Bioeconomy Science Center
Research and cooperation for a sustainable bioeconomy

Bioeconomy Science Center
Research and cooperation for a sustainable bioeconomy
FocusLab CombiCom

Combinatorial creation of structural diversity for novel high-value compounds

 

Scientific Abstract

Natural products represent an invaluable source of bioactive compounds. They can serve as chemical frameworks for developing new agrochemicals and pharmaceuticals that are urgently needed to meet the growing demands of modern society. Reinforcing the change of paradigm from synthetic chemistry to sustainable microbial production, CombiCom will thus exploit secondary metabolite pathways to deliver natural compounds and further extend these structures by exploring the non-natural chemical space beyond. We will pursue an integrated approach by joining forces of experts in biology, chemistry and engineering to create synthetic biology-tailored microbial chassis allowing for the sustainable production of novel high-value compounds, which will be evaluated for their anti-phytopathogenic activity and pharmaceutical potential. This endeavor will be accompanied by the assessment of related socioeconomic implications, aiming to evaluate and optimize the market introduction potential of synthetic biology associated products.

What is the relevance for bioeconomy?

Aiming to reinforce the change of paradigm from synthetic chemistry to sustainable microbial production, key technologies for the sustainable (bio)synthesis of natural and nature-inspired compounds will be developed in a unique and interdisciplinary approach. Inspired by the modular architecture of natural biosynthetic pathways, engineering concepts will be implemented on different pathways, specifically exploiting the joined expertise of CombiCom partners in the fields of biology, chemistry, and engineering.

Biological phyto-protection activities of the new compounds will be evaluated, targeting relevant pathogens of the crop plant rapeseed which represents an important part of the local agricultural landscape. The FocusLab thus aims to promote novel, sustainable, and resource-efficient crop protection strategies. Moreover, CombiCom will specifically address socioeconomic aspects of market introduction of synthetic biology-derived products. Thereby, the dialogue with society and important stakeholders is fostered to ultimately strengthen the acceptance of synthetic biology for a sustainable bioeconomy.

Approach

CombiCom is subdivided into four working units, WU1 – WU4, within which 9 different work packages are integrated.

WU1: Synthetic biology platform – Novel pro- and eukaryotic microbial production chassis are engineered allowing the combinatorial creation of small molecules with structural diversity. Synthetic biology tools for gene transfer, expression and regulation of enzyme activities together with synthetic chemistry will enable the orchestrated biosyntheses of a variety of natural and nature-inspired products (WP1-6).

WU2: Production process – Light-mediated control of cellular processes is evaluated for multifactorial bioprocess engineering. Production performance of microbial chassis will be systematically improved for selected compounds exhibiting promising bioactivities (WP7).

WU3: Multi-step evaluation pipeline – Bio-assays will provide information about the activity, efficacy and specificity of new compounds. Here, CombiCom focuses on the evaluation of anti-phytopathogenic compounds (WP8). Scientific activities within WU1-3 will be closely interconnected by feedback loops of iterative testing and modification of compound structures.

WU4: Social implications – Key barriers and success factors for synthetic biology-derived technologies are elucidated before identifying effective information-framing strategies to foster knowledge transfer and future market introduction of related products (WP9).

 CombiCom is subdivided into four working units, WU1 – WU4, within which 9 different work packages are integrated.
 
CombiCom Work Packages

WP1: Implementation of Rhodobacter capsulatus and Pseudomonas putida as novel bacterial chassis for the production of sesquiterpenes and prodiginines. Synthetic biology tools will be developed and implemented for transplantation and (opto)genetic control of secondary metabolite pathways, enabling effective (muta)synthesis of diverse compounds (Core Group Prof. K.-E. Jaeger/Dr. T. Drepper/Dr. A. Loeschcke, Institute of Molecular Enzyme Technology, HHUD).

WP2: Establishment of Ustilago maydis as a novel basidiomycete fungus chassis for the production of glycolipids and sesquiterpenes. Diverse glycolipid variants will be produced by genetic engineering using homologous and heterologous genes and, in addition, the suitability of this host for sesquiterpene production will be assessed adopting synthetic biology tools (Core Group Prof. M. Feldbrügge/Dr. K. Schipper, Microbiology, HHUD).

WP3: Unlocking eukaryotic green algae Chlorella sp. as next generation phototrophic production hosts. Fast growing Chlorella strains will be characterized and molecular engineering and expression tools will be developed, aiming to evolve the green algae towards small molecule production (Core Group Prof. U. Schurr/Dr. D. Behrendt, IBG-2 – Plant Sciences, FZJ).

WP4: Engineering of pathway regulation and fine-tuning via synthetic (opto)genetic tools. A set of synthetic molecular tools applicable for pro- and eukaryotic chassis will be designed, developed and implemented for the effective pathway transfer, as well as accurate control and regulation of biosynthetic routes (Core Group Prof. M. Zurbriggen, Synthetic Biology, HHUD).

WP5: Enhancing chemical prodiginine diversity via (bio)chemical approaches. Mutasynthesis and semisynthesis will be implemented via introduction of synthetic precursor analoga in vivo and in vitro, respectively. These strategies, together with enzymatic conversion, will enable derivatization, thus generating diverse novel compounds (Core Group Prof. J. Pietruszka/Dr. T. Classen, Bioorganic Chemistry, HHUD).

WP6: Engineering of improved prodiginine and sesquiterpene synthases. Randomized as well as rational methods will be used to evolve prodiginine condensation enzymes for improved mutasynthesis and sesquiterpene synthases towards altered product specificity (Core Group Prof. U. Schwaneberg/Dr. A. J. Ruff/Dr. J. Schiffels, ABBt – Biotechnology, RWTH).

WP7: Process engineering for light-controlled microbial production. A screening platform will be developed for controlling cellular processes based on light-induced gene expression, for process optimization and scale-up for pro- and eukaryotic chassis organisms (Core Group Prof. J. Büchs/Dr. L. Regestein, AVT – Biochemical Engineering (AVT.BioVT), RWTH).

WP8: Evaluation of the anti-phytopathogenic potential of CombiCom-derived compounds. Newly produced compounds will be tested for their impact on relevant fungal and nematode rapeseed pathogens, on plant development, on plant defense responses, and on the plant-associated microbiome (Core Group Prof. F. Grundler/Dr. S. Schleker, INRES – Molecular Phytomedicine, UB).

WP9: Investigation of socioeconomic implications of synthetic biology-driven innovations. Success-factors for market introduction of novel high-value compounds will be examined and the product-related acceptance of synthetic biology explored, in order to develop information framing strategies to cultivate consumer acceptance (Core Group Prof. S. Bröring/Dr. C. Baum, ILR – Technology and Innovation Management in Agribusiness, UB).

 
FocusLab coordinator

Dr. Anita Loeschcke
Institute of Molecular Enzyme Technology of the Heinrich-Heine-University Düsseldorf
located at Forschungszentrum Jülich, Geb. 15.8
Stetternicher Forst
52426 Juelich
Email: a.loeschcke@fz-juelich.de

 more information about the team member
External Partners

Academic partners:

Prof. C. Schmidt-Dannert
Biosynthesis and Designer Microbes
Department of Biochemistry, Molecular Biology & Biophysics
College of Biological Sciences, Medical School
University of Minnesota, Minneapolis (USA)

Prof. H. B. Bode
Fachbereich Biowissenschaften, Merck-Stiftungsprofessur für Molekulare Biotechnologie and
Buchmann Institute for Molecular Life Sciences (BMLS)
Goethe University, Frankfurt (Germany)

Dr. Florian Hennicke
Junior Research Group “Genetics and Genomics of Fungi”
Senckenberg Gesellschaft für Naturforschung, Frankfurt (Germany)

Prof. J. S. Dickshat
Laboratory of Natural Product Chemistry
Kekulé Insitute for Organic Chemistry and Biochemistry
University Bonn, Bonn (Germany)

 
Funding period

01.05.2017 – 30.04.2020

 
Funding

The total budget of CombiCom is € 2.392.370. CombiCom is part of the NRW-Strategieprojekt BioSC and thus funded by the Ministry of Innovation, Science and Research of the German State of North Rhine-Westphalia.

 
Most relevant publications from preliminary studies

WU1
Domröse A*, Klein A*, Hage-Hülsmann J, Thies S, Svensson V, Classen T, Pietruszka J, Jaeger K-E, Drepper T & Loeschcke A (2015) Efficient recombinant production of prodigiosin in Pseudomonas putida. Frontiers in Microbiology 6: 972 *contributed equally

WU2
Binder D, Bier C, Grünberger A, Drobietz D, Hage-Hülsmann J, Wandrey G, Büchs J, Kohlheyer D, Loeschcke A, Wiechert W, Jaeger K-E, Pietruszka J & Drepper T (2016) Photocaged Arabinose: A Novel Optogenetic Switch for Rapid and Gradual Control of Microbial Gene Expression. Chembiochem 17: 296-299

WU3
Bogner W, Kamdem RST, Sichtermann G, Matthäus C, Hölscher D, Popp J, Proksch P, Grundler FMW & Schouten A (2017) Bioactive secondary metabolites with multiple activities from a fungal endophyte. Microbial Biotechnology 10: 175-188

WU4
Bornkessel S, Bröring S, Omta SWFO & van Trijp H (2014) What determines ingredient awareness of consumers? A study on ten functional food ingredients. Food quality and preference 32: 330-339

Klein AS, Domröse A, Bongen P, Brass HUC, Classen T, Loeschcke A, Drepper T, Laraia L, Sievers S, Jaeger KE, Pietruszka J (2017) New Prodigiosin Derivatives Obtained by Mutasynthesis in Pseudomonas putida. ACS Synthetic Biology. doi: 10.1021/acssynbio.7b00099