Buchmann Institute for Molecular Life science

Frankfurt am Main, Germany

Buchmann Institute for Molecular Life science

Frankfurt am Main, Germany
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Ackloo S.,University of Toronto | Brown P.J.,University of Toronto | Muller S.,Buchmann Institute for Molecular Life science
Epigenetics | Year: 2017

Epigenetic chemical probes are potent, cell-active, small molecule inhibitors or antagonists of specific domains in a protein; they have been indispensable for studying bromodomains and protein methyltransferases. The Structural Genomics Consortium (SGC), comprising scientists from academic and pharmaceutical laboratories, has generated most of the current epigenetic chemical probes. Moreover, the SGC has shared about 4 thousand aliquots of these probes, which have been used primarily for phenotypic profiling or to validate targets in cell lines or primary patient samples cultured in vitro. Epigenetic chemical probes have been critical tools in oncology research and have uncovered mechanistic insights into well-established targets, as well as identify new therapeutic starting points. Indeed, the literature primarily links epigenetic proteins to oncology, but applications in inflammation, viral, metabolic and neurodegenerative diseases are now being reported. We summarize the literature of these emerging applications and provide examples where existing probes might be used. © 2017 Taylor & Francis Group, LLC

Kittelmann M.,University of Gottingen | Liewald J.F.,Buchmann Institute for Molecular Life science | Liewald J.F.,Goethe University Frankfurt | Liewald J.F.,Institute of Functional and Applied Anatomy | And 13 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2013

Local recycling of synaptic vesicles (SVs) allows neurons to sustain transmitter release. Extreme activity (e.g., during seizure) may exhaust synaptic transmission and, in vitro, induces bulk endocytosis to recover SV membrane and proteins; how this occurs in animals is unknown. Following optogenetic hyperstimulation of Caenorhabditis elegans motoneurons, we analyzed synaptic recovery by time-resolved behavioral, electrophysiological, and ultrastructural assays. Recovery of docked SVs and of evokedrelease amplitudes (indicating readily-releasable pool refilling) occurred within ∼8-20 s (τ = 9.2 s and τ = 11.9 s), whereas locomotion recovered only after ∼60 s (τ = 20 s). During ∼11-s stimulation, 50- to 200-nm noncoated vesicles ("100nm vesicles") formed, which disappeared ∼8 s poststimulation, likely representing endocytic intermediates from which SVs may regenerate. In endophilin, synaptojanin, and dynamin mutants, affecting endocytosis and vesicle scission, resolving 100nm vesicles was delayed (>20 s). In dynamin mutants, 100nm vesicles were abundant and persistent, sometimes continuous with the plasma membrane; incomplete budding of smaller vesicles from 100nm vesicles further implicates dynamin in regenerating SVs from bulk-endocytosed vesicles. Synaptic recovery after exhaustive activity is slow, and different time scales of recovery at ultrastructural, physiological, and behavioral levels indicate multiple contributing processes. Similar processes may jointly account for slow recovery from acute seizures also in higher animals.

Diaz-Munoz M.D.,Babraham Institute | Bell S.E.,Babraham Institute | Fairfax K.,Babraham Institute | Fairfax K.,Walter and Eliza Hall Institute of Medical Research | And 15 more authors.
Nature Immunology | Year: 2015

Post-transcriptional regulation of mRNA by the RNA-binding protein HuR (encoded by Elavl1) is required in B cells for the germinal center reaction and for the production of class-switched antibodies in response to thymus-independent antigens. Transcriptome-wide examination of RNA isoforms and their abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interactions, revealed that HuR-dependent splicing of mRNA affected hundreds of transcripts, including that encoding dihydrolipoamide S-succinyltransferase (Dlst), a subunit of the 2-oxoglutarate dehydrogenase (α-KGDH) complex. In the absence of HuR, defective mitochondrial metabolism resulted in large amounts of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for the proliferation and differentiation of B cells. © 2015 Nature America, Inc. All rights reserved.

Figge M.T.,Leibniz Institute for Natural Product Research and Infection Biology | Figge M.T.,Frankfurt Institute for Advanced Studies | Figge M.T.,Helmholtz Center for Infection Research | Reichert A.S.,Goethe University Frankfurt | And 4 more authors.
PLoS Computational Biology | Year: 2012

Mitochondrial dynamics and mitophagy play a key role in ensuring mitochondrial quality control. Impairment thereof was proposed to be causative to neurodegenerative diseases, diabetes, and cancer. Accumulation of mitochondrial dysfunction was further linked to aging. Here we applied a probabilistic modeling approach integrating our current knowledge on mitochondrial biology allowing us to simulate mitochondrial function and quality control during aging in silico. We demonstrate that cycles of fusion and fission and mitophagy indeed are essential for ensuring a high average quality of mitochondria, even under conditions in which random molecular damage is present. Prompted by earlier observations that mitochondrial fission itself can cause a partial drop in mitochondrial membrane potential, we tested the consequences of mitochondrial dynamics being harmful on its own. Next to directly impairing mitochondrial function, pre-existing molecular damage may be propagated and enhanced across the mitochondrial population by content mixing. In this situation, such an infection-like phenomenon impairs mitochondrial quality control progressively. However, when imposing an age-dependent deceleration of cycles of fusion and fission, we observe a delay in the loss of average quality of mitochondria. This provides a rational why fusion and fission rates are reduced during aging and why loss of a mitochondrial fission factor can extend life span in fungi. We propose the 'mitochondrial infectious damage adaptation' (MIDA) model according to which a deceleration of fusion-fission cycles reflects a systemic adaptation increasing life span. © 2012 Figge et al.

Geiss C.P.,Buchmann Institute for Molecular Life science | Keramisanou D.,Buchmann Institute for Molecular Life science | Sekulic N.,University of Pennsylvania | Scheffer M.P.,Buchmann Institute for Molecular Life science | And 2 more authors.
Biophysical Journal | Year: 2014

Summary The centromeric histone H3 variant centromeric protein A (CENP-A), whose sequence is the least conserved among all histone variants, is responsible for specifying the location of the centromere. Here, we present a comprehensive study of CENP-A nucleosome arrays by cryo-electron tomography. We see that CENP-A arrays have different biophysical properties than canonical ones under low ionic conditions, as they are more condensed with a 20% smaller average nearest-neighbor distance and a 30% higher nucleosome density. We find that CENP-A nucleosomes have a predominantly crossed DNA entry/exit site that is narrowed on average by 8, and they have a propensity to stack face to face. We therefore propose that CENP-A induces geometric constraints at the nucleosome DNA entry/exit site to bring neighboring nucleosomes into close proximity. This specific property of CENP-A may be responsible for generating a fundamental process that contributes to increased chromatin fiber compaction that is propagated under physiological conditions to form centromeric chromatin. © 2014 Biophysical Society.

Frank M.,Ludwig Maximilians University of Munich | Duvezin-Caubet S.,Ludwig Maximilians University of Munich | Duvezin-Caubet S.,French National Center for Scientific Research | Duvezin-Caubet S.,University of Bordeaux 1 | And 13 more authors.
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2012

Mitochondrial dysfunction is linked to apoptosis, aging, cancer, and a number of neurodegenerative and muscular disorders. The interplay between mitophagy and mitochondrial dynamics has been linked to the removal of dysfunctional mitochondria ensuring mitochondrial quality control. An open question is what role mitochondrial fission plays in the removal of mitochondria after mild and transient oxidative stress; conditions reported to result in moderately elevated reactive oxygen species (ROS) levels comparable to physical activity. Here we show that applying such conditions led to fragmentation of mitochondria and induction of mitophagy in mouse and human cells. These conditions increased ROS levels only slightly and neither triggered cell death nor led to a detectable induction of non-selective autophagy. Starvation led to hyperfusion of mitochondria, to high ROS levels, and to the induction of both non-selective autophagy and to a lesser extent to mitophagy. We conclude that moderate levels of ROS specifically trigger mitophagy but are insufficient to trigger non-selective autophagy. Expression of a dominant-negative variant of the fission factor DRP1 blocked mitophagy induction by mild oxidative stress as well as by starvation. Taken together, we demonstrate that in mammalian cells under mild oxidative stress a DRP1-dependent type of mitophagy is triggered while a concomitant induction of non-selective autophagy was not observed. We propose that these mild oxidative conditions resembling well physiological situations are thus very helpful for studying the molecular pathways governing the selective removal of dysfunctional mitochondria. © 2012 Elsevier B.V.

Khaminets A.,Goethe University Frankfurt | Khaminets A.,Buchmann Institute for Molecular Life science | Behl C.,Johannes Gutenberg University Mainz | Dikic I.,Goethe University Frankfurt | Dikic I.,Buchmann Institute for Molecular Life science
Trends in Cell Biology | Year: 2016

Selective autophagy regulates the abundance of specific cellular components via a specialized arsenal of factors, termed autophagy receptors, that target protein complexes, aggregates, and whole organelles into lysosomes. Autophagy receptors bind to LC3/GABARAP proteins on phagophore and autophagosome membranes, and recognize signals on cargoes to deliver them to autophagy. Ubiquitin (Ub), a well-known signal for the degradation of polypeptides in the proteasome, also plays an important role in the recognition of cargoes destined for selective autophagy. In addition, a variety of cargoes are committed to selective autophagy pathways by Ub-independent mechanisms employing protein-protein interaction motifs, Ub-like modifiers, and sugar- or lipid-based signals. In this article we summarize Ub-dependent and independent selective autophagy pathways, and discuss regulatory mechanisms and challenges for future studies. Ubiquitin is a universal degradation signal used for protein disposal via proteasome and autophagy.Selective autophagy pathways are regulated by phosphorylation and ubiquitination.In contrast to core autophagy machinery, autophagy receptors are divergent and poorly conserved from yeast to humans; however, functional homologs are present.Autophagy receptors target damaged or foreign cytosolic material by recognizing specific protein, sugar, or lipid moieties.Autophagy receptors act together with autophagy adaptors in recognizing and processing cargo via selective autophagy. © 2015 Elsevier Ltd.

Brieke C.,Goethe University Frankfurt | Rohrbach F.,University of Bonn | Gottschalk A.,Buchmann Institute for Molecular Life science | Mayer G.,University of Bonn | Heckel A.,Goethe University Frankfurt
Angewandte Chemie - International Edition | Year: 2012

Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems-from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications. Spot on! Systems which can be regulated by using light as a trigger can be used for very sophisticated experiments in which aspects of space, time, or extent of activation are to be studied. Irreversible photocleavage, reversible photoswitching, and genetically expressible systems are the three possibilities for coupling the trigger to an effect. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stolz A.,Goethe University Frankfurt | Dikic I.,Goethe University Frankfurt | Dikic I.,Buchmann Institute for Molecular Life science
Molecular Cell | Year: 2014

By using quantitative proteomics, Ordureau etal. (2014) provide a comprehensive view on the regulatory steps by which PINK1-mediated phosphorylation of PARKIN and ubiquitin triggers the recruitment of the ubiquitin ligase PARKIN to damaged mitochondria. © 2014 Elsevier Inc.

Stolz A.,Goethe University Frankfurt | Ernst A.,Goethe University Frankfurt | Dikic I.,Goethe University Frankfurt | Dikic I.,Buchmann Institute for Molecular Life science
Nature Cell Biology | Year: 2014

Selective autophagy is a quality control pathway through which cellular components are sequestered into double-membrane vesicles and delivered to specific intracellular compartments. This process requires autophagy receptors that link cargo to growing autophagosomal membranes. Selective autophagy is also implicated in various membrane trafficking events. Here we discuss the current view on how cargo selection and transport are achieved during selective autophagy, and point out molecular mechanisms that are congruent between autophagy and vesicle trafficking pathways. © 2014 Macmillan Publishers Limited. All rights reserved.

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