TOPCAPI will exploit the natural fabrication power of actinomycetes as microbial cell factories to produce three high value compounds: GE2270, a starter compound for the semi-synthesis of NAI-Acne, a new topical anti-acne drug in Phase II clinical trials; 6-desmethyl-tetracycline (6DM-TC) and 6-desmethyl 6-deshydro tetracycline (6DM6DH-TC), intermediates for semi-synthetic conversion to medically important type II polyketide tetracyclines (TC), e.g. minocycline, tigecycline, and the novel omadacycline, which is in Phase III clinical trials, to be used against Methicillin-resistant Staphylococcus aureus infections. Our work will focus on two bacterial host species: Streptomyces coelicolor and Streptomyces rimosus. These host species will be characterised using systems biology approaches, applying integrated data analysis to transcriptomics and metabolomics experiments, combined with predictive mathematical modelling to drive the rapid improvement of these microbial cell factories for industrial drug production using advanced metabolic and biosynthetic engineering approaches. At the same time, we will establish an expanded toolbox for the engineering of actinomycete bacteria as cell factories for other high added-value compounds. In the proposed 4-year project, we will: 1. Host engineer two new actinomycete strains for industry-level improved heterologous compound production through integrating systems biology-driven strain design and state-of-the-art genome editing. 2. Engineer the biosynthesis pathways to obtain high-efficiency synthesis of GE2270 and new pathway variants for 6DM-TC and 6DM6DH-TC as well as improve its production purity. 3. Optimise the expression of the engineered target pathways in pre-engineered strains to achieve industrially viable production levels of ≈1 g/L for GE2270 and ≈24 g/L for 6DM-TC, while creating a complete novel production strain for 6DM6DH-TC.

MARBLES will use a novel and systematic approach to access and exploit marine microbial biodiversity for sustainable bioprospecting to discover microbial consortia and bioactive molecules for application in aqua- and agriculture and in the clinic. MARBLES' ecology-based bioprospecting strategy will focuses on unique host-microbe interactions in marine environments, including marine sponges, microalgae and fish, which rely on their microbiomes and microbial natural products for disease resistance. Partners’ existing microbial collections and new ones generated during MARBLES will be harnessed for the discovery of novel natural products and synthetic microbial communities. For this, MARBLES will use a systems-wide genomics approach to uncover the bioactive agents in disease-suppressive microbiomes. Also, MARBLES will explore host- and microbe-derived chemicals that elicit production of bioactive compounds, as elicitors to revitalise drug screening. The deliverables will be microbes and consortia and bioactive natural products, their derivatives and elicitors, which can be harnessed to fight infectious diseases in the agrochemical and aquaculture industries and in healthcare. Besides highly innovative, the approaches will be cost-effective and will offer advantages from both environmental and health perspectives in comparison to existing alternatives. The sustainable production of bioprotectants will increase the effectiveness of fish production - reducing the pressure on harvesting wild fish - and aid the transition of the crop agriculture sector towards bio-based and circular solutions. MARBLES will work closely together with a panel of SMEs and large companies from the EU aquaculture, crop protection biotechnology and health sectors. MARBLES fully complies with the Nagoya and Cartagena Protocols, and aims to make major contributions to the UN sustainable development goals, SDG 2, 3, 12, 13 and 14, as well as to current UN processes (BBNJ, DSI, SynBio)

The aim of Natalion is to foster innovation excellence of LIOS by the establishment of the Natural Products Research (NPR) group and implementation of the LIOS Innovation Hub as a complementary structural change. The introduction of new research strands and the structural changes will be achieved under the leadership of ERA Chair holder Dr. Stefano Donadio, an experienced Research and Innovation (R&I) professional. Project objectives: O1 Establishment of the NPR group, including its capacity build-up; O2 Setting up the research directions of the NPR group with a focus on new technologies and products; O3 Integration of activities of the NPR group into internal and external collaborative projects including 3I mobility; O4 Increase competitiveness for attraction of external research funding; O5 Establishment of the LIOS Innovation Hub and its integration into institutional, national and EU ecosystems; O6 Development of a motivating and inclusive institutional environment which fosters innovations and entrepreneurial culture; O7 Enabling institutional compliance to ERA priorities and UN Sustainable Development Goals; O8 Dissemination and exploitation of the results of the NPR group according to PEDR and a communication plan; Establishing the NPR group, the international recruitment, as well as the development of environment, fostering innovations will nurture brain circulation for researchers and innovators. The establishment of the LIOS Innovation Hub and its integration into institutional, national and EU ecosystems will deliver institutional reforms with a focus on innovation. Setting up new research directions and integrating the NPR group into internal and external collaboration networks under the competent guidance of the ERA Chair will leverage excellence of R&I and increase the competitiveness for attraction of external research funding. Better communication of R&I results to society will be achieved by Dissemination and Exploitation of the project results.

The discovery of penicillin initiated the antibiotic era and saved millions from dying of life-threatening bacterial infections such as tuberculosis, sepsis, and pneumonia. Penicillin kills bacteria by inhibiting synthesis of peptidoglycan, an important structure of the bacterial cell envelope. Still today, antibiotics targeting the bacterial cell envelope are the most widely used antibiotics in the world. Unfortunately, resistance to these superior antibiotics is becoming highly prevalent and antibiotic-resistant bacteria represent one of the greatest threats to human health and development today. In the CLEAR (Cell Envelope Anti-bacterials) training network, world-leading researchers from academia have gathered with clinicians and 4 highly relevant SME partners to train a new generation of excellent European scientists in finding novel solutions for targeting the cell envelope of bacteria, who know how findings in academia generate assets to SMEs, and who could bring novel antimicrobial solutions to the market. The proposed research program builds on unique findings of the project partners that allow us to take up innovative and yet feasible approaches 1) to identify novel targets in the cell envelope and to evaluate the lead structure potential of novel agents acting on the cell envelope, 2) to re-sensitize resistant bacteria to existing cell wall antibiotics, 3) and to explore novel therapies acting via the cell envelope. Impacts of this proposal are the re-use of safe and cheap antibiotics, and the drugs already approved for treatment of other diseases as novel antimicrobials. The training program combines a broad range of scientific disciplines such as molecular biology, biochemistry, structural biology, screening technologies, pre-clinical testing with complementary courses in innovation, market potential and business strategies ensuring that the 10 PhDs will be highly competitive for both top European research institutions and the pharma/biotech job market.

Genetic tractability of bacterial cells allows generating synthetic microbial chassis platforms (SMCPs) with remarkable biotechnological applications but their functionality currently faces important off-genome limitations due to deficient protein-protein interactions, unfavorable protein stoichiometry or generation of toxic intermediates that ultimately compromise the industrial production processes. To solve this problem, Rafts4Biotech project will take advantage of our recent discovery, that bacteria are able to organize subcellular membrane compartments similar to the so-called lipid rafts of eukaryotic cells, to improve/protect specific cellular processes. Rafts4Biotech project will engineer bacterial cells to confine biotechnologically relevant reactions into bacterial lipid rafts to optimize their stoichiometry and protect cells from undesirable metabolic interferences. Hence, the Rafts4Biotech project will produce new generation reliable and robust SMCPs in which industrial production processes are confined in bacterial lipid rafts, released from their classical off-genome limitations and optimized for industrial production. Moreover, this concept can be applied to many prokaryotes, since lipid rafts happens to occur in many bacterial species. Based on this versatility, Raft4Biotech project will use two biotechnologically relevant biosystems, Bacillus subtilis and Escherichia coli, to engineer synthetic bacterial lipid rafts to optimize the performance of three challenging biochemical processes in the fields of pharmaceutical, cosmetics and feed industrial sectors. To achieve this, Rafts4Biotech consortium combines different expertise in synthetic biology, systems biology and mathematical modeling and it includes a number of SMEs that will actively work in this project and will translate this technology into market application. The technology developed by Rafts4Biotec will optimize multistep industrial processes and invigorate European research.