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Müller, J.B., Geyer, P.E., Colaço, A.R., Treit, P.V., Strauss, M.T., Oroshi, M., Doll, S., Virreira Winter, S., Bader, J.M., Köhler, N., Theis, F., Santos, A., and Mann, M.
(IMPRS-LS students and -alumni are in bold)
Nature, 2020, 582, 592-596.
doi: 10.1038/s41586-020-2402-x

The proteome landscape of the kingdoms of life

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported, advances in mass-spectrometry-based proteomics have enabled increasingly comprehensive identification and quantification of the human proteome. However, there have been few comparisons across species in stark contrast with genomics initiatives. Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides from Bacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.


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Reim, A., Ackermann, R., Font-Mateu, J., Kammel, R., Beato, M., Nolte, S., Mann, M., Russmann, C., and Wierer, M.
Nat Commun, 2020, 11, 3019.
doi: 10.1038/s41467-020-16837-x

Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.


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Lingaraju, M., Schuller, J.M., Falk, S., Gerlach, P., Bonneau, F., Basquin, J., Benda, C., and Conti, E.
Cold Spring Harb Symp Quant Biol, 2020, [Epub ahead of print].
doi: 10.1101/sqb.2019.84.040295

To Process or to Decay: A Mechanistic View of the Nuclear RNA Exosome

The RNA exosome was originally discovered in yeast as an RNA-processing complex required for the maturation of 5.8S ribosomal RNA (rRNA), one of the constituents of the large ribosomal subunit. The exosome is now known in eukaryotes as the major 3'-5' RNA degradation machine involved in numerous processing, turnover, and surveillance pathways, both in the nucleus and the cytoplasm. Yet its role in maturing the 5.8S rRNA in the pre-60S ribosomal particle remains probably the most intricate and emblematic among its functions, as it involves all the RNA unwinding, degradation, and trimming activities embedded in this macromolecular complex. Here, we propose a comprehensive mechanistic model, based on current biochemical and structural data, explaining the dual functions of the nuclear exosome-the constructive versus the destructive mode.


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Bader, J.M., Geyer, P.E., Müller, J.B., Strauss, M.T., Koch, M., Leypoldt, F., Koertvelyessy, P., Bittner, D., Schipke, C.G., Incesoy, E.I., Peters, O., Deigendesch, N., Simons, M., Jensen, M.K., Zetterberg, H., and Mann, M.
(IMPRS-LS students and -alumni are in bold)
Mol Syst Biol, 2020, 16, e9356.
doi: 10.15252/msb.20199356

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

Neurodegenerative diseases are a growing burden, and there is an urgent need for better biomarkers for diagnosis, prognosis, and treatment efficacy. Structural and functional brain alterations are reflected in the protein composition of cerebrospinal fluid (CSF). Alzheimer's disease (AD) patients have higher CSF levels of tau, but we lack knowledge of systems-wide changes of CSF protein levels that accompany AD. Here, we present a highly reproducible mass spectrometry (MS)-based proteomics workflow for the in-depth analysis of CSF from minimal sample amounts. From three independent studies (197 individuals), we characterize differences in proteins by AD status (> 1,000 proteins, CV < 20%). Proteins with previous links to neurodegeneration such as tau, SOD1, and PARK7 differed most strongly by AD status, providing strong positive controls for our approach. CSF proteome changes in Alzheimer's disease prove to be widespread and often correlated with tau concentrations. Our unbiased screen also reveals a consistent glycolytic signature across our cohorts and a recent study. Machine learning suggests clinical utility of this proteomic signature.


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Scacchetti, A., Schauer, T., Reim, A., Apostolou, Z., Campos Sparr, A., Krause, S., Heun, P., Wierer, M., and Becker, P.B.
(IMPRS-LS students are in bold)
Elife, 2020, 9.
doi: 10.7554/eLife.56325

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms

Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.


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Soni, K., Martínez-Lumbreras, S., and Sattler, M.
J Mol Biol, 2020, [Epub ahead of print].
doi: 10.1016/j.jmb.2020.05.012

Conformational dynamics from ambiguous zinc coordination in the RanBP2-type zinc finger of RBM5

The multi-domain RNA binding protein RBM5 is a molecular signature of metastasis. RBM5 regulates alternative splicing of apoptotic genes including the cell death receptor Fas and the initiator Caspase-2. The RBM5 RanBP2-type zinc finger (Zf1) is known to specifically recognize single stranded RNAs with high affinity. Here, we study the structure and conformational dynamics of the Zf1 zinc finger of human RBM5 using NMR. We show that the presence of a non-canonical cysteine in Zf1 kinetically destabilizes the protein. Metal exchange kinetics show that mutation of the cysteine establishes high affinity coordination of the zinc. Our data indicate that selection of such a structurally destabilizing mutation during the course of evolution could present an opportunity for functional adaptation of the protein.


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Schmacke, N.A., and Hornung, V.
Nature, 2020, 581, 266-267.
doi: 10.1038/d41586-020-0133


Fourth defence molecule completes antiviral line-up

Toll-like receptors can initiate an immune response when they detect signs of a viral or microbial threat. New insight into how such receptor activation drives defence programs should aid our efforts to understand autoimmune diseases.


graduationCongratulations on your PhD!


Sophia Hergenhan
Circadian Control of Leukocyte Numbers in the Circulation
RG: Christoph Scheiermann

Tugce Öz Yoldas
What prevents DNA replication between meiosis I and -II in yeast?
RG: Wolfgang Zachariae

 


 

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Yildizoglu, T., Riegler, C., Fitzgerald, J.E., and Portugues, R.
Curr Biol, 2020, [Epub ahead of print].
doi: 10.1016/j.cub.2020.04.043

A Neural Representation of Naturalistic Motion-Guided Behavior in the Zebrafish Brain

All animals must transform ambiguous sensory data into successful behavior. This requires sensory representations that accurately reflect the statistics of natural stimuli and behavior. Multiple studies show that visual motion processing is tuned for accuracy under naturalistic conditions, but the sensorimotor circuits extracting these cues and implementing motion-guided behavior remain unclear. Here we show that the larval zebrafish retina extracts a diversity of naturalistic motion cues, and the retinorecipient pretectum organizes these cues around the elements of behavior. We find that higher-order motion stimuli, gliders, induce optomotor behavior matching expectations from natural scene analyses. We then image activity of retinal ganglion cell terminals and pretectal neurons. The retina exhibits direction-selective responses across glider stimuli, and anatomically clustered pretectal neurons respond with magnitudes matching behavior. Peripheral computations thus reflect natural input statistics, whereas central brain activity precisely codes information needed for behavior. This general principle could organize sensorimotor transformations across animal species.


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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.