Pedro M. Coutinho
A5102987146- Enzyme Production and Characterization
- Biofuel production and bioconversion
- Polysaccharides and Plant Cell Walls
- Genomics and Phylogenetic Studies
- Microbial Metabolites in Food Biotechnology
- Carbohydrate Chemistry and Synthesis
- Glycosylation and Glycoproteins Research
- Enzyme-mediated dye degradation
- Mycorrhizal Fungi and Plant Interactions
- Biomedical Text Mining and Ontologies
- Probiotics and Fermented Foods
- Microbial Metabolic Engineering and Bioproduction
- Fungal Biology and Applications
- Microbial Metabolism and Applications
- Fungal and yeast genetics research
- Plant Pathogens and Fungal Diseases
- Enzyme Catalysis and Immobilization
- Legume Nitrogen Fixing Symbiosis
- Microbial Community Ecology and Physiology
- Peptidase Inhibition and Analysis
- Plant-Microbe Interactions and Immunity
- Phytase and its Applications
- Bioinformatics and Genomic Networks
- Gut microbiota and health
- Protist diversity and phylogeny
Architecture et Fonction des Macromolécules Biologiques
2010-2024
Aix-Marseille Université
2010-2020
Centre National de la Recherche Scientifique
2009-2020
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020
Medical Research Council
2002-2014
Institute of Genetics and Cancer
2009-2014
University of Edinburgh
2013-2014
Western General Hospital
2005-2011
Institut de Neurobiologie de la Méditerranée
2011
MRC Human Genetics Unit
2010
The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence specificity 3D structure of enzymes that assemble, modify breakdown oligo- polysaccharides. Functional structural information is added curated on regular basis based available literature. In addition use by enzymologists seeking CAZymes, dissemination stable nomenclature for these probably major contribution CAZy....
We report the draft genome of black cottonwood tree, Populus trichocarpa . Integration shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction genome. More than 45,000 putative protein-coding genes were identified. Analysis assembled revealed a whole-genome duplication event; about 8000 pairs duplicated from that event survived in A second, older is indistinguishably coincident divergence and Arabidopsis lineages. Nucleotide substitution, tandem gene...
Wood is a major pool of organic carbon that highly resistant to decay, owing largely the presence lignin. The only organisms capable substantial lignin decay are white rot fungi in Agaricomycetes, which also contains non-lignin-degrading brown and ectomycorrhizal species. Comparative analyses 31 fungal genomes (12 generated for this study) suggest lignin-degrading peroxidases expanded lineage leading ancestor reconstructed as species, then contracted parallel lineages mycorrhizal Molecular...
Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand molecular underpinnings of pathogenicity in genus Fusarium, we compared genomes three phenotypically diverse species: graminearum, verticillioides oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions F. that include four entire chromosomes account for more than one-quarter genome. LS rich transposons genes with distinct evolutionary profiles but related to...
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass simple sugars that are converted chemical intermediates biofuels, such as ethanol. We assembled 89 scaffolds (sets ordered oriented contigs) generate 34 Mbp nearly contiguous T. genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering utility effectiveness carbohydrate-active enzymes reesei, its encodes fewer than any other sequenced fungus able hydrolyze...
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them sorely needed. We report the draft genome sequence of root-knot nematode Meloidogyne incognita, a biotrophic parasite many crops, including tomato, cotton coffee. Most assembled this asexually reproducing nematode, totaling 86 Mb, exists in pairs homologous but divergent segments. This suggests that ancient allelic regions M. incognita evolving toward effective haploidy, permitting new...
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for production of enzymes and organic acids, particularly citric acid. We sequenced 33.9-megabase genome A. CBS 513.88, ancestor currently used enzyme strains. A high level synteny was observed with other aspergilli sequenced. Strong function predictions were made 6,506 14,165 open reading frames identified. detailed description components protein secretion pathway striking differences in hydrolytic...
Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described families of that cleave or build complex carbohydrates, namely glycoside hydrolases (GH), polysaccharide lyases (PL), carbohydrate esterases (CE), glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery members CBM33 family GH61 are in fact lytic monooxygenases (LPMO), demands a reclassification these into suitable...
The fungus Laccaria bicolor — seen in its above-ground fruiting body presence as the 'bicoloured deceiver' mushroom lives symbiotically on roots of trees. Its genome has now been sequenced, and key features characterized by transcript profiling. study throws light mechanism mycorrhizal symbiosis, union soil fungi that is vital important to plant productivity. And it will be keen interest evolutionary biologists for revelations about plant–fungus interactions shaping genomes over time....
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges environmental persistence. These attributes have made these species models understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite similarities, two differ in mating behaviour ability to produce asexual spores. We sequenced genomes one strain S. strains B. cinerea. The comparative analysis relative another other fungal is...
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members Proteobacteria, Cyanobacteria, and Fungi. appear to be versatile heterotrophs. Genomic culture indicate use carbon sources that span simple sugars more complex substrates such hemicellulose, cellulose, chitin. encode low-specificity major facilitator superfamily transporters high-affinity ABC for sugars, suggesting...
White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These use extracellular oxidative enzymes are also able to transform related compounds found explosive contaminants, pesticides and toxic waste. We have sequenced 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using whole shotgun approach. The P. reveals an impressive array genes encoding secreted oxidases, peroxidases hydrolytic...
The complex microbiome of the rumen functions as an effective system for conversion plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource degrading enzymes that could be used in production biofuels. gastrointestinal tract harbor dense microbiome. To gain greater understanding ecology metabolic potential this microbiome, we comparative metagenomics (phylotype analysis SEED subsystems-based annotations) examine randomly...
The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and Bacteroidetes. Little known about factors that govern interactions between their members. Here, we examine niches of representatives both in vivo. Finished genome sequences were generated from Eubacterium rectale E. eligens, which belong to Clostridium Cluster XIVa, one most common Firmicute clades. Comparison these 25 other Bacteroidetes indicated possess smaller...
Abstract Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey plant pathogen, providing strategy for biological control of pests protection. Probably, most studied biocontrol agents are species genus Hypocrea / Trichoderma . Results Here we report an analysis genome sequences two atroviride (teleomorph atroviridis ) and virens (formerly Gliocladium , teleomorph ), comparison with reesei jecorina ). These three display...
Rust fungi are some of the most devastating pathogens crop plants. They obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart their hosts. Their lifestyle has slowed dissection molecular mechanisms underlying host invasion avoidance or suppression innate immunity. We sequenced 101-Mb genome Melampsora larici - populina , causal agent poplar leaf rust, 89-Mb Puccinia graminis f. sp. tritici wheat barley stem rust. then compared 16,399 predicted...
The genome of the Périgord black truffle Tuber melanosporum Vittad., a gourmet delicacy that grows symbiotically on roots European oak, has been sequenced. This is largest and most complex fungal so far unusually gene-poor, but rich in mobile genetic elements known as transposons. Comparison with sequence Laccaria bicolor, another ectomycorrhizal symbiotic fungus, reveals contrasting gene sets reflecting two different molecular toolkits have evolved independently to fit root symbiont...
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes the genus Micromonas thrive ecosystems ranging from tropical to polar and could serve as sentinel for biogeochemical fluxes modern oceans during climate change. These broadly distributed primary producers belong an anciently diverged sister clade land plants. Although isolates have high 18S ribosomal RNA gene identity, we found that genomes two shared only...
The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This is economically important in most wheat-growing areas worldwide threatens global food production. Control has been hampered by limited understanding genetic biochemical bases pathogenicity, including mechanisms infection resistance host. Unlike other plant pathogens, M. long latent period during which it...
Family GH13, also known as the α-amylase family, is largest sequence-based family of glycoside hydrolases and groups together a number different enzyme activities substrate specificities acting on α-glycosidic bonds. This polyspecificity results in fact that simple membership this cannot be used for prediction gene function based sequence alone. In order to establish robust show an improved correlation between enzymatic specificity, we have performed large-scale analysis 1691 GH13 sequences...
Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and also largely responsible for the destructive decay wooden structures. Rapid depolymerization cellulose is a distinguishing feature brown-rot, but biochemical mechanisms underlying genetics poorly understood. Systematic examination P. genome, transcriptome, secretome revealed unique extracellular enzyme systems, including an unusual repertoire glycoside hydrolases. Genes encoding exocellobiohydrolases...
The adult human intestine contains trillions of bacteria, representing hundreds species and thousands subspecies. Little is known about the selective pressures that have shaped are shaping this community's component species, which dominated by members Bacteroidetes Firmicutes divisions. To examine how intestinal environment affects microbial genome evolution, we sequenced genomes two normal distal gut microbiota, Bacteroides vulgatus distasonis, comparison with few other non-gut...
Comparative genomic analysis of “dry rot” fungus shows both convergent evolution and divergence among fungal decomposers.