All of the publications that have resulted from the CHASSY project are also available on the project ZENODO page, which you can access here.
Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid
This paper is a collaboration between colleagues in Delft and UCC. They have constructed a plasmid that has shown to be efficient in deactivating the ADE2 gene in four different yeast species. This could open up new paths of research in non-conventional yeasts as previous plasmids and cassettes fro Cas9 and guide-RNA expression were species-specific. The research was published in FEMS Yeast Research.
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Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production
Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci. Recent studies indicate that phenotypic trade-offs, which are often observed after evolution under constant conditions, can be mitigated by using dynamic cultivation regimes. Advances in research on synthetic regulatory circuits offer exciting possibilities to extend the applicability of evolutionary engineering to products of yeasts whose synthesis requires a net input of cellular energy. The review is available to read in Current Opinion in Biotechnology.
CHASSY PI, Jean-Marc Daran of TU Delft and his colleagues have experimented with using a new type of CRISPR technology for genome editing in the industrial yeast, Saccharomyces cerevisiae. They found Cpf1 to be highly efficient at introducing point mutations with high fidelity, and multi-gene editing. The system was also efficient at promoting recombination of the repair fragment.
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints
Genome-scale metabolic models (GEMS) are a useful tool for calculating metabolic phenotypes. Research by CHASSY PI Jens Nielsen and his colleagues have improved the GEMs for Saccharomyces cerevisiae by applying GECKO, a method that also accounts for enzymes as part of reactions. This method is expected to increase the use of model-based design in metabolic engineering. The research is available to read in Molecular Systems Biology.
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