Project description
Protein sequence and function of uncharacterised enzymes in fungi
Fast advances in genome sequencing technology leave ~30 % of predicted proteins as 'orphans', meaning there is no information about their function or about closely related enzymes. Fungi are known as the prolific producers of secondary metabolites, however, the study of the underlying biosynthetic gene clusters is still poorly developed. The EU-funded fORPHAN project aims at developing a de-orphanising pipeline based on the computational and experimental characterisation of enzymes from the fungal kingdom. Researchers propose the use of deep targeted database searches to identify key biosynthetic enzymes in the publicly available genomes of fungi. The promising gene candidates will be expressed in vitro and in recombinant microbial hosts to characterise their activity on a range of substrates and by X-ray crystallography.
Objective
Fast advances in genome sequencing and sequence processing technology leave ~30% of predicted proteins as orphans, meaning without known function or closely related enzymes. Being able to assign a function to such orphans opens avenues to select for and design powerful biocatalysts – individual enzymes, biosynthetic pathways or entire organisms. The herein proposed research aims at developing a de-orphanizing pipeline “fORPHAN” based on computational and experimental characterization of enzymes from the fungal kingdom. Fungi are known to be prolific producers of secondary metabolites, however, the study of the underlying biosynthetic gene clusters is still a fairly young field. The use of automated search and annotation pipelines is currently limited by the small number of experimentally characterized genes and gene clusters that can be used to train the algorithms. Therefore, I propose to use deep targeted database searches to identify key biosynthetic enzymes in the publicly available genomes of fungi. First targets will be the thus-far uncharacterized family of putative chalcone isomerases and the recently discovered family of type III polyketide synthases, which both have great potential for in vivo and in vitro applications. Several gene candidates will be expressed in vitro and in recombinant microbial hosts, and tested for activity on a range of substrates. Interesting candidates will also be characterized by X-ray crystallography. This research will not only yield biotechnologically-relevant catalysts but also provide the bioinformatic foundation for more challenging genome mining projects.
Fields of science
- natural sciencesearth and related environmental sciencesgeologymineralogycrystallography
- natural sciencesbiological sciencesmicrobiologymycology
- natural scienceschemical sciencescatalysisbiocatalysis
- natural sciencesbiological sciencesgeneticsgenomes
- natural sciencesbiological sciencesbiochemistrybiomoleculesproteinsenzymes
Programme(s)
Funding Scheme
MSCA-IF - Marie Skłodowska-Curie Individual Fellowships (IF)Coordinator
9712CP Groningen
Netherlands