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Swietlik JJ, Sinha A, and Meissner F.
Curr Opin Cell Biol. 2020; 63:20–30.

Dissecting intercellular signaling with mass spectrometry-based proteomics

Physiological functions depend on a coordinated interplay of numerous different cell types. Proteins serve as major signaling molecules between cells; however, their comprehensive investigation in physiologically relevant settings has remained challenging. Mass spectrometry (MS)-based shotgun proteomics is emerging as a powerful technology for the systematic analysis of protein-mediated intercellular signaling and regulated post-translational modifications. Here, we discuss recent advancements in cell biological, chemical, and biochemical MS-based approaches for the profiling of cellular messengers released by sending cells, receptors expressed on the cell surface, and their interactions. We highlight methods tailored toward the mapping of dynamic signal transduction mechanisms at cellular interfaces and approaches to dissect communication cell specifically in heterocellular systems. Thereby, MS-based proteomics contributes a unique systems biology perspective for the identification of intercellular signaling pathways deregulated in disease.

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Bartnik, K., Barth, A., Pilo-Pais, M., Crevenna, A.H., Liedl, T., and Lamb, D.C.
J Am Chem Soc, 2019, [Epub ahead of print].
doi: 10.1021/jacs.9b09093

A DNA origami platform for single-pair Forster Resonance Energy Transfer investigation of DNA-DNA interactions and ligation

DNA double-strand breaks (DSBs) pose an everyday threat to the conservation of genetic information and therefore life itself. Several pathways have evolved to repair these cytotoxic lesions by re-joining broken ends, among them the non-homologous end-joining (NHEJ) mechanism that utilizes a DNA ligase. Here, we use a custom-designed DNA origami nanostructure as a model system to specifically mimic a DNA DSB, enabling us to study the end-joining of two fluorescently-labeled DNA double-strands with the T4 DNA ligase on the single-molecule level. The ligation reaction is monitored by Förster Resonance Energy Transfer (FRET) experiments both in solution and on surface-anchored origamis. Due to the modularity of DNA nanotechnology, DNA double-strands with different complementary overhang lengths can be studied using the same DNA origami design. We show that the T4 DNA ligase repairs sticky ends more efficiently than blunt ends and that the ligation efficiency is both influenced by DNA sequence and the incubation conditions. Before ligation, dynamic fluctuations of the FRET signal are observed due to transient binding of the sticky overhangs. After ligation, the FRET signal becomes static. Thus, we can directly monitor the ligation reaction through the transition from dynamic to static FRET signals. Finally, we revert the ligation process using a restriction enzyme digestion and re-ligate the resulting blunt ends. The here presented DNA origami platform is thus suited to study complex multi-step reactions occurring over several cycles of enzymatic treatment.

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Yim, A., Koti, P., Bonnard, A., Marchiano, F., Durrbaum, M., Garcia-Perez, C., Villaveces, J., Gamal, S., Cardone, G., Perocchi, F., Storchova Z., and Habermann, B.
(IMPRS-LS students are in bold)
Nucleic Acids Res, 2019, [Epub ahead of print].
doi: 10.1093/nar/gkz1128

mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations

Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here, we introduce the visual data mining platform mitoXplorer, which integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome containing ∼1200 genes grouped in 38 mitochondrial processes. User-friendly analysis and visualization tools allow to mine mitochondrial expression dynamics and mutations across various datasets from four model species including human. To test the predictive power of mitoXplorer, we quantify mito-gene expression dynamics in trisomy 21 cells, as mitochondrial defects are frequent in trisomy 21. We uncover remarkable differences in the regulation of the mitochondrial transcriptome and proteome in one of the trisomy 21 cell lines, caused by dysregulation of the mitochondrial ribosome and resulting in severe defects in oxidative phosphorylation. With the newly developed Fiji plugin mitoMorph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoXplorer ( is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.

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Baek, K., and Schulman, B.A.
Nat Chem Biol, 2019, [Epub ahead of print].
doi: 10.1038/s41589-019-0414-3

Molecular glue concept solidifies

Molecular-glue-mediated proximity-induced degradation now allows unprecedented therapeutic targeting of previously undruggable proteins. Structures showing how aryl-sulfonamides mediate recruitment of the splicing factor RBM39 to the E3 CRL4DCAF15 broaden the mechanistic principles by which molecular glues target ubiquitylation.

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Glock, P., Brauns, F., Halatek, J., Frey, E., and Schwille, P.
Elife 8, 2019.
doi: 10.7554/eLife.48646

Design of biochemical pattern forming systems from minimal motifs

Although molecular self-organization and pattern formation are key features of life, only very few pattern-forming biochemical systems have been identified that can be reconstituted and studied in vitro under defined conditions. A systematic understanding of the underlying mechanisms is often hampered by multiple interactions, conformational flexibility and other complex features of the pattern forming proteins. Because of its compositional simplicity of only two proteins and a membrane, the MinDE system from Escherichia coli has in the past years been invaluable for deciphering the mechanisms of spatiotemporal self-organization in cells. Here we explored the potential of reducing the complexity of this system even further, by identifying key functional motifs in the effector MinE that could be used to design pattern formation from scratch. In a combined approach of experiment and quantitative modeling, we show that starting from a minimal MinE-MinD interaction motif, pattern formation can be obtained by adding either dimerization or membrane-binding motifs. Moreover, we show that the pathways underlying pattern formation are recruitment-driven cytosolic cycling of MinE and recombination of membrane-bound MinE, and that these differ in their in vivo phenomenology.

graduationCongratulations on your PhD!

Silvia Martinelli
Effect of stress on protein homeostasis mediated by FKBP51 as a possible mechanism underlying stress-related psychiatric disorders
RG: Mathias V. Schmidt / Elisabeth Binder

Andrea Cosolo
Patterning of tissue stress responses by JNK and JAK/STAT
RG: Anne-Kathrin Classen


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Kist, A.M., and Portugues, R.
Cell Rep, 2019, 29, 659-670.e653.
doi: 10.1016/j.celrep.2019.09.024

Optomotor Swimming in Larval Zebrafish Is Driven by Global Whole-Field Visual Motion and Local Light-Dark Transitions

Stabilizing gaze and position within an environment constitutes an important task for the nervous system of many animals. The optomotor response (OMR) is a reflexive behavior, present across many species, in which animals move in the direction of perceived whole-field visual motion, therefore stabilizing themselves with respect to the visual environment. Although the OMR has been extensively used to probe visuomotor neuronal circuitry, the exact visual cues that elicit the behavior remain unidentified. In this study, we use larval zebrafish to identify spatiotemporal visual features that robustly elicit forward OMR swimming. These cues consist of a local, forward-moving, off edge together with on/off symmetric, similarly directed, global motion. Imaging experiments reveal neural units specifically activated by the forward-moving light-dark transition. We conclude that the OMR is driven not just by whole-field motion but by the interplay between global and local visual stimuli, where the latter exhibits a strong light-dark asymmetry.

Congratulations on your PhD!

Alkmini Papadopoulou
An in vitro and in vivo study on the function of Signal Peptide Peptidase-Like 2c and 3
RG: Christian Haass / Regina Fluhrer


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Kashammer, L., Saathoff, J.H., Lammens, K., Gut, F., Bartho, J., Alt, A., Kessler, B., and Hopfner, K.P.
Mol Cell, 2019, [Epub ahead of print].
doi: 10.1016/j.molcel.2019.07.035

Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex

DNA double-strand breaks (DSBs) threaten genome stability throughout life and are linked to tumorigenesis in humans. To initiate DSB repair by end joining or homologous recombination, the Mre11-nuclease Rad50-ATPase complex detects and processes diverse and obstructed DNA ends, but a structural mechanism is still lacking. Here we report cryo-EM structures of the E. coli Mre11-Rad50 homolog SbcCD in resting and DNA-bound cutting states. In the resting state, Mre11's nuclease is blocked by ATP-Rad50, and the Rad50 coiled coils appear flexible. Upon DNA binding, the two coiled coils zip up into a rod and, together with the Rad50 nucleotide-binding domains, form a clamp around dsDNA. Mre11 moves to the side of Rad50, binds the DNA end, and assembles a DNA cutting channel for the nuclease reactions. The structures reveal how Mre11-Rad50 can detect and process diverse DNA ends and uncover a clamping and gating function for the coiled coils.

graduationCongratulations on your PhD!

Markus Höpfler
Slx5/Slx8-dependent Ubiquitin Hotspots on Chromatin Contribute to Stress Tolerance in Saccharomyces Cerevisiae
RG: Stefan Jentsch

Andreas Kist
Cerebellar and Sensory Contributions to the Optomotor Response in Larval Zebrafish
RG: Ruben Portugues