Summary
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.
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More information & hyperlinks
| Web resources: | https://cordis.europa.eu/project/id/893122 |
| Start date: | 01-11-2020 |
| End date: | 20-02-2023 |
| Total budget - Public funding: | 187 572,48 Euro - 187 572,00 Euro |
Cordis data
Original description
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.Status
CLOSEDCall topic
MSCA-IF-2019Update Date
28-04-2024
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