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Microbial catalysis

Our goal is to develop microbial biotechnology concepts that can ultimately be applied to solve grand challenges such as pollution and climate change. Our scientific focus is on the development of microbial catalysts for the bio-based production of chemicals, and the fundamental understanding of the underlying cellular processes. Our main workhorses are bacteria from the genus Pseudomonas and fungi from the Ustilaginaceae family. Our methods revolve around synthetic biology, metabolic engineering, laboratory evolution, systems analysis, and bioprocess technology.


Microbial production of aromatics

Aromatic compounds are versatile building blocks found in numerous applications that we use in everyday life. These aromatics are almost exclusively produced from crude oil and thus contribute to fossil resource depletion and environmental pollution. Microbial catalysis offers alternative production routes for aromatics. By metabolic engineering, we can reprogram microbes to enzymatically convert a renewable substrate into a value-added chemical. For aromatics production, our favorite microbial workhorses are bacteria of the genus Pseudomonas, as they display high tolerance towards toxic aromatic chemicals like toluene and styrene. In our group, we work on the metabolic engineering  of non-pathogenic Pseudomonas species to overproduce the central metabolic precursors phenylalanine and tyrosine, and to convert these precursors into a wide range of aromatics products such as phenol, 4-hydroxybenzoate, cinnamate, and 4-hydroxystyrene. We also develop genetic tools for the domestication of our host strains and use these to engineer chassis Pseudomonads with improved bioprocess features. We want to understand the exceptional stress tolerance of Pseudomonas species and further exploit this tolerance for the production of various chemicals.

Overview of aromatics chemicals produced by our engineered Pseudomonas strainsFigure – Overview of aromatics chemicals produced by our engineered Pseudomonas strains.

Selected literature

Otto, M., B. Wynands, C. Lenzen, M. Filbig, L.M. Blank, N. Wierckx. 2019. Rational engineering of L-phenylalanine accumulation in Pseudomonas taiwanensis to enable high-yield production of trans-cinnamate. Front. Bioeng. Biotechnol. 7:312. link

Wynands, B., M. Otto, N. Runge, S. Preckel, T. Polen, L.M. Blank, N. Wierckx. 2019. Streamlined Pseudomonas taiwanensis VLB120 chassis strains with improved bioprocess features. ACS Synth. Biol. 8:2036-2050. link

Lenzen, C., B. Wynands, M. Otto, J. Bolzenius, P. Mennicken L.M. Blank, N. Wierckx. 2019. High-yield production of 4-hydroxybenzoate from glucose or glycerol by an engineered Pseudomonas taiwanensis VLB120. Front. Bioeng. Biotechnol. 7:130 link

Wynands, B., C. Lenzen, M. Otto, F. Koch, L.M. Blank, N. Wierckx§. 2018. Metabolic engineering of Pseudomonas taiwanensis VLB120 with minimal genomic modifications for high-yield phenol production. Metab. Eng. 47:121-133. link


Plastics degradation

Petroleum-based plastic products and their waste stream management are one of the biggest challenges of our society. Bio-upcycling offers an opportunity to add value to plastic waste by establishing it as substrate for microbial biotechnology. In this concept, monomers resulting from the depolymerization of plastics need to be used as carbon sources by microbes. We are working on engineering these microbes, such as Pseudomonas, to catabolize various plastic monomers. Our research mainly focuses on metabolic engineering and adaptive laboratory evolution to enable the efficient assimilation of plastic monomers like ethylene glycol, 1,4-butanediol, and terephthalate as depolymerization products of PET and PU. On the long run, we want to establish co-utilization of monomer mixtures, and we want to couple the catabolism of plastic monomers to the above-mentioned microbial production of value added-chemicals. This so-called microbial funneling of plastic monomers into diverse chemical compounds offers new opportunities to bio-upcycle plastic waste streams that are currently considered unrecyclable. We also investigate the upcycling of novel plastics with better end-of-life capabilities such as biodegradability.

Graphic A concept for transitioning plastics into the circular bioeconomy through bio-upcyclingFigure – A concept for transitioning plastics into the circular bioeconomy through bio-upcycling.

Selected literature

Li, W., T. Narancic, S.T. Kenny, P.-J. Niehoff, K.E. O'Connor, L.M. Blank, N. Wierckx. 2020. Unraveling 1,4-butanediol metabolism in Pseudomonas putida KT2440. Front. Microbiol. DOI: 10.3389/fmicb.2020.00382. link

Li, W.-J., L.N. Jayakody, M.A. Franden, M. Wehrmann, T. Daun, B. Hauer, L.M. Blank, , G.T. Beckham, J. Klebensberger, N. Wierckx. 2019. Laboratory evolution reveals the metabolic and regulatory basis of ethylene glycol metabolism by Pseudomonas putida KT2440. Environ. Microbiol. 21:3669-3682. link

Wierckx, N., T. Narancic, C. Eberlein, R. Wei, O. Drzyzga, A. Magnin, H. Ballerstedt, S.T. Kenny, E. Pollet, L. Avérous, K.E. O’Connor, W. Zimmermann, H.J. Heipieper, A. Prieto, J. Jiminéz, L.M. Blank. Plastic biodegradation: challenges and opportunities. In: Handbook of Hydrocarbon and Lipid Microbiology. DOI 10.1007/978-3-319-44535-9_23-1. link

Wierckx, N., A. Prieto, P. Pomposiello, V. De Lorenzo, K.E. O ’connor, L.M. Blank. (2015) Plastic waste as a novel substrate for industrial biotechnology. Microb. Biotechnol. 8:900–903. link


Fungal biotechnology

Some of the oldest and most established industrial biotechnology processes involve the fungal production of organic acids. Products such as itaconate, malate, and succinate are produced at large scale with a plethora of applications, for instance in the production of functional polymers including the abovementioned biodegradable plastics. Our research focuses on different strains of Ustilago as biotechnological workhorse with desirable bioprocess features. Unlike traditionally used filamentous fungi such as Aspergillus, Ustilago grows like a yeast. This provides tremendous advantages in reliability, scalability, and handling. We are characterizing and engineering the metabolic networks leading to the production of itaconic acid and other products. These networks span multiple cellular compartments, and the transport of metabolites between these compartments and out of the cell of particular interest. Beyond metabolic engineering, we also engineer the cells’ morphology and their tolerance to organic acids under low pH, and we develop fermentation and in situ product removal strategies. We also aim at enabling the conversion of regional industrial waste streams into organic acids, thereby moving away from pure sugars as substrate and enabling new value chains.

Graphic (Sub-)cellular aspects of fungal itaconic acid productionFigure – (Sub-)cellular aspects of fungal itaconic acid production

Selected literature

  1. Wierckx, G. Agrimi, P.S. Lübeck, M.G. Steiger, N.P. Mira, P.J. Punt. 2020. Metabolic specialization in itaconic acid production: a tale of two fungi. Curr. Opin. Biotech. 62:153-159. link

Becker, J., H. Hosseinpour Tehrani, M. Gauert, J. Mampel, L.M. Blank, N. Wierckx. 2020. An Ustilago maydis chassis for itaconic acid production without by-products. Microb. Biotechnol. 13:350-362. link

Hosseinpour Tehrani, H., K. Saur, A. tharmasothirajan, L.M. Blank, N. Wierckx. 2019. Process engineering of pH tolerant Ustilago cynodontis for efficient itaconic acid production. Microb. Cell Fact. 18:213 link

Hosseinpour Tehrani, H., J. Becker, I. Bator, K. Saur, S. Meyer, A.C. Rodrigues Lóia, L.M. Blank, N. Wierckx. 2019. Integrated strain- and process design enable production of 220 g L-1 itaconic acid with Ustilago maydis. Biotechnol. Biofuels 12:263. link