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Researchers from Goethe University Frankfurt, together with teams from the universities of Marburg and Basel, have shed light on the atomic structure of a bacterial protein that stores hydrogen and carbon dioxide
Microbiologists at Goethe University Frankfurt, together with researchers from Marburg and Basel, have shed light on the structure of an enzyme that produces formic acid from molecular hydrogen (H2) and carbon dioxide (CO2). The enzyme of the bacterium Thermoanaerobacter kivui was discovered a few years previously by microbiologists at Goethe University Frankfurt, and the scientists have recently presented its potential for liquid hydrogen storage. The filamentous structure of the enzyme, now described at atomic level for the first time, acts like a nanowire and is evidently responsible for the extremely efficient conversion rates of the two gases (Nature, DOI 10.1038/s41586-022-04971-z).
FRANKFURT/MARBURG/BASEL. In 2013, a team of microbiologists led by Professor Volker Müller from Goethe University Frankfurt discovered an unusual enzyme in a heat-loving (thermophilic) bacterium: the hydrogen-dependent CO2 reductase HDCR. It produces formic acid (formate) from gaseous hydrogen (H2) and carbon dioxide (CO2), and in the process the hydrogen transfers electrons to the carbon dioxide. That makes this HDCR the first known enzyme which can directly utilise hydrogen. In contrast, all enzymes known until then that produce formic acid take a detour: they obtain the electrons from soluble cellular electron transfer agents, which for their part receive the electrons from the hydrogen with the help of other enzymes.
The bacterium Thermoanaerobacter kivui thrives far away from oxygen, for example in the deep sea, and uses CO2 and hydrogen to produce cellular energy. The HDCR of Thermoanaerobacter kivui consists of four protein modules: one that splits hydrogen, one that produces formic acid and two small modules that contain iron sulphur. “It was already clear to us after our discovery that it had to be the two small subunits that transfer the electrons from one module to the other," says Müller. In 2016, the researchers observed that the enzyme forms long filaments. Müller: “We could see how important this structure was from the fact that filament formation massively stimulates enzyme activity."
The researchers from Goethe University Frankfurt, together with the group led by Dr. Jan Schuller, University of Marburg and LOEWE Centre for Synthetic Microbiology, have now produced a molecular close-up of the enzyme. Through cryo-electron microscopy analysis, Schuller's group has succeeded in determining the HDCR structure at atomic resolution. This made details of the long filaments visible, which the enzyme forms under experimental conditions in the laboratory (in vitro): the filaments' backbone is composed of the two small HDCR subunits, which are arranged together to form a kind of nanowire with thousands of electron-conducting iron atoms. “This is the only enzymatically decorated nanowire discovered so far. On this wire, the hydrogenase module and the formate dehydrogenase module sit like mushroom heads on a cable," explains Schuller.
Helge Dietrich, a doctoral researcher in Volker Müller's group at Goethe University Frankfurt, tested a genetic modification of the small modules that prevented the HDCR filaments from forming. The result: the individual components or monomers were far less active than the filament.
Enzyme monomers arrange themselves into filamentous structures inside bacterial cells too. Professor Ben Engel, a structural cell biologist at the University of Basel, and his team contributed this finding by performing cryo-electron tomography. Using this cutting-edge technique, the researchers discovered something special: “Hundreds of filaments bundle together to form ring-shaped superstructures. These structures are really striking—we informally call them 'portals'," explains Engel. The bundles are evidently anchored in the inner membrane of the bacterial cell and span almost its entire width. Dr. Ricardo Righetto, senior scientist in Ben Engel's team, analyzed the structure of HDCR filaments within the native bacteria: “Cryo-electron tomography allows us to directly look inside cells at very high resolution. Using this approach, we were really surprised to not only confirm the occurrence of HDCR filaments in the cells but to find they form large bundles attached to membrane".
This structure reveals why the HDCR enzyme is orders of magnitude more efficient than all chemical catalysts and far better than all known enzymes at producing formic acid as a “liquid organic hydrogen carrier" from hydrogen and CO2 (cf. background information). Volker Müller: “The hydrogen concentrations in the ecosystem of these bacteria are low, and, in addition, the CO2 and H2 concentrations can switch. Formation of filaments and bundling not only substantially increase the concentration of these enzymes in the cell. The thousands of electron-conducting iron atoms in this 'nanowire' can also store the electrons from hydrogen oxidation intermediately when even just one hydrogen bubble passes by the bacteria."
The team is convinced that not all the enigmas surrounding the HDCR enzyme have yet been solved through the atomic resolution of the structure. Jan Schuller says: “We don't yet know how the wire stores the electrons, why filament formation stimulates enzymatic activity so intensively or how the bundles are anchored in the membrane. We're working on these research questions." But the HDCR's future could be very exciting, believes Volker Müller: “Perhaps one day we'll be able to produce synthetic nanowires which we can use to capture CO2 from the atmosphere. We're also a step closer now to biological hydrogen storage."
Publication: Helge M. Dietrich, Ricardo D. Righetto, Anuj Kumar, Wojciech Wietrzynski, Raphael Trischler, Sandra K. Schuller, Jonathan Wagner, Fabian M. Schwarz, Benjamin D. Engel, Volker Müller & Jan M. Schuller.
Membrane-anchored HDCR nanowires drive hydrogen-powered CO2 fixation. Nature (2022) https://www.nature.com/articles/s41586-022-04971-z
Picture download: https://www.uni-frankfurt.de/122162542
Caption: The filaments of the bacterial enzyme HDCR, which produces formic acid from gaseous H2 and CO2, are wound around each other like a plait. Credit: Verena Resch -- https://luminous-lab.com/
Professor Volker Müller
Department of Molecular Microbiology & Bioenergetics
Institute for Molecular Biosciences
Goethe University Frankfurt
Tel.: +49 (0)69 798-29507
Dr Jan Michael Schuller
KryoEM Molecular Machines
SYNMIKRO Research Center
University of Marburg
Tel.: +49-6421 28 22584
Professor Ben Engel
University of Basel
Tel.: +41 61 207 65 55
Prof. Dr. Luciano Rezzolla elected as Fellow of the International Society on General Relativity and Gravitation
FRANKFURT. Every three years, the International Society on General Relativity and Gravitation hand-picks a few extraordinary scientists as Fellows, among them such famous personalities as Stephen Hawking and Nobel-laureate Roger Penrose. From now on, Luciano Rezzolla, professor for Relativistic Astrophysics at Goethe University Frankfurt, is among them. He has been honoured “for leading contributions to the development of robust numerical relativity simulations of astrophysical phenomena", that is, the very same calculations that are necessary to predict the gravitational-wave signal from merging neutron stars or to produce the image of the Black Hole Sagittarius A* at the centre of our Milky Way.
Rezzolla is the first professor of a German university receiving this special honour. “I was clearly overjoyed to think that my contributions to gravitational physics have been so influential to be enlisted in this very selected group of fellows." he says “I am very passionate about my research, so it is very gratifying when my peers acknowledge the hard work." The ceremony took place on 8 July in Beijing. Unfortunately, Rezzolla was not able to attend personally: “It is a pity. But the fellowship is a big motivation to face all the difficulties that research and academic life inevitably bring."
For the years to come, Rezzolla is focusing on the formation of heavy elements during the merger of neutron stars. As spokesperson of the research cluster ELEMENTS, a collaboration of Goethe University, TU Darmstadt, GSI, and JLU Gießen, he and a variety of physicists from different fields are searching for the origin of heavy elements such as gold and platinum in the universe.
Picture download: https://www.uni-frankfurt.de/121674596
Caption: Luciano Rezzolla, professor for Relativistic Astrophysics at Goethe University Frankfurt (Credit: Uwe Dettmar)
Bartonella bacteria use certain proteins – conserved pathomechanism in other bacterial species
Researchers from University Hospital Frankfurt and Goethe University Frankfurt have unravelled how bacteria adhere to host cells and thus taken the first step towards developing a new class of antibiotics.
FRANKFURT. The adhesion of bacteria to host cells is always the first and one of the decisivesteps in the development of infectious diseases. The purpose of this adhesion by infectious pathogens is first to colonize the host organism (i.e., the human body), and then to trigger an infection, which in the worst case can end fatally. Precise understanding of the bacteria's adhesion to host cells is a key to finding therapeutic alternatives that block this critical interaction in the earliest possible stage of an infection.
Critical interaction with the human protein fibronectin
In collaboration with other researchers, scientists from University Hospital Frankfurt and Goethe University Frankfurt have now explained the exact bacterial adhesion mechanism using the human-pathogenic bacterium Bartonella henselae. This pathogen causes “cat-scratch disease", a disease transmitted from animals to humans. In an international collaborative project led by the Frankfurt research group headed by Professor Volkhard Kempf, the bacterial adhesion mechanism was deciphered with the help of a combination of in-vitro adhesion tests and high-throughput proteomics. Proteomics is the study of all the proteins present in a cell or a complex organism.
The scientists have shed light on a key mechanism: the bacterial adhesion to the host cells can be traced back to the interaction of a certain class of adhesins – called “trimeric autotransporter adhesins" – with fibronectin, a protein often found in human tissue. Adhesins are components on the surface of bacteria which enable the pathogen to adhere to the host's biological structures. Homologues of the adhesin identified here as critical are also present in many other human-pathogenic bacteria, such as the multi-resistant Acinetobacter baumannii, which the World Health Organization (WHO) has classified as the top priority for research into new antibiotics.
State-of-the-art protein analytics were used to visualize the exact points of interaction between the proteins. In addition, it was possible to show that experimental blocking of these processes almost entirely prevents bacterial adhesion. Therapeutic approaches that aim to prevent bacterial adhesion in this way could represent a promising treatment alternative as a new class of antibiotics (known as “anti-ligands") in the constantly growing domain of multi-resistant bacteria.
The research work was funded as part of an Innovative Training Network (“ViBrANT: Viral and Bacterial Adhesin Network Training") under the Marie Skłodowska-Curie Actions (MSCA) of the European Union's HORIZON 2020 research and innovation programme.
The scientific paper has been published in
the prestigious journal “Microbiology Spectrum" of the American Society of
Microbiology (ASM) and was acknowledged as “Paper of the Month" by the German
Society for Hygiene and Microbiology (DGHM) on 18 June 2022.
Publication: Vaca, D. J., Thibau, A., Leisegang, M. S., Malmström, J., Linke, D., Eble, J. A., Ballhorn, W., Schaller, M., Happonen, L., Kempf, V. A. J.; Interaction of Bartonella henselae with Fibronectin Represents the Molecular Basis for Adhesion to Host Cells; Microbiology Spectrum, 18 April, 2022. https://doi.org/10.1128/spectrum.00598-22
https://www.kgu.de/fileadmin/redakteure/Presse/Bilder_Pressmitteilungen/2022/Vaca_Diana_Jaqueline.jpgCaption: First author of the study: Diana Jaqueline Vaca, Institute of Medical Microbiology and Hospital Hygiene at University Hospital Frankfurt. Photo: University Hospital Frankfurt
Adhesion of Bartonella henselae (blue) to human blood vessel cells (red). The bacterium's adhesion to the host cells could be blocked with the help of what are known as “anti-ligands".
Professor Volkhard A. J. Kempf
Director of the Institute of Medical Microbiology and Hospital Hygiene
University Hospital Frankfurt
Tel.: +49 (0)69 6301–5019
Editor: Christoph Lunkenheimer, Press Officer, Staff Unit Communication at Universitätsklinikum Frankfurt, Phone: +49 (0)69 6301–86442, firstname.lastname@example.org
German-American research team deciphers evolution of pathogenic Acinetobacter strains
Hospital-acquired infections (HAIs) are often particularly difficult to treat because the pathogens have developed resistance to common antibiotics. The bacterium Acinetobacter baumannii is particularly dreaded in this respect, and research is seeking new therapeutic approaches to combat it. To look for suitable starting points, an international team led by bioinformaticians at Goethe University Frankfurt has compared thousands of genomes of pathogenic and harmless Acinetobacter strains. This has delivered clues about which properties might have made A. baumannii a successful pathogen – and how it might possibly be combated.
FRANKFURT/ST. LOUIS. Each year, over 670,000 people in Europe fall ill through pathogenic bacteria that exhibit antibiotic resistance, and 33,000 die of the diseases they cause. Especially feared are pathogens that are resistant to several antibiotics at the same time. Among them is the bacterium Acinetobacter baumannii, which is today dreaded above all as a “hospital superbug": up to five percent of all hospital-acquired bacterial infections are caused by this germ alone.
A. baumannii is right at the top of a list of candidates for which, according to the World Health Organization (WHO), new therapies must be developed. This is because the pathogen – due to a flexible genome – easily acquires new antibiotic resistance. At the same time, infections are not only occurring more and more outside the hospital environment but also leading to increasingly severe progression. However, a prerequisite for the development of new therapeutic approaches is that we understand which properties make A. baumannii and its human pathogenic relatives, grouped in what is known as the Acinetobacter calcoaceticus-baumannii (ACB) complex, a pathogen.
A team led by bioinformatician Professor Ingo Ebersberger from Goethe University Frankfurt/ LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) has now reached a milestone in this understanding. The team is composed of members of Research Unit 2251 of the German Research Foundation and other national and international partners, among them scientists of Washington University School of Medicine, St Louis, USA.
For their analysis, the team made use of the fact that a large proportion of the members of the Acinetobacter genus are harmless environmental bacteria that live in water or on plants or animals. Thousands of complete genome sequences both of these as well as of pathogenic Acinetobacter strains are stored in publicly accessible databases.
By comparing these genomes, the researchers were able to systematically filter out differences between the pathogenic and the harmless bacteria. Because the incidence of individual genes was not particularly conclusive, Ebersberger and his colleagues concentrated on gene clusters, that is, groups of neighbouring genes that have remained stable during evolution and might form a functional unit. “Of these evolutionarily stable gene clusters, we identified 150 that are present in pathogenic Acinetobacter strains and rare or absent in their non-pathogenic relatives," says Ebersberger, summing up. “It is highly probable that these gene clusters benefit the pathogens' survival in the human host."
Among the most important properties of pathogens is their ability to form protective biofilms and to efficiently absorb micronutrients such as iron and zinc. And indeed, the researchers discovered that the uptake systems in the ACB group were a reinforcement of the existing and evolutionary older uptake mechanism.
Particularly exciting is the fact that the pathogens have evidently tapped a special source of energy: they can break down the carbohydrate kynurenine produced by humans, which as a messenger substance regulates the innate immune system. The bacteria apparently kill two birds with one stone in this way. On the one hand, breaking down kynurenine supplies them with energy, and on the other hand, they could possibly use it to deregulate the host's immune response.
Ebersberger is convinced: “Our work is a milestone in understanding what's different about pathogenic Acinetobacter baumannii. Our data are of such a high resolution that we can even look at the situation in individual strains. This knowledge can now be used to develop specific therapies against which, with all probability, resistance does not yet exist."
Publication: Bardya Djahanschiri, Gisela Di Venanzio, Jesus S. Distel, Jennifer Breisch, Marius Alfred Dieckmann, Alexander Goesmann, Beate Averhoff, Stephan Göttig, Gottfried Wilharm, Mario F. Feldman, Ingo Ebersberger: Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLOS Genetics (2022) DOI: 10.1371/journal.pgen.1010020 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010020
Scanning electron micrograph of a cluster of Gram-negative, immobile bacteria of the Acinetobacter baumannii species. Photo: Janice Carr
Professor Ingo Ebersberger
Institute of Cell Biology and Neuroscience
Goethe University Frankfurt
Tel.: +49 69 798 42112
Goethe University Frankfurt’s Science Magazine, Forschung Frankfurt, on the topic of motion has now been published in English – New Priority Programme focuses on facial and manual gestures
Communication consists not only of spoken words and phrases. We also convey important information by gesturing with our arms, hands and face. Visual communication, a field so far scarcely studied by theoretical linguistics, is the focus of a new Priority Programme of the German Research Foundation coordinated by Goethe University Frankfurt. Read more in the current issue of “Forschung Frankfurt" entitled “In motion".
FRANKFURT. How gestures and facial expressions can underline, supplement and modify the meaning of words and phrases is something that several disciplines at Goethe University Frankfurt are exploring. Linguistics professor Cornelia Ebert is interested in how the contribution of the meaning of gestures can be modelled. Until recently, visual contributions to meaning were not dealt with in formal linguistics, but instead first and foremost in communication sciences as well as in rhetoric, semiotics and psychology.
Together with Professor Markus Steinbach, sign language researcher at the University of Göttingen, Ebert has successfully applied for a Priority Programme of the German Research Foundation and is responsible for its coordination. The objective is to bring together existing findings from various disciplines and link them with linguistics. You can read about the research questions that the programme will address in the latest issue of Forschung Frankfurt, the Science Magazine of Goethe University Frankfurt, which is dedicated to the topic of motion.
In other articles, scientists from Goethe University Frankfurt report on their research projects related to various aspects of motion, for example how they teach computers to recognise different movements such as “cutting" or “waving", how ADHD can affect adults too or how two movements in quantum physics are superimposed, each of which only occurs with a certain probability. Other articles explore, for example, how smartphones, which are almost ubiquitous, are changing film as a medium or how sports clubs can foster the integration of immigrants.
Journalists can order the current English-language issue of Forschung Frankfurt (2/2021) free of charge from: email@example.com
All articles are available online at
www.forschung-frankfurt.de (then go to EN)
Editor: Dr Markus Bernards, Science Editor, PR & Communication Office, Tel: -49 (0) 69 798-12498, Fax: +49 (0) 69 798-763 12531, firstname.lastname@example.org