“Artificial intelligence and machine learning advances reduce the design possibilities to the most probably ones and can discover new-to-nature solutions,” noted project coordinator Marjan De Mey.
On top of its contribution to decode nature’s building blocks and processes, deCYPher will apply an innovative and holistic approach that seeks to innovate how bioprocesses are developed. deCYPher will develop a standardised artificial intelligence and machine learning platform for biotech applications as well as guiding bioprocesses across all steps of the development chain. Drawing on specific targets for case studies (and decoding CYPs), deCYPher plans to methodically work on taking bioprocess design and control further from an art form to a reproducible and sustainable system.
CSIC's involvement in this research project is facilitated through two of its institutes: the National Centre for Biotechnology (CNB), led by Dr. Juan Nogales, who heads the Systems Biotechnology Group, and the Margarita Salas Center for Biological Research (CIB), directed by Dr. Auxi Prieto, who leads the Polymer Biotechnology Group. Within CSIC, the primary focus is directed towards optimizing the expression and performance of CYP enzymes within specially engineered synthetic microbial compartments. Additionally, CSIC is spearheading efforts to reroute the metabolic pathways of Pseudomonas putida, with the aim of establishing highly efficient microbial cell factories for the production of functionalized flavonoids.
deCYPher is a new European Horizon project that seeks to merge synthetic biology with artificial intelligence and machine learning. Launched with a kick off meeting in Gent, Belgium, representatives of 10 partners from 6 European countries came together to discuss deCYPher’s ambitious goal: overcoming hurdles to produce valuable compounds (usually extracted in small amounts from plants) in industrial biotechnology – specifically terpenoids and flavonoids, natural compounds that encompass about 30.000 different chemical substances.
Flavonoids and terpenoids
Terpenoids and flavonoids are traditionally extracted from plants and have been given much attention due to their importance for a variety of applications and markets, including pharmaceuticals, fragrances, flavours, food preservatives, and insecticides. However, only a tiny fraction of these large and versatile groups of compounds can be commercially extracted from plants, and due to their low contents within the plants such commercial processes require unsustainable large-scale field cultivation. The diversity of terpenoids and flavonoids stems from multiple variations on common molecule structures, which for a majority comes from oxygenation carried out by a vast family of enzymes called Cytochromes P450 (often dubbed CYPs). Terpenoids and flavonoids illustrate once more the complexity involved in biological processes and the difficulty of decoding and re-engineering them in a lab, not to mention at industrial and commercial scales.
