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graduationCongratulations on your PhD!


Jennifer Wells
Structural and Functional Analysis of Transitionally Inactive Eukaryotic Ribosomes:
Regulation of Hibernation with Lso2/CCDC124 and Stalling on the Fungal Arginine
Attenuator Peptide
RG: Roland Beckmann

 


 

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Varga, J., Nicolas, A., Petrocelli, V., Pesic, M., Mahmoud, A., Michels, B.E., Etlioglu, E., Yepes, D., Häupl, B., Ziegler, P.K., Bankov, K., Wild, P.J., Wanninger, S., Medyouf, H., Farin, H.F., Tejpar, S., Oellerich, T., Ruland, J., Siebel, C.W., and Greten, F.R.
J Exp Med, 2020, 217.
doi: 10.1084/jem.20191515

AKT-dependent NOTCH3 activation drives tumor progression in a model of mesenchymal colorectal cancer

Recently, a transcriptome-based consensus molecular subtype (CMS) classification of colorectal cancer (CRC) has been established, which may ultimately help to individualize CRC therapy. However, the lack of animal models that faithfully recapitulate the different molecular subtypes impedes adequate preclinical testing of stratified therapeutic concepts. Here, we demonstrate that constitutive AKT activation in intestinal epithelial cells markedly enhances tumor invasion and metastasis in Trp53ΔIEC mice (Trp53ΔIECAktE17K) upon challenge with the carcinogen azoxymethane. Gene-expression profiling indicates that Trp53ΔIECAktE17K tumors resemble the human mesenchymal colorectal cancer subtype (CMS4), which is characterized by the poorest survival rate among the four CMSs. Trp53ΔIECAktE17K tumor cells are characterized by Notch3 up-regulation, and treatment of Trp53ΔIECAktE17K mice with a NOTCH3-inhibiting antibody reduces invasion and metastasis. In CRC patients, NOTCH3 expression correlates positively with tumor grading and the presence of lymph node as well as distant metastases and is specifically up-regulated in CMS4 tumors. Therefore, we suggest NOTCH3 as a putative target for advanced CMS4 CRC patients.


graduationCongratulations on your PhD!


Itika Saha
Role of Valosin-containing protein (VCP) in tau disaggregation in mammalian cells
(Cellular characterization of polymorphic tau aggregates)
RG: F.-Ulrich Hartl

Francesca Pinci
Tumor necrosis factor (TNF) is a necroptosis-associated alarmin
RG: Veit Hornung

 


 

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Blessing, C., Knobloch, G., and Ladurner, A.G.
Curr Opin Struct Biol, 2020, 65, 130-138.
doi: 10.1016/j.sbi.2020.06.008

Restraining and unleashing chromatin remodelers - structural information guides chromatin plasticity

Chromatin remodeling enzymes are large molecular machines that guard the genome by reorganizing chromatin structure. They can reposition, space and evict nucleosomes and thus control gene expression, DNA replication and repair. Recent cryo-electron microscopy (cryo-EM) analyses have captured snapshots of various chromatin remodelers as they interact with nucleosomes. In this review, we summarize and discuss the advances made in our understanding of the regulation of chromatin remodelers, the mode of DNA translocation, as well as the influence of associated protein domains and remodeler subunits on the specific functions of chromatin remodeling complexes. The emerging structural information will help our understanding of disease mechanisms and guide our knowledge toward innovative therapeutic interventions.


graduationCongratulations on your PhD!


Katarzyna Jonak
Dynamical modeling of the network controlling meiotic divisions
RG: Wolfgang Zachariae

Sriyash Mangal
Elucidating Novel Regulators of Cytokinesis
RG: Barbara Conradt/Esther Zanin

 


 

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Ugur, E., Bartoschek, M.D., and Leonhardt, H.
Methods Mol Biol, 2020, 2175, 109-121
doi: 10.1007/978-1-0716-0763-3_9

Locus-Specific Chromatin Proteome Revealed by Mass Spectrometry-Based CasID

Biotin proximity labeling has largely extended the toolbox of mass spectrometry-based interactomics. To date, BirA, engineered BirA variants, or other biotinylating enzymes have been widely applied to characterize protein interactions. By implementing chromatin purification-based methods the genome-wide interactome of proteins can be defined. However, acquiring a high-resolution interactome of a single genomic locus preferably by multiplexed measurements of several distinct genomic loci in parallel remains challenging. We recently developed CasID, a novel approach where the catalytically inactive Cas9 (dCas9) is coupled to the promiscuous biotin ligase BirA (BirA∗). With CasID, first the local proteome at repetitive telomeric, major satellite, and minor satellite regions was determined. With more efficient biotin ligases and sensitive mass spectrometry, others have successfully identified the chromatin composition at even smaller genomic, non-repetitive regions of a few hundred base pairs in length. Here, we summarize the most recent developments towards interactomics at a single genomic locus and provide a step-by-step protocol based on the CasID approach.


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Wells, J.N., Buschauer, R., Mackens-Kiani, T., Best, K., Kratzat, H., Berninghausen, O., Becker, T., Gilbert, W., Cheng, J., and Beckmann, R.
PLoS Biol, 2020, 18, e3000780
doi: 10.1371/journal.pbio.3000780

Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes

Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes.


Scientists at the Max Planck Institute (MPI) of Biochemistry enable 100-times faster multiplexed DNA-PAINT microscopy using optimized DNA sequences.

• DNA-PAINT uses DNA-barcoded probes to visualize nanoscale biological structures

• Optimized DNA designs enable 100-times faster and multicolor imaging

• High throughput and molecular resolution microscopy might in the future improve our understanding of the interactions between different tumor markers

Super-resolution fluorescence microscopy can be used to visualize structures smaller than 200 nanometers, i.e. below the diffraction limit of light. One of the microscopy techniques, called DNA-PAINT, was developed by Ralf Jungmann, research group leader at the MPI of Biochemistry and Professor for Experimental Physics at the Ludwig Maximilian University Munich together with colleagues. The technique uses short ‘imagers’, dye-labeled DNA strands that temporarily bind to their target molecules in a complementary manner to produce the necessary "blinking" for super-resolution reconstruction of the images. “We have recently improved DNA-PAINT’s traditionally rather slow acquisition speed by an order of magnitude by optimizing DNA sequence design.” says Jungmann. "However, this came at the cost of losing multiplexing, which means that several structures in the cell cannot be observed simultaneously", added Jungmann. The simultaneous observation of several proteins, however, is important for the better understanding of complex signaling cascades between tumor and normal cells.”

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Karayel, O., Tonelli, F., Virreira Winter, S., Geyer, P.E., Fan, Y., Sammler, E.M., Alessi, D., Steger, M., and Mann, M.
Mol Cell Proteomics, 2020, [Epub ahead of print].
doi: 10.1074/mcp.RA120.002055

Accurate MS-based Rab10 phosphorylation stoichiometry determination as readout for LRRK2 activity in Parkinson's disease

Pathogenic mutations in the Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Parkinson's disease (PD). They increase its activity, resulting in augmented Rab10-Thr73 phosphorylation and conversely, LRRK2 inhibition decreases pRab10 levels. Currently, there is no assay to quantify pRab10 levels for drug target engagement or patient stratification. To meet this challenge, we developed an high accuracy and sensitivity targeted mass spectrometry (MS)-based assay for determining Rab10-Thr73 phosphorylation stoichiometry in human samples. It uses synthetic stable isotope-labeled (SIL) analogues for both phosphorylated and non-phosphorylated tryptic peptides surrounding Rab10-Thr73 to directly derive the percentage of Rab10 phosphorylation from attomole amounts of the endogenous phosphopeptide. The SIL and the endogenous phosphopeptides are separately admitted into an Orbitrap analyzer with the appropriate injection times. We test the reproducibility of our assay by determining Rab10-Thr73 phosphorylation stoichiometry in neutrophils of LRRK2 mutation carriers before and after LRRK2 inhibition. Compared to healthy controls, the PD predisposing mutation carriers LRRK2 G2019S and VPS35 D620N display 1.9-fold and 3.7-fold increased pRab10 levels, respectively. Our generic MS-based assay further establishes the relevance of pRab10 as a prognostic PD marker and is a powerful tool for determining LRRK2 inhibitor efficacy and for stratifying PD patients for LRRK2 inhibitor treatment.