Project description:We set out to investigate the genetic adaptions of the known marine fungus Paradendryphiella salina CBS112865 to the degradation of brown macro-algae, expecting to find a repertoire of carbohydrate active enzymes highly specialized to the degradation of algal polysaccharides. We performed whole genome, transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina growing on three species of brown algae and under carbon starvation. The genome comparison to close terrestrial fungal relatives, revealed P. salina to have a similar, but reduced carbohydrate active enzyme (CAZyme) profile, except for the presence of three putative alginate lyase 7 genes, most likely acquired via ancient horizontal gene transfer event from a marine bacterium and a polysaccharide lyase 8 gene with similarity to ascomycete chondroitin AC lyases. The proteomic analysis revealed both PL7 and PL8 enzymes to be highly abundant in the algal fermentations together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the base CAZyme repertoire of saprobic and plant pathogenic ascomycetes with the necessary addition of alginate lyases provide the fungi with the enzymatic capabilities to thrive on brown algae polysaccharides and even cope with the algal defense mechanisms.
Project description:More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.