Biology subjects

Becker, T.

Publications and source records attributed to Becker, T..

At least 19 recordsLinked to original sources

bioRxiv2026

OFC-SV: Interpreting structural variants in African and Asian cohorts with non-syndromic orofacial clefts

OFC-SV is a web-based data portal designed to help interpret structural variants (SVs) in non-syndromic orofacial clefts genomic data published by The Gabriella Miller Kids First Pediatric Research Program. The portal offers a user-friendly way to explore 41 novel SV genes (of these 13 sharing regulatory perturbations already reported in the literature as SNV genes) potentially responsible for non-syndromic OFC (nsOFC) from a cohort of children of African and Asian ancestry. A salient feature of the portal is its unique ability to capture epigenomic disruptions and complex oligogenic interactions in visualized regulatory pathways, thus advancing the frontier of disease etiology through convenient translation of computational signals into biological interpretations.

bioinformatics↗

bioRxiv2026

Msp1-dependent extraction promotes ubiquitylation of translocation-stalled mitochondrial precursor proteins

The translocase of the outer membrane (TOM complex) imports more than 1,000 proteins into mitochondria. Clogging of the TOM pore with a precursor protein causes proteotoxic stress and eventually cell death. Two quality control pathways remove translocation-stalled precursor proteins. In the mitochondrial protein translocation-associated degradation (mitoTAD), Ubx2 recruits the cytosolic AAA-ATPase Cdc48 to clear precursor proteins from the TOM complex. In the mitochondrial compromised protein import response (mitoCPR), the stress-induced Cis1 recruits the AAA-ATPase Msp1 to Tom70. The role of Msp1 for the removal of mitochondrial precursor proteins remains unknown. Here, we demonstrate that parallel loss of Msp1 and Ubx2 strongly affects removal of precursor proteins and cell viability. Msp1 and Ubx2 bind independently of import stress and Cis1 to the TOM complex to remove a large variety of precursor proteins. Msp1-dependent extraction promotes ubiquitylation of precursor proteins, which in turn allows Ubx2-recruited Cdc48 to transfer the substrates to proteasomal degradation. We conclude that two AAA-ATPases cooperate in mitochondrial precursor quality control. Msp1-dependent extraction from the TOM complex facilitates precursor ubiquitylation and Cdc48-mediated transfer to proteasomal degradation.

molecular biology↗

bioRxiv2026

Baseline regulatory programs in larval and adult neural progenitors converge towards an injury-induced state after spinal cord injury

Regeneration after spinal cord injury requires progenitor cells to convert injury-associated signals into coordinated remodeling of gene regulatory programs. Mammalian spinal progenitors show limited neurogenic output after injury, whereas zebrafish regenerate spinal neurons and recover motor function. To investigate the regulatory changes that allow ependymo-radial glia (ERG) cells, the progenitor cells of the zebrafish spinal cord, to generate new neurons, we combined single-nucleus gene expression and chromatin accessibility profiling across embryonic, larval, and adult stages with topic-based gene regulatory network (GRN) inference. We found that larval and adult ERGs enter the injury response from distinct regulatory baselines: larval progenitors are characterized by a gliogenic program, whereas adult progenitors maintain a comparatively quiescent state. Following injury, both populations gradually change their baseline programs and shift towards a lesion-associated module marked by stress-responsive and chromatin-associated regulators, including jun, hmga1a, hmga2, ybx1, and foxj1a. The shift away from homeostatic states is supported by decreased expression of the Notch-associated regulators nuclear factor I A (nfia) and hey1 in larvae, while in adults, downregulation of the same nuclear factor and other TFs such as bhlhe41 is associated with quiescence exit. Pathway analysis showed stage-specific alterations after injury, characterized predominantly by extracellular signaling and cytoskeletal reorganization in larvae and by metabolic and translational remodeling in adults. Despite divergence from the homeostatic states, injury-induced larval and adult GRNs remain distinct from embryonic hERG regulatory programs. Thus, larval and adult progenitors follow different trajectories from their baselines towards a related lesion-reactive state, in which shared regeneration-associated features are acquired within respective contexts.

bioinformatics↗

bioRxiv2026

Diverse origins and transcriptional profiles of macrophages in a spinal lesion in zebrafish

The injury responses of tissue-resident macrophages in the CNS (microglia) and blood-derived macrophages (BDMs) play key roles in successful regeneration of the zebrafish spinal cord, but the origins and dynamic behaviours of these immune cells are not well characterized. Here, we find that microglia, labelled by the p2ry12:GFP reporter gene, migrate long-distance through neural tissue from the brain to the spinal lesion site, while BDMs, labelled by the mpeg1:mCherry reporter gene, migrate mainly from the caudal hematopoietic tissue to the lesion and back. Half of p2ry12:GFP-positive microglia co-express mpeg1:mCherry, while mpeg1:mCherry-positive BDMs are mostly p2ry12:GFP-negative. However, a BDM sub-population starts to express p2ry12:GFP in the lesion. This indicates heterogeneous and dynamic gene expression in macrophage populations. Gene expression profiling reveals several microglia-like and BDM-like clusters in the lesion with gene expression profiles related to proliferation, phagocytosis, pro- and anti-inflammatory phenotypes and distinct expression of regeneration-relevant genes. The most abundant cell cluster are densely-packed microglia-like cells in the lesion core, which express the novel marker g0s2, as well as phagocytosis-related genes. Hence, regenerative success of the zebrafish spinal cord is linked to a heterogeneous and dynamic response of microglia and BDM subpopulations.

neuroscience↗

bioRxiv2026

Spinal injury induces a stem cell-like progenitor state that promotes regenerative neurogenesis via clcf1 in zebrafish.

After spinal injury, zebrafish, in contrast to mammals, show regenerative neurogenesis, characterized by enhanced injury-induced proliferation of ependymo-radial glial cells (ERGs) and an increase in injury-induced generation of neurons from these progenitors. It is unclear whether regenerative neurogenesis simply recapitulates development or uses regeneration-specific mechanisms. Using scRNA-seq and in vivo validation we find a spinal injury-induced state in ERGs (iiERGs) in larval zebrafish. This cell state emerges mostly without proliferation and has stem cell characteristics, including weak expression of neurogenic genes and strong expression of stemness factors, such as lin28a. Expression of lin28a is not detectable during ongoing developmental neurogenesis. Following spinal cord lesion, lin28a disruption increases the numbers of ERGs undergoing neuronal differentiation and of newly-generated neurons, at the expense of proliferating ERGs and iiERGs. This supports a stemness-preserving role of lin28a in iiERGs. Importantly, iiERGs secrete growth factors, including the regeneration-specific cytokine clcf1, which depends in part on lin28a expression. Disruption of clcf1 signalling impairs spinal progenitor proliferation and injury-induced generation of new neurons, but does not affect the emergence of iiERGs. Over-expression of clcf1 is sufficient to augment neurogenesis in unlesioned animals without inducing the iiERG state, indicating that clcf1 acts as a generic growth factor. Hence, we describe an injury-specific stem cell-like ERG population that regulates regenerative neurogenesis by attenuating neuronal differentiation via lin28a and promoting progenitor proliferation via clcf1.

neuroscience↗

bioRxiv2026

Tachykinin neuropeptides are involved in axonal and synaptic differentiation of the pioneer motor axon in zebrafish

In contrast to many other developing systems, in which axon pathfinding and synaptogenesis are separated in time, the pioneering axon of the individually identifiable caudal primary motor neuron in embryonic zebrafish forms en passant synapses during its stereotypical ventral growth. How simultaneous synaptic differentiation and axon pathfinding are coordinated is not fully understood. Here we ask what the role of the tac1 gene, coding for the synaptic tachykinin neuropeptides, is in this unique axon differentiation process. The gene is expressed during axon outgrowth and its disruption results in increased branch length of CaP axons and subtle morphological defects of the pre-synapse. These abnormalities are accompanied by a robust [~]1.5-fold increase in motor neuron activity and in spontaneous early contractions in tac1-deficient embryos. Furthermore, pharmacological inhibition of the tachykinin receptor (Tacr1) leads to altered CaP axonal morphology, mimicking the axonal phenotype observed in tac1-deficient zebrafish. These findings suggest that tachykinin neuropeptides modulate formation and activity of en passant synapses and prevent aberrant axon branching during growth of zebrafish motor axons. HIGHLIGHTS- tac1 refines CaP primary motor axon development in zebrafish - Loss of tac1 disrupts presynaptic maturation at the horizontal myoseptum - tac1 mutants show elevated motor neuron activity and spontaneous contractions

neuroscience↗

bioRxiv2026

Super-resolution complexome of human mitochondria elucidates translocase, morphology and OXPHOS networks

Mitochondria function as cellular powerhouses and central hubs in metabolism, redox and stress reactions, signaling and apoptosis1-5. Defects of mitochondria lead to numerous human diseases1,6-8. The integration of mitochondrial proteins into complexes and networks is crucial for their function. Whereas the composition of the human mitochondrial proteome has been studied8,9, only limited information is available on the organization of the proteome into protein complexes and assemblies. Here we present a systematic mapping of the human mitochondrial complexome from HEK293T cells at super-resolution, resolving more than 7,000 abundance profile peaks of mitochondrial proteins. Proteins functioning in signaling, cell stress, protein biogenesis, turnover and membrane dynamics display particularly high complexities. High resolution and precise quantification enable discrimination between canonical constituents and non-stoichiometric regulatory interactors of the ATP synthase, major metabolite channels and import translocases. The complexome reveals membrane-spanning networks of protein insertase and morphology machinery, and co-assembly of protein import and export components at the major respiratory supercomplex, unraveling a multifunctional organization of mitochondrial machineries. This complexome represents a fully interactive resource for the systematic analysis of human mitochondrial machineries and interaction networks.

biochemistry↗

bioRxiv2026

The multistep quality control of mitochondrial β-barrel protein import

Mitochondrial {beta}-barrel proteins fulfill essential functions for cell viability including transport of proteins, ions and metabolites across the outer membrane. The translocase of the outer membrane (TOM complex) and the sorting and assembly machinery (SAM complex) transport these proteins into the outer membrane. Although {beta}-barrel proteins are essential for cell viability, the quality control mechanisms that monitor their import into the outer membrane remain unknown. We uncovered that Msp1 and Ubx2-recruited Cdc48 cooperate to remove a SAM-arrested Tom40 variant. Prior to degradation, the {beta}-barrel protein is deposited in cytosolic protein storages, termed MitoStores, to minimize accumulation of aberrant proteins in the cell. The cytosolic AAA ATPase Hsp104 disaggregates these proteins to facilitate their proteasomal degradation. Altogether, mitochondrial and cytosolic factors cooperate to degrade translocation-arrested mitochondrial {beta}-barrel proteins.

molecular biology↗

bioRxiv2026

Aberrant FICD-mediated AMPylation drives α-Synuclein pathology and overall protein dyshomeostasis in dopaminergic neurons in Parkinson's disease

BackgroundFilamentation induced by cAMP domain-containing protein (FICD) is an endoplasmic reticulum (ER)-resident adenylyltransferase that catalyzes protein AMPylation, a post-translational modification. Although FICD-mediated AMPylation has been linked to the fine-tuning of proteostasis and neuronal integrity, its role in neurodegenerative diseases characterized by protein dyshomeostasis remains unclear. Parkinsons disease (PD) is defined by dopaminergic neurodegeneration and aggregation of -synuclein (aSyn) as a consequence of impaired protein homeostasis. We therefore investigated whether dysregulated FICD-mediated AMPylation contributes to PD pathogenesis. MethodsWe combined analyses of human post-mortem PD brain tissue with complementary models, including midbrain dopaminergic neurons derived from human induced pluripotent stem cells (hiPSCs) of a PD patient carrying an SNCA gene duplication and its isogenic gene dosage-corrected control line, transgenic mouse models of synucleinopathy, and an aSyn-overexpressing H4 neuroglioma cell model. Genetic and pharmacological modulation of FICD activity was integrated with multi-proteomic approaches, including chemical proteomics-based AMPylation profiling, stable isotope labelling with amino acids in cell culture-based global protein turnover analysis, and whole-proteome profiling to identify AMPylation-associated molecular pathways. ResultsFICD was preferentially expressed in dopaminergic neurons and was upregulated in SNCA duplication PD patient-derived neurons, as well as in the basal ganglia of PD post-mortem brains and synucleinopathy mice. Despite this overall increase, the proportion of FICD-expressing dopaminergic neurons was reduced under PD conditions, suggesting selective vulnerability of dopaminergic neurons to FICD. Mechanistically, FICD selectively AMPylated lysosomal proteins, thereby linking AMPylation to the regulation of degradative pathways. Moreover, hyperactivation of FICD-induced AMPylation triggered ER stress, impaired lysosomal function, reduced protein turnover, and ultimately promoted aSyn aggregation and apoptotic cell death. Importantly, pharmacological inhibition of AMPylation reversed aSyn pathology and neurite degeneration in PD patient-derived neurons. ConclusionsWe identify the pathological relevance of FICD-mediated AMPylation in PD-related neurodegeneration and its contribution to aSyn aggregation through a bidirectional interplay with aSyn pathology. Our findings support FICD-mediated AMPylation as a defining molecular switch regulating intracellular protein homeostasis in PD and highlight the FICD-AMPylation pathway as a potential therapeutic target for restoring aSyn pathology and mitigating disease progression.

neuroscience↗

bioRxiv2026

A reparative neutrophil subpopulation promotes spinal cord regeneration in zebrafish by controlling macrophage inflammation via Il-4

In mammals, a dysregulated immune response is detrimental to spinal cord repair. In zebrafish, which are capable of spinal cord regeneration, the immune response promotes regeneration. Neutrophils are the first immune cells to arrive at a spinal cord injury site, but their role in successful regeneration is not fully understood. Here we show that ablating neutrophils, including a subpopulation that expresses the cytokine il4, increases expression of il1b (coding for Il-1{beta}) in macrophages/microglia and impairs anatomical and functional recovery after a spinal cord injury in larval zebrafish. Regeneration is fully rescued by over-expression of il4 alone or experimentally reducing Il-1{beta} levels. Disruption of il4 mimics the detrimental effect of neutrophil ablation for axonal regeneration and is also rescued by reducing Il-1{beta} levels. Hence, after spinal cord injury, a pro-regenerative neutrophil subpopulation promotes spinal cord regeneration in larval zebrafish by controlling expression of il1b in macrophages/microglia. For this neutrophil action, il4 expression is necessary and sufficient. HIGHLIGHTS- Neutrophil ablation impairs spinal cord repair in zebrafish - The neutrophil response can be replaced by reducing Il-1{beta} levels - A pro-regenerative subpopulation of neutrophils expresses il4 - il4 overexpression fully rescues effects of neutrophil ablation

neuroscience↗

bioRxiv2025

Substrate-induced assembly and functional mechanism of the bacterial membrane protein insertase SecYEG-YidC

The Sec translocon and the YidC/Oxa1-type insertases universally mediate biogenesis of -helical membrane proteins, but the molecular basis of their cooperation has remained disputed. Recent discoveries of multi-subunit insertases assembled at the back of the translocon in fungi and higher eukaryotes have raised the question about the architecture and mechanism of the putative bacterial ortholog SecYEG-YidC. Here, we combine cryogenic electron microscopy with cell-free protein synthesis to visualize biogenesis of SecYEG/YidC-dependent multipass membrane protein NuoK. We demonstrate that the nascent chain of NuoK does not enter the lateral gate of SecYEG, but crosses over the translocon towards its back side, whereto YidC is recruited in the nascent chain-dependent manner. The SecY-YidC interface promotes folding of the transmembrane helices prior their insertion, in agreement with thermodynamic principles of membrane protein folding. YidC forms extensive contacts with the nascent chain, suggesting its key role in the insertion event. Our data provide detailed insights on the insertase machinery, suggest the evolutionary conservation of the gate-independent insertion route, and offer an expanded view on membrane protein biogenesis.

biochemistry↗

bioRxiv2024

Macrophage crosstalk with neural progenitors and fibroblasts controls regenerative neurogenesis via Sema4ab after spinal cord injury in zebrafish

Zebrafish, in contrast to mammals, regenerate neurons after spinal cord injury, but little is known about the control mechanisms of this process. Here we use scRNA-seq and in vivo experiments to show that sema4ab, mainly expressed by lesion-reactive microglia, attenuates regenerative neurogenesis by changing the complex lesion environment. After spinal injury, disruption of sema4ab doubles the number of newly generated progenitor cells and neurons but attenuates axon regrowth and recovery of swimming function. Disruption of the plxnb1a/b receptors, selectively expressed by neural progenitor cells, increases regenerative neurogenesis. In addition, disruption of sema4ab alters activation state and cytokine expression of microglia, such that fibroblasts increase expression of the cytokine tgfb3, which strongly promotes regenerative neurogenesis. Hence, sema4ab in microglia attenuates regenerative neurogenesis in multiple ways, likely directly through plxnb1a/b receptors and indirectly, by controlling the inflammatory milieu and tgfb3 levels. Targeting Sema4A-dependent signalling in non-regenerating vertebrates may be a future strategy to improve regenerative outcomes. HIGHLIGHTS- Microglia suppress pro-regenerative fibroblast signalling in a spinal injury site - Fibroblasts promote regenerative neurogenesis via Tgfb3 signalling - sema4ab promotes microglia activation state after spinal injury - scRNA-seq reveals full complement of sema4ab-dependent changes on different cell types during repair of a spinal lesion site

neuroscience↗

bioRxiv2024

The RNA helicase HrpA rescues collided ribosomes in E. coli

Although many antibiotics inhibit bacterial ribosomes, loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryo-EM structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA, such that by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.

molecular biology↗

bioRxiv2024

Temperature drives seagrass recovery across the Western North Atlantic

Climate-driven shifts in herbivores, temperature and nutrient runoff threaten coastal ecosystem resilience. However, our understanding of ecological resilience, particularly for foundation species, remains limited due to a rarity of field experiments that are conducted across appropriate spatial and temporal scales and that investigate multiple stressors. This study aimed to evaluate the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and how this is impacted by environmental gradients in (a)biotic factors. We assessed the resilience (i.e. recovery) of turtlegrass to a simulated disturbance (complete above- and belowground biomass removal) over a year. Contrary to temperate studies, higher temperature generally enhanced seagrass recovery. While nutrients and light availability had minimal impact, combined high levels of nutrients and herbivore grazing (meso and megaherbivore) reduced aboveground recovery. Our results suggest that the resilience of some tropical species, especially in cooler subtropical waters, may initially increase with warming.

ecology↗

bioRxiv2024

Wound closure after brain injury relies on force generation by microglia in zebrafish

Wound closure after a brain injury is critical for tissue restoration but this process is still not well characterised at the tissue level. We use live observation of wound closure in larval zebrafish after inflicting a stab wound to the brain. We demonstrate that the wound closes in the first 24 hours after injury by global tissue contraction. Microglia accumulation at the point of tissue convergence precedes wound closure and computational modelling of this process indicates that physical traction by microglia could lead to wound closure. Indeed, genetically or pharmacologically depleting microglia leads to defective tissue repair. Live observations indicate centripetal deformation of astrocytic processes contacted by migrating microglia. Severing such contacts leads to retraction of cellular processes, indicating tension. Weakening tension by disrupting the F-actin stabilising gene lcp1 in microglial cells, leads to failure of wound closure. Therefore, we propose a previously unidentified mechanism of brain repair in which microglia has an essential role in contracting spared tissue. Understanding the mechanical role of microglia will support advances in traumatic brain injury therapies Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/597300v3_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@112aorg.highwire.dtl.DTLVardef@6712c4org.highwire.dtl.DTLVardef@101179borg.highwire.dtl.DTLVardef@b4ecb6_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

C9ORF72 deficiency results in degeneration of the zebrafish retina in vivo

G4C2 Hexanucleotide repeat expansions within the gene C9ORF72 are the most common cause of the neurodegenerative diseases Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). This disease-causing expansion leads to a reduction in C9ORF72 expression levels in patients, suggesting haploinsufficiency could contribute to disease. To further understand the consequences of C9ORF72 deficiency in vivo, we generated a c9orf72 mutant zebrafish line. Analysis of the spinal cord revealed no appreciable neurodegenerative pathology such as loss of motor neurons, or increased levels of neuroinflammation. However, detailed examination of c9orf72-/- retinas showed prominent neurodegenerative features, including a decrease in retinal thickness, gliosis, and an overall reduction in neurons of all subtypes. Structurally, analysis of rod and cone cells within the photoreceptor layer showed a disturbance in the outer cells of the retina and rhodopsin mis-localisation from rod outer segments to their cell bodies and synaptic endings. Thus, C9ORF72 may play a previously unappreciated role in retinal homeostasis and suggests C9ORF72 deficiency can induce tissue specific neuronal loss.

neuroscience↗

bioRxiv2023

The human cytomegalovirus-encoded pUS28 antagonizes CD4+ T-cell recognition by targeting CIITA

Human cytomegalovirus (HCMV) is a relevant pathogen especially for individuals with impaired immunity. Harnessing potent immune antagonists, HCMV circumvents sterile immunity. Given that HCMV prevents the upregulation of human leukocyte antigen (HLA)-DP and HLA-DR, we screened a library of HCMV genes by co-expression with the HLA class II (HLA-II)-inducing transcription coordinator class II transactivator (CIITA). We identified the latency regulator pUS28 as interaction factor and potent viral antagonist of CIITA-driven expression of CD74, HLA-DR, HLA-DM, HLA-DQ, and HLA-DP. Both wt-pUS28 and a mutant incapable to induce G-protein-coupled signaling (R129A), but not a mutant lacking the C-terminus, drastically reduced the CIITA protein abundance post-transcriptionally. While control CD4+ T cells from HCMV-seropositive individuals vigorously responded to CIITA-expressing cells decorated with HCMV antigens, pUS28 expression was sufficient to inhibit HLA-II induction and immune recognition by HCMV-specific CD4+ T cells. Our data uncover a mechanism employed by HCMV to evade HLA-II-mediated recognition by CD4+ T cells.

immunology↗

bioRxiv2023

Ribosomal A-site interactions with near-cognate tRNAs drive stop codon readthrough

tRNAs serve as a dictionary for the ribosome translating the genetic message from mRNA into a polypeptide chain. Besides this canonical role, tRNAs are involved in other processes like programmed stop codon readthrough (SC-RT). There, tRNAs with near-cognate anticodons to stop codons must outcompete release factors and incorporate into the ribosomal decoding center to prevent termination and allow translation to continue. However, not all near-cognate tRNAs promote efficient SC-RT. Here, we demonstrate that those that do, establish critical contacts between their anticodon stem (AS) and ribosomal proteins Rps30/eS30 and Rps25/eS25 forming the decoding site. Unexpectedly, the length and well-defined nature of the AS determines the strength of these contacts, which is reflected in organisms with reassigned stop codons. These findings open a new direction in tRNA biology that should facilitate the design of artificial tRNAs with specifically altered decoding abilities.

molecular biology↗