News | IMPRS for Molecules of Life

Publication of IMPRS-LS student Kheewoong Baek

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Baek, K., Krist, D.T., Prabu, J.R., Hill, S., Klügel, M., Neumaier, L.-M., von Gronau, S., Kleiger, G., and Schulman, B.A.
Nature, 2020 578, 461-466.
doi: 10.1038/s41586-020-2000-y

NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly

Eukaryotic cell biology depends on cullin-RING E3 ligase (CRL)-catalysed protein ubiquitylation, which is tightly controlled by the modification of cullin with the ubiquitin-like protein NEDD8. However, how CRLs catalyse ubiquitylation, and the basis of NEDD8 activation, remain unknown. Here we report the cryo-electron microscopy structure of a chemically trapped complex that represents the ubiquitylation intermediate, in which the neddylated CRL1^β-TRCP promotes the transfer of ubiquitin from the E2 ubiquitin-conjugating enzyme UBE2D to its recruited substrate, phosphorylated IκBα. NEDD8 acts as a nexus that binds disparate cullin elements and the RING-activated ubiquitin-linked UBE2D. Local structural remodelling of NEDD8 and large-scale movements of CRL domains converge to juxtapose the substrate and the ubiquitylation active site. These findings explain how a distinctive ubiquitin-like protein alters the functions of its targets, and show how numerous NEDD8-dependent interprotein interactions and conformational changes synergistically configure a catalytic CRL architecture that is both robust, to enable rapid ubiquitylation of the substrate, and fragile, to enable the subsequent functions of cullin-RING proteins.

Graduation of Yunmin Wu and Mahesh Lingaraju

Congratulations on your PhD!

Yunmin Wu
Neural Basis of Visual Motion Perception: An Illusory Perspective
RG: Herwig Baier

Mahesh Lingaraju
Structural and Biochemical Characterization of Interactions Centered on RNA Decay Factors: MTR4 and SMG1
RG: Elena Conti

Publication of IMPRS-LS student Chia-Wei Lee

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Lee, C.-W., Wilfling, F., Ronchi, P., Allegretti, M., Mosalaganti, S., Jentsch, S., Beck, M., and Pfander, B.
Nat Cell Biol, 2020 22, 159-166.
doi: 10.1038/s41556-019-0459-2

Selective autophagy degrades nuclear pore complexes

Nuclear pore complexes (NPCs) are very large proteinaceous assemblies that consist of more than 500 individual proteins1,2. NPCs are essential for nucleocytoplasmic transport of different cellular components, and disruption of the integrity of NPCs has been linked to aging, cancer and neurodegenerative diseases3-7. However, the mechanism by which membrane-embedded NPCs are turned over is currently unknown. Here we show that, after nitrogen starvation or genetic interference with the architecture of NPCs, nucleoporins are rapidly degraded in the budding yeast Saccharomyces cerevisiae. We demonstrate that NPC turnover involves vacuolar proteases and the core autophagy machinery. Autophagic degradation is mediated by the cytoplasmically exposed Nup159, which serves as intrinsic cargo receptor and directly binds to the autophagy marker protein Atg8. Autophagic degradation of NPCs is therefore inducible, enabling the removal of individual NPCs from the nuclear envelope.

Shaping the social networks of neurons

Identification of a protein complex that attracts or repels nerve cells during development

The three proteins Teneurin, Latrophilin and FLRT hold together and bring neighboring neurons into close contact, enabling the formation of synapses and the exchange of information between the cells. In the early phase of brain development, however, the interaction of the same proteins leads to the repulsion of migrating nerve cells, as researchers from the Max Planck Institute of Neurobiology and the University of Oxford have now shown. The detailed insight into the molecular guidance mechanisms of brain cells was possible due to the structural analyses of the protein complex.

Well anchored, the proteins Teneurin and FLRT are located on the surface of nerve cells. They are on the lookout for their partner protein, Latrophilin, on other neurons. When the three proteins come into contact, they interconnect and hold the membranes together. They then trigger still largely unknown signaling cascades and thus promote the formation of a synapse at this site. Teneurin and its partner proteins are known to establish these important cell contacts in the brain. Teneurin is also an evolutionary very old protein, with related proteins found in diverse organisms ranging from bacteria to worms, fruit flies and vertebrates. However, the role of these proteins during brain development, when neurons are not yet forming synapses, remained unknown.

Graduation of Samira Parhizkar

Congratulations on your PhD!

Samira Parhizkar
Loss of TREM2 function increases amyloid seeding but reduces plaque associated ApoE
RG: Christian Haass

Publication of IMPRS-LS student Sophia Hergenhan

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Hergenhan S, Holtkamp S, and Scheiermann C.
J Mol Biol. 2020;S0022-2836(20)30028-0.
(*IMPRS-LS students are in bold)
doi:10.1016/j.jmb.2019.12.044

Molecular interactions between components of the circadian clock and the immune system

The immune system is under control of the circadian clock. Many of the circadian rhythms observed in the immune system originate in direct interactions between components of the circadian clock and components of the immune system. The main means of circadian control over the immune system is by direct control of circadian clock proteins acting as transcription factors driving the expression or repression of immune genes. A second circadian control of immunity lies in the acetylation or methylation of histones to regulate gene transcription or inflammatory proteins. Furthermore, circadian clock proteins can engage in direct physical interactions with components of key inflammatory pathways such as members of the NFκB protein family. This regulation is transcription independent and allows the immune system to also reciprocally exert control over circadian clock function. Thus, the molecular interactions between the circadian clock and the immune system are manifold. We highlight and discuss here the recent findings with respect to the molecular mechanisms that control time-of-day dependent immunity. This review provides a structured overview focusing on the key circadian clock proteins and discusses their reciprocal interactions with the immune system.

Publication of IMPRS-LS student Tia Tyrsett Kuo

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Kuo TT, and Ladurner AG.
Front Genet. 2019;10:1210.
doi:10.3389/fgene.2019.01210

Exploiting the Circadian Clock for Improved Cancer Therapy: Perspective From a Cell Biologist

Since the discovery of the biological clock, the concept of treating cancer according to biological rhythms, here termed cancer chronotherapy, has rapidly evolved. Its fundamental aim is to improve the efficacy of drugs and to minimize adverse effects by administering chemotherapeutic drugs at the appropriate time-of-day. In the last two decades, several experimental and clinical studies have reported positive associations between the circadian clock and drug response in cancer patients. However, the lack of mechanistic insights into critical, deterministic clock-controlled genetic, and metabolic variations between and within individual cancer patients continue to cast a shadow on the potential benefits cancer chronotherapy may provide. Here, we provide first a simplified overview on our biological clocks and how our life-style induces complex biochemical reactions and genetic interactions. Next, we summarize how these reactions directly and indirectly modulate the effectiveness and toxicity of oncological drug treatments. Since cytotoxic chemotherapy represents the most common and affordable of cancer treatments, a case should be made that we need to ensure these treatments are used in the best possible manner. Thus, we list current challenges and future directions toward that goal.

Publication of IMPRS-LS student Jonathan Swietlik

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Swietlik JJ, Sinha A, and Meissner F.
Curr Opin Cell Biol. 2020; 63:20–30.
doi:10.1016/j.ceb.2019.12.002

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.

Publication of IMPRS-LS student Kira Bartnik

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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.

Publication of IMPRS-LS student Annie Yim

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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 (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.