Biology subjects

Johnson, S. L.

Publications and source records attributed to Johnson, S. L..

At least 19 recordsLinked to original sources

bioRxiv2026

Glucosylceramide synthase is required for C6-ceramide nanoliposome-induced organelle stress and cell death

Sphingolipids are bioactive lipids that regulate key signaling pathways both directly as ligands and through membrane re-organization. Ceramide sits at the center of this network and is considered pro-death in many contexts, making ceramide accumulation an attractive therapeutic strategy. Given the wide-ranging regulation of cellular responses this network exerts, better understanding ceramide metabolism may promote therapeutic efficacy of sphingolipid-based therapeutics. Ceramide glycosylation, catalyzed by glucosylceramide synthase (GCS; UGCG), is in turn widely regarded as a detoxification route thus limiting efficacy of ceramide- based therapeutics. Here we show the opposite. Delivery of short-chain C6-ceramide via a ceramide nanoliposome (CNL) induced organelle stress and cell death in chronic lymphocytic leukemia (CLL) via the accumulation of glycosphingolipids (GSLs), rather than through ceramide itself. Pharmacologic and genetic blockade of GCS protected B-cell leukemia, breast carcinoma, glioblastoma, lung adenocarcinoma, and non- malignant embryonic kidney cells from CNL-induced death. Conversely, exogenous C8-glucosylceramide was sufficient to kill cells that cannot degrade it. We show that GSL accumulation drives an ordered organelle response beginning with lysosomal deacidification, endoplasmic reticulum stress, followed by mitochondrial respiratory capacity decline, each attenuated by inhibition of GSL synthesis. These effects were accompanied by MLKL phosphorylation, increased activity of the stress sensor JNK and CHOP induction, with JNK inhibition partially protecting from death. These findings invert the prevailing view of ceramide glycosylation as a resistance mechanism and identify glycosphingolipid flux as a required effector arm of ceramide-directed therapy.

cancer biology↗

bioRxiv2026

Estrogen-related receptor gamma is required for normal auditory innervation and is essential for hearing.

Estrogen-related receptor gamma (ESRRG), an orphan nuclear receptor with structural homology to the classical estrogen receptors, is widely recognised as a key metabolic regulator involved in mitochondrial, synaptic, and ion-homeostatic pathways. Previous clinical studies suggest a link between ESRRG and auditory function; for example, ESRRG has been associated with susceptibility to age-related hearing loss in women and implicated in congenital hearing loss. However, the biological mechanisms by which ESRRG may mediate hearing function remain largely unknown. Here, using a combination of in vivo auditory physiological recordings, immunofluorescence analyses, single hair-cell electrophysiology, and transcriptomic approaches, we characterise the phenotype of a new inner-ear conditional Esrrg knockout (Esrrg-cKO) to investigate the role of Esrrg in the auditory system. We found that Esrrg-cKO mice of both sexes develop early-onset hearing loss, as evidenced by elevated auditory brainstem response thresholds and reduced wave 1 amplitudes from two weeks of age. These auditory deficits arise from a combination of early-onset cochlear neuronal and innervation malformations, together with inner hair cell synaptic defects and delayed myelination that persist into adulthood. Furthermore, distortion product otoacoustic emissions and endocochlear potential recordings are normal in Esrrg-cKO mice, and although sensory hair cells are preserved, IHCs retain immature biophysical properties. These findings are consistent with auditory neuropathy, and together with our comparative transcriptome analyses, indicate that Esrrg is an essential molecular driver of normal cochlear innervation and maturation.

neuroscience↗

bioRxiv2026

Cell-specific isotope labeling identifies myo-inositol transfer between neurons and oligodendroglia to support myelin repair

Neurons and glial cells are biochemically coupled through the exchange of nutrients, but our knowledge of which metabolites are transferred between them remains limited due to technical challenges. Here, we introduce a strategy to label specific cell types with isotopic tracers so that metabolite transfer can be measured directly in the intact brain. By engineering neurons in mice to metabolize 13C-labeled cellobiose, a glucose dimer that wild-type cells cannot catabolize, we selectively track neuron-derived metabolites by using mass spectrometry-based metabolomics. Applying this approach enabled us to identify myo-inositol as a critical metabolite synthesized by neurons and transferred to oligodendrocyte progenitor cells (OPCs) via the SLC5A3 transporter. The transfer of myo-inositol from neurons to OPCs promotes OPC proliferation and differentiation by enhancing phosphatidylinositol synthesis and upregulating expression of myelin-associated genes. During demyelination, deficient nutrient transfer can be rescued by dietary supplementation of myo-inositol, which accelerates myelin repair. These findings establish a generalizable technology for tracing intercellular metabolite transfer in vivo and identify a previously unrecognized mechanism of myo-inositol transfer from neurons to glial cells in support of CNS regeneration, revealing a potential metabolic target for therapeutic intervention in neurodegenerative disease.

biochemistry↗

bioRxiv2025

Cell type diversification and phenotype convergence underlying white fin-ornamentation of cyprinid fishes

Neural crest derived cells offer valuable opportunities to dissect mechanisms of cell fate specification and differentiation within individual ontogenies and the underpinnings of cell type diversification over evolutionary time. Particularly useful for such analyses are pigment cells of ectothermic vertebrates that arise from neural crest cells, or via latent neural crest derived stem cells, and comprise several classes with cell-type specific pigmentary phenotypes. Among these are white cells, "leucophores," present in a variety of species that contribute to patterns on the body or ornamentation on the fins. To better understand developmental and evolutionary origins of these cells we have examined leucophores harboring deposits of yellow/orange carotenoids, "xantholeucophores," of zebrafish and leucophores of white cloud minnow, within the same family Cyprinidae. We show that white phenotypes of both cell types require sepiapterin reductase that promotes accumulation of pale and colorless pteridines. We further demonstrate that xantholeucophores develop directly from yellow sepiapterin rich xanthophore-like cells and that this transition requires both gap junctional activity and permeability of the aquaglyceroporin / peroxiporin channel Aquaporin 3. These findings identify these white cells as distinct developmentally, genetically, and biochemically from another type of white cell in zebrafish and other white cells present across phylogenetic lineages. Our results highlight remarkable convergences and parallelisms in the acquisition of white cell phenotypes within and between species and identify this as a rich system for enquiries into the evolutionary individuation of novel cell types. SignificanceUnderstanding how cell types arise is fundamental to explaining animal complexity. Pigment cells offer opportunities to address this question because they display striking variation. We show that white pigment cells comprise multiple classes with independent origins. In zebrafish, white cells on one fin develop from melanophores whereas white cells on another fin develop from yellow precursors that convert their pigments to colorless ones. White cells of a related minnow require the same colorless pigments yet differ in other ways. These findings illuminate remarkable convergence: white cells have arisen repeatedly from different progenitor cell lineages by different mechanisms. This diversity--even within and between closely related species--identifies a powerful model for understanding the evolution of cell types with distinct identities and functions.

developmental biology↗

bioRxiv2025

Induced ubiquitination bypasses canonical ERAD to drive ER protein degradation

Heterobifunctional proteolysis-targeting chimeras (PROTACs) have emerged as a powerful strategy to degrade disease-relevant proteins, enabling targeting of previously "undruggable" proteins. Current degrader molecules primarily target cytosolic substrates, yet nearly one-third of the proteome resides in or transits the endoplasmic reticulum (ER), including receptors, secreted factors, and biosynthetic enzymes with high therapeutic relevance. Whether ER-localized proteins can be broadly targeted for induced degradation remains an open question. To address this gap, we employed a panel of fluorescent reporter cell lines and used the dTAG chemical-genetic system to recruit cytosolic E3 ligases. While lumenal substrates segregated from the cytosol were resistant to degradation, recruitment of cytosolic ligases effectively degraded ER membrane proteins across multiple topologies and with post-translational modifications. CRISPR genetic screens revealed that the induced degradation required the expected cullin RING ligase complexes but surprisingly bypassed ER-associated degradation (ERAD) machinery, with the exception of the AAA ATPase VCP. Mechanistic studies demonstrated that substrate ubiquitination was essential for VCP binding, and cleavage of ubiquitin chains released VCP, suggesting a model in which VCP directly extracts substrates independent of a dislocation apparatus. Extending this strategy to an endogenous substrate, we synthesized an HMGCR ERAD-TAC by linking atorvastatin to a cereblon E3 ligase recruiter and found that HMGCR degradation was likewise VCP-dependent. Together, these findings demonstrate that ER membrane proteins are generally susceptible to induced degradation via cytosolic ligase recruitment, uncovering a VCP-centered mechanism that operates independently of membrane-embedded ERAD machinery. This work establishes foundational principles for extending targeted protein degradation to the early secretory pathway. SIGNIFICANCE STATEMENTTargeted protein degradation has transformed drug discovery. Nearly one-third of the proteome reside in or transit the endoplasmic reticulum (ER), a compartment rich in therapeutically relevant but structurally complex targets. Whether these ER proteins can be broadly degraded using PROTACs has remained unknown. Here, we define the minimal requirements for degrading ER membrane proteins by recruiting cytosolic E3 ligases. Using chemical-genetic tools, genetic screens, and a statin-based degrader, we show that ubiquitination engages the VCP extraction machinery, enabling degradation of diverse ER membrane proteins independent of canonical ER-associated degradation components. These findings reveal a ubiquitin-driven route for membrane protein turnover, expand the landscape of druggable ER proteins, and establish principles for designing degraders operating in the early secretory pathway.

cell biology↗

bioRxiv2025

Aging Alters Hair Cell Physiological Properties in Mice with Late-Onset Age-Related Hearing Loss.

Cochlear hair cells convert sound stimuli into electrical signals. Age-related hearing loss (ARHL) is characterized by the progressive reduction of these hair cells and their synapses, but the underlying mechanisms remain poorly understood. In this study, we tested the hypothesis that hair cell function declines with age in CBA/CaJ mice, a strain known for its very slow ARHL progression. We found that hair cell size began to decrease from 10 months of age, before hearing loss was detectable. This structural change was associated with a significant decrease in the total current response and a distinct reduction in the expression of large conductance calcium-activated potassium (BK) channel currents (IK,f). However, the magnitude of the mechanoelectrical transducer (MET) currents at the hair cell stereociliary bundles remained unaffected. This observation challenges the common conception that stereocilia are the most fragile component of sensory cells in aging. Our results provide clear evidence of an early decline in hair cell function with age, which precedes measurable hearing loss, suggesting that these cellular deficits define a distinct pathological route to ARHL in the CBA/CaJ mouse model.

physiology↗

bioRxiv2025

Misophonia Symptoms Severity is Attributed to Impaired Flexibility and Heightened Rumination

Misophonia is a disorder involving sensitivity to certain sounds and related stimuli. Here, we explore the relationship between misophonia and affective flexibility, which describes cognitive shifting abilities in the face of emotion-evoking stimuli. Previous evidence suggests impaired subjective cognitive flexibility in misophonia, but this relationship has not been confirmed behaviourally or in emotionally-salient contexts. The secondary aim of this study is to test the potential association between misophonia and cognitive flexibility, building upon findings from previous research. The third objective is to examine the relationship between misophonia and rumination, a maladaptive cognitive process characterized by repetitive negative thinking and linked to both cognitive and affective inflexibility. One hundred and forty participants completed the recently developed Memory and Affective Flexibility Task (MAFT), designed to assess affective flexibility, as well as a battery of self-report measures to evaluate misophonia severity, cognitive flexibility and rumination. Results suggested an inverse relationship between affective flexibility as measured by switch accuracy, but not reaction time, and misophonia severity. Cognitive flexibility was also inversely associated with misophonia severity, but notably did not attribute to task-based affective flexibility, suggesting two independent constructs both involved in misophonia manifestation. Rumination associated positively with misophonia severity and inversely with cognitive flexibility, but not affective flexibility. Taken together, these findings highlight a unique cognitive profile of misophonia, characterized by rigidity at the psychological level through cognitive inflexibility and rumination, as well as at the executive-function level in terms of affective switching difficulties.

pathology↗

bioRxiv2024

Variable Presence of an Evolutionarily New Brain Structure is Related to Trait Impulsivity

BackgroundImpulsivity is a multidimensional construct reflecting poor constraint over ones behaviors. Clinical psychology research identifies separable impulsivity dimensions that are each unique transdiagnostic indicators for psychopathology. Yet, despite this apparent clinical importance, the shared and unique neuroanatomical correlates of these factors remain largely unknown. Concomitantly, neuroimaging research identifies variably present human brain structures implicated in cognition and disorder: the folds (sulci) of the cerebral cortex located in the latest developing and most evolutionarily expanded hominoid-specific association cortices. MethodsWe tethered these two fields to test whether variability in one such structure in anterior cingulate cortex (ACC)--the paracingulate sulcus (PCGS)--was related to individual differences in trait impulsivity. 120 adult participants with internalizing or externalizing psychopathology completed a magnetic resonance imaging scan and the Three-Factor Impulsivity Index. Using precision imaging techniques, we manually identified the PCGS, when present, and acquired quantitative folding metrics (PCGS length and ACC local gyrification index). ResultsNeuroanatomical-behavioral analyses revealed that participants with leftward or symmetrical PCGS patterns had greater severity of Lack of Follow Through (LFT)--which captures inattention and lack of perseverance--than those with rightward asymmetry. Neuroanatomical-functional analyses identified that the PCGS co-localized with a focal locus found in a neuroimaging meta-analysis on a feature underlying LFT. Both quantitative folding metrics did not relate to any impulsivity dimension. ConclusionsThis study advances understanding of the neuroanatomical correlates of impulsivity and establishes the notion that the topographical organization of distinct, hominoid-specific cortical expanses underlie separable impulsivity dimensions with robust, transdiagnostic implications for psychopathology.

neuroscience↗

bioRxiv2024

Emotion-related impulsivity is related to orbitofrontal cortical sulcation

BackgroundEmotion-related impulsivity (ERI) describes the trait-like tendency toward poor self-control when experiencing strong emotions. ERI has been shown to be elevated across psychiatric disorders and predictive of the onset and worsening of psychiatric syndromes. Recent work has correlated ERI scores with the neuroanatomy of the orbitofrontal cortex (OFC). Informed by a growing body of research indicating that the morphology of cortical folds (sulci) can produce insights into behavioral outcomes, the present study modeled the association between ERI and the sulcal morphology of OFC at a finer scale than previously conducted. MethodsAnalyses were conducted in a transdiagnostic sample of 118 individuals with a broad range of psychiatric syndromes. We first manually defined over 2000 sulci across the 118 participants. We then implemented a model-based LASSO regression to relate OFC sulcal morphology to ERI and test whether effects were specific to ERI as compared to non-emotion-related impulsivity. ResultsThe LASSO regression revealed bilateral associations of ERI with the depth of eight OFC sulci. These effects were specific to ERI and were not observed in non-emotion-related impulsivity. In addition, we identified a new transverse component of the olfactory sulcus in every hemisphere that is dissociable from the longitudinal component based on anatomical features and correlation with behavior, which could serve as a new transdiagnostic biomarker. ConclusionsThe results of this data-driven investigation provide greater neuroanatomical and neurodevelopmental specificity on how OFC is related to ERI. As such, findings link neuroanatomical characteristics to a trait that is highly predictive of psychopathology.

neuroscience↗

bioRxiv2023

An epigenome-wide association study of child appetitive traits and DNA methylation

Childhood appetitive traits are consistently associated with obesity risk, and yet their etiology is poorly understood. Appetitive traits are complex phenotypes which are hypothesized to be influenced by both genetic and environmental factors, as well as their interactions. Early-life epigenetic processes, such as DNA methylation (DNAm), may be involved in the developmental programming of appetite regulation in childhood. In the current study, we meta-analyzed epigenome-wide association studies (EWASs) of cord blood DNAm and early-childhood appetitive traits. Data were from two independent cohorts: the Generation R Study (n=1,086, Rotterdam, the Netherlands) and the Healthy Start study (n=236, Colorado, USA). DNAm at autosomal methylation sites in cord blood was measured using the Illumina Infinium HumanMethylation450 BeadChip. Parents reported on their childs food responsiveness, emotional undereating, satiety responsiveness and food fussiness using the Childrens Eating Behaviour Questionnaire at age 4-5 years. Multiple regression models were used to examine the association of DNAm (predictor) at the individual site- and regional-level (using DMRff) with each appetitive trait (outcome), adjusting for covariates. Bonferroni-correction was applied to adjust for multiple testing. There were no associations of DNAm and any appetitive trait at the individual site-level. However, at the regional level, we identified 45 associations of DNAm with food responsiveness, 7 associations of DNAm with emotional undereating, 13 associations of DNAm with satiety responsiveness, and 9 associations of DNAm with food fussiness. This study shows that DNAm in the newborn may partially explain variation in appetitive traits expressed in early childhood and provides preliminary support for early programming of child appetitive traits through DNAm. Investigating differential DNAm associated with appetitive traits could be an important first step in identifying biological pathways underlying the development of these behaviors.

genetics↗

bioRxiv2023

High-throughput single molecule tracking identifies drug interactions and cellular mechanisms

The regulation of cell physiology depends largely upon interactions of functionally distinct proteins and cellular components. These interactions may be transient or long-lived, but often affect protein motion. Measurement of protein dynamics within a cellular environment, particularly while perturbing protein function with small molecules, may enable dissection of key interactions and facilitate drug discovery; however, current approaches are limited by throughput with respect to data acquisition and analysis. As a result, studies using super-resolution imaging are typically drawing conclusions from tens of cells and a few experimental conditions tested. We addressed these limitations by developing a high-throughput single-molecule tracking (htSMT) platform for pharmacologic dissection of protein dynamics in living cells at an unprecedented scale (capable of imaging > 106 cells/day and screening > 104 compounds). We applied htSMT to measure the cellular dynamics of fluorescently tagged estrogen receptor (ER) and screened a diverse library to identify small molecules that perturbed ER function in real time. With this one experimental modality, we determined the potency, pathway selectivity, target engagement, and mechanism of action for identified hits. Kinetic htSMT experiments were capable of distinguishing between on-target and on-pathway modulators of ER signaling. Integrated pathway analysis recapitulated the network of known ER interaction partners and suggested potentially novel, kinase-mediated regulatory mechanisms. The sensitivity of htSMT revealed a new correlation between ER dynamics and the ability of ER antagonists to suppress cancer cell growth. Therefore, measuring protein motion at scale is a powerful method to investigate dynamic interactions among proteins and may facilitate the identification and characterization of novel therapeutics.

cell biology↗

bioRxiv2022

HDAC6 inhibition partially alleviates mitochondrial trafficking defects and restores motor function in human motor neuron and zebrafish models of Charcot-Marie-Tooth Disease Type 2A

Charcot Marie Tooth Disease (CMT) is a group of inherited progressive conditions affecting distal motor and sensory neurons, leading to muscle weakness, pain and loss of sensation in limbs. There are currently no treatments for this debilitating disease. To investigate disease mechanisms and facilitate treatment discovery, here we developed an in vitro model for CMT type 2A by introducing the patient-specific MFN2R94Q mutation into human embryonic stem cells (hESCs). Isogenic mutant and wild-type hESCs differentiated to spinal motor neurons with similar efficiency and gave rise to functional motor neurons in vitro. However, MFN2R94Q/+ spinal motor neurons displayed impaired mitochondrial trafficking, resulting in reduced numbers of mitochondria in distal parts of axons. Importantly, we showed that mitochondrial trafficking defects can be alleviated by treatment with an HDAC6 inhibitor. Chemical and genetic inhibition of HDAC6 also significantly rescued the motor phenotype in a zebrafish CMT2A model. Taken together, our study reveals a mutation-specific insight into CMT2A disease mechanism and confirms HDAC6 as a promising target for further therapeutic development.

cell biology↗

bioRxiv2021

Novel regulators of growth identified in the evolution of fin proportion in flying fish

Identifying the genetic foundations of trait variation and evolution is challenging as it is often difficult to parse meaningful signals from confounding signatures such as drift and epistasis. However, identification of the genetic loci underlying morphological and physiological traits can be honed through the use of comparative and complementary genetic approaches, whereby shared sets of genes that are repeatedly implicated across large evolutionary time periods as under selection can illuminate important pathways and epistatic relationships that function as novel regulators of trait development. Here we intersect comparative genomic analyses with unbiased mutagenesis screens in distantly related species to define the control of proportional growth, as changes in the size and relative proportions of tissues underlie a large degree of the variant forms seen in nature. Through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors, key innovations for flying fishes and flying halfbeaks. To refine our analysis, we intersected convergent phylogenomic signatures with mutants identified in distantly related zebrafish with altered fin size. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter, lat4a, and the potassium channel, kcnh2a, in the regulation of fin proportion. We show that specific epistatic interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to a conserved, non-canonical signaling interaction that integrates bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.

developmental biology↗

bioRxiv2020

ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme

ATP-dependent chromatin remodelers are essential enzymes that restructure eukaryotic genomes to enable all DNA-based processes. The diversity and complexity of these processes are matched by the complexity of the enzymes that carry them out, making remodelers a challenging class of molecular motors to study by conventional methods. Here we use a single molecule biophysical assay to overcome some of these challenges, enabling a detailed mechanistic dissection of a paradigmatic remodeler reaction, that of sliding a nucleosome towards the longer DNA linker. We focus on how two motors of a dimeric remodeler coordinate to accomplish such directional sliding. We find that ATP hydrolysis by both motors promotes coordination, suggesting a role for ATP in resolving the competition for directional commitment. Furthermore, we show an artificially constitutive dimer is no more or less coordinated, but is more processive, suggesting a cell could modulate a remodelers oligomeric state to modulate local chromatin dynamics.

biophysics↗

bioRxiv2020

Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes

Sporulation is a complex morphophysiological process resulting in a cellular structure that is more resistant than the vegetative form. In Firmicutes, this structure is produced within the mother cell, and is called an endospore. Endospore formation is thought to have evolved in the common ancestor of Firmicutes. However, sporulation has apparently been lost in some extant lineages that are defined as asporogenic. We isolated strain 11kri321, a representative of the genus Kurthia, from an oligotrophic geothermal reservoir. While Kurthia spp. is considered to comprise only asporogenic species, strain 11kri321 produced spores. Genomic reconstruction of the sporulation pathway shows elements typical of sporulation in Bacilli, including the signaling for sporulation onset. However, key genes were missing, including those involved in engulfment and dipicolinic acid synthesis. Based on the results for strain 11kri321, sporulation was investigated in other Kurthia strains. Genes involved in signaling, cell division and spore coat formation were detected in three available Kurthia genomes. Moreover, endosporulation was clearly visualized in at least two of the four strains tested. These results show that Kurthia is an endospore-forming Firmicute lineage. However, the genetic background of sporulation in this genus deviates from the known sporulation pathway in Firmicutes and even within Bacilli, suggesting that a revision of the minimal set of genes used for genomic detection of sporulation is required. Based on our findings we propose the term cryptosporulant to refer to putative asporogenic Firmicutes for which a detailed genomic and physiological characterization of sporulating is missing. ImportanceEndospore-forming Firmicutes include many environmental and medical relevant bacterial clades. In these microorganisms, the ability to produce endospores is essential for survival in the environment and even for pathogenesis. The minimum core of genes required to produce a viable and resistant spore, the distinction between endospore-forming and asporogenic groups, as well as the evolution of sporulation have been a subject of investigation and debate for decades. Here, we demonstrate endosporulation in the genus Kurthia, considered as asporogenic. Morphological, physiological and genomic analyses were undertaken to demonstrate that sporulation is not lost within this lineage. Based on our results we propose a re-examination of the minimal genetic requirements of sporulation and the use of the term cryptosporulant to describe lineages of Firmicutes that have not previously been observed to sporulate, but for which a detailed analysis is still missing.

microbiology↗

bioRxiv2019

Environmental unpredictability shapes glucocorticoid regulation across populations of tree swallows

Responding appropriately to challenges is an important contributor to fitness. Variation in the regulation of glucocorticoid hormones, which mediate the phenotypic response to challenges, can therefore influence the ability to persist in a given environment. We compared stress responsiveness in four populations of tree swallows (Tachycineta bicolor) along an environmental gradient to evaluate support for different selective pressures in driving the evolution of glucocorticoid regulation. In accordance with the environmental unpredictability hypothesis, stronger stress responses were seen in more unpredictable environments. Contrary to the reproductive value hypothesis, the stress response was not lower in populations engaging in more valuable reproductive attempts. Populations with stronger stress responses also had stronger negative feedback, which supports a "mitigating" rather than a "magnifying" effect of negative feedback on stress responses. These results suggest that combining a robust stress response with strong negative feedback may be important for persisting in unpredictable or rapidly changing environments.

evolutionary biology↗

bioRxiv2019

GABA-A signaling maintains melanocyte stem cell quiescence in larval zebrafish

Adult stem cells (ASCs) contribute to long-term homeostasis and regeneration of many adult tissues. Some ASCs proliferate continuously, others remain quiescent awaiting activation. To identify pathways that regulate ASC quiescence and tissue homeostasis, we study melanocyte stem cells (MSCs) that drive vertebrate pigmentation. In larval zebrafish, MSCs are quiescent, but can be recruited to regenerate the larval pigment pattern following melanocyte ablation. Through pharmacological experiments, we found that inhibition of GABA-A receptor function, specifically the GABA-A rho subtype, induces excessive melanocyte production in larval zebrafish. Conversely, pharmacological activation of GABA-A inhibited melanocyte regeneration. We used CRISPR to generate two mutant alleles of gabrr1, a subtype of GABA-A. Both alleles exhibited robust melanocyte overproduction, while conditional overexpression of gabrr1 inhibited larval melanocyte regeneration. Our data suggest that gabrr1 signaling is necessary and sufficient to maintain MSC quiescence and prevent excessive pigmentation of the larval zebrafish.

developmental biology↗

bioRxiv2019

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome.

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, are disordered. The disordered acidic patch is expected to inhibit the second SNF2h promoter, while disorder near the dyad is expected to promote DNA translocation. The other structure doesnt show octamer deformation, but surprisingly shows a 2bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation. One sentence summaryCryo-EM structures capture different conformational states of chromatin remodeler-nucleosome complexes.

biophysics↗