Say hi to Hiroyuki Seebach! Hiro is working on enzymes that produce molecules, which help plants scavenge metals from the soil. He started his project back in October 2018 in the group of Prof. Ute Krämer after completing his master's degree at the University of Bayreuth.
What are you doing in the lab, Hiro?
The enzyme nicotianamine synthase (NAS) is essential for plant metal homeostasis. The product nicotianamine is a metal chelator for several transition metals like iron, copper or zinc and is involved in the uptake and transport of these metals. Interestingly, in recent years, NAS genes were identified in nearly all taxonomic kingdoms, for example in the bacterium Staphylococcus aureus or the archaeon Methanothermobacter thermoautotrophicus. My research is focusing on the differences between these different NAS species. We established an activity assay for NAS enzymes, which made it possible to directly compare the activities of different species with one single assay. This approach also allowed us to analyse, for the first time, an extended C-terminal region that is unique to plant NAS and may play a role in regulating enzyme activity.
Another research topic is the elucidation of the reaction mechanism catalysed by plant NAS. Nicotianamine contains an azetidine-ring structure, which is also found in antibiotics but rarely in other biomolecules. Currently there is not much known about the mechanism. By generating NAS mutants and identifying reaction intermediates by mass spectrometry, we hope to gain insight into the reaction mechanism.
How do you benefit from being a member of MiCon?
During my PhD in the MiCon group, I came into contact with many people, especially other PhD students. They helped me to discuss my experiments and problems in a relaxed atmosphere, since we all have the same goal in mind. This was especially helpful for me to connect with other groups, e.g. Prof. Marc Nowaczyk or Prof. Frank Schulz , to use machines that are not available in our lab and new techniques. I would highly recommend other students to join MiCon to benefit from these opportunities as well. And to everyone who just started his/her/their PhD: We´re all in the same boat, which will eventually reach its destination!
Another month, a new face! Meet Kai Vocke, who is an associated MiCon member since November 2019 in the lab of Prof. Eckhard Hofmann. Kai works on the structural and mechanistic elucidation of important membrane proteins since his master's studies. Kai earned his bachelor's degree in science engineering at RTWH Aachen, Germany.
What are you doing in the lab, Kai?
ABC transporter gain importance in the field of medical research, as they are involved in a number of essential metabolic pathways in prokaryotes and eukaryotes. Structural and biochemical information on essential ABC transporters leads to targets for application research in the field of, for example, cancer therapy, certain metabolic diseases and antibiotics. In my research, I focus on the coupling of substrate transport and ATP consumption as well as the mechanism of the transport itself. For the energetic coupling to the conformational changes in substrate transport, I concentrate on MsbA, an ABC exporter from Escherichia coli. MsbA has been subject to research for over a decade so that structure, transport characteristics and several effector molecules are well known. I investigate the role of selected residues with Fourier transform infrared spectroscopy. This method allows for the investigation of single amino acids and their influence on ATP binding and hydrolysis. Combined with transport activity data this allows for the discrimination of important residues in substrate and allocrite binding sites. Additionally, recent research on the proposed ABC importer Rv1819c from Mycobacterium tuberculosis suggests a new type of ABC importer, whose mode of action is unknown to this point. For a better understanding of the transport mechanism, I collaborate with groups specialized in FTIR and EPR spectroscopy as well as electron microscopy to elucidate conformational changes during transport.
How do you benefit from being a member of MiCon?
This program can really broaden your methodological knowledge if you follow up on the projects set up and development by MiCon researchers in the various fields. Interaction with PIs and other graduate students through the seminars and other events can lead to new perspectives on problems that arise and ultimately to synergistic effects for one's own research.
Today we talk to Jan Burnik, who is a PhD student working on protein crystallography in Prof. Eckhard Hofmann's group. He joined MiCon as a full-member immediately after the start of the graduate college in summer 2018.
What are you doing in the lab, Jan?
During my studies, I always wanted to work with enzymes that matter. That is why I’m working in the field of Hydrogenases ever since. The long-term hope is to contribute to a cleaner and greener future of our society.
My experimental focus is protein crystallography. The best phrase to describe this method might be ‘seeing is believing’. My students and I currently working on three [FeFe]-Hydrogenases. The first one’s a classic: HydA1 from Chlamydomonas reinhardtii, our model enzyme. Furthermore, we are investigating the two less considered enzymes CpII and CpIII of the soil bug Clostridium pasteurianum. We want to find out what the structural differences are between the three hydrogenases and how these contribute to the different catalytic properties of the enzymes. My second project is some kind of ‘heart project’: I refuse to believe that it is impossible to solve the structure of holo-HydA1. If the native protein does not crystallize, we simply have to create a solution that works. Therefore, I strengthen and stabilize the holoform covalently and non-covalently before attempting to crystallize these improved variants.
What do you like about the RTG?
Regarding the covalent stabilisation of protein variants, I got some ideas when I asked one of our PI’s, Dirk Tischler, for help. That’s probably the best part of the RTG. As we (the PhD students) meet frequently with all PI's during MiCon events and in between, the exchange of ideas and solutions to individual, and sometimes very specific research problems is high. Also, it often helps to share your own misery with your fellow researchers, and often you get a different and useful perspective on your own project, which helps you solve your problems, and vice versa.
Anna Frank has been on board with the RTG MiCon since its inception in 2018 and is part of the management team. She works in the group of Prof. Marc Nowaczyk on the elucidation of molecular mechanisms of photosynthesis.
What are you doing in the lab, Anna?
In my project I am seeking for a way to utilize natural photosynthesis to drive desired reactions – just by the power of (sun)light. Wiring enzymatic catalysts to the photosynthetic machinery of cyanobacteria allows a production of e.g. biofuels or fine chemicals in an environmentally friendly process, without the need for harmful chemical components, high temperatures or pressure. My particular focus is on enzymes of the Cytochrome P450 family that convert naturally occurring fatty acids in cyanobacteria into precursor molecules that can be used for the production of fine chemicals, pharmaceuticals and advanced materials. Additionally, the coupling of the cyanobacterial-own hydrogenase to Photosystem I, done in the lab of our collaboration partner Dr. Gutekunst at the University of Kiel, is promising to allow light-driven production of biohydrogen as a clean biofuel. For the project, we work together with several groups from Germany, Israel and Japan and are happy to share our progress at the Cyano 2019, Biohybrid 2020 and other conferences to come.
What's the best part about being in a collaborative RTG?
I am very fortunate to have benefited from close collaboration with various groups within MiCon. Especially the group of Prof. Dr. Tischler supports my work by providing the Cyt P450 enzymes that are a key component of my project and by enabling the regular use of their gas chromatography facilities for sample analysis. Prof. Hofmann’s group provided us with a quick and easy technique for cell disruption of cyanobacteria via a microfluidizer.
My advice: Take the opportunity to discuss your problems in a large audience with members of different groups. The combined experience of interdisciplinary groups is immense and chances are very high, that you will get surprising ideas and help offers from others that you would have never come to by yourself.
Jan Plewka-Mandelkow is a PhD student in the group of Professor Dr. Ute Krämer, Chair of Molecular Genetics and Physiology of Plants. He did his Master thesis at the University of Cologne in cooperation with the Max Planck Institute for Plant Breeding Research before joining the Ruhr University at the beginning of 2020.
What are you doing in the lab, Jan?
I am a plant scientist focusing on plant-microbe-interactions. To be more specific, I explore bacteria living on or inside plant leaves. It is well-known that colonizing microbiota have a significant influence on their host’s health. Consequently, plant hosts can shape their microbiota structure and behavior by the production and accumulation of secondary metabolites, for example coumarins, glucosinolates, or camalexin. This was demonstrated in the well-recognized model organism Arabidopsis thaliana. Another possible mechanism to shape the microbiota in a leaf might be the accumulation or depletion of trace elements in the plant apoplast. In my first project, I am investigating the variation of metal tolerances among bacterial isolates of the phyllosphere of A. thaliana. In a second project, I isolated around 300 zinc- and cadmium-tolerant endophytic bacteria from the metal hyperaccumulator Arabidopsis halleri, which is able to grow on soils containing extremely high metal concentrations. I will use these strains as a model system to explore plant-microbe interactions in metal hyperaccumulators. Additionally, I am comparing the microbiota from wild type plants and mutant lines impaired in zinc and cadmium hyperaccumulation and from plants vastly contrasting in leaf metal accumulation in the field.
What is your personal benefit from participating in an interdisciplinary graduate program?
I profited a lot from the networking opportunities created by the RTG. I already got several helpful bits of advice from scientists from outside my research group. I also got help, in an efficient and uncomplicated manner, from other groups that pushed my projects important steps forward. Moreover, I received travel funding to visit the group of Professor Dr. Julia Vorholt at the ETH Zürich, from where I transferred the A. thaliana phyllosphere collection to our institute and learnt how to work with it. For the next generations of fellows or associated scientists, I highly recommend using these networking opportunities for their own projects to improve their science. I am still in my first year, so I am looking forward to the future opportunities organized by and with the RTG.
Anna Christina Lienkamp is a MiCon member of the first hour and works in the group of Professor Dr. Dirk Tischler on the interface between microbiology, biotechnology and biochemistry. She started her PhD work back in July 2018 working on new enzymes and pathways in Actinobacteria.
What are you doing in the lab, Anna?
My research project is about the glutathione-dependent degradation of xenobiotics in actinobacterial pathways. Actinobacteria, which can grow on rare and mostly toxic carbon sources like isoprene or styrene, gain this unique ability through specific sets of enzymes. I am working on some of these enzymes regarding their characteristics and role in the native degradation pathways. It has been shown that the actinobacterium Gordonia rubripertincta converts a styrene derivative to ibuprofen, which is just one example of many for a potential biotechnological application. Generally, the production of substituted phenylacetic acids in the course of this pathway can serve a broad range of industrial applications for not only several drugs but also flavours and fragrances. My project combines protein biochemistry with analytical methods and requires a wide set of techniques and devices, which keeps it challenging and broadens the development of my scientific skills. My favourite part so far is the identification of reaction products by liquid chromatography mass spectrometry and the most exciting part is to currently write my first publication about the recent results.
How did you personally benefit from being part of this RTG? Do you have any advice for the next generation of fellows?
Being part of the MiCon RTG is an experience I would highly recommend to my fellow students. The biggest scientific benefit is the permanent exchange of knowledge and techniques. Outstanding herein is the diversity of scientific backgrounds by the members but a shared common basic knowledge and thematic proximity of the overall topics. This helps to critically examine each other’s research projects by giving and receiving many constructive advices and thus more solutions to potential problems. Additionally, we complement and help each other with sets of devices, protocols and techniques giving more options for everyone’s research. Personally, I value the scientific and personal exchange about doing a PhD and being part of an interdisciplinary and international scientific community. Sharing similar experiences and enjoying the social activities offered definitely adds up to the quality of my PhD and helped me a lot in being a more professional researcher. My advice for the new students to come would be to use the benefit of networking because it raises the quality of overall education and science in general.
Prof. Dr. Franz Narberhaus
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Last update: Aug 31, 2023
