Biotechnology with focus on Bioprocess Engineering

Data-driven development of enzyme cascades

Several impressive biocatalytic multi-step reactions, so-called in vitro enzyme cascades, have been developed for the synthesis of complex molecules with pharmaceutical relevance. However, the development and optimization of enzyme cascades is challenging because the performance might be affected by destabilizing or inhibitory interactions between cascade components. In the project, an iterative data-driven approach combining modelling and simulation with wet-lab experiments is developed to optimize a cascade for the synthesis of pharmaceutically relevant molecules in terms of production performance. 

Sustainable, biocatalytic production of cyclic dinucleotides

Cyclic dinucleotides serve bacteria and mammals as secondary messengers in signal transduction and immune defense. The cyclic dinucleotide 2'3'-cGAMP in particular is widely used in immuno-oncological research. Previous chemical synthesis methods are complex (15 steps), which leads to high production costs. In order to make production more efficient, cost-effective and environmentally friendly, an optimized chemoenzymatic process for the synthesis of 2'3'-cGAMP and derivatives is being established in this project. This innovative approach makes it possible to avoid toxic reagents and intermediates in future and drastically reduce energy-intensive processing steps. 

Cell-free protein synthesis of membrane proteins

Heterologous production of integral membrane proteins in vivo is challenging due to toxicity, limited space for proper folding, and inefficient transport and incorporation into the membrane. These problems are a setback for the structural and functional characterization of existing or engineered membrane proteins. Cell-free protein synthesis (CFPS) might be an alternative in these cases due to its openness and potential for high throughput screening, allowing modification of the system as needed to support the synthesis of functional membrane proteins. To date, only a few membrane proteins with intact functionality have been synthesized using CFPS. In this project, integral membrane proteins are synthesized with CFPS. First, a suitable hydrophobic environment must be created. Subsequently, the CFPS synthesis is combined with activity assays for membrane proteins.

• Do you always need replicates for biocatalysis experiments? In close collaboration with Prof. Dr. Eric von Lieres (Forschungszentrum Jülich), we focused on overcoming the complexity of optimizing enzyme cascades by using machine learning techniques. In contrast to conventional biocatalysis experiments, we did not use replicates and relied on Bayesian optimization with inherent uncertainty quantification to guide the design of the experiments.
  This project highlights the power of data-driven optimization strategies to determine the optimal reaction conditions most efficiently. https://doi.org/10.1002/cctc.202400777
• Can the synthesis of proteins by the cellular machinery take place under non-physiological conditions? A wide parameter space was tested for high viscosities, concentrations of inorganic ions and osmolarity using various technical additives, including organic solvents, polymers and salts. This study shows that the protein synthesis machinery is very robust to various technical additives. https://doi.org/10.3762/bjoc.20.192
• Biotechnology is recognized as a key technology for achieving the Sustainable Development Goals and requires environmental assessment methods to refocus research at an early stage of development. In the study, we have shown that Life Cycle Assessments (LCAs) for early-stage bioprocesses face challenges, especially the limited availability of process data and specialized databases. Therefore, recommendations are given on how Life Cycle Assessments can be performed at an early stage of bioprocess development. https://doi.org/10.1016/j.tibtech.2023.03.011

The Rosenthal Group has one postdoc, two PhD students, one technician, and is supported by several undergraduates. The group is funded by the Deutsche Forschungsgemeinschaft and the Bundesministerium für Wirtschaft und Klimaschutz.

• Malzacher S., Meißner D., Range J., Findrik Blažević Z., Rosenthal K., Woodley J.M., Wohlgemuth R., Wied P., Nidetzky B., Giessmann R.T., Prakinee K., Chaiyen P., Bommarius A., Rohwer J., de Souza R. O. M. A., Halling P., Pleiss J., Kettner C., Rother D.
  The STRENDA Biocatalysis Guidelines for Cataloguing Metadata
  Nature Catalysis, 2024, accepted article.
• Becker M, Nowak I., Hildebrand K., Lütz S., Rosenthal K.
  Development of a multi-enzyme cascade for 2’3’-cGAMP synthesis from nucleosides Catalysis Science & Technology, 2024, 14(12), 3335-3345. https://doi.org/10.1039/D4CY00147H
• Becker M., Ziemińska-Stolarska A., Markowska D., Lütz S., Rosenthal K.
  Comparative life cycle assessment of chemical and biocatalytic 2'3'‐cyclic GMP‐AMP synthesis ChemSusChem, 2023, 16(5), e202201629. https://doi.org/10.1002/cssc.202201629
• Wowra K., Hegel E., Scharf A., Grünberger A., Rosenthal K.
  Estimating environmental impacts of early-stage bioprocesses Trends in Biotechnology, 2023, 41(9), 1199-1212. https://doi.org/10.1016/j.tibtech.2023.03.011
• K. Rosenthal, UT. Bornscheuer, S. Lütz
  Cascades of Evolved Enzymes for the Synthesis of Complex Molecules
  Angewandte Chemie International Edition, 2022, 61(39), e202208358. https://doi.org/10.1002/anie.202208358

E-Mail: krosenthal@constructor.university

Homepage: https://constructor.university/katrin-rosenthal 
LinkedIn profile: https://www.linkedin.com/in/katrin-rosenthal-07a46b240

Scopus profile: https://www.scopus.com/authid/detail.uri?authorId=55549749000 
ORCiD: https://orcid.org/0000-0002-6176-6224 
Google Scholar profile: https://scholar.google.com/citations?user=EeqcN0AAAAAJ&hl=de