Biology subjects

Johnson, A.

Publications and source records attributed to Johnson, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

An integrated workflow for structural virology with a 100 keV electron microscope

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

biochemistry↗

bioRxiv2025

Insights into Aspergillus fumigatus morphogenesis and pathogenesis through the putative lipid transporter ArvA

Aspergillus fumigatus poses a significant threat to human well-being, in part due to the increasing emergence of strains resistant to frontline antifungal therapy. In this study, we observe that the gene, arvA, is required for A. fumigatus morphogenesis, antifungal drug susceptibility, and cell wall homeostasis. Intriguingly, our study reveals novel morphological and growth aberrations in the absence of arvA. Loss of arvA results in hyper-swollen conidia that give rise to stunted, polarity-deficient hyphae in numerous environmental conditions, indicating a pivotal role for arvA in A. fumigatus morphogenesis. Surprisingly, despite these severe in vitro morphological and cell wall defects, arvA was not required for morbidity and mortality in immunologically distinct murine models of invasive pulmonary aspergillosis (IPA). However, growth in natural calf lung surfactant was able to normalize{Delta} arvA growth with the wild-type strain suggesting lung surfactant may partially complement the severe in vitro morphological defects of arvA loss in vivo. Taken together our observations reveal arvA as a mediator of A. fumigatus antifungal drug susceptibility and highlight the complex and ill-defined pulmonary nutrient environments role in mediating A. fumigatus pathogenesis and disease progression. IMPORTANCEAspergillus fumigatus is a challenging fungal pathogen in the clinic in part due to increasing azole drug resistance. In this study, we observe that loss of the A. fumigatus gene arvA results in increased azole susceptibility and significant in vitro morphological changes highlighted by hyper-swollen conidia that yield stunted and polarity deficient hyphae. Importantly, despite these severe in vitro morphological and growth abnormalities,{Delta} arvA surprisingly retains full pathogenicity and virulence in two immunologically distinct murine models of invasive pulmonary aspergillosis. These results challenge our understanding of the in-host environment and how it mediates fungal morphogenesis and pathogenesis. These results, consequently, not only enhances our understanding of the role of arvA in A. fumigatus morphogenesis and drug susceptibility, but further emphasizes the importance of in vivo animal models in fully evaluating potential antifungal drug targets.

microbiology↗

bioRxiv2025

Affiliative behavioural phenotype and microglial activation predict social decision-making following immune activation

Social animals are faced with a critical decision when sick: to affiliate or withdraw. The behavioural response during an immune challenge varies by individual and species. However, the social and biological factors leading to variation in this decision during an immune challenge are unknown. Here, we explore the affiliative behavioural phenotype, "huddlers" and "non-huddlers," as a social predictor, and microglial activation and peripheral cytokine expression as biological predictors of social-decision making during an immune challenge. To measure social-decision making, we recorded social approach and time spent in proximity to a familiar same-sex conspecific versus a novel object in the social California mouse following lipopolysaccharide (LPS) treatment. Behavioural phenotype predicted both the social response to LPS and the relationship between cytokine activity and social behaviour, suggesting that social experience regulates social decision-making during sick versus healthy conditions. Additionally, we found that elevated microglia activity in the dentate gyrus (DG) and medial prefrontal cortex (mPFC) negatively correlated with social behaviour, positioning these regions for future exploration for the role of microglia on social decision-making. Our results identify the predictive power of behavioural phenotypes on social response to sickness and a link between microglia and decision-making during sickness.

neuroscience↗

bioRxiv2025

Gene editing in "cell villages" enables exploring disease-relevant mutations in many genetic backgrounds

Understanding how individual genetic backgrounds shape the effects of disease-associated mutations is central to elucidating the biology of complex psychiatric disorders. We developed a scalable village editing strategy that enables simultaneous genome editing across multiple induced pluripotent stem cell (iPSC) lines, allowing systematic assessment of how polygenic context modulates the impact of specific mutations. Using pooled CRISPR editing in 15 iPSC lines spanning a range of schizophrenia (SCZ) polygenic risk scores, we generated homozygous and heterozygous knockouts in two known SCZ-associated genes: LRP1, involved in cholesterol import, and NRXN1, a presynaptic adhesion molecule. By mixing all lines prior to editing and de-multiplexing them afterward, we efficiently produced multi-donor knockout neurons at scale. Transcriptomic profiling revealed that LRP1 and NRXN1 loss produce both shared and donor-specific effects on neuronal gene expression, with variable perturbation of neurotransmitter transport and cholesterol biosynthesis pathways across genetic backgrounds. These results demonstrate that village editing enables systematic dissection of gene-background interactions in human neurons, offering a powerful framework for studying the polygenic architecture of psychiatric disease.

cell biology↗

bioRxiv2025

The gut microbiota directs vitamin A flux to regulate intestinal T cell development

The intestinal microbiota shapes adaptive immunity, but the mechanisms remain incompletely defined. Here, we show that the microbiota initiates the movement of retinoids--dietary vitamin A derivatives including retinol and retinoic acid--through a sequential pathway from epithelial cells to myeloid cells and ultimately to T cells in the mesenteric lymph nodes (mLNs). This cellular axis is traversed over three days. Microbe-associated molecular patterns (MAMPs) initiate retinoid flux by inducing expression of serum amyloid A (SAA) proteins. These epithelial retinol-binding proteins are necessary and sufficient for epithelial-to-myeloid cell retinoid transfer and for myeloid cell migration to the mLNs. In the mLNs, microbial antigen drives retinoid transfer from myeloid cells to developing T cells, culminating in T cell retinoid uptake and transcriptional programming. This pathway is activated during postnatal development, when gut adaptive immunity is first established. These findings reveal that the microbiota programs intestinal adaptive immunity by regulating immune cell access to a nutrient-derived developmental signal. HighlightsO_LIThe gut microbiota enables vitamin A flux to developing intestinal CD4 T cells. C_LIO_LIMicrobiota-induced SAA initiates vitamin A flux along a gut myeloid-T cell axis. C_LIO_LIMicrobial molecular patterns and antigen drive distinct steps of vitamin A flux. C_LIO_LIMicrobiota-driven vitamin A flux programs intestinal T cell homing and maturation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/674524v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@13b3906org.highwire.dtl.DTLVardef@11ceee3org.highwire.dtl.DTLVardef@87913forg.highwire.dtl.DTLVardef@50c9a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Lack of mRNA Methylation in Schwann Cells Results in Demyelination and Regenerative Failure

Schwann cells are essential for peripheral nerve myelination and regeneration. N6-methyladenosine (m6A) RNA methylation, regulated by methyltransferase-like 14 (Mettl14), is a critical post-transcriptional modification, but its role in Schwann cell biology remains unclear. Using a conditional knockout (cKO) mouse model, we investigated the impact of Mettl14-mediated m6A methylation on Schwann cells. Mice born with Schwann cell-specific genetic deletion of Mettl14 developed normally but starting in young adulthood exhibited progressive motor deficits, severe demyelination, and axonal degeneration, confirmed by behavioral assessments and histological analyses. Mettl14-deficient Schwann cells displayed impaired proliferation and mitochondrial dysfunction in vitro. Following sciatic nerve injury, Mettl14 cKO mice showed defective macrophage recruitment, slowed axonal degeneration, and impaired regeneration. These findings suggest that Mettl14-mediated m6A methylation is critical for Schwann cell maintenance but not development. Given that Mettl14 cKO mice developed a demyelinating polyneuropathy, it is possible that manipulation of m6A methylation in Schwann cells is a promising therapeutic strategy targeting peripheral nerve repair and myelination.

neuroscience↗

bioRxiv2025

Redesigning petal shape, size, and color in soybean reveals unexpected phenotypes for floral organ development

Soybean (Glycine max) has not yet benefited from large-scale hybrid breeding efforts due to its small, self-fertilizing flowers that are difficult to emasculate, and limited attractiveness to pollinators. This study explores targeted floral trait engineering to enhance pollinator attraction, aiming to overcome barriers to soybean hybridization. We generated a high-resolution floral organ expression atlas and H3K4 trimethylation ChIP-Seq dataset to identify candidate genes involved in petal development, nectar sugar content, and petal pigmentation. Using CRISPR-based activation and repression systems, we modified the expression of AINTEGUMENTA (GmANT), BIGPETAL (GmBPE), and SUCROSE TRANSPORTER2 (GmSUC2). Contrary to expectations based on Arabidopsis homologs, transcriptional activation of GmANT_B and repression of GmBPE led to reduced, rather than increased, petal size, highlighting divergent regulatory mechanisms in soybean. Complementation of the W1 gene that controls petal pigmentation successfully converted white petals to purple, with preliminary evidence indicating that this color conversion may increase pollinator visitation. These results underscore the complexity of floral development in soybean and provide foundational tools and resources for future efforts to engineer reproductive traits for hybrid seed production.

plant biology↗

bioRxiv2025

Human genetic variation shapes the response of neurons to interferons

Inflammation is increasingly recognized as important to neuropathology, including more classic neuroimmune disease as well as neurodegenerative and neuropsychiatric disorders. Interferons (IFN) are important mediators of central nervous system inflammation. Individuals appear to vary in susceptibility to neuroinflammatory pathology, suggesting that identifying human genetic modifiers of the neuronal IFN response might provide insight into disease pathophysiology. To identify potential modifiers, we stimulated neuronal "cellular villages" of iPSC-derived neurons from over one hundred donors with IFN-alpha (IFNa) or IFN-gamma (IFNg). We then correlated allele states of common variable SNPs to gene expression to identify hundreds of expression quantitative trait loci (eQTLs), many of which emerged specifically upon IFN treatment. We characterized the distinct but overlapping neuronal transcriptional responses to IFNa and IFNg, and identified specific response QTLs. Functional annotation of STAT1 binding to the genome in response to IFN stimulus identified STAT1 binding sites as enriched for response-regulating human genetic variation and also enabled identification of loci with IFN-dependent allele-specific binding of STAT1. These results demonstrate how human genetic variation can influence IFN-dependent mechanisms in neurons in disease-relevant ways.

molecular biology↗

bioRxiv2025

Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase

Prior to ejaculation, sperm are stored in the epididymis in a resting metabolic state. Upon ejaculation, sperm must alter their metabolism to generate the energy needed to support the motility and maturation process known as capacitation to reach and fertilize the oocyte. How sperm regulate the capacitation-induced increase in carbon flux is unknown. Here, we use 13C stable isotope labeling to follow glucose metabolism through sperm central carbon metabolic network before and after sperm activation. We identify regulatory steps which sperm use to alter their metabolic state from resting to highly active. In activated sperm, glucose flux through glycolysis is increased at the expense of the pentose phosphate pathway to increase energy yield. Increased glycolytic activity seems to be due to capacitation-induced stimulation of flux through aldolase. In the mitochondria-containing midpiece, glycolytically generated pyruvate feeds the TCA cycle to further maximize energy yield via oxidative phosphorylation. In the mitochondria-free principal piece of the tail, pyruvate produced from glycolysis is reduced to lactate by lactate dehydrogenase. Reduction to lactate regenerates oxidized NAD+ ensuring a sufficient supply to support glycolysis. The resultant lactate is at least partially secreted. Finally, we find evidence that there is an as yet unknown endogenous source of energy in sperm feeding the upregulation of TCA cycle intermediates. These studies provide the most complete picture of the metabolic shift which occurs in capacitating sperm. Significance statementA rapid switch from a quiescent to a high energy-demanding state during ejaculation is essential for sperm to reach and fertilize the oocyte. Somatic cells also undergo bioenergetic switches from low to very high energy demand. However, because metabolic processes essential for proliferation are going on in parallel, it is difficult to identify the molecular mechanisms regulating the increase in ATP production. This study represents the first complete picture of the metabolic reprogramming that happens in sperm upon ejaculation. Using stable isotope labeling, we identify rate-limiting enzymatic steps and points of regulation directing the changes in metabolic flux. Our sperm metabolic studies allow us to identify conserved mechanisms of metabolic regulation that are crucial for the survival of mammalian cells.

biochemistry↗

bioRxiv2025

The functional organization of chromosome territories in single nuclei during zygotic genome activation

Chromosome territories (CTs) are intricately organized and regulated within the nucleus. Despite remarkable advances in our understanding of genome packaging and gene expression, the interplay among CTs, pairing of parental homologous chromosomes, and genome function during development remains elusive. Here, we employ an Oligopaints-based high-resolution imaging approach to examine variable CT organization in single nuclei during the developmental process of zygotic genome activation. We reveal large-scale chromosome changes with extensive homolog pairing at the whole-chromosome level that decreases locally due to spatial variability in chromosome conformations. In the absence of one homolog copy, the dynamics of CT compaction and RNA polymerase II recruitment are supported by transcriptional changes in haploid embryos. Finally, global inhibition of transcription results in decreased CT opening and no significant impact on CT pairing levels. These findings enhance our understanding of parental genome folding and regulation, which may inform strategies for chromosome-based diseases.

developmental biology↗

bioRxiv2025

Molecular characterisation of common Culicoides Biting Midges (Diptera: Ceratopogonidae) in Ireland

BackgroundBiting midges in the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including Bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques. MethodsAdult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. Additionally, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland. ResultsDNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of Bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides sp. which could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector. ConclusionDNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.

molecular biology↗

bioRxiv2024

An alternative route for β-hydroxybutyrate metabolism supports fatty acid synthesis in cancer cells

Cancer cells are exposed to diverse metabolites in the tumor microenvironment that are used to support the synthesis of nucleotides, amino acids, and lipids needed for rapid cell proliferation1-3. Recent work has shown that ketone bodies such as {beta}-hydroxybutyrate ({beta}-OHB), which are elevated in circulation under fasting conditions or low glycemic diets, can serve as an alternative fuel that is metabolized in the mitochondria to provide acetyl-CoA for the tricarboxylic acid (TCA) cycle in some tumors4-7. Here, we discover a non-canonical route for {beta}-OHB metabolism, in which {beta}-OHB can bypass the TCA cycle to generate cytosolic acetyl-CoA for de novo fatty acid synthesis in cancer cells. We show that {beta}-OHB-derived acetoacetate in the mitochondria can be shunted into the cytosol, where acetoacetyl-CoA synthetase (AACS) and thiolase convert it into acetyl-CoA for fatty acid synthesis. This alternative metabolic routing of {beta}-OHB allows it to avoid oxidation in the mitochondria and net contribute to anabolic biosynthetic processes. In cancer cells, {beta}-OHB is used for fatty acid synthesis to support cell proliferation under lipid-limited conditions in vitro and contributes to tumor growth under lipid-limited conditions induced by a calorie-restricted diet in vivo. Together, these data demonstrate that {beta}-OHB is preferentially used for fatty acid synthesis in cancer cells to support tumor growth.

cancer biology↗

bioRxiv2024

Deficiency of Hv1 Proton Channel Enhances Macrophage Antigen Presentation and Anti-Tumor Responses in Glioma

In the tumor microenvironment of glioblastoma, myeloid cells act as a double-edged sword--they are a major cellular component modulating the immune response while presenting a potential therapeutic target. Our study highlights the voltage-gated proton channel Hv1, predominantly expressed in myeloid cells, as a crucial regulator of their physiological functions. We discovered a strong correlation between increased Hv1 expression and poor prognosis in glioblastoma patients. Depleting Hv1 significantly extended survival in a mouse model of glioma. Employing multiple novel transgenic mouse lines, we demonstrated that Hv1 is upregulated in response to tumor presence, with glioma-associated macrophages as the principal contributors. Specifically, we identified that Hv1 in infiltrating macrophages as the major driver of survival phenotype differences. Through a combination of in vivo two-photon imaging, spectral flow cytometry, and spatial transcriptomic sequencing, we found that Hv1 depletion leads to reduced macrophage infiltration and enhanced antigen presentation, ultimately fostering a stronger adaptive immune response. These findings establish the Hv1 channel as a crucial new immune regulator within the brain tumor milieu, offering a promising target for reprogramming macrophage function to combat glioblastoma.

neuroscience↗

bioRxiv2024

Octahedral small virus-like particles of dengue virus type 2

Flavivirus envelope (E) and precursor M (prM) proteins, when ectopically expressed, assemble into empty, virus-like particles (VLPs). Cleavage of prM to M and loss of the pr fragment converts the VLPs from immature to mature particles, mimicking a similar maturation of authentic virions. Most of the VLPs obtained by prM-E expression are smaller than virions; early, low-resolution cryo-EM studies suggested a simple, 60-subunit, icosahedral organization. We describe here the cryo-EM structure of immature, small VLPs from dengue virus type 2 and show that they have octahedral rather than icosahedral symmetry. The asymmetric unit of the octahedral particle is an asymmetric trimer of prM-E heterodimers, just as it is on icosahedral immature virions; the full, octahedrally symmetric particle thus has 24 such asymmetric trimers, or 72 prM-E heterodimers in all. Cleavage of prM and release of pr generates ovoid, somewhat irregular, mature particles. Previous work has shown that mature smVLPs have fusion properties identical to those of virions, consistent with local, virion-like clustering of 36 E dimers on their surface. The cryo-EM structure and the properties of these VLPs described here relate directly to on-going efforts to use them as vaccine immunogens. IMPORTANCEEctopic expression of flavivirus envelope (E) and precursor M (prM) proteins leads to formation and secretion of empty, virus-like particles (VLPs), which are candidate, non-infectious, virion-like components of flavivirus vaccines. We show that the immature particles of a major class of VLPs -- "small VLPs" (smVLPs), which have smaller diameter than those of virion size, -- are octahedrally (rather than icosahedrally) symmetric, with the same clustering of prM and E, as asymmetric trimers of prM-E heterodimers, found on immature virions. Cleavage of prM and formation of mature, smVLPs yields somewhat irregular, ovoid particles. Design and characterization of VLPs as vaccine components will need to take these properties into account.

microbiology↗

bioRxiv2024

Single-nanoparticle electrophoretic mobility and trapping using active-feedback 3D tracking

Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EPM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EPM on a per-particle basis. Single-nanoparticle EPM is determined by using active feedback to "lock on" to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EPM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EPM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EPM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EPM in various ionic strengths (0.25-5 mM) and found decreased EPM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EPM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EPM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.

biophysics↗

bioRxiv2024

NRF2-dependent regulation of the prostacyclin receptor PTGIR drives CD8 T cell exhaustion

The progressive decline of CD8 T cell effector function--also known as terminal exhaustion--is a major contributor to immune evasion in cancer. Yet, the molecular mechanisms that drive CD8 T cell dysfunction remain poorly understood. Here, we report that the Kelch-like ECH-associated protein 1 (KEAP1)-Nuclear factor erythroid 2-related factor 2 (NRF2) signaling axis, which mediates cellular adaptations to oxidative stress, directly regulates CD8 T cell exhaustion. Transcriptional profiling of dysfunctional CD8 T cells from chronic infection and cancer reveals enrichment of NRF2 activity in terminally exhausted (Texterm) CD8 T cells. Increasing NRF2 activity in CD8 T cells (via conditional deletion of KEAP1) promotes increased glutathione production and antioxidant defense yet accelerates the development of terminally exhausted (PD-1+TIM-3+) CD8 T cells in response to chronic infection or tumor challenge. Mechanistically, we identify PTGIR, a receptor for the circulating eicosanoid prostacyclin, as an NRF2-regulated protein that promotes CD8 T cell dysfunction. Silencing PTGIR expression restores the anti-tumor function of KEAP1-deficient T cells. Moreover, lowering PTGIR expression in CD8 T cells both reduces terminal exhaustion and enhances T cell effector responses (i.e. IFN-{gamma} and granzyme production) to chronic infection and cancer. Together, these results establish the KEAP1-NRF2 axis as a metabolic sensor linking oxidative stress to CD8 T cell dysfunction and identify the prostacyclin receptor PTGIR as an NRF2-regulated immune checkpoint that regulates CD8 T cell fate decisions between effector and exhausted states. One Sentence SummaryThe KEAP1-NRF2 pathway is hyperactivated in terminally exhausted CD8 T cells and drives T cell dysfunction via transcriptional regulation of the prostacyclin receptor, Ptgir.

immunology↗

bioRxiv2024

Zinc-starved Brassicaceae Plants Secrete Peptides thatInduce Root Expansion

Zinc (Zn) deficiency is recognized as a global crisis as it is observed in half of all agricultural soils. However, the molecular mechanisms that drive plant physiological responses to soil Zn deficiency are not well understood. We used an untargeted metabolomics approach to search for metabolites exuded from roots during Zn deficiency stress, which led to the discovery of a collection of secreted small defensin-like peptides in Arabidopsis thaliana (named Zinc-Deficiency Responsive Peptides (ZDRPs)). Phylogenetic analysis and untargeted metabolomics revealed ZDRPs in at least eleven accessions of A. thaliana and nine members of the Brassicaceae family. Analysis of Arabidopsis gene mutants and overexpressing lines, in combination with chemical complementation experiments, unveiled a critical role of these peptides in plant root growth. We hypothesize that Brassicaceae secreted peptides enable plants to expand their root mass to reach Zn-rich soil layers and optimize Zn uptake. These data reveal a critical relationship between plant survival, Zn status, root morphology and peptide production. Taken together, our results expand our knowledge regarding micronutrient deficiency responses in plants and could enable in engineering approaches to make plants more resilient to low Zn conditions. SignificanceZinc deficiency is the most abundant micronutrient deficiency affecting about 50% of arable lands thus presenting a high burden for plant health and agriculture globally. In this study, we reveal a metabolic strategy by Brassicaceae to deal with low Zn concentrations. We characterize the role of peptides expressed upon zinc deficiency in a variety of important crop plants. The discovery of a cryptic class of peptides that are made by plant roots specifically suffering from Zn deficiency provides critical insight into the molecular mechanisms by which plants dynamically acclimate to nutrient-limited soils. The identification of peptides actively secreted by zinc-deprived plants has translational value for sustainable agriculture, human health, and bioengineering approaches to enable tolerance to low zinc.

plant biology↗

bioRxiv2024

Cooperativity of weak actomyosin interaction

We report the discovery of a new regulatory mechanism of the actomyosin system in muscle. We show that the weak binding of the myosin-nucleotide complex with unregulated F-actin is a cooperative process. Hundreds of myosin heads must work together for efficient force production in muscle, but the precise mechanism by which they coordinate remains elusive. It is known that myosin initially binds actin weakly, then transitions into a strongly bound state to produce force. Using the contiguous cooperative binding model, we interpreted our experimental results in terms of a cooperativity parameter defined as an increased probability for a myosin head to bind to the actin filament next to the already bound head. Considering the geometric organization of a sarcomere, we propose the formation of cross-bridge clusters composed of up to six myosin heads bound consecutively to actin. The cooperativity of weak actomyosin interaction may explain several challenging questions in muscle physiology, such as the role of myosin isoforms in mixed-isoform hybrid muscles, or the yield of supramaximal rate of force production in decorated skinned muscle fibers. Significance StatementForce in striated muscle results from myosin interacting with actin. Initially, myosin attaches weakly to the thin filament, transitioning to a strongly bound state, generating force. Our experiments show high cooperativity in myosins weak interaction with unregulated actin filament. This cooperative behavior may facilitate the formation of cross-bridge clusters and the cooperative steps of myosin heads between clusters. Consequently, the thin- and thick-filament regulation could govern the spacing between cross-bridge clusters and influence the probability of a myosin head stepping along the thin filament during force development in muscle.

biophysics↗