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Bittmann, J., Grigaitis, R., Galanti, L., Amarell, S., Wilfling, F., Matos, J., and Pfander, B.
(IMPRS-LS students are in bold)
Elife, 2020, 9.
doi: 10.7554/eLife.52459

An advanced cell cycle tag toolbox reveals principles underlying temporal control of structure-selective nucleases

Cell cycle tags allow to restrict target protein expression to specific cell cycle phases. Here, we present an advanced toolbox of cell cycle tag constructs in budding yeast with defined and compatible peak expression that allow comparison of protein functionality at different cell cycle phases. We apply this technology to the question of how and when Mus81-Mms4 and Yen1 nucleases act on DNA replication or recombination structures. Restriction of Mus81-Mms4 to M phase but not S phase allows a wildtype response to various forms of replication perturbation and DNA damage in S phase, suggesting it acts as a post-replicative resolvase. Moreover, we use cell cycle tags to reinstall cell cycle control to a deregulated version of Yen1, showing that its premature activation interferes with the response to perturbed replication. Curbing resolvase activity and establishing a hierarchy of resolution mechanisms are therefore the principal reasons underlying resolvase cell cycle regulation.

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Blessing, C., and Ladurner, A.G.
Nat Struct Mol Biol, [Epub ahead of print].
doi: 10.1038/s41594-020-0412-x

Tickling PARPs into serine action

Poly-(ADP-ribosylation) is a post-translational modification with broad roles in cell signaling. A recently reported crystal structure reveals how the accessory factor HPF1 extends the catalytic active site of PARP1 and PARP2 to promote the specific ADP-ribosylation of serine residues, a prerequisite for dynamic chromatin changes induced by DNA damage.

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Kober-Hasslacher, M., Oh-Strauß, H., Kumar, D., Soberón, V., Diehl, C., Lech, M., Engleitner, T., Katab, E., Fernandez Saiz, V., Piontek, G., Li, H., Menze, B., Ziegenhain, C., Enard, W., Rad, R., Böttcher, J.P., Anders, H.J., Rudelius, M., Schmidt-Supprian, M. (IMPRS-LS students are in bold)
J Clin Invest, 2020, [Epub ahead of print].
DOI: 10.1172/JCI124382

c-Rel gain in B cells drives germinal center reactions and autoantibody production

Single nucleotide polymorphisms and locus amplification link the NF-κB transcription factor c-Rel to human autoimmune diseases and B cell lymphomas, respectively. However, the functional consequences of enhanced c-Rel levels remain enigmatic. Here, we overexpressed c-Rel specifically in mouse B cells from BAC-transgenic gene loci and demonstrate that c-Rel protein levels linearly dictated expansion of germinal center (GC) B cells and isotype-switched plasma cells. c-Rel expression in B cells of otherwise c-Rel-deficient mice fully rescued terminal B cell differentiation, underscoring its critical B cell-intrinsic roles. Unexpectedly, in GCB cells transcription-independent regulation produced the highest c-Rel protein levels amongst B cell subsets. In c-Rel overexpressing GCB cells this caused enhanced nuclear translocation, a profoundly altered transcriptional program and increased proliferation. Finally, we provide a link between c-Rel gain and autoimmunity by showing that c-Rel overexpression in B cells caused autoantibody production and renal immune complex deposition.

Congratulations on your PhD!

Irene Riera Tur
Artificial amyloid-like aggregating proteins cause cytotoxicity in vitro and in vivo
RG: Rüdiger Klein


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Libicher, K., Hornberger, R., Heymann, M., and Mutschler, H.
Nat Commun, 2020, 11, 904.
doi: 10.1038/s41467-020-14694-2

In vitro self-replication and multicistronic expression of large synthetic genomes

The generation of a chemical system capable of replication and evolution is a key objective of synthetic biology. This could be achieved by in vitro reconstitution of a minimal self-sustaining central dogma consisting of DNA replication, transcription and translation. Here, we present an in vitro translation system, which enables self-encoded replication and expression of large DNA genomes under well-defined, cell-free conditions. In particular, we demonstrate self-replication of a multipartite genome of more than 116 kb encompassing the full set of Escherichia coli translation factors, all three ribosomal RNAs, an energy regeneration system, as well as RNA and DNA polymerases. Parallel to DNA replication, our system enables synthesis of at least 30 encoded translation factors, half of which are expressed in amounts equal to or greater than their respective input levels. Our optimized cell-free expression platform could provide a chassis for the generation of a partially self-replicating in vitro translation system.

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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 CRL1β-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.

graduationCongratulations 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


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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.

Congratulations on your PhD!

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


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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)

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.