Biology subjects

Schmid, M.

Publications and source records attributed to Schmid, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Evolutionary signatures of self-incompatibility genes in grasses: high diversity, trans-generic polymorphism and co-evolution

In many flowering plants, self-incompatibility (SI) is a genetically controlled recognition system that prevents self-fertilization, thereby promoting outcrossing and maintaining genetic diversity within populations. The gametophytic SI system in grasses (Poaceae) is governed by two multiallelic loci, S and Z, each locus comprising of three genes governing the initial recognition between pollen and stigma. Identifying these genes establishes the molecular basis of SI in grasses, but how its unique two-locus architecture has shaped the evolution of the underlying loci and recognition genes remains largely unexplored. Here, we report targeted sequence capture of SI genes in 362 genotypes across nine forage grass species, revealing extensive allelic richness and sequence diversity. The SI genes exhibited elevated nucleotide diversity ({pi}) (0.134 < {pi} < 0.403) and great amino acid sequence divergence, ranging between 48.2-58.0% for the female determinants (sS and sZ) and 66.5-83.4% for the male determinants (SI-DUF247). The SI-DUF247 proteins also displayed trans-generic polymorphism, indicating that alleles predate speciation. Phylogenetic analysis of SI determinants showed congruence at both S- and Z-locus, consistent with co-evolution of recognition partners. Our results demonstrate that the unique two-locus SI system in grasses shares evolutionary characteristics with other SI systems, suggesting that their reproductive function is shaping their evolution. These findings also indicate that the grass SI loci are under long-term balancing selection to maintain recognition specificity while creating sufficient allelic diversity. Our study provides comprehensive sequence resources for SI genes and new insights into the evolution of the unique two-locus SI system of grasses.

plant biology↗

bioRxiv2026

GenomeCompendium: A database for the integrated analysis of repeats, assembly quality and functional content of complete prokaryotic genomes

Microorganisms hold great promise for urgent global needs such as increasing sustainable agricultural production while reducing chemical fertilizer and pesticide use or providing novel classes of antimicrobials/therapeutics. Moving from analyzing microbiome composition to applying synthetic communities and studying their functions requires access to isolates and complete genome sequences. By spanning the frequent repeats, long-read sequencing can resolve complex prokaryotic genomes, yet error-prone short-read assemblies dominate. We here release the GenomeCompendium, a public database and interactive analysis tool for complete prokaryotic genomes (https://genome-compendium.com/). Using NCBI RefSeq (~47,000) and GenBank (~13,000) genomes, we integrated available metadata, GTDB taxonomy and computed features including repeat classes and gene content screening, intragenomic 16S rRNA sequence identity, and biosynthetic gene cluster co-occurrences. Evaluating repeat content and assembly complexity metrics, we identify taxonomic ranks dominated by difficult-to-assemble genomes and show that complex, repeat-rich genomes are more common than previously estimated. By mining metadata, our quality control flags 6.3% of RefSeq assemblies as potentially erroneous or incomplete. As valuable reference for data mining and to track taxonomic coverage, the GenomeCompendium links ~90 features across genomes, offers downloadable reports and -as unique features- pre-computed proteogenomics databases to improve genome annotations of RefSeq strains and the ability to analyze any uploaded prokaryotic genome.

genomics↗

bioRxiv2026

Nemo2.4: fast and accurate quantitative genetics forward-time simulations

We present Nemo 2.4, an advanced forward-time individual-based simulation framework designed to model the complex eco-evolutionary dynamics and genetic basis of quantitative traits. This tool addresses current challenges in evolutionary quantitative genetics by providing unprecedented flexibility and computational efficiency. Nemo 2.4s modular architecture allows researchers to design custom life cycles by combining specialized Life Cycle Event (LCE) modules, from reproduction and dispersal to selection, crossing, and phenotype expression. The software supports diverse population models, including both Wright-Fisher (WF) and non-WF dynamics, spatially explicit models, and varying demography. Nemo 2.4 handles a wide range of genetic architectures, including both multi-allelic Quantitative Trait Loci (QTL) for general trait studies, and dense di-allelic Quantitative Trait Nucleotides (QTN) implemented with highly optimized bit-wise data structures. Crucially, it allows the simulation of QTNs on comprehensive genetic maps that incorporate other genetic elements, providing genomic-scale resolution. Key biological complexities are integrated natively: the model accommodates modular pleiotropy, dominance, and pairwise epistasis across multiple traits, facilitating the study of complex genotype-phenotype mappings. Furthermore, Nemo 2.4 models phenotypic plasticity through reaction norms and incorporates underlying liability thresholds, enabling the simulation of environmental influences on trait evolution with various forms of selection (e.g., Gaussian, linear, truncation). Due to its compiled design and memory-efficient data representations for large numbers of loci, Nemo provides a robust platform for running high-throughput simulations critical for testing theoretical predictions in polygenic adaptation and understanding evolutionary responses to changing environments.

evolutionary biology↗

bioRxiv2026

Anthropogenic-driven loss of an adaptive radiation reduces thermal response diversity

Biodiversity is predicted to stabilize ecosystems if species have different environmental responses. How this response diversity is shaped by ecological and evolutionary processes remains poorly understood. We determine the drivers of thermal response diversity of 16 Swiss peri-alpine lake-fish communities. We report the first evidence that evolutionary diversification of lineages through adaptive radiation can increase the response diversity of an ecosystem. In-situ diversification increases response diversity in the cold-deep lake environment, but non-endemic and non-native species contributed only weakly to response diversity. The loss of endemic species during historical anthropogenic eutrophication led to a negative legacy on present thermal response diversity in cold and deep lake strata. Overall, the interplay of evolutionary diversification, ecological assembly and anthropogenic impacts drives variation in response diversity. Conserving and restoring processes that generate diversity may help maintain ecosystem stability beyond the Anthropocene.

ecology↗

bioRxiv2026

Activation of the bridge-like lipid transfer protein Atg2 by Atg1-mediated phosphorylation

Bridge-like lipid transfer proteins (BLTPs) have emerged as major contributors to lipid flux and thus cellular organization. BLTPs harbor a hydrophobic channel connecting two membranes to enable the bulk flow of lipids between them. The regulation of BLTPs is incompletely understood. Employing in vitro reconstitution, molecular dynamics simulations, and cell biology, we discovered that the BLTP Atg2, which mediates lipid transfer during autophagosome biogenesis, is activated by the Atg1 kinase. Atg1 phosphorylates two serines in the N-terminal region of Atg2. This triggers membrane binding and opening of the channel to enable lipid transfer. The Atg1 kinase complex is localized to the endoplasmic reticulum through binding of its Atg13 subunit to the VAP protein Scs2. Phosphorylated Atg2 can subsequently establish contacts with Atg9 vesicles. Our study delineates a pathway for the Atg1 kinase mediated activation of the BLTP Atg2 to establish membrane contact site formation and lipid flux.

cell biology↗

bioRxiv2026

Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics

Structural alphabets have transformed protein phylogenetics by enabling sequence-style alignment and maximum-likelihood inference to be applied directly to structural data. However, a coordinate-explicit alphabet, in which character states are derived from three-dimensional atomic positions, encodes not only evolutionary signal but also the conformational variability inherent to protein structure. This source of noise has not previously been quantified in a phylogenetic context, and no framework exists for comparing alphabets with respect to their conformational sensitivity. Here, we introduce the Normalised Noise Index (NNI), a Shannon entropy-based metric for quantifying conformational sensitivity in structural alphabet encodings, and apply it alongside ensemble-wide Robinson-Foulds (RF) variance as a framework for characterising the impact of conformational noise on phylogenetic inference. Across 3,749 single-chain NMR ensembles from the Protein Data Bank, we show that 3Di character variability is a pervasive feature of experimentally observed conformational spread, with NNI negatively correlated with within-ensemble structural stability. A 100 ns molecular dynamics simulation of myoglobin confirmed that thermal fluctuations alone are sufficient to generate comparable 3Di character variation and, in 2.9% of cases, to redirect maximum-likelihood tree search away from the expected topology in a 4-taxon globin benchmark with independently established relationships. Exhaustive enumeration of 4,800 conformational replicates across three NMR ensembles revealed that topological variance under 3Di encoding is approximately 1.7-fold greater than under structural distance, based on 11,517,600 pairwise RF comparisons, a source of uncertainty invisible to standard bootstrap analysis. By contrast, TEA, a sequence-derived structure-aware alphabet inferred from ESM-2 embeddings rather than directly from atomic coordinates, is insulated from conformational sampling by construction and yields zero topological variance across all conformational replicates, serving here as a noise-insulated reference rather than a proposed replacement for 3Di. Together, these results demonstrate that alphabet choice is a methodological variable in structural phylogenetics, and that the NNI metric and RF variance frame-work introduced here provide a practical basis for principled noise characterisation as new structural alphabets continue to emerge.

bioinformatics↗

bioRxiv2026

Intrinsic disorder in elicitin-like effectors: Molecular shields in the arms race of biotrophic pathogens

Plant pathogens establish colonization through effector secretion to modulate host immune responses. Within bacterial effectors intrinsically disordered regions (IDRs) contribute to diverse functions and pathogenicity, but their role in effectors of phytopathogenic oomycetes remains poorly understood. Here, analysis of oomycete secretomes across lifestyles reveal widespread intrinsic disorder in secreted proteins, particularly in apoplastic elicitin and elicitin-like effectors (ELLs). Combining in vitro and in planta experiments, we show that IDRs in ELLs from the biotrophic pathogen Albugo candida reduce immune recognition, consistent with an IDR-mediated shielding mechanism. This function is transferable, as fusion of an ELL-derived IDR to the immunogenic elicitin INF1 from Phytophthora infestans abolishes its recognition. These findings identify intrinsic disorder as a functional feature of apoplastic effectors that modulates host detection and promotes pathogen fitness. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/717489v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1363e05org.highwire.dtl.DTLVardef@21f34dorg.highwire.dtl.DTLVardef@ec6e5borg.highwire.dtl.DTLVardef@41327b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Periweaning diet-induced activation of an IFNγ-mediated regulatory circuit promotes the homeostasis of cytotoxic CD8+ T Cells

Balancing pathogen defence with maintaining tolerance to environmental antigens, such as food or commensals, in neonates is essential for survival and the establishment of life-long immune homeostasis. Instructed by environmental signals type 1 conventional dendritic cells (cDC1) drive either T cell tolerance or immunity. Here, we uncover an interferon (IFN)-{gamma}-driven regulatory circuit in early life that relays dietary cues to spleen cDC1. Loss-of-function demonstrates that IFN{gamma}-mediated STAT1-signaling induces an immunogenic maturation program in spleen cDC1 that instructs cDC1 to expand effector memory CD8 T cells. This program emerges during weaning, when IFN{gamma} production from lymphocytes rises, it occurs in germ-free mice and remains responsive to dietary intervention in adult mice. During the transition from breastfeeding to solid food at weaning, this circuit relays dietary information to spleen cDC1 to shape the effector phenotype of food-antigen specific CD8+ T cells in a feed-forward manner, allowing cDC1 to recalibrate the T cell pool at the moment of nutritional independence.

immunology↗

bioRxiv2025

Systemic and local regulation of root growth by vascular trehalose 6-phosphate is correlated with re-allocation of primary metabolites between shoots and roots

Trehalose 6-phoshpate (Tre6P) is a key signalling molecule that reflects carbon status and integrates it with developmental decision making. Tre6P has been demonstrated to regulate various developmental processes, including vegetative growth, shoot branching, flowering, and root branching. Here, we investigate how vasculature-derived Tre6P influences root system architecture by expressing heterologous Tre6P synthase (TPS) or Tre6P phosphatase (TPP) specifically in the plant vasculature. Plants with elevated vascular-derived Tre6P levels had smaller root systems, reduced sucrose levels, and lower root metabolite levels, whereas vascular TPP overexpression had the opposite effect. Using reciprocal grafting experiments, we identified shoot-derived vascular Tre6P to be the main driver of these systemic responses. In lines with increased Tre6P in the shoot vasculature, the shoot-to-root metabolite ratios were consistently increased, indicating that Tre6P modulates metabolite allocation and utilization to balance carbon partitioning between shoot and root growth. Our data further suggest that vascular Tre6P contributed to optimizing the carbon-to-nitrogen ratio to support growth and fitness. Besides this systemic function, this study shows that root-derived Tre6P also plays a critical local role in modulating root development. Collectively, our results demonstrate that Tre6P in the vasculature functions both systemically and locally to coordinate metabolic status with root growth and architecture.

plant biology↗

bioRxiv2025

Retargeted adenoviruses for local IgA and CD47 blocker production as a novel cancer therapy

Despite advances in IgG-based cancer immunotherapy, challenges remain in effectively engaging innate immune responses against solid tumors. Here, IgA antibodies hold promise due to their ability to activate neutrophils and macrophages. We present a novel retargeted adenovirus-mediated approach that transforms cancer cells into "biofactories" for localized production of monomeric or dimeric IgA antibodies and a CD47 blocker to potentiate the effect of IgA antibodies. With our approach tumor cells effectively produced IgA antibodies against tumor antigens such as EGFR or EpCAM and a soluble SIRP-Fc fusion protein, which blocks the CD47-SIRP axis. In a perfused tumor-on-a-chip model, locally produced IgA triggered neutrophil- and macrophage-mediated tumor cell killing, further potentiated by SIRP-Fc co-production. In FcRI-transgenic, tumor-bearing mice, intratumoral adenoviral injection induced strong local IgA and SIRP-Fc expression, immune cell infiltration, and more than 50% tumor volume reduction after a single treatment. We found that dimeric IgA exerts stronger effects than monomeric IgA, which is of particular interest since dimeric IgA necessitates a local production approach. Together, these results demonstrate that adenovirus-mediated, tumor-restricted delivery of IgA antibodies and CD47 blockade effectively engages innate immune mechanisms, providing a promising new avenue to enhance cancer immunotherapy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/686998v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@183dd88org.highwire.dtl.DTLVardef@452624org.highwire.dtl.DTLVardef@1cb10e8org.highwire.dtl.DTLVardef@c2fa85_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Plastic germination, temporal niche partitioning, and emergent assortative mating in annual plants

Temporal fluctuations in environmental conditions can promote coexistence via the storage effect, which requires a mechanism buffering different variants during adverse periods. This mechanism readily occurs in annual plants whose seeds do not necessarily germinate each year but instead remain dormant in a seed bank. Yet, how plasticity in germination timing affects genetic diversification and ecological speciation under temporally varying conditions remains poorly understood. Here, we use mathematical modeling and individual-based simulations to investigate the joint evolution of a combination of traits controlling plastic seed germination and plant fecundity under interannual environmental fluctuations. We show that adaptive plasticity in germination readily evolves via a genetic association between seed and plant traits, allowing seeds to germinate preferentially in years favorable for their subsequent growth and reproduction. Such adaptive plasticity enhances the storage effect and promotes genetic divergence among different morphs specialized to distinct yearly conditions. Because these morphs germinate preferentially in different years, plastic germination indirectly generates temporal assortative mating, thereby maintaining genetic associations among seed and plant traits despite the absence of physical linkage between loci controlling these traits. This temporal assortative mating ultimately leads to reproductive isolation between morphs, thus laying the foundation for ecological speciation. Our findings show that adaptive plasticity and genetic diversification are not mutually exclusive but can interact synergistically to enhance biodiversity.

evolutionary biology↗

bioRxiv2025

Post-translational modifications of microtubules are crucial for malaria parasite transmission

Microtubules, composed of - and {beta}-tubulin polymers, are essential components of the eukaryotic cytoskeleton. They maintain cellular shape and structural integrity and play critical roles in cell division and in intracellular vesicular transport. In Plasmodium, the parasite that causes malaria, nuclear replication during the liver stage is among the fastest known in eukaryotic cells and relies heavily on microtubules for DNA segregation and cytoskeletal organization. Despite their importance, the role of microtubules in liver stage development remains largely unexplored. Here, we investigated microtubule dynamics during liver stage development using a combination of cell and molecular biology techniques, expansion microscopy, and live-cell imaging. By employing antibodies specific for -tubulin post-translational modifications (PTMs), we found that the Plasmodium sporozoites subpellicular microtubules (SSPM) persist during liver infection, giving rise to liver stage parasite microtubule bundles (LSPMB). These LSPMB form multimeric tubulin structures within hepatocytes and are redistributed to the hemi-spindle poles of parasite nuclei during schizogony. Deletion of the C-terminal region encompassing all known Plasmodium -tubulin PTM sites prevented sporozoite migration from the mosquito midgut to the salivary glands, effectively blocking parasite transmission. Using Plasmodium microtubule-specific depolymerisation drugs, we found that while LSPMB are stable in sporozoites, they exhibit dynamic behavior during hepatocyte infection. Given the regulatory role of PTMs in microtubule dynamics, we generated parasite mutants by substituting and deleting key -tubulin C-terminal residues involved in PTMs. Substitution of the polyglutamylation site with alanine and deletion of the C-terminal tyrosination/detyrosination motifs impaired parasite growth during liver infection. Together, our findings reveal extensive microtubule remodeling during liver stage development and establish -tubulin C-terminal modifications as critical regulators of both intracellular development and parasite transmission of Plasmodium parasites.

cell biology↗

bioRxiv2025

Disrupted Forward Connectivity in Parieto-temporal Network Impairs Memory Performance in Alzheimer's Disease

Alzheimers disease (AD) is characterised by the accumulation of beta-amyloid (A{beta}) and tau proteins, leading to neurodegeneration and cognitive decline. While A{beta} and tau are known to disrupt synaptic function, the mechanisms linking these molecular pathologies to network-level dysfunction and memory impairment remain poorly understood. Here we investigated the effects of A{beta} and tau pathology (CSF A{beta}42/40 ratio and tau phosphorylated at position 181, p-tau-181, respectively) on effective connectivity (EC) related to memory encoding, which may constitute a link between synaptic pathology and cognitive outcomes. Functional magnetic resonance imaging (fMRI) during visual memory encoding was acquired from participants of the multicentric DZNE Longitudinal Cognitive Impairment and Dementia Study (DELCODE), including 203 cognitively normal older participants (CN) as well as individuals with subjective cognitive decline (SCD; N = 204), mild cognitive impairment (MCI; N = 65), and early dementia due to AD (DAT; N = 21). EC was assessed by applying Dynamic causal modelling (DCM) to the fMRI data, using brain regions previously implicated in memory-encoding: the parahippocampal place area (PPA), the hippocampus (HC) and the precuneus (PCU). Disruptions in forward connectivity from the PPA to the HC and PCU were associated with both memory impairment and indices of AD pathology. Specifically, reduced excitatory EC from the PPA to the HC was associated with higher p-tau-181 levels and correlated with poorer memory performance. Diminished inhibitory EC from the PPA to the PCU was driven by both tau and amyloid pathology and was likewise linked to memory decline. Our findings suggest that disrupted forward connectivity within the temporo-parietal memory network constitutes a candidate mechanism mediating the relationship between molecular pathology and cognitive dysfunction.

neuroscience↗

bioRxiv2025

ReCycled: A Tool to Reset the Start of Circular Bacterial Chromosomes

Summary (two sentences)For many publicly available bacterial genomes the chromosome start is not set at the replication initiation protein. This is a burden for comparative genomics studies as the synteny between such genomes cannot readily be assessed. Here, we present ReCycled, a tool for identifying and resetting the start of circular bacterial chromosomes. Availability and implementationFreely available on GitHub at https://github.com/Freevini/ReCycled under the GPL-3.0 license. Runs on all tested GNU/Linux systems. ContactVincent Somerville, vincent@somerville.earth Supplementary InformationThe analyses, scripts and data to test the different pipelines are deposited online on zenodo (10.5281/zenodo.15170502).

bioinformatics↗

bioRxiv2025

Transcriptional Dynamics and Chromatin Accessibility in the Regulation of Shade-Responsive Genes in Arabidopsis

Open chromatin regions host DNA regulatory motifs that are accessible to transcription factors and the transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio (LRFR). Under shade, phytochromes become inactive, enabling PHYTOCHROME INTERACTING FACTORs (PIFs), particularly PIF7, to promote genome-wide reprogramming essential for LRFR responses. An initial strong and fast regulation of shade-responsive genes is followed by attenuation of this response under prolonged shade. We wanted to determine whether the transcriptional response to shade depends on chromatin accessibility. For this, we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. We found that PIF7 binding sites were accessible for most early target genes before LRFR treatment. The transcription pattern of most acute shade-responsive genes correlated with a rapid increase in PIF levels and chromatin association at 1h, and its decrease at 25h of shade exposure. For a small subset of acutely responding genes, PIFs also modulate chromatin accessibility at their binding sites early and/or late in the response to shade. Our results suggest that in seedlings a state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in PIF stability and gene occupancy, accompanied by changes in chromatin accessibility in a minority of genes.

plant biology↗

bioRxiv2024

Time and temperature-resolved transcriptomic analysis of Arabidopsis splicing-related mutants

Temperature plays a crucial role in plant growth and development, influencing numerous physiological processes throughout the plant life cycle. Ambient temperature fluctuations can significantly affect transcriptomic adjustments, which are essential for plants to adapt to ever-changing environmental conditions. Despite the known impacts of extreme temperatures on plant physiology, there remains a knowledge gap regarding the specific effects of moderate changes in ambient temperatures on transcriptomic responses. This study employs strand-specific mRNA sequencing (RNA-seq) to assess how different splicing-related mutants respond to varying ambient temperatures, providing a valuable resource to the research community. Analysis of our time-resolved temperature-regulated alternative RNA splicing data reveals that common and exclusive use of the splicing machinery plays pivotal roles in thermoresponsive growth. Furthermore, our analyses demonstrate that moderate temperature changes are translated into widespread transcriptomic responses, including adjustments of the circadian clock and significant splicing changes in light and temperature genes. These results highlight the importance of these particular signaling pathways in adapting to new temperature regimes and suggest future experiments to study the role of alternative RNA splicing in temperature adaptation. Taken together, our results provide insights regarding the role of RNA splicing in plant responses to ambient temperature changes, highlighting the biological relevance of transcriptomic adjustments in enhancing plant resilience and adaptation to climate variability. SIGNIFICANCE STATEMENT- This is the first comprehensive study on how mutants involved in multiple steps of the splicing process modulate splicing activity in response to low and high ambient temperature changes. - We assessed early and acclimated transcriptomic responses and created a valuable resource to investigate the biological outputs.

plant biology↗

bioRxiv2024

Dysfunction of the episodic memory network in the Alzheimer's disease cascade

Alzheimers disease (AD) is a major cause of dementia and cognitive decline. Here we assessed how episodic memory circuit dysfunction, a hallmark of AD, is related to the longitudinal cascade of AD biomarkers, neurodegeneration and cognition using data from the DZNE Longitudinal Cognitive Impairment and Dementia study. This data set is unique by including over 1000 longitudinal functional magnetic resonance imaging (fMRI) measurements during episodic memory encoding. We leveraged a disease progression model (DPM) to obtain AD progression scores. Voxel-wise analyses revealed widespread loss of deactivation (hyperactivation) and activation (hypoactivation) with increasing disease stage. Hyperactivation trajectories were nonlinear and visually preceded trajectories of cognition. Overall, hyperactivation was independently associated with co-occurrence of amyloid- and tau-positivity and neurodegeneration, suggesting synaptic dysfunction and neurodegeneration as two independent drives of cognitive decline. Our results therefore provide evidence for a critical time window in which pharmacological treatments targeting the synapse may improve cognition.

neuroscience↗

bioRxiv2024

An ALPK3 truncation variant causing autosomal dominant hypertrophic cardiomyopathy is partially rescued by mavacamten

The ALPK3 gene encodes alpha-protein kinase 3, a cardiac pseudo-kinase of unknown function. Heterozygous truncating variants (ALPK3tv) can cause dominant adult-onset Hypertrophic Cardiomyopathy (HCM). Here we confirm an excess of ALPK3tv in sarcomere-gene negative HCM patients. Moreover, we generated a novel knock-in mouse model carrying an ALPK3tv (K201X). Homozygous animals displayed hypertrophy and systolic dysfunction. Heterozygous animals demonstrated no obvious baseline; however, they had an aggravated hypertrophic response upon chronic adrenergic challenge. Isolated cardiomyocytes from heterozygous and homozygous mice showed reduced basal sarcomere length with prolonged relaxation, whilst calcium transients showed increased diastolic calcium levels and prolonged re-uptake. We also observed reduced fractional shortening. Protein kinase A-mediated phosphorylation, including that of cardiac troponin I, was significantly decreased. In agreement with the cellular HCM phenotype, reduced ratios of myosin heads in the super-relaxed state were measured. Contractile and calcium handling defects were partly corrected by treatment with mavacamten, a novel myosin inhibitor. For the first time with a non-sarcomere HCM variant, we have demonstrated hallmark changes in cardiac contractility and calcium handling, some resembling sarcomere-positive HCM, while others are distinct and DCM-like. Mavacamten is able to partially rescue the cellular phenotype, hence could be beneficial to HCM patients with ALPK3tv.

genetics↗