Biology subjects

Schmitt, J.

Publications and source records attributed to Schmitt, J..

15 recordsLinked to original sources

bioRxiv2026

A Cell-Based Assay to Categorize Variants of Human Succinate Semialdehyde Dehydrogenase Associated with Autism Spectrum Disorder

Many genes are implicated in autism spectrum disorder (ASD) as a result of sequencing the genomes of individuals with ASD, however in most cases it remains unclear which genes are playing causative roles. ALDH5A1, which encodes the enzyme succinate semialdehyde dehydrogenase (SSADH), an important regulator of GABA metabolism, is causative in the syndrome SSADH deficiency and is also implicated in ASD. However, it is unknown how variants found in ASD affect SSADH function. We developed a yeast growth assay that models SSADH deficiency to quantify the functional impact of seven ALDH5A1 variants found in ASD. In this assay, expression of human ALDH5A1 partially complemented the growth defect caused by deletion of the ALDH5A1 ortholog UGA2. Using growth rate measurements, we calculated functional scores for 27 variants divided into calibration and ASD test variant groups. Functional scores for benign and pathogenic calibration variants segregated accordingly, validating the assay, while ASD variants displayed a range of activities from complete loss to normal function. Comparisons with published enzymatic assays and computational predictions showed broad agreement, while also identifying some limitations of these approaches. SUMMARY STATEMENTWe introduce a simple yeast assay to measure how autism-linked gene variants in ALDH5A1, which encodes the enzyme succinate semialdehyde dehydrogenase, affect its function, helping clarifying its role in autism.

neuroscience↗

bioRxiv2025

Structural basis for co-translational assembly of homo-oligomeric proteins

The efficient formation of protein complexes is essential for cellular function. Across all kingdoms of life, protein complexes frequently assemble co-translationally, either when one subunit is fully synthesized before interaction with nascent partner subunits (co-post) or when multiple nascent subunits interact co-translationally (co-co), with homomeric proteins particularly enriched among co-co assembling complexes. However, it is unknown whether co-co assembly of homomers occurs on the same mRNA in cis or across neighbouring mRNAs in trans, and how ribosomes spatially organize to enable co-co assembly. Using E. coli homodimeric protein PheA as a proof-of-concept model, we show by ribosome profiling and cryo-EM structural analysis that it employs the co-co assembly route. Co-co assembly of PheA is facilitated by the proximity of polypeptide exit tunnels, but does not rely on fixed ribosomal orientations. Surprisingly, PheA was identified as an exceptional candidate where trans-assembly is potentially the primary mode of PheA co-co assembly, generating large polysomal networks for PheA synthesis. Cis-assembly of PheA was less frequent and occurred mainly between non-adjacent ribosomes on the mRNA due to spatial restraints imposed by the arrangement of directly neighbouring ribosomes in polysomes. These findings reveal fundamental principles of how cells structurally organise fast and efficient co-translational protein complex assembly.

molecular biology↗

bioRxiv2025

Continuous theta-burst stimulation of the ventromedial prefrontal cortex reduces Pavlovian go-invigoration and enhances thalamo-striatal reward prediction error signals

The ventromedial prefrontal cortex (vmPFC) represents value, i.e. whether environmental cues are good or bad. Rewarding cue value is aligned with a tendency to act or to inhibit in case of potential punishment, a so-called Pavlovian Bias. Value-related vmPFC activation may therefore impact Pavlovian bias. However, it remains unknown how the activity in the vmPFC modulates the Pavlovian bias. Thus, we applied continuous theta-burst stimulation (cTBS), a non-invasive protocol that transiently reduces cortical excitability, over the vmPFC in a single-blinded, between-subject study. 90 healthy adults performed a motivational Go/NoGo learning task during fMRI after receiving cTBS (n=45) or sham (n=45) stimulation. Behaviourally, cTBS reduced overall Go response rates and slowed reaction times. Computational modelling showed a decrease in the learning rate, selectively for rewarding outcomes. Computational fMRI analysis showed stronger reward prediction error (RPE) signals in the vmPFC, mediodorsal thalamus, and left dorsal striatum after cTBS, without changes in neural signals at cue onset. These findings provide causal evidence that the vmPFC drives the action-invigoration component of the Pavlovian bias. Significance statementWe causally link ventromedial prefrontal cortex (vmPFC) function to motivated action in humans. In a single-blind cTBS-fMRI study (n=90), transient vmPFC inhibition reduced Go responding, slowed reaction times, and selectively lowered the positive learning rate early in learning. At the same time, reward-prediction-error signals increased in mediodorsal thalamus, dorsal striatum, and vmPFC, while cue-onset value/choice signals were unchanged. Together, the results indicate that vmPFC normally speeds value updating and invigorates actions; when inhibited, control shifts toward slower, subcortically supported learning under higher uncertainty.

neuroscience↗

bioRxiv2025

Adaptational lag at high elevations depends on life stage in a California wildflower.

O_LIHigh elevation populations are expected to receive reduced snowpack, warmer temperatures, and more variable precipitation patterns, potentially putting them at risk if rates of adaptation do not keep pace with climate change. Populations from climates more closely aligned with the changing high elevation conditions may prove better suited to current climate than the current local populations. Thus, it is essential to assess 1) whether high elevation populations are locally adapted to current climate, and 2) whether fitness of lower elevation populations from warmer climates is higher than for local populations in high elevation conditions. C_LIO_LIWe conducted a common garden study with Streptanthus tortuosus at a high elevation site. Twenty-three populations from across the species range were measured weekly for mortality, and reproductive output was measured at the end of the growing season. We examined the effects of climatic distance from the site of origin on plant performance. The effects of weekly weather on mortality were also assessed. C_LIO_LIWe observed adaptational lag for high elevation populations, including the native population, but only for some life stages. Low elevation populations had higher survival through the first year and over winter. Additionally, the probability of reproducing was highest for populations from the warmest climates. Warmer ambient temperatures at the high elevation garden were also associated with higher weekly mortality across populations. However, survival to reproduction in the second year was higher in populations from climates closer to the garden, i.e. high elevation populations. Thus, adaptational lag differed among life stages. C_LIO_LISynthesis: This study highlights the importance of considering variation in life history and seasonal conditions when evaluating how species that occur across an elevational gradient may respond to climate change. This adds to a growing body of evidence that reveals warming temperatures as a threat to high elevation populations. However, unlike previous studies, this threat was not consistent across life stages. These results suggest that strategic assisted gene flow that combines the benefits of warm-adapted low elevation populations with the benefits of snow-adapted life history from high elevation populations may be beneficial in this species, and similar systems. C_LI

ecology↗

bioRxiv2025

Translation-driven temporal control for intertwined protein assembly

Protein complexes are essential to cells. However, how structurally intertwined protein subunits can assemble faithfully is poorly understood. Here, we reveal a "temporal control" mechanism driven by coupled ribosomes to form intertwined dimers. Using Disome Selective Profiling and optical tweezers, we show that the BTB domains of KEAP1, KLHL12, and PATZ1 form stable closed states as monomers, thus impeding proposed domain-swapping assembly routes. By contrast, the timed emergence of nascent chain segments during translation enables alternative folding-assembly pathways that bypass the closed monomeric state. Analysis indicates that this mechanism works in concert with dimerization quality control by the E3 ligase SCF-FBXL17, and is relevant across the BTB domain family. This study shows that ribosome cooperation expands the range of possible protein architectures.

molecular biology↗

bioRxiv2025

The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis

Natural proteins are structurally diverse and often form intricate multidomain, oligomeric architectures. This presents a prima facie challenge to cellular homeostasis, as topologically complex proteins seldom refold efficiently in vitro. How cells overcome sequence-intrinsic folding limitations to optimize protein biogenesis is incompletely understood. Here, we show that efficient folding and assembly of the model five-domain homotetramer {beta}-galactosidase is obligatorily coupled to its synthesis on the ribosome, and define the underlying mechanisms. During refolding of full-length protein from denaturant, maturation of the catalytic domain is frustrated. Assembly outpaces monomer folding, and non-native oligomers accumulate. The ribosome directs the order of folding events and specifies the pathway of oligomer assembly. Efficient de novo folding is characterised by segmental domain folding, shaped by binding of a nascent amphipathic helix to a cryptic pocket on the ribosome surface. Homomer assembly initiates cotranslationally via recruitment of a full-length subunit to the nascent polypeptide, and the failure to do so results in misassembly. Our results reveal how the ribosome can dictate the timing of folding and assembly to enable efficient biogenesis of a topologically complex protein.

biochemistry↗

bioRxiv2025

Herbarium specimens reveal a constrained seasonal climate niche despite diverged annual climates across a wildflower clade

Quantifying species niches across a clade reveals how environmental tolerances evolve, and offers insights into present and future distributions. We use herbarium specimens to explore climate niche evolution across 14 annual species of the Streptanthus (s.l.) clade (Brassicaceae), which originated in deserts and diversified into cooler, moister areas. To understand how climate niches evolved, we used historical climate records to estimate each species 1) classic annual climate niche, averaged over specimen collection sites; 2) growing season niche, from estimated specimen germination date to collection date, averaged across specimens (specimen-specific niche); and 3) standardized seasonal niche based on average growing seasons of all species (clade-seasonal niche). In addition to estimating how phenological variation maps onto climate niche evolution, we explored how spatial refugia shape the climate experienced by species by 1) analyzing how field soil texture changes relative to the climate space that species occupy and 2) comparing soil water holding capacity from each specimen locality to that of surrounding areas. Specimen-specific niches exhibited less clade-wide variation in climatic water deficit than did annual or clade-seasonal niches, and specimen-specific temperature niches showed no phylogenetic signal, in contrast to annual and clade-seasonal temperature niches. Species occupying cooler regions tracked hotter and drier climates by growing later into the summer, and by inhabiting refugia on drought-prone soils. These results underscore how phenological shifts, spatial refugia, and germination timing shape "lived" climate. Despite occupying a large range of annual climates, we found these species are constrained in the conditions under which they thrive. Significance statementHere, we show that closely related species that appear to have diverged in their climate niches based on highly differentiated annual conditions are actually tracking very similar seasonal climate conditions. This climate similarity, estimated from collection locations and associated weather data of nearly 2000 herbarium specimens, is achieved through the evolution of germination timing and plant flowering phenology, as well as establishment in spatial refugia with suitable microclimates. Our results highlight how occupation of a subset of seasonal conditions can be conserved across diverse species, resulting in less climate niche evolution than expected. Restricted climate niches imply that species may be less adaptable than we expect based on annual climates, and have implications for conservation, management and persistence under hotter climates.

ecology↗

bioRxiv2025

Specimen-tailored "lived" climate reveals precipitation onset and amount best predict specimen phenology, but only weakly predict specimen reproductive success across a clade

Herbarium specimens are broadly distributed in space and time, enabling investigation of climate impacts on phenology and fitness. We reconstructed specimen "lived" climate from knowledge of germination cues and collection dates for 14 annual species in the Streptanthus (s.l.) clade (Brassicaceae) to ask: Which climate attributes, including the timing of precipitation onset, best explain specimen phenological stage and estimated reproduction? We also asked whether climate effects on phenology and reproduction were evolutionarily conserved. Precipitation amount and onset date, more than temperature, best predicted specimen phenology, but only weakly predicted reproduction. Earlier rainfall onset was associated with more phenologically advanced specimens, a relationship that showed phylogenetic signal. Few climate predictors explained variation in specimen reproduction. The lack of association between specimen reproduction and climate may arise from phenological shifts that buffer impacts of climate, interactions with other species, or challenges in estimating total reproduction from specimens. Our results highlight the value of specimen-tailored growing season conditions for reconstructing climate, incorporating evolutionary relationships in assessing responses to climate, and the complexities of estimating fitness from specimens. For the latter, we propose supplemental herbarium collections and community science protocols to increase the utility of these data for understanding climate impacts on populations.

ecology↗

bioRxiv2024

A multi-model approach defines function altering MECP2 missense variants identified in individuals with autism spectrum disorder

Pathogenic variants in MECP2 commonly lead to Rett syndrome, where MECP2s function as a DNA cytosine methylation reader is believed critical. MECP2 variants are also catalogued in individuals with autism spectrum disorder (ASD), including nine missense variants which had no known clinical significance at the start of this study. To assess these nine variants as risk alleles for ASD, we developed MECP2 variant functional assays using budding yeast and Drosophila. We calibrated these assays with known pathogenic and benign variants. Our data predict that four ASD variants are loss of function and five are functional. Protein destabilization offers insight into the altered function of some of these variants. Notably, yeast and Drosophila lack DNA methylation, yet all Rett pathogenic and ASD variants located in the methyl DNA binding domain that we analyzed proved to be loss of function, suggesting a clinically-relevant role for non-methyl DNA-binding by MECP2.

neuroscience↗

bioRxiv2024

Accelerated phenology fails to buffer fitness loss from delayed rain onset in a clade of wildflowers

The timing of early life cycle events has cascading effects on phenology and fitness. These effects may be critical for climate resilience of plant populations, especially in Mediterranean environments, where delayed rainfall onset causes delayed germination. To examine impacts of germination timing on ten species of the Streptanthus/Caulanthus clade, we induced germination across a range of dates in ambient seasonal conditions and recorded phenological and fitness traits. Later germination cohorts accelerated flowering, partially stabilizing flowering date, but the degree of this compensatory plasticity differed across species. Fitness declined with later germination; the magnitude of this decline depended on the balance between direct negative effects of later germination and compensatory positive effects of accelerated flowering. The resulting species differences in fitness responses suggest differential vulnerability to climate change. Species from wetter, cooler, less variable habitats accelerated flowering more and declined less in seed set with later germination, suggesting climate adaptation. However, other fitness responses to germination timing, like first year fitness, were evolutionarily labile across the clade and unrelated to climate. Although compensatory phenological plasticity may buffer the impacts of delayed germination, it cannot prevent long term declines in population fitness as fall rains come later with climate change.

evolutionary biology↗

bioRxiv2023

Co-translational ribosome pairing enables native assembly of misfolding-prone subunits

Protein complexes are pivotal to most cellular processes. Emerging evidence indicates that pairs of ribosomes ubiquitously drive the synchronized synthesis and assembly of two protein subunits into homodimeric complexes1-5. These observations suggest protein folding mechanisms of general importance enabled by contacts between nascent chains6,7 - which have thus far rather been considered detrimental8,9. However, owing to their dynamic and heterogeneous nature, the folding of interacting nascent chains remains unexplored. Here, we show that co-translational ribosome pairing allows their nascent chains to chaperone each other, thus enabling the formation of coiled-coil homodimers from subunits that misfold individually. We developed an integrated single-molecule fluorescence and force spectroscopy approach to probe the folding and assembly of two nascent chains extending from nearby ribosomes, using the intermediate filament lamin as a model system. Ribosome proximity in early translation stages was found to be critical: when interactions between nascent chains are inhibited or delayed, they become trapped in stable misfolded states that are no longer assembly competent. Conversely, early interactions allow the two nascent chains to nucleate native-like quaternary structures that grow in size and stability as translation advances. We conjecture that protein folding mechanisms enabled by ribosome cooperation are more broadly relevant to intermediate filaments and other protein classes.

molecular biology↗

bioRxiv2023

Germination responses to experimental rainfall timing identify potential vulnerability to climate change across a clade of California wildflowers

The timing of germination, driven by seasonal cues, is critical for the life cycle of plants. Variation among species in germination responses can reflect evolutionary processes and adaptation to local climate and can affect vulnerability to changing conditions. Indeed, climate change is altering the timing of precipitation and associated temperatures, which may interact with germination cueing to affect the timing, quantity, and speed of germination. Germination responses to change can then have consequences for individual fitness, population dynamics, and species distributions. Here, we assessed responses to the timing of germination-triggering rains and corresponding temperatures for 11 species spanning the Streptanthus (s.l.) clade (Brassicaceae). To do so, we experimentally manipulated the onset date of rainfall events, measured effects on germination fraction and rate, and evaluated whether responses were constrained by evolutionary relationships across the phylogeny. We then explored the possible consequences of these responses to contemporary shifts in precipitation timing. Later onset rains and cooler temperatures significantly reduced germination rates for all species. Germination fractions decreased with later rains and cooler temperatures for all but three Caulanthus species. Species germination responses to the timing of rainfall and seasonal temperatures were phylogenetically constrained, with Caulanthus species appearing less sensitive. Further, six species are likely already experiencing significant decreases in germination fractions or rates (or both) with observed climate change, which has shifted the timing of rainfall towards the cooler, winter months in California. Overall, our findings highlight the importance of the germination responses to seasonal timing, how they have evolved across the clade, and their implications under climate change.

plant biology↗

bioRxiv2022

Spatial modeling reveals nuclear phosphorylation and subcellular shuttling of YAP upon drug-induced liver injury

The Hippo signaling pathway controls cell proliferation and tissue regeneration via its transcriptional effectors yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). In this context, the canonical pathway topology is characterized by sequential phosphorylation of kinases in the cytoplasm that define the subcellular localization of YAP and TAZ. However, the molecular mechanisms controlling the nuclear/cytoplasmic shuttling dynamics of both factors under physiological and tissue-damaging conditions are poorly understood. By implementing experimental data, partial differential equation (PDE) modeling, as well as automated image analysis, we demonstrate that nuclear phosphorylation contributes to differences between YAP and TAZ localization in the nucleus and cytoplasm. Treatment of hepatocyte-derived cells with hepatotoxic acetaminophen (APAP) overdose induces a biphasic protein phosphorylation eventually leading to nuclear protein enrichment of YAP but not TAZ. APAP-dependent regulation of nuclear/cytoplasmic YAP shuttling is not an unspecific cellular response but relies on the sequential induction of reactive oxygen species (ROS), RAC-alpha serine/threonine-protein kinase (AKT, synonym: protein kinase B), as well as elevated nuclear interaction between YAP and AKT. Mouse experiments confirm this consecutive sequence of events illustrated by the expression of ROS-, AKT-, and YAP-specific gene signatures upon APAP administration. In summary, our data illustrate the importance of nuclear processes in the regulation of Hippo pathway activity. YAP and TAZ exhibit different shuttling dynamics, which explains distinct cellular responses of both factors under physiological and tissue-damaging conditions. SignificanceWe show that canonical view on the Hippo pathway must be extended by additional regulatory processes in cell nuclei. These processes significantly contribute to the activity of YAP and TAZ under unchallenged conditions (e.g., with cell density as physiological regulator of the Hippo kinase cassette) or under cell damaging conditions (e.g., after administration of APAP overdose). APAP-induced cellular damage activates YAP via distinct molecular processes as part of a cell-protective response.

molecular biology↗

bioRxiv2022

Alteration of myocardial structure and function in RAF1associated Noonan syndrome: Insights from cardiac disease modeling based on patient-derived iPSCs

Noonan syndrome (NS), the most common among the RASopathies, is caused by germline variants in genes encoding components of the RAS-MAPK pathway. Distinct variants, including the recurrent Ser257Leu substitution in RAF1, are associated with severe hypertrophic cardiomyopathy (HCM). Here, we investigated the elusive mechanistic link between NS-associated RAF1S257L and HCM using three-dimensional cardiac bodies and bioartificial cardiac tissues generated from patient-derived induced pluripotent stem cells (iPSCs) harboring the pathogenic RAF1 c.770C>T missense change. We characterize the molecular, structural and functional consequences of aberrant RAF1 -associated signaling on the cardiac models. Ultrastructural assessment of the sarcomere revealed a shortening of the I-bands along the Z disc area in both iPSC-derived RAF1S257L cardiomyocytes, and myocardial tissue biopsies. The disease phenotype was partly reverted by using both MEK inhibition, and a gene-corrected isogenic RAF1L257S cell line. Collectively, our findings uncovered a direct link between a RASopathy gene variant and the abnormal sarcomere structure resulting in a cardiac dysfunction that remarkably recapitulates the human disease. These insights represent a basis to develop future targeted therapeutic approaches.

cell biology↗

bioRxiv2022

Excessive self-grooming of Shank3 mutant mice is associated with gene dysregulation and imbalance between the striosome and matrix compartments in the striatum

Autism is characterised by atypical social communication and stereotyped behaviours. Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are detected in 1-2% of patients with autism and intellectual disability (ID), but the mechanisms underpinning the symptoms remain largely unknown. Here, we characterised the behaviour of Shank3{Delta}11/{Delta}11 mice from three to twelve months of age. We observed decreased locomotor activity, increased stereotyped self-grooming and modification of socio-sexual interaction compared to wild-type littermates. We then used RNAseq on four brain regions of the same animals to identify differentially expressed genes (DEG). DEGs were identified mainly in the striatum and were associated with synaptic transmission (e.g. Grm2, Dlgap1), G-protein-signalling pathways (e.g. Gnal, Prkcg1, and Camk2g), as well as excitation/inhibition balance (e.g. Gad2). Downregulated and upregulated genes were enriched in the gene clusters of medium-sized spiny neurons expressing the dopamine 1 (D1-MSN) and the dopamine 2 receptor (D2-MSN), respectively. Several DEGs (Cnr1, Gnal1, Gad2, and Drd4) were reported as striosome markers. By studying the distribution of the glutamate decarboxylase GAD65, encoded by Gad2, we showed that the striosome compartment of Shank3{Delta}11/{Delta}11 mice was enlarged and displayed much higher expression of GAD65 compared to wild-type mice. Altogether, these results indicate altered gene expression in the striatum of SHANK3-deficient mice and strongly suggest, for the first time, that the impairment in behaviour of these mice are related to an imbalance striosomes/matrix.

neuroscience↗