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Karayel, O., Michaelis, A.C., Mann, M., Schulman, B.A., and Langlois, C.R.
Proc Natl Acad Sci U S A, 2020, online ahead of print.
doi: 10.1073/pnas.2020197117

DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift

The yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome-based readouts can serve as comprehensive systems-level assays in all cellular systems.



Scientists at the Max Planck Institute of Biochemistry have now discovered why JAK2 mutant tumor cells can survive cancer therapy. Myeloproliferative neoplasms (MPN) is a chronic cancers of the hematopoietic system. In simple terms it is a cancer of blood cells. This can be caused by mutations in JAK2 protein, because this important protein regulates cell division and differentiation. In order to heal the diseases, drugs are needed that prevent the diseased cells from proliferation in the long term. Patients with JAK2 mutations are treated with JAK inhibitors but the treatment often fails. With the currently used drugs, there are some cells that are either resistant to the drugs in advance or get used to the drug. Therefore, these cancer cells continue to divide unintentionally. Scientists around Matthias Mann, from the MPI of Biochemistry together with scientist from the Leibniz Institut on Aging in Jena, have investigated the mechanism that enables cancer cells to survive a drug treatment.

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Bauernfried, S., Scherr, M.J., Pichlmair, A., Duderstadt, K.E., and Hornung, V.
(IMPRS-LS students are in bold)
Science, 2020, Online ahead of print.
doi: 10.1126/science.abd0811

Human NLRP1 is a sensor for double-stranded RNA

Inflammasomes function as intracellular sensors of pathogen infection or cellular perturbation and thereby play a central role in numerous diseases. Given the high abundance of NLRP1 in epithelial barrier tissues, we screened a diverse panel of viruses for inflammasome activation in keratinocytes. We identified Semliki Forest virus (SFV), a positive-strand RNA virus, as a potent activator of human, but not murine NLRP1. SFV replication and the associated formation of double-stranded (ds) RNA was required to engage the NLRP1 inflammasome. Moreover, delivery of long dsRNA was sufficient to trigger activation. Biochemical studies revealed that NLRP1 binds dsRNA via its LRR, resulting in its NACHT domain gaining ATPase activity. Altogether, these results establish human NLRP1 as a direct sensor for dsRNA and thus RNA virus infection.



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Karayel, Ö., Xu, P., Bludau, I., Velan Bhoopalan, S., Yao, Y., Ana Rita, F.C., Santos, A., Schulman, B.A., Alpi, A.F., Weiss, M.J., and Mann, M.
Mol Syst Biol 16, e9813.
doi: 10.15252/msb.20209813

Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis

Human erythropoiesis is an exquisitely controlled multistep developmental process, and its dysregulation leads to numerous human diseases. Transcriptome and epigenome studies provided insights into system-wide regulation, but we currently lack a global mechanistic view on the dynamics of proteome and post-translational regulation coordinating erythroid maturation. We established a mass spectrometry (MS)-based proteomics workflow to quantify and dynamically track 7,400 proteins and 27,000 phosphorylation sites of five distinct maturation stages of in vitro reconstituted erythropoiesis of CD34+ HSPCs. Our data reveal developmental regulation through drastic proteome remodeling across stages of erythroid maturation encompassing most protein classes. This includes various orchestrated changes in solute carriers indicating adjustments to altered metabolic requirements. To define the distinct proteome of each maturation stage, we developed a computational deconvolution approach which revealed stage-specific marker proteins. The dynamic phosphoproteomes combined with a kinome-targeted CRISPR/Cas9 screen uncovered coordinated networks of erythropoietic kinases and pinpointed downregulation of c-Kit/MAPK signaling axis as key driver of maturation. Our system-wide view establishes the functional dynamic of complex phosphosignaling networks and regulation through proteome remodeling in erythropoiesis.



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Libicher, K., and Mutschler, H.
Chem Commun (Camb), 2020, Online ahead of print.
doi: 10.1039/d0cc06515c

Probing self-regeneration of essential protein factors required for in vitro translation activity by serial transfer

The bottom-up construction of bio-inspired systems capable of self-maintenance and reproduction is a central goal in systems chemistry and synthetic biology. A particular challenge in such systems is the continuous regeneration of key proteins required for macromolecular synthesis. Here, we probe self-maintenance of a reconstituted in vitro translation system challenged by serial transfer of selected key proteins. We find that the system can simultaneously regenerate multiple essential polypeptides, which then contribute to the maintenance of protein expression after serial transfer. The presented strategy offers a robust methodology for probing and optimizing continuous self-regeneration of proteins in cell-free environments.



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Scacchetti, A., and Becker, P.B.
Curr Opin Cell Biol, 2020, 70, 1-9.
doi: 10.1016/

Variation on a theme: Evolutionary strategies for H2A.Z exchange by SWR1-type remodelers

Histone variants are a universal means to alter the biochemical properties of nucleosomes, implementing local changes in chromatin structure. H2A.Z, one of the most conserved histone variants, is incorporated into chromatin by SWR1-type nucleosome remodelers. Here, we summarize recent advances toward understanding the transcription-regulatory roles of H2A.Z and of the remodeling enzymes that govern its dynamic chromatin incorporation. Tight transcriptional control guaranteed by H2A.Z nucleosomes depends on the context provided by other histone variants or chromatin modifications, such as histone acetylation. The functional cooperation of SWR1-type remodelers with NuA4 histone acetyltransferase complexes, a recurring theme during evolution, is structurally implemented by species-specific strategies.



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Finogenova, K., Bonnet, J., Poepsel, S., Schäfer, I.B., Finkl, K., Schmid, K., Litz, C., Strauss, M., Benda, C., and Müller, J.
Elife, 2020, 9.
doi: 10.7554/eLife.61964

Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3

Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and trimethylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro. Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.



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Schwach, J., Kolobynina, K., Brandstetter, K., Gerlach, M., Ochtrop, P., Helma, J., Hackenberger, C.P.R., Harz, H., Cardoso, M.C., Leonhardt, H., and Stengl, A.
(IMPRS-LS students are in bold)
Chembiochem, 2020, [Epub ahead of print].
doi: 10.1002/cbic.202000727

Site-Specific Antibody Fragment Conjugates for Reversible Staining in Fluorescence Microscopy

Antibody conjugates have taken a great leap forward as tools in basic and applied molecular life sciences, which was enabled by the development of chemoselective reactions for the site-specific modification of proteins. Antibody-oligonucleotide conjugates combine the antibody's target specificity with the reversible, sequence-encoded binding properties of oligonucleotides like DNAs or PNAs, allowing sequential imaging of large numbers of targets in a single specimen. In this report, we use the Tub-tag Ⓡ technology in combination with Cu-catalyzed azide-alkyne-cycloaddition for the site-specific conjugation of single DNA and PNA strands to an eGFP-binding nanobody. We show binding of the conjugate to recombinant eGFP and subsequent sequence-specific annealing of fluorescently labelled imager strands. Furthermore, we reversibly stain eGFP-tagged proteins in human cells, thus demonstrating the suitability of our conjugation strategy to generate antibody-oligonucleotides for reversible immunofluorescence imaging.



The German Society for Cell Biology (DGZ) and ZEISS honor Petra Schwille, Director at the Max Planck Institute of Biochemistry, with the Carl Zeiss Lecture. With this award, the DGZ internationally acknowledges her major contributions to Cell Biology, in particular the introduction of fluorescence cross correlation spectroscopy for understanding fundamental aspects of life.

What is the minimum equipment required by the cell as the smallest living unit in an organism? Petra Schwille is looking into this question with her department "Cellular and Molecular Biophysics". Together they aim to (re)construct cellular processes and ultimately minimal living cells from dramatically simplified functional subsystems such as proteins and protein assemblies. The microscope is not sufficient to observe the interactions between the single, tiny molecules in the cell and the processes underlying them. The Biophysicist has therefore developed the fluorescence cross correlation spectroscopy, a method which visualizes processes in and around the cell. This method allows to analyze the dynamics and interactions of fluorescence-labeled molecules with highest resolution down to the level of single molecules.

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Baek, K., Scott, D.C., and Schulman, B.A.
Curr Opin Struct Biol, 2020, 67, 101-109
doi: 10.1016/

NEDD8 and ubiquitin ligation by cullin-RING E3 ligases

RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s - including the cullin-RING ligase family - are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms - interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners - directing cullin-RING E3-E2 enzyme active sites to modify their specific targets.