified while the ergosterol synthesis is not affected by the deuterated culture medium. Our results confirm that the production of well defined natural unsaturated perdeuterated lipids is possible and gives also new insights about the process of desaturase enzymes.
    PLoS ONE 01/2014; 9(4):e92999. · 3.53 Impact Factor
  • Laurence Boudière, Eric Maréchal
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    ABSTRACT: The knowledge of the membrane lipid metabolism in photosynthetic cells is expected to benefit from the availability of inhibitors acting at the level of specific enzymes like MGD1 (E.C. 2.4.1.46) that catalyzes the synthesis of monogalactosyldiacylglycerol (MGDG) in chloroplasts. MGDG is a major lipid of photosynthetic membrane, interacting with photosystems. It is the precursor of digalactosyldiacylglycerol that serves as a phospholipid surrogate when plants are deprived of phosphate, and it is a source of polyunsaturated fatty acids for jasmonic acid syntheses. MGD1 is activated by phosphatidic acid and thus a coupling point between phospholipid and galactolipid metabolisms. Here we describe a method to screen for inhibitors of MGD1 assayed in liposomes. Selected compounds can therefore reach the core of the biological membranes in which the target sits. We then describe a secondary screen to evaluate the efficiency of developed compounds at the whole plant level. Major issues raised by the screening of inhibitors acting on membrane proteins are discussed and can be useful for similar targets.
    Methods in molecular biology (Clifton, N.J.) 01/2014; 1056:79-93. · 1.29 Impact Factor
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    ABSTRACT: The understanding of chloroplast function requires the precise localization of proteins in each of its sub-compartments. High-sensitivity mass spectrometry has allowed the inventory of proteins in thylakoid, stroma, and envelope fractions. Concerning membrane association, proteins can be either integral or peripheral or even soluble proteins bound transiently to a membrane complex. We sought a method providing information at the surface of the outer envelope membrane (OEM), based on specific tagging with biotin or proteolysis using thermolysin, a non-membrane permeable protease. To evaluate this method, envelope, thylakoid, and stroma proteins were separated by two-dimensional electrophoresis and analyzed by immunostaining and mass spectrometry. A short selection of proteins associated to the chloroplast envelope fraction was checked after superficial treatments of intact chloroplasts. We showed that this method could allow the characterization of OEM embedded proteins facing the cytosol, as well as peripheral and soluble proteins associated via tight or lose interactions. Some stromal proteins were associated with biotinylated spots and analyzes are still needed to determine whether polypeptides were tagged prior import or if they co-migrated with OEM proteins. This method also suggests that some proteins associated with the inner envelope membrane (IEM) might need the integrity of a trans-envelope (IEM-OEM) protein complex (e.g., division ring-forming components) or at least an intact OEM partner. Following this evaluation, proteomic analyzes should be refined and the putative role of inter-membrane space components stabilizing trans-envelope complexes demonstrated. For future comprehensive studies, perspectives include the dynamic analyses of OEM proteins and IEM-OEM complexes in various physiological contexts and using virtually any other purified membrane organelle.
    Frontiers in Plant Science 01/2014; 5:203. · 3.60 Impact Factor
  • Cyrille Y Botté, Eric Maréchal
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    ABSTRACT: In structural, functional, and evolutionary terms, galactoglycerolipids are signature lipids of chloroplasts. Their presence in nongreen plastids has been demonstrated in angiosperms and diatoms. Thus, galactoglycerolipids are considered as a landmark of green and nongreen plastids, deriving from either a primary or secondary endosymbiosis. The discovery of a plastid in Plasmodium falciparum, the causative agent of malaria, fueled the search for galactoglycerolipids as possible targets for treatments. However, recent data have provided evidence that the Plasmodium plastid does not contain any galactoglycerolipids. In this opinion article, we discuss questions raised by the loss of galactoglycerolipids during evolution: how have galactoglycerolipids been lost? How does the Plasmodium plastid maintain four membranes without these lipids? What are the main constituents instead of galactoglycerolipids?
    Trends in Plant Science 11/2013; · 11.81 Impact Factor
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    ABSTRACT: Glycerolipids constituting the matrix of photosynthetic membranes, from cyanobacteria to chloroplasts of eukaryotic cells, comprise monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol and phosphatidylglycerol. This review covers our current knowledge on the structural and functional features of these lipids in various cellular models, from prokaryotes to eukaryotes. Their relative proportions in thylakoid membranes result from highly regulated and compartmentalized metabolic pathways, with a cooperation, in the case of eukaryotes, of non plastidic compartments. This review also focuses on the role of each of these thylakoid glycerolipids in stabilizing protein complexes of the photosynthetic machinery, which might be one of the reasons for their fascinating conservation in the course of evolution. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.
    Biochimica et Biophysica Acta 09/2013; · 4.66 Impact Factor
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    ABSTRACT: The human malaria parasite Plasmodium falciparum harbors a relict, nonphotosynthetic plastid of algal origin termed the apicoplast. Although considerable progress has been made in defining the metabolic functions of the apicoplast, information on the composition and biogenesis of the four delimiting membranes of this organelle is limited. Here, we report an efficient method for preparing highly purified apicoplasts from red blood cell parasite stages and the comprehensive lipidomic analysis of this organelle. Apicoplasts were prepared from transgenic parasites expressing an epitope-tagged triosephosphate transporter and immunopurified on magnetic beads. Gas and liquid chromatography MS analyses of isolated apicoplast lipids indicated significant differences compared with total parasite lipids. In particular, apicoplasts were highly enriched in phosphatidylinositol, consistent with a suggested role for phosphoinositides in targeting membrane vesicles to apicoplasts. Apicoplast phosphatidylinositol and other phospholipids were also enriched in saturated fatty acids, which could reflect limited acyl exchange with other membrane phospholipids and/or a requirement for specific physical properties. Lipids atypical for plastids (sphingomyelins, ceramides, and cholesterol) were detected in apicoplasts. The presence of cholesterol in apicoplast membranes was supported by filipin staining of isolated apicoplasts. Galactoglycerolipids, dominant in plant and algal plastids, were not detected in P. falciparum apicoplasts, suggesting that these glycolipids are a hallmark of photosynthetic plastids and were lost when these organisms assumed a parasitic lifestyle. Apicoplasts thus contain an atypical melange of lipids scavenged from the human host alongside lipids remodeled by the parasite cytoplasm, and stable isotope labeling shows some apicoplast lipids are generated de novo by the organelle itself.
    Proceedings of the National Academy of Sciences 04/2013; · 9.81 Impact Factor
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    ABSTRACT: Microalgae of the genus Nannochloropsis are capable of accumulating triacylglycerols when exposed to nutrient limitation (in particular nitrogen, N) and are therefore considered promising organisms for biodiesel production. Here, after nitrogen removal from the medium, Nannochloropsis gaditana cells show extensive triacylglycerol accumulation (38%TAG on a dry-weight basis). Triacylglycerols accumulated during N deprivation harbor signatures indicating they mainly stem from freshly synthesized fatty acids with a small proportion originating from a recycling of membrane glycerolipids. The amount of chloroplast galactoglycerolipids, which are essential for the integrity of thylakoids, decreases while their fatty acid composition appears unaltered. In starved cells, galactolipids are kept at a sufficient level to maintain chloroplast integrity as confirmed by electron microscopy. Consistently, N starved Nannochloropsis cells contain less photosynthetic membranes but are still efficiently performing photosynthesis. N starvation leads to a modification of photosynthetic apparatus with a change in pigment composition and a decrease in the content of all the major electron flow complexes, including Photosystem II, Photosystem I and the Cytochrome b6f complex. The Photosystem II content is particularly affected, leading to the inhibition of linear electron flow from water to CO2. Such a reduction, however, is partially compensated for by activation of alternative electron pathways such as cyclic electron transport. Overall, these changes allow cells to modify their energetic metabolism in order to maintain photosynthetic growth.
    Eukaryotic Cell 03/2013; · 3.59 Impact Factor
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    ABSTRACT: Monogalactosyldiacylglycerol, the major lipid of plants and algal plastids, is synthesized by MGDG synthases (MGD). MGDs belong to the large glycosyltransferase family. They catalyze the transfer of a galactose residue from the donor UDP-Gal to an 1,2-sn-diacylglycerol acceptor. MGDs are monotopic proteins localized in the plastid envelope and, as such, they are difficult to purify. This study re-examined previous purification procedures and aimed to set up a standard protocol for expression and purification of recombinant MGD1, addressing problems frequently encountered with the purification of glycosyltransferases, particularly protein aggregation, and enabling crystallization for structural studies. Briefly, His-tagged versions of MGD1 were expressed in E. coli and purified by a two-step procedure, including immobilized metal affinity chromatography and size-exclusion chromatography. We demonstrated that E. coli is an appropriate host cell to produce a soluble and active form of MGD1. We also investigated the effects of various buffers and additives used during the purification and concentration steps on the biochemical behavior of the enzyme. The protocol we developed typically yields milligram quantities of pure and homogenous protein material and proved suitable for crystallization and biochemical studies. We also revisited the conditions for activity tests and effects of known positive effectors of MGD1 such as phosphatidic acid and phosphatidylglycerol.
    Biochimie 11/2012; · 3.14 Impact Factor
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    ABSTRACT: Plastids are semiautonomous organelles derived from cyanobacterial ancestors. Following endosymbiosis, plastids have evolved to optimize their functions, thereby limiting metabolic redundancy with other cell compartments. Contemporary plastids have also recruited proteins produced by the nuclear genome of the host cell. In addition, many genes acquired from the cyanobacterial ancestor evolved to code for proteins that are targeted to cell compartments other than the plastid. Consequently, metabolic pathways are now a patchwork of enzymes of diverse origins, located in various cell compartments. Because of this, a wide range of metabolites and ions traffic between the plastids and other cell compartments. In this review, we provide a comprehensive analysis of the well-known, and of the as yet uncharacterized, chloroplast/cytosol exchange processes, which can be deduced from what is currently known about compartmentation of plant-cell metabolism. Expected final online publication date for the Annual Review of Genetics Volume 46 is November 02, 2012. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
    Annual Review of Genetics 08/2012; · 17.44 Impact Factor
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    ABSTRACT: Plant cells are characterized by the presence of chloroplasts, membrane lipids of which contain up to ∼80% mono- and digalactosyldiacylglycerol (MGDG and DGDG). The synthesis of MGDG in the chloroplast envelope is essential for the biogenesis and function of photosynthetic membranes, is coordinated with lipid metabolism in other cell compartments and is regulated in response to environmental factors. Phenotypic analyses of Arabidopsis using the recently developed specific inhibitor called galvestine-1 complete previous analyses performed using various approaches, from enzymology, cell biology to genetics. This review details how this probe could be beneficial to study the lipid homeostasis system at the whole cell level and highlights connections between MGDG synthesis and Arabidopsis flower development.
    Molecular BioSystems 05/2012; 8(8):2023-35, 2014. · 3.35 Impact Factor
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    ABSTRACT: Malaria is one of the major global health problems. About 500 million humans are infected each year, and 1 million, mostly African children, die from malaria annually. No vaccine is yet in sight, and those drugs that have previously served us well are now losing ground against the disease as parasites become resistant to our best compounds. The need for development of new antimalarials is now more urgent than ever. An exciting avenue for development of new drugs emerged recently when it was discovered that the malaria parasites have a previously unrecognized evolutionary history aligned to plants. These parasites contain a subcellular compartment--the apicoplast--which is homologous to the chloroplast of plants and algae, in which photosynthesis occurs. The malaria chloroplast (apicoplast) has lost photosynthesis but it retains many chloroplast pathways, which are otherwise unique to plants. These pathways obviously do not exist in the human host and there has been considerable excitement about using the apicoplast as a parasite-specific Achilles' Heel. We propose to review the current state of development of novel compounds directed against this emerging target of malaria parasites with emphasis on the chemistry.
    Current pharmaceutical design 05/2012; 18(24):3490-504. · 4.41 Impact Factor
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    ABSTRACT: Glutamine amidotransferase/aminodeoxychorismate synthase (GAT-ADCS) is a bifunctional enzyme involved in the synthesis of p-aminobenzoate, a central component part of folate cofactors. GAT-ADCS is found in eukaryotic organisms autonomous for folate biosynthesis, such as plants or parasites of the phylum Apicomplexa. Based on an automated screening to search for new inhibitors of folate biosynthesis, we found that rubreserine was able to inhibit the glutamine amidotransferase activity of the plant GAT-ADCS with an apparent IC(50) of about 8 μM. The growth rates of Arabidopsis thaliana, Toxoplasma gondii, and Plasmodium falciparum were inhibited by rubreserine with respective IC(50) values of 65, 20, and 1 μM. The correlation between folate biosynthesis and growth inhibition was studied with Arabidopsis and Toxoplasma. In both organisms, the folate content was decreased by 40-50% in the presence of rubreserine. In both organisms, the addition of p-aminobenzoate or 5-formyltetrahydrofolate in the external medium restored the growth for inhibitor concentrations up to the IC(50) value, indicating that, within this range of concentrations, rubreserine was specific for folate biosynthesis. Rubreserine appeared to be more efficient than sulfonamides, antifolate drugs known to inhibit the invasion and proliferation of T. gondii in human fibroblasts. Altogether, these results validate the use of the bifunctional GAT-ADCS as an efficient drug target in eukaryotic cells and indicate that the chemical structure of rubreserine presents interesting anti-parasitic (toxoplasmosis, malaria) potential.
    Journal of Biological Chemistry 05/2012; 287(26):22367-76. · 4.65 Impact Factor
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    ABSTRACT: Hidden Markov Models (HMMs) are a powerful tool for protein domain identification. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in new sequenced organisms. In Pfam, each domain family is represented by a curated multiple sequence alignment from which a profile HMM is built. In spite of their high specificity, HMMs may lack sensitivity when searching for domains in divergent organisms. This is particularly the case for species with a biased amino-acid composition, such as P. falciparum, the main causal agent of human malaria. In this context, fitting HMMs to the specificities of the target proteome can help identify additional domains. Using P. falciparum as an example, we compare approaches that have been proposed for this problem, and present two alternative methods. Because previous attempts strongly rely on known domain occurrences in the target species or its close relatives, they mainly improve the detection of domains which belong to already identified families. Our methods learn global correction rules that adjust amino-acid distributions associated with the match states of HMMs. These rules are applied to all match states of the whole HMM library, thus enabling the detection of domains from previously absent families. Additionally, we propose a procedure to estimate the proportion of false positives among the newly discovered domains. Starting with the Pfam standard library, we build several new libraries with the different HMM-fitting approaches. These libraries are first used to detect new domain occurrences with low E-values. Second, by applying the Co-Occurrence Domain Discovery (CODD) procedure we have recently proposed, the libraries are further used to identify likely occurrences among potential domains with higher E-values. We show that the new approaches allow identification of several domain families previously absent in the P. falciparum proteome and the Apicomplexa phylum, and identify many domains that are not detected by previous approaches. In terms of the number of new discovered domains, the new approaches outperform the previous ones when no close species are available or when they are used to identify likely occurrences among potential domains with high E-values. All predictions on P. falciparum have been integrated into a dedicated website which pools all known/new annotations of protein domains and functions for this organism. A software implementing the two proposed approaches is available at the same address: http://www.lirmm.fr/∼terrapon/HMMfit/
    BMC Bioinformatics 05/2012; 13:67. · 3.02 Impact Factor

Publication Stats

1k Citations
436.04 Total Impact Points

Institutions

  • 2014
    • Cea Leti
      Grenoble, Rhône-Alpes, France
  • 2001–2014
    • Atomic Energy and Alternative Energies Commission
      • • Cell and Plant Physiology (PCV)
      • • Institute of life sciences research and technologies (iRTSV)
      Gif, Île-de-France, France
    • Tokyo Institute of Technology
      • Graduate School of Bioscience and Biotechnology
      Tokyo, Tokyo-to, Japan
  • 1995–2014
    • University Joseph Fourier - Grenoble 1
      • Laboratoire de Physiologie Cellulaire Végétale
      Grenoble, Rhône-Alpes, France
  • 2013
    • University of Grenoble
      Grenoble, Rhône-Alpes, France
  • 1994–2013
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France
  • 2012
    • University of Lille Nord de France
      Lille, Nord-Pas-de-Calais, France
  • 2011
    • Paris Diderot University
      Lutetia Parisorum, Île-de-France, France
  • 2006
    • University of Pretoria
      • Faculty of Natural and Agricultural Sciences
      Pretoria, Gauteng, South Africa
  • 2002
    • Philipps University of Marburg
      Marburg, Hesse, Germany
  • 1999
    • The Rockefeller University
      • Laboratory of Plant Molecular Biology
      New York City, NY, United States
    • Institut de Génétique et de Biologie Moléculaire et Cellulaire
      Strasburg, Alsace, France