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Introduction
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February 2007 - present
April 2006 - February 2007
Publications
Publications (132)
In photosynthetic organisms, light acts as an environmental signal to control their development and physiology, as well as energy source to drive the conversion of CO2 into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular e...
Diatoms are a major phylum of microalgae, playing crucial ecological roles. They derive from secondary endosymbiosis of a red alga by an unknown heterotrophic eukaryote, leading to a complex intracellular organization. In response to unfavorable conditions (stress), diatoms store oil in lipid droplets (LD), raising interest for applications, in par...
In photosynthetic organisms light acts as an environmental signal to control their development and physiology, and as energy source to drive the conversion of CO2 into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energy...
In photosynthetic organisms light acts as an environmental signal to control their development and physiology, and as energy source to drive the conversion of CO 2 into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energ...
Background
Many organisms rely on mineral nutrients taken directly from the soil or aquatic environment, and therefore, developed mechanisms to cope with the limitation of a given essential nutrient. For example, photosynthetic cells have well-defined responses to phosphate limitation, including the replacement of cellular membrane phospholipids wi...
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and reg...
Photoautotrophs’ environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells...
Phosphate is vital for plant and algae growth, yield, and survival, but in most environments, it is poorly available. To cope with phosphate starvation, photosynthetic organisms used their phospholipids as a phosphate reserve. In microalgae, betaine lipids replace phospholipids whereas, in higher plants, betaine lipid synthesis is lost, driving pla...
Photoautotrophs environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells or organs. Furthermore, cells w...
The early steps in germination and development of angiosperm seedlings often occur in the dark, inducing a special developmental programme called skoto-morphogenesis. Under these conditions photosynthesis cannot work and all energetic requirements must be fulfilled by mitochondrial metabolization of storage energies. Here, we report the physiologic...
Diatoms are unicellular heterokonts, living in oceans and freshwaters, exposed to frequent environmental variations. They have a sophisticated membrane compartmentalization and are bounded by a siliceous cell-wall. Formation of lipid droplets (LDs), filled with triacylglycerol (TAG), is a common response to stress. The proteome of mature-LDs from P...
During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylo...
Tetrahydrofolate and its derivatives, commonly known as folates, are essential for almost all living organisms. Besides acting as one-carbon donors and acceptors in reactions producing various important biomolecules such as nucleic and amino acids, as well as pantothenate, they also supply one-carbon units for methylation reactions. Plants along wi...
Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures em...
Photosynthesis is a unique process that allows independent colonization of the land by plants and of the oceans by phytoplankton. Although the photosynthesis process is well understood in plants, we are still unlocking the mechanisms evolved by phytoplankton to achieve extremely efficient photosynthesis. Here, we combine biochemical, structural and...
Photosynthetic membranes, or thylakoids, are the most extensive membrane system found in the biosphere. They form flattened membrane cisternae in the cytosol of cyanobacteria and in the stroma of chloroplasts. The efficiency of light energy capture and conversion, critical for primary production in ecosystems, relies on the rapid expansion of thyla...
This presentation is related to H. Hessami’s Ph.D. Thesis on group based epidemiological models.
Rubisco and fructose-1,6-bisphosphate aldolases (FBAs) are involved in CO2 fixation in chloroplasts. Both enzymes are trimethylated at a specific lysine residue by the chloroplastic protein methyltransferase LSMT. Genes coding LSMT are present in all plant genomes but the methylation status of the substrates varies in a species-specific manner. For...
Photosynthetic membranes, or thylakoids, are the most extensive membrane system found in the biosphere. They form flattened membrane cisternae in the cytosol of cyanobacteria and in the stroma of chloroplasts. The efficiency of light energy capture and conversion, critical for primary production in ecosystems, relies on the rapid expansion of thyla...
Abstract. By nature, epidemic phenomena are catastrophic. However, when shall we begin to consider an event as catastrophic ? from which scale ? how can we measure them ? and especially, beyond the observation, how can we control them ? New data promised by the « Big Data » coupled to hybrid modelling approaches let hope for a possible return on in...
Diatoms constitute a major phylum of phytoplankton biodiversity in ocean and fresh water ecosystems. They are known to respond to some chemical variations of the environment by the accumulation of triacylglycerol, but the relative changes occurring in membrane glycerolipids has not yet been studied. Our goal was first to define a reference for the...
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 ha...
Pairwise comparison of data vectors represents a large part of computational biology, especially with the continuous increase
in genome-wide approaches yielding more information from more biological samples simultaneously. Gene clustering for function
prediction as well as analyses of signalling pathways and the time-dependent dynamics of a system...
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 va...
Natural immunity or resistance to pathogens most often relies on the genetic make-up of the host. In a LEW rat model of refractoriness to toxoplasmosis, we previously identified on chromosome 10 the Toxo1 locus that directs toxoplasmosis outcome and controls parasite spreading by a macrophage-dependent mechanism. Now, we narrowed down Toxo1 to a 89...
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...
microRNAs were recently found to be regulators of the host response to infection by apicomplexan parasites. In this study, we identified two immunomodulatory microRNAs, miR-146a and miR-155, that were coinduced in the brains of mice challenged with Toxoplasma in a strain-specific manner. These microRNAs define a characteristic fingerprint for infec...
Uranium is a natural element which is mainly redistributed in the environment due to human activity, including accidents and spillages. Plants may be useful in cleaning up after incidents, although little is yet known about the relationship between metal speciation and plant response. Here, J-Chess modeling was used to predict U speciation and expo...
After invading host cells, Toxoplasma gondii multiplies within a parasitophorous vacuole (PV) that is maintained by parasite proteins secreted from organelles called dense granules. Most dense granule proteins remain within the PV, and few are known to access the host cell cytosol. We identify GRA16 as a dense granule protein that is exported throu...
Artificial neural systems have been for the past thirty years a fascinating research topic with contributions from both theoreticians as well as from researchers implementing novel computational learning techniques into numerous application fields. Starting as an attempt to emulate human brain processing and cognition, supervised and unsupervised l...
All plastid membranes are characterized by the presence of large amounts of galactolipids. The galactolipid content of thylakoids
is especially high since galactolipids represent up to 80% of the membrane glycerolipids, out of which monogalactosyldiacylglycerol
(MGDG) constitutes the main part (50%). In its first part, this chapter describes the st...
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 a...
The number N of detectable (i.e. communicating) extraterrestrial
civilizations in the Milky Way galaxy is usually done by using the Drake
equation. This equation was established in 1961 by Frank Drake and was the
first step to quantifying the SETI field. Practically, this equation is rather
a simple algebraic expression and its simplistic nature le...
Plant hormones, in addition to regulating growth and development, are involved in biotic and abiotic stress responses. To investigate whether a hormone signalling pathway plays a role in the plant response to the heavy metal cadmium (Cd), gene expression data in response to eight hormone treatments were retrieved from the Genevestigator Arabidopsis...
Monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the main lipids in photosynthetic membranes in plant cells. They are synthesized in the envelope surrounding plastids by MGD and DGD galactosyltransferases. These galactolipids are critical for the biogenesis of photosynthetic membranes, and they act as a source of polyun...
Comparison of the Ramlibacter tataouinensis TTB310 genome against the closest proteobacterial genomes. Similarity searches were carried out between strain TTB310 and all the complete proteomes present in NCBI database, using BLASTP. The figure was generated with the results of the thirteen most similar genomes (12 betaproteobacteria, 1 alphaproteob...
Genes of
Ramlibacter tataouinensis
TTB310 potentially involved in peroxide scavenging pathways.
(TIFF)
Biosynthesis of even- and odd-numbered, straight and branched chain fatty acids from acetyl-CoA, propionyl-CoA and branched chain amino acids derivatives as starting units in Ramlibacter tataouinensis TTB310. Determining steps for the distribution of fatty acid molecular species in the final profile include the branched chain amino acid transaminas...
Experimental conditions for live optical imaging of
Ramlibacter tataouinensis
TTB310 (video S1).
(DOC)
Glycerolipid composition of Ramlibacter tataouinensis TTB310 membranes. PE, phosphatidylethanolamine, PC, phosphatidylcholine, PG, phosphatidylglycerol, DPG, diphosphatidylglycerol, PI, phosphoinositides. Glycerolipids (100 µg) were resolved by two-dimensional thin layer chromatography (first dimension, chloroform/methanol/water 65∶25∶4; second dim...
Characteristics of cell envelope transport systems in Ramlibacter tataouinensis TTB310. This table contains genes involved in: general export pathway (Sec translocation, SRP insertion and Tat translocation pathways, including predicted Tat substrates), Outer Membrane Protein (OMP) insertion machinery, Outer Membrane (OM) lipoproteins synthesis (inc...
Additional signal transduction, regulator and bifunctional proteins in
Ramlibacter tataouinensis
TTB310.
(DOC)
Live optical imaging of
Ramlibacter tataouinensis
TTB310 exhibiting both “cyst-to-rod” division step (in the middle of the screen) and “
rod-rod
” division (last images) (See Text S1 for details).
(AVI)
Sequence alignment of KaiC proteins centered on SynKaiC phosphorylable residues (T426, S431 and T432). Conserved T, ST are red coloured, S replacing T are green coloured, Y replacing T are blue coloured, T replacing S are pink coloured and other replacement with a non phosphorylable residue are italicized. KaiC proteins exhibiting one or several re...
Genes involved in autotrophic dicarboxylate/hydroxybutyrate cycle (carbohydrate metabolism), energetic metabolism, dissimilative nitrate reduction and cofactors and vitamins synthesis in Ramlibacter tataouinensis TTB310. Note that: i) ATP is generated by classical and complete oxidative phosphorylation including the five complexes [complex I (NADH...
DNA-binding proteins in Ramlibacter tataouinensis TTB310. This figure represents the distribution of the transcription factors found in R. tataouinensis.
(TIFF)
Representation of prokaryotic predicted KaiC proteins according to (1) their TULIP tree position, (2) nature of their phosphorylable sites and (3) their genetic organization. Proteins were classified using a distance matrix derived from Z-value probabilities (see Materials and Methods). We have integrated the RecA protein (Rta_37450, 351 residues)...
Carbohydrate-active enzymes (CAZymes) found in Ramlibacter tataouinensis TTB310. Note that this table contains: i) a list of CAZymes found in strain TTB310, ii) a comparison of CAZymes from strain TTB310 against seven betaproteobacterial genomes, and iii) a list of exported and potentially secreted glycosyl hydrolases.
(XLS)
Fatty acid composition of each membrane glycerolipid class extracted from Ramlibacter tataouinensis TTB310 cells. PE, phosphatidylethanolamine, PC, phosphatidylcholine, PG, phosphatidylglycerol, DPG, diphosphatidylglycerol, PI, phosphoinositol, FA, fatty acid.
(DOC)
Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-...
Whatever the phylogenetic method, genetic sequences are often described as strings of characters, thus molecular sequences can be viewed as elements of a multi-dimensional space. As a consequence, studying motion in this space (ie, the evolutionary process) must deal with the amazing features of high-dimensional spaces like concentration of measure...
Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focu...
Quantile-quantile plot of (top-left) the Gumbel theoretical quantile versus the data quantile. (top-right) the gamma theoretical quantile versus the data quantile. (down-left) our model theoretical quantile versus the data quantile. (top-left) our model theoretical quantile versus the Gumbel theoretical quantile.
Histogram of the distribution of random scores between the Response Regulator NtrC family proteins in Pseudomonas fluorescens Pf-5 and homologous proteins in Pseudomonas fluorescens Pf0-1 (Accession numbers PFL_0091 and Pfl01_0046). Only the second sequence was shuffled 1000 times. Red curve: Gumbel distribution with parameters θ = 33.27876 and β =...
Histogram of the distribution of random scores between the two-component system, NarL family, sensor histidine kinase in Pseudomonas fluorescens Pf-5 and homologous proteins in Pseudomonas fluorescens Pf0-1 (Accession numbers PFL_4451 and Pfl01_4222). Only the second sequence was shuffled 1000 times. Red curve: Gumbel distribution with parameters θ...
(Top Left) Histogram of the distribution of random scores between the rod shape-determining protein MreB in Pseudomonas fluorescens Pf-5 and the homologous protein in Pseudomonas fluorescens Pf0-1 (Accession numbers PFL_0896 and Pfl01_0838). Only the second sequence was shuffled 1000 times. Red curve: Gumbel distribution with parameters θ = 33.2078...
(Top Left) Histogram of the distribution of random scores between a hypothetical protein in Pseudomonas fluorescens Pf-5 and the homologous protein of Pseudomonas fluorescens Pf0-1 (Accession numbers PFL_5654 and Pfl01_5140). Only the second sequence was shuffled 1000 times. Red curve: Gumbel distribution with parameters θ = 32.25266 and β = 5.9411...
Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distribution...
Characteristics of Tg-miR-15 and -49. The miR-15/miR-49a (A) and miR49b (B) production hot spots in chromosome VIIb are shown alongside the predicted structure and the sequence conservation across parasite species. The mature region is shown in red for miR15 and miR49b and in green for miR-49a. Same legend as in Figure S2A.
(0.71 MB TIF)
Characteristics of Tg-miR-56. (A) A miR-56 production hot spot in chromosome XI is shown along with the predicted structure (B) and the sequence conservation across parasite species (C). The mature region is shown in red. Same legend as in Figure S2A.
(0.42 MB TIF)
Characteristics of Tg-miR-66. (A) A miR-66 production hot spot in chromosome XII is shown along with the predicted structure and (B) the sequence conservation across parasite species. The mature region is shown in red and the passenger strand (microRNA*) in blue. Same legend as in Figure S2A.
(0.59 MB TIF)
Characteristics of Tg-miR-65. (A) A miR-65 production hot spot in chromosome IX is shown along with the predicted structure and (B) the sequence conservation across parasite species. The mature region is shown in red and the passenger strand (microRNA*) in blue. Same legend as in Figure S2A.
(0.45 MB TIF)
T. gondii small RNAs cloning. (A) Ethidium bromide was used to visualize small RNAs in total RNA extracted from Toxoplasma cultures. A spiked synthetic RNA oligonucleotides were used as a size reference. RNA markers (middle lane) are 19, 24 and 33 nucleotides. (B) Genome distribution of Toxoplasma small RNAs.
(1.20 MB TIF)
Tg-microRNA-60 family. (A) A miR-60b production spot on chromosome VIIa is depicted with the representative secondary structure of the precursor and the conservation across parasite species. Small RNAs with perfect matches were plotted within a 800-bp sliding window. Short thin lines above the long bars represent small RNAs derived from the antisen...
Tg-microRNA-4 family. (A) A miR-4 production hot spot in chromosome V is shown along with the predicted structure and the sequence conservation across parasite species. Same legend as in Figure S2A. The mature region is shown in red. (B) Toxoplasma Tg-miR-4 family variants are aligned. The numbers of reads are indicated for each species. There is 3...
Characteristics of Tg-miR-43. (A) A miR-43 production hot spot in chromosome IX is shown along with the predicted structure (B) and the sequence conservation across parasite species (C). The mature region is shown in red. Same legend as in Figure S2A.
(0.44 MB TIF)
Characteristics of Tg-miR-62. (A) A miR-62 production hot spot in chromosome IX is shown along with the predicted structure and (B) the sequence conservation across parasite species. The mature region is shown in red and the passenger strand (microRNA*) in blue. Same legend as in Figure S2A.
(0.46 MB TIF)
Characteristics of Tg-miR-64. (A) A miR-64 production hot spot in chromosome XI is shown along with the predicted structure and (B) the sequence conservation across parasite species. The mature region is shown in red. Same legend as in Figure S2A.
(0.52 MB TIF)
Characteristics of Tg-miR-61 and -63. (A) Predicted structure of miR-61 is shown along with (B) the sequence conservation across parasite species. The pre-miR-61 stem-loop structure is conserved across three loci on chromosomes IX and Ia. (C) Predicted structure of miR-63 is shown along with (D) the sequence conservation across parasite species. Th...
Toxoplasma REP-derived small RNAs (rdsRNAs).
(0.03 MB PDF)
Characteristics of the Tg-miR-40 family. The miR-40a (A) and miR40b (B) production hot spots in chromosomes X and VIIb respectively are shown along with the predicted structure and the sequence conservation across parasite species. The mature region is shown in red. A new cloned Tg-miR candidate is labelled in green. Same legend as in Figure S2A.
(...
Characteristics of the Tg-miR-24 family. (A) miR-24a/miR-24b production hot spots are shown in chromosome VIII along with the predicted structure and (B) the sequence conservation across parasite species. The mature region is shown in red and the passenger strand (microRNA*) in blue. Same legend as in Figure S2A.
(0.95 MB TIF)
Northern analysis of Tg-miR and Tg-rdsRNAs. Full-size images of RNA blot phosphoimager scans used to generate panels A and B in Figures 4 and 5, respectively. Same legend as in Figures 2A and 3A. RNA markers (left lane) are 19, 21 and 23 nucleotides.
(2.37 MB TIF)
Identification of putative Toxoplasma proto-microRNAs. Secondary structure of T. gondii proto-miR-1 (A), -2 (B), -3 (C) and -4 (D) foldbacks compared to predicted secondary structure of the orthologous sequences from N. caninum. The red line indicates the cloned mature T. gondii miRNA sequence, while the blue line refers to the corresponding N. can...
Prediction of Toxoplasma miRNA target genes. (A) The number of predicted target genes are shown for 12 Tg-microRNAs. (B) Genes targeted by the 14 Tg-miRNA families were functionally classified using the eukaryotic Clusters of Orthologous Groups (KOG) database.
(1.07 MB TIF)
Toxoplasma tg-microRNAs.
(0.03 MB PDF)
Predicted binding sites of selected T. gondii tg-miRNA.
(0.04 MB PDF)
Summary of Tg-AGO-associated proteins identified by mass spectrometry.
(0.12 MB PDF)
In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC) to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a p...
One of the major characteristics of chloroplast membranes is their enrichment in galactoglycerolipids, monogalactosyldiacylglycerol
(MGDG), and digalactosyldiacylglycerol (DGDG), whereas phospholipids are poorly represented, mainly as phosphatidylglycerol
(PG). All these lipids are synthesized in the chloroplast envelope, but galactolipid synthesis...
A configuration space of homologous protein sequences (or CSHP) has been recently constructed based on pairwise comparisons, with probabilities deduced from Z-value statistics (Monte Carlo methods applied to pairwise com-parisons) and following evolutionary assumptions. A Z-value cut-off is applied so as proteins are placed in the CSHP only when th...
