Skip to main content

Synthetic microbial consortia-based platform for flavonoids production using synthetic biology

Periodic Reporting for period 1 - SynBio4Flav (Synthetic microbial consortia-based platform for flavonoids production using synthetic biology)

Reporting period: 2019-01-01 to 2020-06-30

The one aim of this Project is the setup of a standardized pipeline for manufacturing flavonoids by using cutting edge synthetic biology tools and microbial chassis, supported by systems biology, synthetic biochemistry, protein engineering, and chemical engineering. SynBio4Flav endeavours not just to reassemble the biochemical pathways thereof but also to break down specific portions of the necessary biochemical routes and split them between different microbial species, each of them genetically programmed to deliver the optimal output for subsequent biosynthetic steps, i.e. distributed catalysis within an engineered microbial consortium.
Ongoing efforts in SynBio are mainly targeted to the standardization of low complexity parts such as genes, operons and pathways while less attention has been paid to cellular systems and microbial communities. The current low yields obtained in the production of flavonoids calls for further progress in the optimization and standardization of the hierarchy abstraction of SynBio large-scale production, particularly at the high-complexity levels such as cell systems and microbial communities.
Synbio4Flav focuses on the entire SynBio hierarchy abstraction chain, including i) DNA/proteins, enzymatic reactions and metabolic pathways (Objective 1), ii) cells (Objective 2), iii) microbial consortia (Objective 3) and iv) downstream processing (Objective 4). These four objectives match the scope of work packages 2, 3, 4 & 5, respectively. Despite being addressed individually, their inputs and outputs are narrowly intertwined within the overarching conceptual and technical framework of synthetic biology.
In addition, two accessory WPs (WP6 and WP7) support optimization by providing the proper standardized and complementary SynBio tools and systems design & analysis required for optimal integration, respectively. Besides fuelling SynBio4Flav's optimization chain, WP6 and WP7 provide new SynBio and computational tools with potential applicability beyond this project, and thus have a strong merit on their own. In each of these WPs, several partners are contributing a synergistic set of tools and expertise to develop specific technologies needed for the implementation of the final envisioned synthetic microbial consortia-based platform for flavonoid production.
Within the framework provided by Synbio4Flav, the work done during this first reporting period has mainly targeted the optimization of the synthetic pathways responsible for flavonoids biosynthesis (WP2) and the development of the required SynBio and SysBio tools that will be critical in upcoming implementation steps (WP6, WP7). In addition, tasks involving the optimization of selected microbial hosts’ metabolic backgrounds have already started. These actions are mainly directed to removing undesirable metabolic features, such as competing pathways (WP3). During this first reporting period, mathematical models and novel devices for rational and standardized assembly of synthetic consortia have been developed (WP4). Similarly, basic setup and protocols for the envisioned bioprocesses have been developed (WP5). Finally, a huge effort on dissemination and exploitation has already been done, thus placing the project in the showcase of microbial biotechnology and circular economy.
The new approach proposed by SynBio4Flav includes the de-composition of flavonoid pathways into minimal modules and further re-assembly at microbial community level. In these first 18 months, the project has made significant progress towards this objective. Work done in WP2 and WP3 has demonstrated the suitability of optimizing precursor, assembly and decoration pathways in the context of different bacterial chassis, thus delivering a proof of concept of the SynBio4Flav approach. Furthermore, the development of new devices and mathematical models for the optimization of synthetic consortia developed in WP4 and WP7 pave the way for the validation of this new approach in the next reporting periods.

Promising advances in the synthesis of basic flavonoid synthons have been achieved during this reporting period. In addition, the identification of new decoration enzymes such as new glucosidases and hydrolases will facilitate the achievement of SynBio4Flav's expected impacts, e.g. “production of at least 10 natural complex glycosylated flavonoids difficult to synthetize by chemical approaches and, at least, 5 novel glycosylated flavonoids”.

SynBio4Flav has largely contributed to standardization in synthetic biology during this first reporting period, including the extension of SEVA standards toward genome editing in P. putida and S. albus and the design and validation of new standardized biological parts in the context of Modular Cloning. Therefore, new promoters, enzymes and regulators have been standardized and will be publicly accessible through DOULIX www.doulix.com

During this first reporting period, the SynBio4Flav consortium has implemented a large array of dissemination actions contributing not only to put the project on the map, but also to bring synthetic biology and the benefits of flavonoids to society. We have been approached by a broad variety of stakeholders ranging from press reporters to school children (WP8). Society's overall reaction to the project has been very positive, which seems to confirm that our outreach efforts have also contributed to a public acceptance of synthetic siology and biotechnology as enabling technologies for solving societal challenges. The first scientific outputs are also being generated in the form of conference presentations and peer-reviewed publications.

In the context of the current COVID-19 pandemic, SynBio4Flav has swiftly shifted gears expand its research effort in order to deliver reliable production of functionalized flavonoids with antiviral activity, thus contributing to the development of effective treatments. The SynBio4Flav consortium liaised with the Project Officer and other EU officials to update them on the project's planned response to the pandemic. Subsequent coverage of the project on the EC's dedicated websites and relevant officers' social media are expected to further increase the overall visibility of the project in the short term.