Essential Machineries of Methanogenesis

Almost all biogenic methane – whether produced in swamps, landfills, the digestive tract of ruminants, or any other environment – is made by ancient microbes called methanogens. Although their single-celled body plan is simple, methanogens are master biochemists, catalysing many sophisticated reactions to make a living in low-free-energy anaerobic landscapes. We are especially interested in the processes of flavin-based electron bifurcation, which allows methanogens to fix CO2 from their environments, and in the large structures that have evolved for direct electron transfer of strongly reducing electrons. We are interested in understanding the mechanism of methane release, which is only poorly understood from a structural perspective. Several projects are carried out in collaboration with the lab of Seigo Shima, Max Planck Institute for Terrestrial Microbiology, Marburg.

Structural and Functional Conservation of Proton-translocating Machineries of the Complex I Superfamily

A major unresolved question in bioenergetics is how respiratory complex I and its relatives couple redox turnover in the soluble arm to proton translocation across the membrane. We are taking a parallel approach to this question by evaluating the proton-translocating ancestors of the superfamily, membrane-bound hydrogenases (MBHs). Sequence and structural conservation suggests that a single fundamental mechanism facilitates coupling across the superfamily, in spite of the fact that MBHs reduce protons at the site analogous to the quinone-reducing site of complex I. An answer to this question is of interest in understanding energetic coupling in many microorganisms but would also allow us to better understand energetic coupling across the complex I superfamily and thus, across the tree of life.

Mechanisms of CO2 Fixation

Fixing CO2 to organic molecules is a challenge faced not only by photosynthetic organisms but by diverse autotrophs. With increasing atmospheric CO2 levels driving climate change, efficient and cheap CO2 fixation has also become a pressing challenge for human society. Working together with the group of Tristan Wagner, Max Planck Institute for Marine Microbiology, we aim to understand, at an atomic level, the evolved mechanisms of CO2 fixation. Our long-term aspiration is for this work to inspire and inform strategies for climate change mitigation.

Mitochondrial Iron-Sulfur Cluster Biogenesis

Mitochondria are known as the ‘powerhouses’ of eukaryotic cells, as they carry out many of the essential reactions that convert energy from food molecules and oxygen to the so-called energy currency of the cell, ATP. But an even more widely conserved function of mitochondria is in biogenesis of redox cofactors called iron-sulfur clusters, which are essential for a wide range of cellular functions. Even in fully aerobic organisms, the iron-sulfur cluster biosynthesis pathway is sensitive to oxygen. Applying tools for generating cryo-EM samples under anaerobic, stably reducing and turnover conditions, we are working to understand the atomic mechanism of mitochondrial iron-sulfur cluster biogenesis in collaboration with the lab of Roland Lill at the Philipps University Marburg.

Bioenergetic Complexes of Sulfate-Reducing Metabolism

An important but poorly studied group of organisms use sulfate as terminal electron acceptor, releasing sulfide. In addition to their obvious role in sulfur cycling, these microbes play essential roles in the global carbon cycle (carbon mineralisation and methane release), in shaping soil and marine environments, and in human health and disease. In spite of their importance, very little is known about how sulfate reduction is linked to energy conservation. Working together with the labs of Inês Pereira and Margarida Archer at ITQB-Nova in Lisbon, we are working to understand the structural basis for energy conservation in sulfate reducing microorganisms.

Reactive Oxygen Species Production

Reactive oxygen species (ROS) play essential roles in cellular defense, signalling, cell death, and many other essential functions. ROS can be produced as by-products of a number of different reactions, or by dedicated protein complexes. Our work aims to better understand the structure and mechanism of ROS-producing enzymes in human cells and bacterial pathogens.

Development of Elemental Mapping in Macromolecular Complexes by EM

When we determine a protein’s structure by single-particle cryo-EM, we use image processing tools to combine information from many individual copies of the same protein complex, generating a three-dimensional map of the complex, which we use to build an atomic model. Although these reconstructions can now reach high resolutions, allowing us to confidently build many parts of complexes including the polypeptide and polynucleotide scaffold, we often have difficulty unambiguously identifying other densities in our maps including bound metals and other ions, lipids, substrates and inhibitors. Because these species often play out-sized roles in the activity and regulation of complexes, the uncertainty in assigning these densities has large consequences for the accuracy of the atomic models, and of future work carried out based on these models. Therefore, we see the need for a technique that would allow us to map elements in the 3D particle space. Several techniques already exist for elemental mapping in the electron microscope, but these require much higher doses than our biological samples will tolerate. We are working to combine techniques from analytical electron microscopy with the many ’tricks’ of biological cryo-EM: low-dose acquisition, cryogenic temperatures, automated data acquisition, and image processing techniques that allow a large total dose to be spread across many identical copies of a given object.
This project is carried out in collaboration with CEOS GmbH, and Holger Stark and Dietmar Riedel of the Max Planck Institute for Multidisciplinary Sciences.


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