A5000482521- Enzyme Catalysis and Immobilization
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Amino Acid Enzymes and Metabolism
- Enzyme Production and Characterization
- Chromosomal and Genetic Variations
- Biofuel production and bioconversion
- Plant nutrient uptake and metabolism
- Metabolism and Genetic Disorders
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Carbohydrate Chemistry and Synthesis
- Chemical Synthesis and Analysis
- Legume Nitrogen Fixing Symbiosis
- Synthesis and Catalytic Reactions
- Biochemical and Molecular Research
- Protist diversity and phylogeny
- Protein Structure and Dynamics
- Plant Reproductive Biology
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Porphyrin Metabolism and Disorders
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2011-2020
CEA Paris-Saclay
2018-2020
Centre National de la Recherche Scientifique
2011-2020
Génomique Métabolique du Genoscope
1997-2020
Genoscope
2009-2020
Université Paris-Saclay
2005-2020
Université d'Évry Val-d'Essonne
2010-2019
Direction de la Recherche Fondamentale
2016
Université Clermont Auvergne
2015
Centre National de Recherche en Génomique Humaine
2012
Sink strength of growing potato tubers is believed to be limited by sucrose metabolism and/or starch synthesis. Sucrose synthase (Susy) most likely responsible for the entire cleavage in sink tubers, rather than invertases. To investigate unique role with respect and transgenic plants were created expressing Susy antisense RNA corresponding T‐type isoform. Although constitutive 35S CaMV promotor was used drive expression inhibition activity tuber‐specific, indicating that independent...
Prochlorococcus marinus , the dominant photosynthetic organism in ocean, is found two main ecological forms: high-light-adapted genotypes upper part of water column and low-light-adapted at bottom illuminated layer. P. SS120, complete genome sequence reported here, an extremely form. The SS120 composed a single circular chromosome 1,751,080 bp with average G+C content 36.4%. It contains 1,884 predicted protein-coding genes size 825 bp, rRNA operon, 40 tRNA genes. Together 1.66-Mbp MED4, one...
Article4 March 2008Open Access A complete collection of single-gene deletion mutants Acinetobacter baylyi ADP1 Véronique de Berardinis Corresponding Author Genoscope, Institut Génomique (CEA), Evry, France UMR8030 CNRS-Genoscope-Université d'Evry, Search for more papers by this author David Vallenet Vanina Castelli Marielle Besnard Agnès Pinet Corinne Cruaud Sumitta Samair Christophe Lechaplais Gabor Gyapay Céline Richez Maxime Durot Annett Kreimeyer François Le Fèvre Vincent Schächter...
Sucrose synthase, an important enzyme in carbohydrate metabolism, catalyzes the reversible conversion of sucrose and UDP to UDP‐glucose fructose vitro . To investigate vivo function both gene ( Asus 1) a corresponding cDNA from roots Arabidopsis were isolated. The 1 has homologies 67–72% synthase genes other species. Histochemical GUS analysis tobacco plants transformed with 1.5 kb promoter fragment transcriptionally fused β‐glucuronidase reporter showed that is expressed phloem leaves,...
Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on evolution of cereals and other grasses. Therefore, decoding its entire genome will be prerequisite applied basic research this all cereals.We have determined analyzed complete sequences two chromosomes, 11 12, which total 55.9 Mb (14.3% length), based set overlapping clones. A 5,993 non-transposable element related genes are present these chromosomes. Among them 289 disease...
Abstract Background Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded "gold mine" for novel biochemical reactions is used model organism studying metabolic aspects such the Stickland reaction, coenzyme-B12- selenium-dependent acids. With goal revisiting its carbon, nitrogen, metabolism, comparing studies with other clostridia, genome...
Microbial metabolism of plant polysaccharides is an important part environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), anaerobic growth screening. We apply this study the bacterium Clostridium phytofermentans ferments biomass components including glucans, mannans, xylans,...
Abstract Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy the oceans. While their roles as primary producers grazers well appreciated, other aspects life histories remain obscure due to challenges culturing sequencing natural diversity. Here, we exploit single-cell genomics metagenomics data from circumglobal Tara Oceans expedition analyze genome content apparent oceanic distribution seven prevalent lineages uncultured...
Biocatalytic potential of a new wild-type amine dehydrogenase used in an enzyme-catalyzed synthesis enantiomerically pure primary amine.
Genome-scale metabolic models are powerful tools to study global properties of networks. They provide a way integrate various types biological information in single framework, providing structured representation available knowledge on the metabolism respective species.We reconstructed constraint-based model Acinetobacter baylyi ADP1, soil bacterium interest for environmental and biotechnological applications with large-spectrum biodegradation capabilities. Following initial reconstruction...
Abstract A high‐throughput screening of candidate nitrilases against 25 structurally diverse substrates allowed us to create a wide collection 125 experimentally validated nitrilases. The enzymes were selected by genomic approach from 700 prokaryotic species and one metagenome as representative the nitrilase family diversity. enzymatic this expands biocatalytic toolbox for chemical synthesis providing large number tested with their assigned substrates. Three examples illustrate synthetic...
Abstract Iron(II)/α‐ketoacid‐dependent oxygenases (αKAOs) are enzymes that mainly catalyse hydroxylation reaction. By using a genomic approach combining sequence comparison and protein‐domain sharing, set of 131 αKAO was prepared. The screening various substrates revealed five new αKAOs. Four αKAOs were found to be active towards L ‐lysine, ‐ornithine ‐arginine with total regio‐ stereoselectivities yielding the corresponding 3‐ or 4‐hydroxyamino acids. enzymatic cascade reaction two...
To evaluate the existing annotation of Arabidopsis genome further, we generated a collection evolutionary conserved regions (ecores) between and rice. The ecore analysis provides evidence that gene catalog is not yet complete, number these annotations require re-examination. improve used novel “full-length” enriched cDNA prepared from several tissues. An additional 1931 genes were covered by new sequences, raising annotated with corresponding sequence to about 14,000. Detailed comparisons...
Although the proteins of lysine fermentation pathway were biochemically characterized more than thirty years ago, genes encoding that catalyze three steps this are still unknown. We combined gene context, similarity enzymatic mechanisms, and molecular weight comparisons with known to select candidate for these orphan proteins. used a wastewater metagenomic collection sequences find characterize missing pathway. After recombinant protein production purification following cloning in...
For the ornithine fermentation pathway, described more than 70 years ago, genetic and biochemical information are still incomplete. We present here experimental identification of last four missing genes this metabolic pathway. They encode L-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, two subunits 2-amino-4-ketopentanoate thiolase. While only for Clostridiaceae to date, pathway is shown be widespread.
Significance The experimental dissection of novel metabolic pathways, from genes and enzymes to metabolites, is a key issue for improving our knowledge the enzymatic capabilities microbial world providing accurate functional annotation genomes. We used an integrative methodology combining phenotyping complete genome-scale mutant collection Acinetobacter baylyi ADP1 with untargeted liquid chromatography/MS-based approach uncover degradation pathway trigonelline (TG), widespread osmolyte....