Biology subjects

Koenig, C.

Publications and source records attributed to Koenig, C..

24 records · Page 2Linked to original sources

bioRxiv2022

Structure of the lysosomal membrane fusion machinery

Lysosomes are of central importance in cellular recycling, nutrient signaling 1,2 and endocytosis, and are tightly connected to autophagy 3 and the invasion of pathogenic bacteria and viruses 1,4. Lysosomal fusion events are fundamental to cell survival and require HOPS, a conserved heterohexameric tethering complex 5,6. HOPS recognizes and binds small membrane-associated GTPases on lysosomes and organelles, and assembles membrane bound SNAREs for fusion 7,8. Through tethering, HOPS brings membranes in close proximity to each other and significantly increases fusion efficacy by catalysing SNARE assembly. Consequently, different HOPS mutations are causative for severe diseases 6. Despite its fundamental cellular duties, it remained speculative how HOPS fulfils its function as high-resolution structural data were unavailable. Here, we used cryo-electron microscopy to reveal the structure of HOPS. In the complex, two central subunits form the backbone and an assembly hub for the functional domains. Two GTPase binding units extend to opposing ends, while the SNARE binding module points to the side, resulting in a triangular shape of the complex. Unlike previously reported, HOPS is surprisingly rigid and extensive flexibility is confined to its extremities. We show that HOPS complex variants with mutations proximal to the backbone can still tether membranes but fail to efficiently promote fusion indicating, that the observed integrity of HOPS is essential to its function. In our model, the core of HOPS acts as a counter bearing between the flexible GTPase binding domains. This positions the SNARE binding module exactly between the GTPase anchored membranes to promote fusion. Our structural and functional analysis reveals the link between the spectacular architecture of HOPS and its mechanism that couples membrane tethering and SNARE assembly, to catalyse lysosomal fusion.

biophysics↗

bioRxiv2020

Associative learning in larval and adult Drosophila is impaired by the dopamine-synthesis inhibitor 3-Iodo-L-tyrosine

Across the animal kingdom, dopamine plays a crucial role in conferring reinforcement signals that teach animals about the causal structure of the world. In the fruit fly Drosophila melanogaster, the dopamine system has largely been studied using a rich genetic toolbox. Here, we suggest a complementary pharmacological approach applying the dopamine-synthesis inhibitor 3-Iodo-L-tyrosine (3IY), which causes acute systemic inhibition of dopamine signaling. Using Pavlovian conditioning, across developmental stages (3rd instar larva versus adult), valence domains (reward versus punishment), and types of reinforcement (natural versus optogenetically induced), we find that 3IY feeding specifically impairs associative learning, whereas additional feeding of L-3,4-dihydroxyphenylalanine (L-DOPA), a precursor of dopamine, rescues this impairment. This study establishes a simple, quick, and comparably low-cost approach that can be combined with the available genetic tools to manipulate and clarify the functions of the dopaminergic system - in D. melanogaster and other animals.

neuroscience↗

bioRxiv2019

The Human Exonuclease-1 Interactome And Phosphorylation Sites

Error-free repair of DNA double-strand break is orchestrated by homologous recombination (HR) pathways and requires the concerted action of several factors. Among these, EXO1 and DNA2/BLM execute extensive resection of DNA ends to produce 3-overhangs, which are key intermediates for downstream steps of HR. To help shedding light on regulatory aspects of DNA repair pathways in which EXO1 participates, we set out to identify proteins interacting with EXO1. Affinity purification of EXO1 followed by Orbitrap mass spectrometry led to the identification of novel partners that are involved in RNA processing or that are the causative agents of rare X-linked disorders. Depletion of a selected subset of EXO1 interacting proteins led to reduction of the DNA damage response. Among those, we examined the RRP5-homologue and NF{kappa}B-interacting protein PDCD11/ALG-4, which has roles in apoptosis and is a putative driver gene in cutaneous T-cell lymphoma. We provide evidence that depletion of PDCD11 decreased the formation of {gamma}H2AX foci and the phosphorylation of DNA damage response signaling intermediates in response to camptothecin or bleomycin, resulting in increased cellular resistance to DNA damage. Furthermore, extensive coverage of EXO1 sequence (>85%) by mass spectrometry allowed conducting an in-depth analysis of its phosphorylation sites, with the identification of 26 residues that are differentially modified in untreated conditions or upon induction of DNA damage.\n\nAs a whole, these results provide the basis for future in-depth studies on novel roles of EXO1 in genome stability and indicate targets for pharmacological inhibition of pathways of cancer development.\n\nHIGHLIGHTS O_LIProteome-wide analysis of Exonuclease-1 (EXO1) interacting proteins revealed novel partners involved in RNA processing or that are the causative agents of rare X-linked disorders.\nC_LIO_LIWe provide evidence for a role of PDCD11 in the DNA Damage Response.\nC_LIO_LIWe conducted a comprehensive identification of EXO1 phosphorylation sites.\nC_LI

cell biology↗

bioRxiv2019

GIFT - A Global Inventory of Floras and Traits for macroecology and biogeography

To understand how traits and evolutionary history shape the geographic distribution of plant life on Earth, we need to integrate high-quality and global-scale distribution data with functional and phylogenetic information. Large-scale distribution data for plants are, however, often restricted to either certain taxonomic groups or geographic regions. For example, range maps only exist for a small subset of all plant species and digitally available point-occurrence information is strongly biased both geographically and taxonomically. An alternative, currently rarely used resource for macroecological and botanical research are regional Floras and checklists, which contain highly curated information about the species composition of a clearly defined area, and which together virtually cover the entire global land surface. Here we report on our recent efforts to mobilize this information for macroecological and biogeographical analyses in the GIFT database, the Global Inventory of Floras and Traits. GIFT integrates plant distributions, functional traits, phylogenetic information, and region-level geographic, environmental and socioeconomic data. GIFT currently holds species lists for 2,893 regions across the whole globe including ~315,000 taxonomically standardized species names (i.e. c. 80% of all known land plant species) and ~3 million species-by-region occurrences. In addition, GIFT contains information about the floristic status (native, endemic, alien and naturalized) and takes advantage of the wealth of trait information in the regional Floras, complemented by data from global trait databases. Based on a hierarchical and taxonomical derivation scheme, GIFT holds information for 83 functional traits and more than 2.3 million trait-by-species combinations and achieves unprecedented coverage in categorical traits such as woodiness (~233,000 spp.) or growth form (~213,000 spp.). Here we present the structure, content and automated workflows of GIFT and a corresponding web-interface (http://gift.uni-goettingen.de) as proof of concept for the feasibility and potential of mobilizing aggregated biodiversity data for global macroecological and biogeographical research.

ecology↗

bioRxiv2019

Disharmony of the world’s island floras

Disharmony is a key concept in island biology that describes the biased representation of higher taxa on islands compared to their mainland source regions. Although differential colonization success of taxa is predicted by selective dispersal, environmental and biotic filtering, the empirical evidence for disharmony remains largely anecdotal. Here, we develop a novel method for delineating island source regions and present the first global quantitative assessment of island disharmony. We analyzed the overall compositional bias of 320 island floras and examined the over- or under-representation on islands for 450 plant families. We found that the compositional bias of island floras is strongly predicted by geographical and climatic island characteristics (isolation, area, geologic origin, temperature, precipitation), whereas the representation of individual families is only weakly related to family-specific characteristics (family size, family age, taxonomic group, functional traits), indicating that the taxonomic scope of the disharmony concept has historically limited its wider applicability. Our results provide a strong foundation for integrating disharmony with quantitative functional and phylogenetic approaches in order to gain a deeper understanding of assembly processes on islands.

ecology↗

bioRxiv2018

Pharmacophore-guided discovery of CDC25 inhibitors causing cell cycle arrest and cell death

CDC25 phosphatases have a key role in cell cycle transitions and are important targets for cancer therapy. Here, we set out to discover novel CDC25 inhibitors. Using a combination of computational approaches we defined a minimal common pharmacophore in established CDC25 inhibitors and performed a virtual screening of a proprietary library. Taking advantage of the availability of crystal structures for CDC25A and CDC25B and using a molecular docking strategy, we carried out hit expansion/optimization. Enzymatic assays revealed that naphthoquinone scaffolds were the most promising CDC25 inhibitors among selected hits. At the molecular level, the compounds acted through a mixed-type mechanism of inhibition of phosphatase activity, involving reversible oxidation of cysteine residues. In 2D cell cultures, the compounds caused arrest of the cell cycle at the G1/S or at the G2/M transition. Mitotic markers analysis and time-lapse microscopy confirmed that CDK1 activity was impaired and that mitotic arrest was followed by death. Finally, studies on 3D organoids derived from intestinal crypt stem cells of Apc/K-Ras mice revealed that the compounds caused arrest of proliferation.

cancer biology↗