Contributions to Max Planck Society Yearbooks

Nature uses antimicrobial peptides as broad-spectrum antibiotics: they are the first line of defense against invading pathogens. Bacteria, however, have developed ways to evade these defenses. Our project group has investigated how a small protein establishes a sensitive alarm system of bacteria to be on the lookout for antimicrobial peptides. Our work provides the molecular basis for the development of new peptide-based drugs.

The central biocatalyst in photosynthesis, Rubisco, is the most abundant enzyme on earth. But how did Rubisco evolve, and how did it adapt to environmental changes during Earth’s history? By reconstructing billion-year-old enzymes, our team has deciphered one of the key adaptations of early photosynthesis. Our results not only provide insights into the evolution of modern photosynthesis but also offer new synthetic impulses for improving it.

Ustilago maydis is one of numerous fungal pathogens that destroy large quantities of crops worldwide each year. Its highly specific interaction with the host plant maize is a valuable model system for studying molecular details of fungal-plant interactions. We found a fungal complex of seven proteins forming a structure with an essential role in disease development. Our findings potentially a fungal complex of seven proteins forming a structure with an essential role in disease development. Our findings potentially open up novel approaches to plant protection.

Bacteria such as Salmonella or Yersinia are equipped with tiny "injection needles" for shooting proteins into their host cells. For years, researchers have thought of using bacterial injection devices to introduce proteins into eukaryotic cells. We now succeeded in controlling the injection system optogenetically by using light as a trigger, enabling its targeted utilization in biotechnological or medical applications.

Glycolic acid is a direct by-product of photosynthesis and one of the most important compounds in the carbon cycle of the oceans. Though marine bacteria convert some of its carbon back into carbon dioxide, the exact metabolic pathways remained largely unknown. We rediscovered a long forgotten pathway, the BHA cycle. This cycle was overlooked so far, but actually represents the major pathway for glycolic acid degradation in ubiquitous marine Proteobacteria. Its detailed and multidisciplinary elucidation enables reassessment of the global carbon dioxide balance.

Single-molecule localization microscopy offers unprecedented insights into living cells. In practice, however, many difficulties persist. By improving an important group of fluorophores, we were able to significantly reduce the damage the method causes in the imaged cells and to establish a novel, aberration-free multi-color strategy. This enables, among other things, the four-dimensional reconstruction of multi-protein-complexes such as the kinetochore in Schizosaccharomyces pombe.

Methane is an end product of anaerobic degradation of organic materials and is a potent greenhouse gas. Roughly, half of the world-wide methane emission is biologically performed by methanogenic archaea. We are interested in the enzymes involved in hydrogenotrophic methanogenesis. Here, we report on the crystal structure of the formyl-methanofuran dehydrogenase (Fwd) and heterodisulfide-reductase/hydrogenase complexes (Hdr/Mvh). These enzyme complexes are involved in the sequential reactions of ferredoxin reduction and CO₂-reduction/fixation within the methanogenic pathway.

The conversion of the greenhouse gas carbon dioxide (CO₂) into organic compounds is a key process in the global carbon cycle. In the past years, several novel pathways and enzymes for the conversion of CO₂ were discovered in microorganisms. In parallel to these discoveries, new approaches were followed by using the methods of synthetic biology to establish artificial pathways for the fixation of CO₂ that are more efficient compared to naturally existing CO₂-fixation pathways. Synthetic CO₂-fixation could pave the way towards novel applications in biotechnology and nanotechnology.

Many bacterial species colonize surfaces and form dense three-dimensional structures, known as biofilms, which are resistant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. The developmental process that gives rise to biofilms is largely unknown. It was recently discovered that between the initial surface attachment and mature tower-shaped biofilm structures, the cellular architecture undergoes several critical transitions.

In clostridia the exergonic reduction of crotonyl-CoA to butyryl-CoA by NADH is coupled to the endergonic reduction of ferredoxin by NADH – a process called flavin-based electron bifurcation, catalyzed by a two-FAD-containing electron transferring flavoptrotein (Etf) and butyryl-CoA dehydrogenase (Bcd). This, and similar systems are wide-spread in anaerobic bacteria and archaea, which reduce ferredoxin for H₂ formation in fermentations, for generation of ΔµNa⁺ via a ferredoxin-NAD reductase (Rnf) and in aceto-and methanogenesis for CO₂ reduction by H₂.

Hydrogen is an atmospheric trace gas which is mainly decomposed in soils. Already in the 1970s it was obvious that the decomposition process must be based on biological activity. However, it took more than 40 years until the decomposition process was finally understood. Today we know that nickel-iron hydrogenases of the group 5 are responsible for the oxidation of the atmospheric hydrogen. These hydrogenases are mainly found in Actinobacteria, e.g., Streptomyces or Mycobacterium, which are common microorganisms in soils.

Methane (CH₄) is an important intermediate in the global carbon cycle. Per year about 1 Gt methane is formed from biomass and further oxidized to CO₂. The formation of methane involves mainly anaerobic microorganisms, whereas in the oxidation of methane both anaerobic and aerobic microorganisms participate. In the atmosphere, where methane acts as a greenhouse gas, methane is predominantly re-mineralized photochemically. Investigations of the biochemistry of the methane cycle have led over and over again to new discoveries. On two of the most recent discoveries will be reported here.

Iron-sulfur (Fe/S) clusters serve as ancient cofactors of proteins with a function in catalysis, electron transport and the regulation of gene expression. The synthesis of a Fe/S cluster and its insertion into target proteins is a complex process which in eukaryotes requires more than 30 proteins in mitochondria and cytosol. These components were analyzed both in vivo and in vitro for their molecular function and a mechanistic model of Fe/S protein biogenesis was proposed. In humans, malfunctions in this pathway cause numerous diseases.

Hydrogen (H₂) plays a crucial role in global carbon cycles. Hydrogenases - H₂ producing and utilizing enzymes - are pivotally involved in biological systems for the turnover of H₂. Three types of hydrogenases are known: [NiFe]-, [FeFe]- and [Fe]-hydrogenases. The [Fe]-hydrogenase functions in the methanogenic pathway of hydrogenotrophic methanogenic archaea. This new type of hydrogenase contains a unique iron-guanylylpyridinol (FeGP) cofactor. We are studying the structure and function of both the enzyme and cofactor as well as the FeGP cofactor biosynthesis.

Numerous bacterial species are motile and almost all of them are capable of forming sessile surface-associated communities, often referred to as biofilms. Both abilities are crucial for successful propagation and spreading in the natural environment. Using species of the soil and sediment bacteria Shewanella we study how these organisms regulate motility and biofilm formation to adapt to environmental conditions.

A nearly invisible battle rages on between Bacteria and Archaea on one side and viruses and other mobile elements on the other. This tug-of-war leaves its traces in the genomes of the involved parties and thus can be analyzed in respect of their co-evolution. One of the antiviral defense systems of Bacteria, the CRISPR system, contains pieces of viral DNA that provide direct insight into the history of previous viral attacks. Another indication of this battle is the disruption of transfer RNA genes used by viruses as attachment sites to facilitate their integration into the host genome.

The key question of our research is how do new pathogens emerge and how fast can they adapt to new environments and host species. We investigate evolutionary processes during pathogen speciation and host specialization by comparison of 12 genomes of closely related grass pathogens. Agriculture strongly affects the rate of pathogen adaptation as crop species more rapidly accumulate beneficial mutations compared to its wild relatives. Analyses of more than 9500 genes facilitated the identification of candidate genes involved in speciation and host specialization of pathogens.

Members of the third domain of life, the Archaea, exhibit a number of different cell surface structures which are similar in assembly and function to bacterial type IV pili. Type IV pili play an important role in surface motility and adhesion, DNA transfer and invasion of eukaryotic host cells. Archaeal type IV pili like filaments are build from a minimal set of subunits facilitating the progress of understanding the mechanism of how these and other bacterial type IV pili are assembled.

The fungus Ustilago maydis is the causative agent of maize smut disease. During this biotrophic interaction, plant defense is suppressed immediately upon penetration. We identified the secreted effector-protein Pep1. Pep1 deletion mutants failed to suppress plant defense and are not able to colonize maize tissue. Therefore, Pep1 is an essential factor for the compatible interaction between U. maydis and its host plant. Elucidation of the Pep1 function will help to understand the molecular mechanisms that determine compatibility in biotrophic plant-fungal interactions.

Recent advances in the study of bacterial cell biology have demonstrated that bacteria use complex regulatory mechanisms to ensure proper temporal and spatial regulation of cellular processes. In this article, the complexity of such systems is illustrated by the molecular pathway that coordinates chromosome segregation with cell division in Caulobacter crescentus.

Myxococcus xanthus is a bacterium with multicellular behaviors: In nutrient-limited environments, the cells enter a developmental program leading to spore-filled fruiting bodies. Regulation of the program involves intra- and intercellular signals and coordination of distinct cell populations. To facilitate this behavior, the developmental program is comprised of unusual signal transduction systems that integrate multiple signals.

Sexual development of the phytopathogenic fungus Ustilago maydis is governed by the mating type loci a and b. The a2 locus genes lga2 and rga2 encode mitochondrial proteins, whose expression is coupled to the sexual cycle. These proteins compromise mitochondrial integrity and pathogenesis in the absence of the mitochondrial p32 family protein Mrb1. Lga2 interferes with mitochondrial fusion and together with Rga2 has a possible function in controlling mitochondrial inheritance.

Denitrifying microorganisms play a key role in the global nitrogen cycle. Denitrification is one of the main processes of this cycle and trace gases originating from it cause climatic effects. Application of molecular techniques in the field of microbial ecology allowed fundamental insights into diversity and structure of denitrifier communities. This is a prerequisite to understand the interrelationship of structure and function of denitrifier communities and the influence of parameters that drive the development of these microbial communities and their activity in the environment.

Successful infection by the corn pathogen Ustilago maydis is accompanied by a number of morphological transitions that resemble simple developmental programs. Prerequisite for plant penetration is the formation of an infectious filament that exhibits polar tip growth and forms empty sections at its distal pole. In order to investigate the impact of RNA-binding proteins on such developmental processes, members of this protein class were identified according to sequence similarities with well characterized RNA-binding domains. Out of 94, 25 candidates were chosen and respective gene deletion strains were constructed and tested for pathogenic development. The loss of Rrm4, a protein with three N-terminal RNA recognition motifs (RRM) and a C-terminal protein interaction domain, resulted in reduced filamentation and virulence. Further analysis revealed that deletion strains form shorter, bipolar growing filaments. Subcellular localisation in vivo showed that Rrm4 forms particles that move bi-directionally along microtubules. Further mutational analysis of the various protein domains revealed that the N-terminal RNA contact regions RRM1 and RRM2 are most likely necessary to contact cargo whereas the C-terminal protein interaction domain is crucial for particle formation. These results indicate that Rrm4-containing particles transport RNA from the nucleus to the cell poles and that this process is important for unipolar tip growth of the infectious hyphae. A role for long distance transport of RNA along microtubules has already been implicated for embryo development and neuronal signal transmission. Our results obtained in U. maydis constitute the first example for long distance RNA transport in microorganisms indicating that the basic concept is evolutionarily more conserved than previously anticipated.

Bacterial cells communicate extensively with each other using intercellular signaling molecules. In most cases these signals are small diffusible molecules and part of a communication system that helps the bacteria to assess population size. Analyses of the formation of the magnificently shaped, multicellular, spore-filled fruiting bodies in Myxococcus xanthus revealed a unique intercellular communication system in which the signaling molecule is a 17 kDa, non-diffusible, cell surface-associated protein. This signaling molecule is tailored to guide the slow moving cells of M. xanthus into the fruiting bodies and to coordinate temporally and spatially the two morphogenetic events, aggregation and sporulation, during fruiting body formation.

The associations of insects with microorganisms are often related to a nutrient-poor or recalcitrant diet. There are many indications that the symbionts provide metabolic capacities unavailable to the host. The gut microbiota of termites is involved in cellulose degradation and plays important roles in further digestion and in the nitrogen budget. The highly structured microbial communities are also excellent model systems for the investigation of fundamental problems in microbial ecology.