SCIENTIFIC REPORT 2010–2014 LOEWE CENTER FOR SYNTHETIC MICROBIoloGY 3 Preface Research on microorganisms has been a long-stand- The collaboration between groups from the Philipps- ing focus of the Philipps-Universität and has made Universität with departments and research groups Marburg one of the best places in Germany to study from the Max Planck Institute for Terrestrial Microbi- microbiology. The fruitful collaborations between ology laid the foundation for further projects like the groups working at the university and the local Max international Max Planck Research School and DFG- Planck Institute for Terrestrial Microbiology have funded coordinated programs, including the micro- heightened the national and international visibility biology-oriented Collaborative Research Center 987. of Marburg and have fortified its reputation for excel- Regionally, SYNMIKRO interacts with groups at the lence. These concerted activities provided the appro- Justus-Liebig-Universität Giessen and the Technische priate framework for the foundation of the Center for Hochschule Mittelhessen and thereby strengthens the Synthetic Microbiology (SYNMIKRO) within the LOEWE research alliance among the universities. SYNMIKRO excellence program of the state of Hessen in a joint is thus also a prime example of fruitful collaborations effort between Philipps-Universität and Max Planck between institutions. Society in the year 2010. We are grateful for the con- tinued support of the state of Hessen without which The manifold research activities and the broad range the center could not have been established. On the oc- of microorganisms studied under the umbrella of casion of the fifth anniversary since its inception, this SYNMIKRO extend to dedicated teaching activities brochure surveys the many activities of SYNMIKRO. that provide superb training for the next generations As the president of the Philipps-Universität Marburg, of microbiologists. Excellence in teaching in the field I am very proud of what has been achieved in this time. of microbiology is a nationally and internationally recognized hallmark of the Philipps-Universität. Scientific progress requires creative minds, excellent working conditions and a stimulating environment. Along with the many scientists working in SYNMIKRO, All these elements come together in an ideal manner I feel that it is both necessary and worthwhile to sum- in SYNMIKRO. Research at the center is carried out by marize for a broader audience what has been accom- internationally highly regarded and recognized scien- plished so far and to look forward to future activities tists. The center provides access to a state-of-the-art of the center. I thank the group leaders, scientists, infrastructure for modern molecular biology. The large and the large number of students for their hard work number of cooperations across the traditional disci- and their concentrated efforts to make SYNMIKRO a plines from life sciences and natural sciences all the success. They have all contributed to making this bro- way to the humanities shows that Marburg provides chure an interesting and stimulating read that I hope an atmosphere that is conducive for interdisciplinary you will enjoy. and trans-disciplinary research. In the near future, key groups in synthetic microbiology from both the Prof. Katharina Krause Philipps-Universität and the Max Planck Institute President will be housed in a large, well-equipped new research Philipps-Universität Marburg building in the center of the science campus Lahn- berge. This new building will foster even closer sci- entific interactions and the cost-effective sharing of equipment. 4 Welcome 5 Freisleben Mösch Hüllermeier Klebe Kolb Thauer Bölker Li Kahmann Essen Lill Bremer Becker Structural Biology Thanbichler Maier Lenz Super Buckel Resolution Microscopy Voigt Albers Mass Spectrometry Synthetic Microbiology in Marburg Laboratory Heider Automation Electron Microorganisms are omnipresent in the biosphere. and interaction of cellular components generates Microscopy Conrad They occupy even the most exotic ecological niches emergent properties is required before we can use Liesack Bange Marahiel and have developed an impressive variety of physi- natural systems as prototypes for the construction Sourjik Waldming- ological and sensory functions that allow them to of predictable, streamlined and robust systems with haus S gaard- respond to and cope with environmental challenges. novel properties. Vice versa, the process of building Andersen Some of these traits already provide the basis for synthetic systems or of modifying natural systems Randau Fritz large-scale production of chemicals and pharmaceu- facilitates understanding, as the performance of Eckhardt ticals, for biofuels, food-processing, biosensing or bio- these constructs helps to understand their function. remediation. Nevertheless, the vast natural toolbox All of this is made possible by advances and new tech- Jonas Graumann developed by microorganisms over billions of years of nologies in several disciplines, in particular in cell Dahlke evolution undoubtedly contains many undiscovered biology, genetics, molecular biology, structural Brune Kostina Flow processes that wait to be explored and harnessed. The biology, biochemistry, and computational biology. Interactome map of SYNMIKRO. Cytometry field of synthetic microbiology is at the center of this enterprise. Much of the fascination with this emer- In 2010, the Philipps-Universität Marburg and the Max gent field derives from the ability to freely combine Planck Institute for Terrestrial Microbiology joined myriads of genes, cellular processes, and biochemical forces to bring synthetic microbiology to Marburg. develop synthetic microbiology, from the identification discourse on pioneering developments. The public is functions in very much the same way as engineers They established SYNMIKRO, the Center for Synthetic and characterization of modules in natural systems regularly invited to learn about synthetic microbiol- combine different parts to form larger functional Microbiology, within the LOEWE excellence program of to the development of synthetic modules and their ogy in open lectures and plenary discussions, and a units and products. the state of Hessen. Research at the center follows the integration into natural host organisms or synthetic fruitful dialogue between basic natural sciences and two-pronged approach – building to understand and chassis-cells. the humanities was initiated. understanding to build – to gain insights into the basic Modeling & Bioethics principles of microbial life and to provide the funda- For optimal support of the scientific projects, With this brochure, we introduce the members of mental knowledge and tools needed to tap in novel SYNMIKRO has invested in state-of-the-art infra- SYNMIKRO and their projects, explain the work of the Microbial Communities ways the potential of microorganisms as cell factories structural units for laboratory automation, flow infrastructural units and describe key activities of Chassis and Genomes or sensor/reporter systems. Since its foundation, the cytometry, protein spectroscopy, super resolution the center in the years 2010-2014. We hope that you center has grown to become a major, internationally microscopy, electron microscopy, structural biology can see from this report that SYNMIKRO provides a Metabolism Cellular visible research institution that today represents one and mass spectrometry. These infrastructural units vibrant environment for top-level education and first- Organization of the hot spots of research in quantitative and syn- provide critical support for the projects pursued by Cellular Signal class science, and that it’s worth to keep an eye on Processing and thetic microbiology in Europe. SYNMIKRO researchers and their collaboration part- SYNMIKRO and its diverse activities. Regulation ners, and are engaged in the development of enabling SYNMIKRO is an interdisciplinary center that consists technologies in key areas in synthetic microbiology. Bruno Eckhardt Anke Becker of members from seven faculties of the university Director Vice Director and the four departments of the Max Planck Insti- The impact of SYNMIKRO goes well beyond the dedi- tute. Drawing on Marburg’s highly-rated expertise in cated research projects. With the thematic focus in Topics integrated within SYNMIKRO. microbiology, it integrates almost 30 laboratory synthetic microbiology within the M.Sc. program groups at the university and the Max Planck Insti- Molecular and Cellular Biology and with our success- However, the challenges encountered by synthetic tute to cover all aspects of microbial life from the ful iGEM team, we recruit graduate and undergradu- biology in its early years revealed that many processes molecular level to whole cells and communities. In ate students to this fascinating new field early in their within cells are still poorly understood and that not addition, theory- and ethics-focused groups provide career. Furthermore, a structured doctoral program, all synthetic pathways sketched on the drawing board testable mathematical models, systematic overviews summer schools, workshops and seminars aim at actually work in cells. A better quantitative, dynamic, and guidance. With its inter- and trans-disciplinary scientists in academia and industry. In addition, we and theoretical understanding of how organization expertise, SYNMIKRO offers a unique opportunity to are committed to promoting the public and scientific 6 Welcome