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)

Global terrestrial plant biodiversity remains a largely untapped source of natural bioactive compounds. In fact, valid sources are even “hiding in plain sight”, yet not “within reach” due to lack of effective technical solutions to unlock their potential. In this context, the PROSPLIGN consortium has developed an innovative bioprospecting approach that uses cutting-edge and complementary chemical and enzymatic methods, supported by statistical analysis and coupled with high-throughput detection methods, to enable the discovery of bioactive molecules from lignin, one of the fractions of the most abundant biopolymer on Earth (lignocellulose). Lignin “chemical biodiversity” will enable PROSPLIGN to cover three target markets (pharmaceuticals, cosmetics and fragrances) with a combined market of >€1.4 trillion. The project will use lignin derived from 9 different species and investigate at least 3 different chemical approaches and 10 different enzymes to obtain up to 1000 mixtures of lignin-derived compounds, and then pass a progressively narrower “hit validation funnel” in industrially relevant environments, being screened via up to 17 different bioactivity assays. Sustainable production routes for at least 2 of the most promising compounds per sector, directly or following derivatisation, will be proposed. Compared to traditional approaches, PROSPLIGN's bioprospecting avoids animal cruelty, expensive exploration efforts (no novel animal/plants discovery), disruptive extractions (seeking “hidden gems” in an abundant but underexploited “biomass mine”), and directly targets the liberation of readily testable bio/chemical-functionality present in plant material, superior to other approaches relying on “manipulation-intensive” microbial strain culture or “extrapolation” from DNA/RNA). Ultimately, PROSPLIGN will contribute to a new generation of biobased bioactives, unlocking more value from existing sources whose immense potential has yet to be harnessed.

The HOTBIO consortium will train a new generation of early-stage scientists to take marine microbial natural products from the seabed to the bedside. They will be involved in every stage of the pipeline from microbial isolation through compound purification and identification to making analogues with desirable drug-like properties. They will gain associated skills in access and benefit sharing, intellectual property and entrepreneurship. Students graduating from HOTBIO will be in a unique position to enter a challenging labour market as they will have received multidisciplinary training at world leading research groups in academia as well as at industry partners. Mentorship will be provided by industrial scientists and recent graduates from the MSCA ITN MarPipe. The HOTBIO consortium consists of eight beneficiaries from seven European countries, including two members from non-academic sectors, that will host ten PhD students. Three more PhD students hosted by two Swiss associated partners will be funded by the Swiss State Secretariat for Education, Research and Innovation. In addition to secondments at the partners in Europe, students will also get the opportunity to do secondments in low-to-middle income countries (LMICs) in Africa and Asia to get a deeper understanding of how modern research can be done in resource-limited setting. HOTBIO expands a conventional marine biodiscovery pipeline by including computer aided drug design (CADD), chemical synthesis of optimized compounds (i.e. medicinal chemistry), target deconvolution and extensive ADMET profiling. This will advance the bioactive microbial secondary metabolites to the later stages of preclinical development, and it will also inform the decisions and priorities of what kind of compounds that should be targeted in the initial phase of the drug discovery process. The downstream development will include hit compounds from earlier projects.