Biology subjects

Luck, K.

Publications and source records attributed to Luck, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Cellular context defines brain-specific functions of genes associated with neurodevelopmental disorders

Differential gene expression rarely explains why certain genes, e.g. associated with tissue-specific manifestations of human disease, exert tissue-specific functions. To understand how gene expression and molecular context act in concert to drive tissue-specific gene function, we focus on Neurodevelopmental disorders (NDDs), for which underlying disease mechanisms are still poorly understood. We developed a computational framework that harmonizes and integrates spatiotemporal transcriptome datasets enabling us to systematically quantify preferential gene expression across tissues and developmental stages. Applying this pipeline to approximately 1,000 NDD-associated genes, we find that only about 10% show brain-preferential expression, with distinct gene clusters instead exhibiting significant upregulation in non-brain tissues. Investigation of these clusters reveals regulatory mechanisms that govern mitochondrial function to meet neurons' high energetic demands, which are mechanistically distinct from those employed by other energy-intensive tissues such as heart and skeletal muscle. Furthermore, by integrating tissue-agnostic protein-protein interaction data with our expression resource, we identify putative brain-specific interaction partners for 22 uniformly expressed NDD-associated genes. We experimentally validate these interactions for QRICH1 and demonstrate that disease-associated mutations disrupt them, providing a molecular hypothesis for how QRICH1 acquires brain-specific function and how its disruption might cause Ververi-Brady syndrome. Together, our findings highlight the importance of molecular context for brain-specific gene function in the context of neurodevelopmental disease. We provide a framework for dissecting molecular mechanisms of tissue-specific Mendelian-like disorders and for exploring how biological processes are adapted to tissue-specific needs.

bioinformatics↗

bioRxiv2026

Foldseek-Interface reveals a protein interface universe far from complete

Protein-protein interactions mediate a vast range of cellular functions, requiring diverse modes of binding. While recent years have seen major efforts to chart and classify the protein structure universe, we lack comparable methods to assess and cluster that diversity in interface structure at interactome scale. Here, we present Foldseek-Interface, a method that converts 3D interface structures into searchable sequences to enable fast alignment and clustering of protein interaction interfaces. It matches the accuracy of state-of-the-art tools while running up to 230 times faster. Applying it to all biological assemblies in the PDB, we cluster 3.1 million dimers into 77{,}167 interface clusters and use this resource to characterise interface diversity, evolution, and pathogen mimicry. Application of Foldseek-Interface to resources of predicted protein complex structures rapidly revealed putatively novel interface types worth further experimental interrogation. Foldseek-Interface and the interface cluster resource are freely available as webservers for search https://search.foldseek.com/interface and exploration https://interface.foldseek.com.

bioinformatics↗

bioRxiv2026

The phosphoproteomic landscape of the DNA damage response

The DNA damage response (DDR) comprises an intricate network of protein-protein interactions and signaling pathways activated by DNA lesions and genomic instability. Central to this response is protein phosphorylation, which orchestrates DNA repair, cell cycle checkpoint activation, and chromatin organization. The response of the human phosphoproteome to different DNA damage-inducing agents and the functional role of regulated phosphorylation sites remains insufficiently characterized. Here, we systematically profiled the cellular phosphoproteome following exposure to eleven DNA damage-inducing agents that humans encounter physiologically or during cancer therapy. We identified a core set of DNA damage responsive phosphorylation sites, along with DDR signatures associated with DNA double strand breaks, replication stress and a pleiotropic response. Regulated phosphorylation sites are enriched within intrinsically disordered regions (IDRs), often forming clusters of nearby modifications that can affect IDR conformations or overlap with short linear interaction motifs. We discover that the RNA damage response predominantly shapes the changes induced by reactive aldehyde formaldehyde, alkylating agent methyl methanesulfonate and oxidative stress. Finally, we demonstrate that the proteasome-associated ubiquitin E3 ligase UBE3A is targeted by ATM and ATR kinases, thus linking proteasome regulation with the DDR.

cell biology↗

bioRxiv2026

Systematic drug profiling across BAF complex perturbations reveals distinct dependencies

Chromatin remodeling by BAF complexes regulates access to DNA with implications in transcription, replication and the sensing and repair of DNA lesions, processes that are closely coupled to cell growth control. BAF complexes exist in three major subtypes each composed of a unique subset of about a dozen subunits. While for individual BAF subunits direct functions in DNA repair and cell growth have been described, we lack a more systematic interrogation of BAF perturbation and its implications in these processes. To fill this need, we subjected an isogenic BAF knockout collection to treatment with diverse genotoxic and cytotoxic compounds quantifying proliferation, cell cycle phase distributions, cell fate decisions, DNA double-strand break signaling, and transcriptional responses. The screen uncovered vulnerabilities of selected BAF-deficient cells to MEK and EGFR pathway inhibition, as well as unexpected resistance toward checkpoint inhibitors and certain DNA-damaging agents. Notably, loss of distinct ARID paralogs produced markedly divergent phenotypes, indicating limited functional redundancy and subtype-specific contributions to genome stability and cell cycle regulation. Collectively, these results provide a comparative resource linking BAF complex composition to genotoxic and cytotoxic stress responses, highlighting candidate synthetic-lethal interactions and generating hypotheses for mechanistic studies of BAF complexes in genome maintenance and cell growth control.

molecular biology↗

bioRxiv2026

The floral illusion: A parasitic beetle mimics the scent of flowers to attract bees

Animals are not known to biosynthesize floral signals to manipulate pollinators, although such mimicry could profoundly shape plant-pollinator interactions. Larvae of the poisonous European blister beetle Meloe proscarabaeus parasitize multiple solitary bee species, yet the mechanism enabling host attraction has remained unresolved. Here we show that these larvae lure bees by emitting a bouquet of volatile compounds that closely resembles floral scent. Chemical analyses reveal a complex blend of monoterpenoids derived from (S)-linalool, a ubiquitous floral volatile. Behavioral assays demonstrate that these compounds function as floral cues, eliciting attraction in bees. Transcriptomic and functional analyses identify cytochrome P450 enzymes that oxidize (S)-linalool, demonstrating that larvae biosynthesize these plant-like volatiles de novo. Together, these findings broaden the scope of interkingdom chemical mimicry and uncover a striking form of sensory deception in which an insect chemically assumes the signal identity of a flower, revealing that animals can evolve biosynthetic pathways to exploit plant-pollinator communication.

ecology↗

bioRxiv2026

Short linear motifs - Unexplored players driving Toxoplasma gondii infection

Pathogens infect hosts by interacting with host proteins and exploiting their functions to their advantage. Short linear motifs, small functional regions within intrinsically disordered protein regions, are common mediators of host-pathogen protein interactions. While motifs have been more extensively studied in viruses and bacteria, the extent to which eukaryotic unicellular parasites use motifs during infection remains unexplored. Toxoplasma gondii is a widespread intracellular Apicomplexan parasite capable of infecting all warm-blooded animals and invading any of their nucleated cells. Toxoplasmas secreted proteins are key in interacting with host proteins during infection, making them potential sources for motifs. To highlight the role of motifs in Toxoplasma gondii infection, we curated 21 known motif instances in Toxoplasma proteins from the scientific literature. To identify more motifs in Toxoplasma secreted proteins, we developed a computational pipeline that annotates putative motif matches with structural and functional features. Through this approach, we identified a set of 24,291 motif matches in 295 secreted proteins. We highlight strategies for further prioritisation of likely functional motif matches by focusing on integrin motifs, degrons and TRAF6-binding motifs. We subjected four predicted TRAF6-binding motifs to experimental validation, supporting the predicted motifs in the Toxoplasma proteins RON10 and GRA15. Our motif predictions provide a valuable resource for generating hypotheses and designing experiments to study infection mechanisms. The characterisation of motifs in Toxoplasma will be key to understanding the molecular principles underlying its broad host range and more comprehensive Apicomplexan infection strategies. ImportanceToxoplasma gondii is a widely distributed intracellular parasite that achieves a successful infection by interacting with different host cell proteins. Short linear motifs are small functional modules found in unstructured protein regions and recognised by folded protein domains. Given that unstructured protein regions are a common feature of Toxoplasmas proteins, we hypothesise that motifs play important roles during its infection cycle. Here, we highlight the role of motifs during the Toxoplasma host cell invasion cycle through a curated set of motif examples. Through a computational pipeline, we predict thousands of motifs in secreted proteins, outline strategies for working with these predictions and finally experimentally test proteins containing a motif involved in the innate immune response, successfully showing the binding of two motifs. Our work provides a resource for further motif testing in Toxoplasma proteins, aiming at understanding the molecular mechanisms of its infection strategies and its broad host range.

bioinformatics↗

bioRxiv2025

Bidirectional control of a metabolic transition by the GID ubiquitin ligase

The GID/CTLH ubiquitin ligase is a multisubunit E3 conserved across eukaryotes. GID/CTLH has been implicated in a variety of processes, including metabolic regulation, cell proliferation, embryonic development and cell differentiation. However, our understanding of substrate recognition by GID/CTLH remains incomplete. Here, we characterize the regulation, specificity and functions of the putative substrate receptor Gid11 in budding yeast. We find that upon its expression during the switch of carbon source from glucose to ethanol, Gid11 associates with the core GID complex, likely forming a large ring assembly. Through systematic mutagenesis, we identify a negatively charged pocket on Gid11 that binds substrates carrying N-terminal degrons starting with threonine and define the Thr/N-degron motif. Such Thr/N-degrons are exposed upon co-translational removal of the initiator methionine, while escaping N-terminal acetylation. Finally, we show that during the switch to ethanol, GIDGid11 targets for degradation factors linked to glycolysis, opposing the established role of GID in the degradation of gluconeogenic enzymes during the reverse switch from ethanol to glucose. Taken together, our results establish Gid11 as a bona fide GID substrate receptor and highlight GID as a regulator of metabolic transitions.

molecular biology↗

bioRxiv2025

Variant characterization in the intrinsically disordered human proteome

Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in the characterization of missense variants in folded protein regions. However, 37% of all annotated missense variants reside in 25% of the proteome that is intrinsically disordered, lacking positional sequence conservation and stable structures. To significantly advance variant effect prediction in disordered protein regions, we combined sequence pattern searches with AlphaFold and experiments to structurally annotate 1,300 protein-protein interactions with interfaces mediated by short disordered motifs binding to folded domains in partner proteins. These interfaces were selected based on their overlap with uncertain missense variants enabling reliable prediction of deleterious effects of 1,187 uncertain variants in disordered protein regions. Extensive experimental efforts validate predicted interfaces and deleterious variant effects that were predicted as benign by AlphaMissense. This study demonstrates how critical structural information on protein interaction interfaces is for variant effect prediction especially in disordered protein regions and provides a clear avenue towards its system-wide implementation.

systems biology↗

bioRxiv2024

Highjacked by a pseudoenzyme: How eudicot plants make indole

Indole is crucial for plant defense, where it is released as a signaling volatile upon herbivore attack and also serves as a starting precursor for defensive specialized metabolites. Indole is known to be synthesized in plants from indole-3-glycerol phosphate by the enzyme indole-3-glycerol phosphate lyase. Here we report that in core eudicots, indole production for plant defense occurs via an alternative pathway. The subunit of tryptophan synthase (TSA), an enzyme of core metabolism, normally binds to tryptophan synthase {beta} subunit (TSB) to produce tryptophan. However, we show that a non-catalytic TSB paralogue (TSB-like) can highjack TSA to produce indole. The widespread occurrence of TSB-like genes in eudicots suggests that this alternative mechanism for indole formation is widespread throughout the plant kingdom.

plant biology↗

bioRxiv2024

Streamlined screening platforms lead to the discovery of pachysiphine synthase from Tabernanthe iboga

Plant-specialized metabolism is largely driven by the oxidative tailoring of key chemical scaffolds catalyzed by cytochrome P450 (CYP450s) enzymes. The monoterpene indole alkaloids tabersonine and pseudo-tabersonine, found in the medicinal plant Tabernanthe iboga, are extensively modified by oxidative reactions. Here we developed a streamlined screening strategy to screen the activity of T. iboga CYP450s in Nicotiana benthamiana. Using multigene constructs encoding the biosynthesis of tabersonine and pseudo-tabersonine scaffolds, we set out to uncover the CYP450s responsible for oxidative transformations of these scaffolds. Our approach identified two T. iboga cytochrome P450 enzymes: pachysiphine synthase (PS) and 16-hydroxy-tabersonine synthase (T16H). These enzymes catalyze an epoxidation and site-specific hydroxylation of tabersonine to produce pachysiphine and 16-OH-tabersonine, respectively. We further demonstrated that these genes produced the expected products when expressed in Catharanthus roseus flowers. This work provides new insights into the biosynthetic pathways of MIAs and underscores the utility of N. benthamiana and C. roseus as platforms for the functional characterization of plant enzymes.

biochemistry↗

bioRxiv2024

Phenylphenalenones and Linear Diarylheptanoid Derivatives are Biosynthesized via Parallel Routes in Musella lasiocarpa, the Chinese Dwarf Banana

Phenylphenalenones (PPs) are complex polycyclic natural products that play an important role in the chemical defense system of banana and plantain (Musaceae). Although suggestions for how plants synthesize the PP scaffold were first proposed more than 50 years ago, no biosynthetic information is yet available at the enzyme level. Here, we use transcriptomic data from seeds of Musella lasiocarpa, the Chinese dwarf banana, to identify five biosynthetic genes involved in the formation of dihydrocurcuminoids. Characterization of the substrate specificities of the enzymes reveals two distinct dihydrocurcuminoid pathways leading to the two types of major aromatic seed metabolites, the PPs and the linear diarylheptanoid derivatives. Furthermore, through multiple rounds of feeding potential intermediates to M. lasiocarpa root protein extract, followed by high-resolution mass spectrometry profiling, product isolation, and NMR-based elucidation, we demonstrate the stepwise conversion of a dihydrocurcumin-type precursor to the PP 4-hydroxylachnanthocarpone. In contrast to the commonly hypothesized Diels-Alder cyclization mechanism, we propose an unexpected two-step cyclization route to the PP scaffold.

biochemistry↗

bioRxiv2023

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation

Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. We thoroughly assessed AlphaFold-Multimer accuracy for structure prediction of interactions involving folded domains binding to short linear motifs from the ELM database. The structure predictions were highly sensitive but not very specific when using small protein fragments. Sensitivity decreased substantially when using long protein fragments or full length proteins with intrinsically disordered regions. We delineated a fragmentation strategy to optimize sensitivity and applied it to interactions between proteins associated with neurodevelopmental disorders. This enabled prediction of highly confident and likely disease-related novel interfaces, but also resulted in many high scoring false positive predictions. Experiments supported predicted interfaces between CREBZF-HCFC1, FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

systems biology↗

bioRxiv2023

Dynamic X-chromosomal reactivation enhances female brain resilience

While random X-chromosome inactivation in female cells of placental mammalians silences one allele of the majority of X-chromosomal genes, a considerable fraction is only incompletely and variably inactivated resulting in a tissue-specific pattern of mono- and biallelic expression. Here we used clonal human female induced pluripotent stem cells (iPSCs) allowing to trace the (in)activation status of the two X-chromosomes individually along neural differentiation trajectories. We discovered X-chromosome-wide locus- and lineage-specific dynamic usage of the two X-chromosomal alleles in female cells induced by differentiation. Leveraging iPSCs derived from patients with an X-linked neurodevelopmental disorder, we demonstrate that activation of alleles on the inactive X-chromosome can exert protective effects on the manifestation of disease phenotypes in female neural cells and tissue. Taken together, our data demonstrate that alleles on the inactive X-chromosome can serve as a critical reservoir reactivated during differentiation, thereby enhancing resilience of female neural tissue.

neuroscience↗

bioRxiv2023

An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori

Piwi-interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping-pong amplification loop. Within this process, piRNA-associated PIWI proteins (piRISC) enter the nuage to cleave target RNA, which is stimulated by Gtsf proteins. The resulting cleavage product gets loaded into an empty PIWI protein to form a new piRISC complex. However, for piRNA amplification to occur, it is required that new RNA substrates, Gtsf-piRISC and empty PIWI proteins are all in physical proximity. In this study we show that BmGtsf1L binds to piRNA-loaded BmAgo3 and co-localizes to BmAgo3-BmVreteno positive granules. Biochemical assays further revealed that conserved residues within the unstructured tail of BmGtsf1L directly interact with BmVreteno. Using a combination of AlphaFold modeling, atomistic molecular dynamics simulations and in vitro assays we identified a novel binding interface on a BmVreteno-eTudor domain, which is required for BmGtsf1L binding. Our study reveals that a single eTudor domain within BmVreteno provides two binding interfaces and thereby interconnects piRNA-loaded BmAgo3 and BmGtsf1L.

molecular biology↗

bioRxiv2022

Biosynthesis of iridoid sex pheromones in aphids

Iridoid monoterpenes, widely distributed in plants and insects, have many ecological functions. While the biosynthesis of iridoids has been extensively studied in plants, little is known about how insects synthesize these natural products. Here, we elucidated the biosynthesis of the iridoids cis-trans-nepetalactol and cis-trans-nepetalactone in the pea aphid Acyrthosiphon pisum [Harris], where they act as sex pheromones. The exclusive production of iridoids in hind legs of sexual female aphids allowed us to identify iridoid genes by searching for genes specifically expressed in this tissue. Biochemical characterization of candidate enzymes revealed that the iridoid pathway in aphids proceeds through the same sequence of intermediates as described for plants. The six identified aphid enzymes are unrelated to their counterparts in plants, conclusively demonstrating an independent evolution of the entire iridoid pathway in plants and insects. In contrast to the plant pathway, at least three of the aphid iridoid enzymes are likely membrane-bound. We demonstrated that a lipid environment facilitates the cyclization of a reactive enol intermediate to the iridoid cyclopentanoid-pyran scaffold in vitro, suggesting that membranes are an essential component of the aphid iridoid pathway. Altogether, our discovery of this complex insect metabolic pathway establishes the genetic and biochemical basis for the formation of iridoid sex pheromones in aphids and this discovery also serves as a foundation for understanding the convergent evolution of complex metabolic pathways between kingdoms. Significance StatementPlants, animals and microbes produce a plethora of natural products that are important for defense and communication. Most of these compounds show a phylogenetically restricted occurrence, but in rare instances, the same natural product is biosynthesized by organisms in two different kingdoms. The monoterpene-derived iridoids, for example, have been found in more than 50 plant families, but are also observed in several insect orders. The aphid iridoid pathway discovered in this study, one of the longest and most chemically complex insect-derived natural product biosynthetic pathways reported to date, is compared with iridoid biosynthetic pathways in plants and highlights the mechanisms underlying the convergent evolution of metabolic enzymes in insects and plants.

biochemistry↗

bioRxiv2022

Next-generation large-scale binary protein interaction network for Drosophila

Generating reference maps of the interactome networks underlying most cellular functions can greatly illuminate genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. Here, we applied state-of-the-art experimental and bioinformatics methods to identify high-confidence binary protein-protein interactions (PPIs) for Drosophila melanogaster. We performed four all-by-all yeast two-hybrid (Y2H) screens of >10,000 Drosophila proteins, resulting in the FlyBi dataset of 8,723 PPIs among 2,939 proteins. As part of this effort, we tested subsets of our data and data from previous PPI datasets using an orthogonal assay, which allowed us to normalize data quality across datasets. Next, we integrated our FlyBi data with previous PPI data, resulting in an expanded, high-confidence binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6,511 proteins. These data are accessible through the Molecular Interaction Search Tool (MIST) and other databases. To assess the utility of the PPI resource, we used novel interactions from the FlyBi dataset to generate an autophagy interaction network that we validated in vivo using two different autophagy-related assays. We found that deformed wings (dwg) encodes a protein that is both a regulator and a target of autophagy. Altogether, the resources generated in this project provide a strong foundation for building high-confidence new hypotheses regarding protein networks and function.

cell biology↗

bioRxiv2021

Binary Interactome Models of Inner- Versus Outer-Complexome Organization

Hundreds of different protein complexes that perform important functions across all cellular processes, collectively comprising the "complexome" of an organism, have been identified1. However, less is known about the fraction of the interactome that exists outside the complexome, in the "outer-complexome". To investigate features of "inner"- versus outer-complexome organisation in yeast, we generated a high-quality atlas of binary protein-protein interactions (PPIs), combining three previous maps2-4 and a new reference all-by-all binary interactome map. A greater proportion of interactions in our map are in the outer-complexome, in comparison to those found by affinity purification followed by mass spectrometry5-7 or in literature curated datasets8-11. In addition, recent advances in deep learning predictions of PPI structures12 mirror the existing experimentally resolved structures in being largely focused on the inner complexome and missing most interactions in the outer-complexome. Our new PPI network suggests that the outer-complexome contains considerably more PPIs than the inner-complexome, and integration with functional similarity networks13-15 reveals that interactions in the inner-complexome are highly detectable and correspond to pairs of proteins with high functional similarity, while proteins connected by more transient, harder-to-detect interactions in the outer-complexome, exhibit higher functional heterogeneity.

systems biology↗

bioRxiv2019

A reference map of the human protein interactome

Global insights into cellular organization and function require comprehensive understanding of interactome networks. Similar to how a reference genome sequence revolutionized human genetics, a reference map of the human interactome network is critical to fully understand genotype-phenotype relationships. Here we present the first human \"all-by-all\" binary reference interactome map, or \"HuRI\". With ~53,000 high-quality protein-protein interactions (PPIs), HuRI is approximately four times larger than the information curated from small-scale studies available in the literature. Integrating HuRI with genome, transcriptome and proteome data enables the study of cellular function within essentially any physiological or pathological cellular context. We demonstrate the use of HuRI in identifying specific subcellular roles of PPIs and protein function modulation via splicing during brain development. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI thus represents an unprecedented, systematic reference linking genomic variation to phenotypic outcomes.

systems biology↗