A5033034669- Fungal and yeast genetics research
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Yeasts and Rust Fungi Studies
- DNA and Nucleic Acid Chemistry
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Coral and Marine Ecosystems Studies
- Biofuel production and bioconversion
- Fermentation and Sensory Analysis
- Gut microbiota and health
- Aquaculture disease management and microbiota
- Analytical Chemistry and Chromatography
- Bacteriophages and microbial interactions
- DNA Repair Mechanisms
- Chromosomal and Genetic Variations
- Antimicrobial Peptides and Activities
- Advanced biosensing and bioanalysis techniques
- Tannin, Tannase and Anticancer Activities
- Marine and coastal ecosystems
- Gene expression and cancer classification
- Bacterial Genetics and Biotechnology
- Genomics and Chromatin Dynamics
- Thermodynamic properties of mixtures
- Gene Regulatory Network Analysis
Sorbonne Université
2010-2023
Centre National de la Recherche Scientifique
2009-2023
Institut de Biologie Physico-Chimique
2001-2023
Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues
2017-2023
Laboratoire de Biologie Computationnelle et Quantitative
2014-2017
Biologie du chloroplaste et perception de la lumière chez les micro-algues
2017
Institut de Biologie Paris-Seine
2016-2017
Institut de Systématique, Évolution, Biodiversité
2017
Institut Pasteur
2004-2015
Université Paris Cité
2015
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and consequences its ancestral duplication, leaving evolution entire class hemiascomycetes only partly explored. We concentrate here five species Saccharomycetaceae , a large subdivision hemiascomycetes, that we call “protoploid” because they diverged from S. lineage prior to genome duplication. determined complete sequences three these species: Kluyveromyces (Lachancea)...
New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying understanding how transition from noncoding to coding occurs are key problems in evolutionary biology. However, is a difficult task, hampered by presence remote homologs, fast evolving sequences erroneously annotated genes. To overcome these limitations, we developed...
The Metagenomics and Metadesign of the Subways Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised experts across many fields, including genomics, data analysis, engineering, public health, architecture. ultimate goal MetaSUB to improve city utilization planning through detection, measurement, design metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, human activity, longitudinal,...
Reconstructing genome history is complex but necessary to reveal quantitative principles governing evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of architecture and gene repertoire. Here, we reconstructed genus Lachancea that appeared cover continuous range from closely related more diverged yeast species. Our approach integrated generation high-quality data set; development AnChro, new algorithm for reconstructing ancestral...
The recent release of sequences several unexplored yeast species that cover an evolutionary range comparable to the entire phylum chordates offers us a unique opportunity investigate how genes involved in adaptation have been shaped by evolution. We examined three different sets genes, all related adaptative processes at genomic level, evolved hemiascomycetes: (1) mating-type govern sexuality, (2) silencing are connected regulation cassettes and telomere position effect, (3) gene families...
The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant osmotolerant. sequencing strain LS3 revealed that the nuclear genome A. 11.8 Mb long consists four chromosomes with regional centromeres. closest sequenced relative Yarrowia lipolytica, although mean...
Among genes conserved from bacteria to mammals are those involved in replicating and repairing DNA. Following the complete sequencing of four hemiascomycetous yeast species during course Genolevures 2 project, we have studied conservation 106 replication, repair, recombination Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica compared them with their Saccharomyces cerevisiae orthologues. We found that proteins belonging replication fork nucleotide excision...
We investigated the claim that symbiotic dinoflagellates from corals and sea anemones release lipid droplets in vitro. Putative droplet secretion vitro is taken as evidence for translocation algae to host hospite cnidarians. confirmed isolated tropical anemone Condylactis gigantea exhibited surface “blebs” attached droplets. The entities stained positively with DNA‐specific fluorochrome Hoechst 33258 chromosome stain lacto‐aceto‐orcein, but not lysochrome Sudan Black B. In contrast, bona...
Transfer of fragments mtDNA to the nuclear genome is a general phenomenon that gives rise NUMTs (NUclear sequences MiTochondrial origin). We present here first comparative analysis NUMT content entirely sequenced species belonging monophyletic group, hemiascomycetous yeasts (Candida glabrata, Kluyveromyces lactis, thermotolerans, Debaryomyces hansenii and Yarrowia lipolytica, along with updated Saccharomyces cerevisiae). This study revealed huge diversity in number organization across six...
Abstract We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in multicopy plasmid with tetracycline-regulatable (Tet-off) promoter. selected 714 such mean size 700 base-pairs out around 84,000 clones tested. These include 493 in-frame open reading frame corresponding to 454 distinct genes (of which 91 are unknown function), and 162 out-of-frame, antisense intergenic genomic fragments, representing largest...
The genome of the basidiomycete pathogenic yeast Cryptococcus neoformans carries two UDP-glucose epimerase genes (UGE1 and UGE2). UGE2 maps within a galactose cluster composed galactokinase homologue gene galactose-1-phosphate uridylyltransferase. This clustered organization GAL is similar to that in most hemiascomycete genomes Schizosaccharomyces pombe but otherwise not generally conserved fungal kingdom. UGE1 has been identified as necessary for galactoxylomannan biosynthesis virulence....
Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, its significance increases when several genomes related organisms can be compared. Among yeasts, only the S. cerevisiae reference strain has been analyzed so far for pseudogenes.We present here first comparative analysis within fully sequenced annotated eight yeast species, spanning entire...
Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in nucleo-cytosol host organelle-targeted via acquisition N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment their physico-chemical properties, we show that organelle targeting peptides, which are distinct signal peptides other subcellular compartments, group with subset antimicrobial peptides. We demonstrate extant...
Abstract Motivation: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, insert-size (Mate-Pair libraries) provide higher physical coverage the genome and give access to repeat-containing regions. They thus theoretically overcome previous limitations as they are becoming...
Abstract Copy number variation of chromosomal segments is now recognized as a major source genetic polymorphism within natural populations eukaryotes, well possible cause diseases in humans, including cancer, but its molecular bases remain incompletely understood. In the baker’s yeast Saccharomyces cerevisiae , variety low-order amplifications (segmental duplications) were observed after adaptation to limiting environmental conditions or recovery from gene dosage imbalance, and interpreted...
Abstract Notre travail a consisté mesurer la constante diélectrique de 20 composés organiques purs, soit dans un intervalle température s'étendant −150°C à ‐ 70°C, aux températures 20,0°C et 25,0°C. Nous redonnons une description l'appareil résonance utilisé précédemment par J. Timmermans, A. M. Piette R. Philippe. avons eu l'occasion d'étudier le comportement anormal, l'état liquide, association bimoléculaire. concluons aperçu des travaux très controversés concernant globulaire du succinonitrile.
Antimicrobial peptides (AMPs) represent an ancient mechanism for antagonizing microbial opponents, being generated by eukaryotes, eubacteria, and archaea alike [1,2]. Given the dearth in new antibiotics, there has been increasing interest AMPs. As our understanding grown, a tantalizing possibility taken shape: Might these agents of competition be at heart cooperative success story that gave rise to mitochondria chloroplasts? Striking similarities suggest system protein import into...
We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm build nucleotides that contain all four standard bases in variable proportions. These enable us search very rapidly base sequences energetically favor chosen types of DNA deformation or DNA-protein DNA-ligand interactions. Sequences satisfying the criteria can be found by energy minimization, combinatorial...
Convergent gene pairs can produce transcripts with complementary sequences. We had shown that mRNA duplexes form in vivo Saccharomyces cerevisiae via interactions of overlapping 3'-ends and lead to posttranscriptional regulatory events. Here we show duplex formation is restricted convergent genes separated by short intergenic distance, independently their 3'-untranslated region (UTR) length. disclose an enrichment involved biological processes related stress among these genes. They are...
Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over past two decades, breakthroughs in genomics and ecosystem biology, as well development genetic resources model species, have redrawn boundaries our knowledge relevance these microbes global ecosystems. However, considering their vast biodiversity complex evolutionary history, comprehension algal biology remains limited. As algae rely light, both main source energy information...
Abstract Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in nucleo-cytosol host organelle-targeted via acquisition N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment their physico-chemical properties, we show that organelle targeting peptides, which are distinct signal peptides other subcellular compartments, group with subset antimicrobial peptides. We...