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CORDIS

From protein sequence to function – computational and experimental de-orphanization of uncharacterized enzymes in fungi

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.

Coordinator

RIJKSUNIVERSITEIT GRONINGEN
Net EU contribution
€ 187 572,48
Address
Broerstraat 5
9712CP Groningen
Netherlands

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Region
Noord-Nederland Groningen Overig Groningen
Activity type
Higher or Secondary Education Establishments
Links
Total cost
€ 187 572,48