Sylvain Darnet

Plant sterol biosynthesis: identification of two distinct families of sterol 4alpha-methyl oxidases.

In plants, the conversion of cycloartenol into functional phytosterols requires the removal of the two methyl groups at C-4 by an enzymic complex including a sterol 4alpha-methyl oxidase (SMO). We report the cloning of candidate genes for SMOs in Arabidopsis thaliana, belonging to two distinct families termed SMO1 and SMO2 and containing three and two isoforms respectively. SMO1 and SMO2 shared low sequence identity with each other and were orthologous to the ERG25 gene from Saccharomyces cerevisiae which encodes the SMO. The plant SMO amino acid sequences possess all the three histidine-rich motifs (HX3H, HX2HH and HX2HH), characteristic of the small family of membrane-bound non-haem iron oxygenases that are involved in lipid oxidation. To elucidate the precise functions of SMO1 and SMO2 gene families, we have reduced their expression by using a VIGS (virus-induced gene silencing) approach in Nicotiana benthamiana. SMO1 and SMO2 cDNA fragments were inserted into a viral vector and N. benthamiana inoculated with the viral transcripts. After silencing with SMO1, a substantial accumulation of 4,4-dimethyl-9beta,19-cyclopropylsterols (i.e. 24-methylenecycloartanol) was obtained, whereas qualitative and quantitative levels of 4alpha-methylsterols were not affected. In the case of silencing with SMO2, a large accumulation of 4alpha-methyl-Delta7-sterols (i.e. 24-ethylidenelophenol and 24-ethyllophenol) was found, with no change in the levels of 4,4-dimethylsterols. These clear and distinct biochemical phenotypes demonstrate that, in contrast with animals and fungi, in photosynthetic eukaryotes, these two novel families of cDNAs are coding two distinct types of C-4-methylsterol oxidases controlling the level of 4,4-dimethylsterol and 4alpha-methylsterol precursors respectively.

Ultra-Deep Sequencing Reveals the microRNA Expression Pattern of the Human Stomach

Background While microRNAs (miRNAs) play important roles in tissue differentiation and in maintaining basal physiology, little is known about the miRNA expression levels in stomach tissue. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia. Methodology/Principal Findings A small RNA library of stomach tissue was sequenced using high-throughput SOLiD sequencing technology. We obtained 261,274 quality reads with perfect matches to the human miRnome, and 42% of known miRNAs were identified. Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue. Subsequently, the expression of these miRNAs was validated in 10 healthy individuals by RT-PCR showed a significant correlation of 83.97% (P<0.05). Six miRNAs showed a low variable pattern of expression (miR-29b, miR-29c, miR-19b, miR-31, miR-148a, miR-451) and could be considered part of the expression pattern of the healthy gastric tissue. Conclusions/Significance This study aimed to validate normal miRNA profiles of human gastric tissue to establish a reference profile for healthy individuals. Determining the regulatory processes acting in the stomach will be important in the fight against gastric cancer, which is the second-leading cause of cancer mortality worldwide.

High-throughput sequencing of black pepper root transcriptome

BackgroundBlack pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper.ResultsThe root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology.ConclusionsThis dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

Nutritional composition, fatty acid and tocopherol contents of buriti (Mauritia flexuosa) and patawa (Oenocarpus bataua) fruit pulp from the amazon region

O buriti e o pataua sao duas palmeiras endemicas da regiao Amazonica. As polpas destes frutos sao tradicionalmente consumidas pela populacao local, mas ainda nao ganharam os mercados nacional e internacional. A composicao nutricional em acidos graxos e tocoferol foi determinada com metodologias analiticas modernas de cromatografia gasosa (CG) e cromatografia liquida de alta eficiencia (CLAE) baseadas nos padroes da AOCS (AMERICAN..., 2002) e AOAC (ASSOCIATION..., 1997), respectivamente. As duas polpas se mostraram bastante energeticas, com uma alta concentracao em acidos graxos, respectivamente 38,4% e 29,1% em massa seca (MS), em proteinas, 7,8% e 7,4% MS e em fibras dieteticas, 46% e 44,7%. A polpa de buriti pode ser considerada uma otima fonte de vitamina E devido ao seu alto teor de tocoferol (1169 µg.g-1 MS). O perfil de acidos graxos encontrados para a polpa de pataua foi muito semelhante ao de azeite de oliva.

Molecular and Enzymatic Characterizations of Novel Bifunctional 3β-Hydroxysteroid Dehydrogenases/C-4 Decarboxylases from Arabidopsis thaliana

We have isolated two cDNAs from Arabidopsis thaliana encoding bifunctional 3β-hydroxysteroid dehydrogenase/C-4 decarboxylases (3βHSD/D) involved in sterol synthesis, termed At3βHSD/D1 and At3βHSD/D2. Transformation of the yeast ergosterol auxotroph erg26 mutant, which lacks 3βHSD/D activity, with the At3βHSD/D1 isoform or with At3βHSD/D2 isoform containing a C-terminal At3βHSD/D1 endoplasmic reticulum-retrieval sequence restored growth and ergosterol synthesis in erg26. An in vitro enzymatic assay revealed high 3βHSD/D activity for both isoenzymes in the corresponding microsomal extracts. The two At3βHSD/D isoenzymes showed similar substrate specificities that required free 3β-hydroxyl and C-4-carboxyl groups but were quite tolerant in terms of variations of the sterol nucleus and side chain structures. Data obtained with 4α-carboxy-cholest-7-en-3β-ol and its 3α-deuterated analog revealed that 3α-hydrogen-carbon bond cleavage is not the rate-limiting step of the reaction. In planta reduction on the expression of the 3βHSD/D gene as a consequence of VIGS-mediated gene silencing in Nicotiana benthamiana led to a substantial accumulation of 3β-hydroxy-4β,14-dimethyl-5α-ergosta-9β,19-cyclo-24(241)-en-4α-carboxylic acid, consistent with a decrease in 3βHSD/D activity. These two novel oxidative decarboxylases constitute the first molecularly and functionally characterized HSDs from a short chain dehydrogenase/reductase family in plants.

Enzymological properties of sterol-C4-methyl-oxidase of yeast sterol biosynthesis.

Despite genes of the sterol methyl-oxidase component (SMO) of the sterol-C4-demethylation multienzymatic complex have been identified in a variety of organisms and the key role played by SMO in yeast sterol biosynthesis, the enzymological properties of yeast SMO have not been investigated. An enzymatic assay for measuring specifically sterol 4alpha-methyl-oxidase activity in Saccharomyces cerevisiae has been developed for the first time by using [14C]-4,4-dimethyl-zymosterol as substrate. It allowed enzymatically formed C4 mono- and di-demethylated products to be characterized as well as two novel C4-hydroxymethyl-zymosterol derivatives to be identified as immediate oxidative metabolites by the yeast 4,4-dimethyl-zymosterol 4alpha-methyl-oxidase (ScSMO). The properties of microsomal ScSMO have been established with respect to cofactor requirements and kinetics and the substrate selectivity examined with a number of 4,4-dimethyl- and 4alpha-methyl-sterols. Remarkably, ScSMO showed very low activity with 24-methylene-24-dihydrocycloartenol, the natural substrate of maize 4,4-dimethyl-sterol-C4-methyl-oxidase. Conversely, maize sterol-C4-methyl-oxidases showed extremely reduced activity with the natural substrate of ScSMO. The previously described antifungal agent, 6-amino-2-n-pentylbenzothiazole was shown to directly inhibit the microsomal ScSMO activity in vitro. The yeast system was more than 500 times more sensitive to this derivative than the maize systems. These distinct substrate specificities and inhibitor sensitivities between yeast and plant sterol-4alpha-methyl-oxidases probably reflect diversity in the structure of their active sites in relation to the distinct sterol biosynthetic pathways.

Functional identification of sterol-4α-methyl oxidase cDNAs from Arabidopsis thaliana by complementation of a yeast erg25 mutant lacking sterol-4α-methyl oxidation1

Specific primers derived from both genomic sequence data and EST cDNA sequences were used to polymerase chain reaction amplify two full‐length cDNA sequences (AtSMO1 and AtSMO2), 801 and 783 bp, respectively, from an Arabidopsis thaliana cDNA library. The predicted proteins show 32 and 29% identity to the ERG25 gene from Saccharomyces cerevisiae which encodes the sterol‐4α‐methyl oxidase (SMO), a membrane‐bound non‐heme di‐iron oxygenase involved in lipid metabolism. Heterologous expression of AtSMO1 and AtSMO2 in a yeast erg25 ergosterol auxotroph, lacking SMO activity, restored growth and endogenous ergosterol synthesis. These results represent the first functional identification of SMO genes from plants.

Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme.

Salamanders are the only living tetrapods capable of fully regenerating limbs. The discovery of salamander lineage-specific genes (LSGs) expressed during limb regeneration suggests that this capacity is a salamander novelty. Conversely, recent paleontological evidence supports a deeper evolutionary origin, before the occurrence of salamanders in the fossil record. Here we show that lungfishes, the sister group of tetrapods, regenerate their fins through morphological steps equivalent to those seen in salamanders. Lungfish de novo transcriptome assembly and differential gene expression analysis reveal notable parallels between lungfish and salamander appendage regeneration, including strong downregulation of muscle proteins and upregulation of oncogenes, developmental genes and lungfish LSGs. MARCKS-like protein (MLP), recently discovered as a regeneration-initiating molecule in salamander, is likewise upregulated during early stages of lungfish fin regeneration. Taken together, our results lend strong support for the hypothesis that tetrapods inherited a bona fide limb regeneration programme concomitant with the fin-to-limb transition.

MiRNA expression profile for the human gastric antrum region using ultra-deep sequencing.

Background MicroRNAs are small non-coding nucleotide sequences that regulate gene expression. These structures are fundamental to several biological processes, including cell proliferation, development, differentiation and apoptosis. Identifying the expression profile of microRNAs in healthy human gastric antrum mucosa may help elucidate the miRNA regulatory mechanisms of the human stomach. Methodology/Principal Findings A small RNA library of stomach antrum tissue was sequenced using high-throughput SOLiD sequencing technology. The total read count for the gastric mucosa antrum region was greater than 618,000. After filtering and aligning using with MirBase, 148 mature miRNAs were identified in the gastric antrum tissue, totaling 3,181 quality reads; 63.5% (2,021) of the reads were concentrated in the eight most highly expressed miRNAs (hsa-mir-145, hsa-mir-29a, hsa-mir-29c, hsa-mir-21, hsa-mir-451a, hsa-mir-192, hsa-mir-191 and hsa-mir-148a). RT-PCR validated the expression profiles of seven of these highly expressed miRNAs and confirmed the sequencing results obtained using the SOLiD platform. Conclusions/Significance In comparison with other tissues, the antrum’s expression profile was unique with respect to the most highly expressed miRNAs, suggesting that this expression profile is specific to stomach antrum tissue. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in the regulation of the molecular processes of the human stomach.

Identifying Sequences Potentially Related to Resistance Response of Piper tuberculatum to Fusarium solani f. sp. piperis by Suppression Subtractive Hybridization

Piper tuberculatum is an exotic Piper from the Amazon region that shows resistance to infection by Fusarium solani f. sp. piperis, causal agent of Fusarium disease in black pepper (Piper nigrum L.). In this work we aimed to study the interaction between P. tuberculatum and F. solani f. sp. piperis at a molecular level, using suppression subtractive hybridization to identify genes potentially related to Fusarium disease resistance. Comparative sequence analysis confirmed that clones isolated here show a high identity with genes coding for proteins that have a known role in plant defense response mechanisms, such as peroxidase, hydroxyproline-rich glycoprotein and CBL-interacting protein kinase. The present study constitutes the first effort to understand the molecular basis of this plant-pathogen interaction, identifying genes which may be used in the future genetic improvement of black pepper.