Algal biomass is underexploited and high value products based on algal polysaccharides and oligosaccharides remain rare. Indeed, commercial enzymes essentially originate from terrestrial organisms which degrade plant biomass and thus are inefficient or inactive on algal biomass. In the context
A major challenge in modern biology is the discovery of in vivo metabolic or physiological functions of unknown proteins. Our institute has developed an integrated strategy based on in silico prediction of enzymatic activities and in vitro screening of enzymes
MetX and MetA are two phylogenetically unrelated protein families, but both are implied in the first step of the L-methionine biosynthesis pathway. MetX proteins are known as L-homoserine O-acetyltransferases (HAT), while MetA proteins are generally annotated as L-homoserine O-succinyltransferase (HST).
GROOLS (Genomic Rule Oriented Object Logic System) is a bioinformatics software that helps biologists in the evaluation of genome functional annotation through biological processes like metabolic pathways. GROOLS is an expert system that uses paraconsistent logic. It evaluates the completeness
Nearly 35% of the proteins from large-scale sequencing of microbial genomes are annotated with unknown function. Our objective is to explore, by analogy, active sites from proteins of unknown function using 3D tools in order to suggest enzymatic activities. The
Endless improvements of Next-Generation Sequencing (NGS) lead to constantly increasing sequencing data that serve various studies such as metagenomics, transcriptomics or WGS projects. De novo assembly of raw data from WGS projects has been a tedious task requiring a strong expertise for a while but the recent development of powerful tools has brought the technical part of this process within the reach of “standard” bioinformaticians. However, the choice of the appropriate tool depends on the nature of the data (huge amount of short high quality reads vs few long and noisy reads) and probably the issue to address (assembling an isolate vs a collection of genomes included in a complex sample).
In addition to being time consuming and irrelevant for detection of a wide panel of pathogenic targets, current diagnostic methods for pathogens detection (microbial cultures, PCR-RFLP, test strips…) are almost useless in case of complex biological threats (e.g. several pathogens in a mixed sample). Thus, High-throughput sequencing (HTS) becomes undoubtedly a relevant tool for biodefense activities because besides being now affordable, it allows rapid identification of microorganisms without a priori, without isolation or prior cultivation, and can be even applied to microorganisms embedded in extremely complex matrices (i.e. metagenomic samples; e.g. soil samples, clinical samples, contaminated food…).
There is a massive amount of sequence and structural data available, and the accumulation rate exceeds the pace of functional studies. One way to enhance functional assessment is to mine the available data to inform a strategy that can be
The proportion of protein sequences of unknown function in public databases stills very important (42% of UniProt sequences are labelled as “hypothetical”, “uncharacterized”, “unknown” or “putative”). On the other hand, a number of enzyme activities (about 30%) remain orphan (i.e.
Genome-resolved metagenomics have profoundly reshaped our understanding of the distribution, functionalities and roles of Archaea. Within the domain, major supergroups are Euryarchaeota, which includes many methanogens, the TACK, which includes Thaumarchaeaota that impact ammonia oxidation in soils and the ocean,
Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs).