Prof. Dr. Wolfgang Streit
The Streit lab pursues two main aspects of research
I. Functional metagenomics and provision of new biocatalysts for biotechnology. Based on this, we have, among other things, been very successful in identifying plastic-degrading enzymes. Watch a short film by the Biology Department or the ZDF program Leschs Kosmos "Die Plastik-Zeitbombe: Wege aus der Krise" (The plastic time bomb: ways out of the crisis).
II. Identification of important parameters for the targeted control of microbial biofilms. We have a great deal of expertise in the (meta) genomic and structural analysis of biofilms.
Click here for PAZy – a database listing exclusively biochemically characterized plastic-active enzymes – curated in collaboration between the University of Stuttgart, Institute of Biochemistry and Technical Biochemistry and the University of Hamburg, Department of Microbiology & Biotechnology.
I. New enzymes and valuable biomolecules for biotechnology
In one of the central research areas, we use metagenomics (genomes of all microorganisms) to provide new biocatalysts and other valuable biomolecules for various biotechnology applications. A central aspect of our research is the utilization of non-cultivated organisms or their metagenomes for biotechnology. Today we know that 99 % of all microorganisms are not or only with difficulty cultivable. We want to exploit this almost unlimited potential of new enzymes and molecules. In order to use this immense potential, we are developing new technologies on the one hand and identifying many biocatalysts on the other. This is done against the background of both basic and applied research.
- Biocatalysts from the metagenome for the chemical industry: With regard to the identification and supply of biocatalysts, we have worked on relatively different classes of enzymes, but our focus is on the isolation of lipases, esterases and other hydrolases for industrial applications. In this respect we now have one of the largest lipase/esterase enzyme collections with over 150 active and characterize biocatalysts (Metacat collection) and about 80 active cellulolytic enzymes. In addition, there are lactonases, hydrogenases, glycosyltransferases, decarboxlyases and other enzymes, which we have often characterized up to the 3D structure. In our work we are also interested in identifying completely new reactions and enzymes (dark and grey matter proteins). In addition, we usually develop reporter assays for the detection of the reactions in high-throughput procedures. We are constantly expanding our metagenome enzyme collection, which forms the basis for many of our research projects.
- Enzymes for the degradation of synthetic polymers: In the course of the above mentioned metagenome searches we started to isolate PET-degrading enzymes a few years ago. We currently have about 60-PET-active enzymes from a wide variety of organisms that have been identified and partially characterized in our laboratories. These enzymes are currently the focus of two BMBF projects (LipoBiocat and Plastisea) and represent the largest collection of such enzymes worldwide. We are currently extending this work to other plastics for which there are no known enzymes. In principle, we assume that not only the degradation is of interest, but also the use of the enzymes for the synthesis of new biodegradable polymers and materials. This work currently forms the basis for a number of ongoing doctoral theses.
- Establishment of a digital platform for enzyme searches: A challenge in many of our projects, which we often carry out in cooperation with industrial partners, is caused by the relatively long runtimes. The usual development time is usually 3-5 years, calculated from the identification of the enzyme to the first upscaling trials. In order to shorten this period, we are working at full speed on an automated platform. We want to achieve the provision of robust enzymes or entire metabolic pathways for biotechnology in relatively short periods of time of maximum 3-6 months. Here, we are working on the development of in vitro systems in order to gain really fast access to non-cultivated organisms. In combination with sequence-based metgenome searches and in vitro approaches, the aim is to provide a few thousand active enzymes for initial screening in a very short time and only in a second step to enter upscaling. The platform will be available in a few years. Currently we can provide about 30-50 enzymes within a very short time.
II. Microbial biofilms
Microbial biofilms are often unwanted growths on surfaces and they pose a real challenge in both clinical and industrial environments.
- Biofilms - detection and analysis: Biofilm analysis and reliable diagnostics are often very difficult and costly in industry and also in the clinical environment. For this purpose we analyse metagenomes of complex biofilms and thus gain deep insights into the functioning of these consortia. We use the whole range of omics analysis and image-representing methods, such as electron microscopy, are an integral part of such analyses. We have also established EPS analysis.
- Control and management of growth at interfaces: To this end, we are working intensively on the elucidation of processes that play a role in bacterial communication during biofilm formation. In this field of research we are particularly interested in how microorganisms talk to each other. On the one hand, we are looking for new signalling molecules, on the other hand we are also investigating how growth in a biofilm can be specifically controlled. We are working with mixed consortia on the level of entire populations as well as in the field of single cell analysis. In this work we also reconstruct multi-species biofilms and try to simulate the natural conditions in the process or clinical environment. In this way we gain very deep insight into 3D biofilm structures and omics.
- Avoidance of microbial biofilms: In principle, it is better to inhibit biofilms very early in growth. Here we are working together with colleagues from the Chemistry department on both enzymatic and compound-driven approaches to inhibit microbial biofilms. We have achieved initial successes with enzymes that intervene in cell-cell communication, but also with molecules from the group of flavonoids and diorcinols. The long-term goal of this work is to change the biofilm population in such a way that no (hardly) biofilms are formed or that a rapid detachment takes place.
Available range of methods
Methodologically, the lab is very broadly based due to the diversity of topics and has a great deal of expertise in the fields of DNA and RNA technologies, genomics and metagenomics, transcriptomics, GC and HPLC analysis and protein purification. In addition, the laboratory has expertise in the handling of a number of model organisms that are particularly important in biotechnology and industrial microbiology. These include Pseudomonas sp., Burkholderia sp. and others. Within the scope of biotechnological work, we also develop microorganisms for production. We have established genetic systems for all organisms. Finally, in recent years we have just begun to establish single cell technology in the laboratory and have established the first laser trapping system for this purpose. We also have 3D biofilm systems and a confocal laser scanning system for biofilm analysis. Furthermore, we often develop new techniques for the detection of enzyme activities in metagenome banks.
3D-structure of the metagenome derived Lipase LipS (Chow et al., 2012, PDB: 4FBL). LipS is a true lipase derived from a non-cultivated Symbiobacterium sp. It has a high potential for application in biotechnology.
3D-structure of a bacterial biofilm in a flow cell produced by Stenotrophomonas maltophilia K279a, an emerging pathogen (Cells were visualized with the life dead stain). The biofilms of Stenotrophomonas maltophilia clinical isolates were grown in flow cells under flow conditions at 28 °C for 72 hours (Alio et al., in preparation, 2020).
Cellulolytic bacteria forming colonizing cellulose fibres (unpublished image)
Mikrobieller Biofilm von Janthinobacterium sp HH102 (rot) auf Filamenten des pflanzenpathogenen Pilzes Fusarium graminearum (grün) (Haack et al., 2016)
Mining metagenomes for active hydrolases. Image derived from the cover of Green Chemistry issue 7, 2009 and Pottkämper et al., 2009
Microbes colonizing microalga surfaces of Micrasterias crux melitensis. Small image shows a magnification of the core region of the microalga (unpublished).
A zoom into the center of the microalga Crux melitensis
Comamonas sp. forming biofilms on PET fibres. From the cover of AEM 19 and modified after Danso et al., 2019
3D-Structure prediction model of PET2 a metagenome-derived PET esterase and Bishydroxyethyl Therepthalic (BHET) acid fitting into the active site. The image was derived from Danso et al., 2018
3D-structure of the metagenome-derived and optimized cellulase CelA2 from the cover of Green Chemistry issue 10, 2012 and Lehmann et al., 2012
Stenotrophomonas maltophilia forming very long filamentous cells and outer membrane vesicles. Image derived from Abda et al., 2015
Stenotrophomonas maltophilia is a gloabl emerging opportunistic pathogen that is of clinical relevance. Macrophages pose the first line of immune defence during bacterial infection. Employing various clinical isolates of S. maltophilia we are currently investigating the interaction of this bacteria with primary human macrophages. Staining Macrophage F-Aktin with Phalloidin 568 (red) cell nucleus with DAPI (blue), S. maltophilia are tagged with GFP (green)
Crystal structure of the PET-hydrolyzing bacteroidetal PET30∆PorC including active site and hydrophobicity comparison. (A) Overall structure of PET30∆PorC. The structure was solved by X-ray crystallography to a resolution of 2.1 Å. (B) Comparison of active site residues. All three enzymes PET30∆PorC (light blue), PET27 (orange) and IsPETase (light yellow) have the typical residues of Ser-hydrolases at the catalytically active positions (Ser, His and Asp). The residues of IsPETase are indicated in black. (C) Surface hydrophobicity around the tunnel leading to the active site of four PET-degrading enzymes. Hydrophilic regions are displayed in turquoise and hydrophobic in gold. Taken from Zhang et al. 2022 (Front. Microbiol. 12:803896. doi: 10.3389/fmicb.2021.803896)
Photo: Pablo Pérez-García
Plastic polluted beach in Mallorca, July 2021