AbstractReplication of the epigenome occurs concurrently with DNA replication. A major component of epigenetic memory is contained in histones, and this memory is preserved via recycling of parental histones onto the leading and lagging strands of the replication fork. The histones of one parental strand must be incorporated into two nascent strands, a process governed by the replisome's histone chaperones. These chaperones determine which strand each histone is incorporated into and the frequency with which each strand receives parental histones, a determination that is essential for preserving epigenetic landscapes and ensuring proper gene expression following DNA replication. Here, we describe recent developments in our understanding of how parental histone recycling occurs and the effects it has on cells in developmental contexts. Although histones are generally recycled symmetrically to the leading and lagging strands, asymmetric histone recycling can occur naturally in some asymmetrically dividing cells or be induced by manipulating replisome components. Asymmetric histone recycling generates distinct epigenetic states at a given genomic locus, which can result in differential gene expression and ultimately different cell fates following cell division in multicellular organisms. This is important for future studies examining the role of epigenetics in both development and disease contexts.
Mitosis is triggered when the rising activity of CDK1-Cyclin B, amplified by the CDK1/Cdc25/Wee1 feedback loop, overcomes inhibitory signalling from Wee1 and counteracting phosphatases. CDK-opposing phosphatases PP1, PP2A-B55 and PP2A-B56 are regulators of mitosis. A screen for differentially phosphorylated sites in a ΔPP1dis2 genetic background in Schizosaccharomyces pombe identified phosphorylation of T73 or T75 in the regulatory B56Par1 subunit. The B56Par1.T73T75 phosphorylation is directly mediated by CDK1-Cyclin B, and a phospho-mimetic mutation increased while a non-phosphorylatable mutation reduced PP2A-B56Par1 phosphatase activity. Blocking B56Par1.T73T75 phosphorylation reduced cell length in unperturbed divisions from 14 to 12 µm, without causing pleiotropic defects. Therefore, blocking phosphorylation at T73T75 alone prematurely unlocked amplification of the CDK1/Cdc25/Wee1 feedback loop, advancing cells into mitosis. Signalling from T73T75 reveals for the first time that timely mitotic commitment in unperturbed cycles is mediated by PP2A-B56.
AbstractInflammatory bowel diseases (IBDs) are a major public and veterinary health concern, but the causes are poorly understood. In this review, we discuss the potential of mycobacteria as causative factors for such diseases. We focus on similarities between the most common human IBD, Crohn's disease, and a common IBD in cattle, Johne's disease. Both are multifactorial diseases, leading to a chronic hyperinflammatory immune response of the intestines. However, the underlying genetic and environmental factors, such as variations in the intestinal microbiome, are still poorly understood. While Johne's disease has been shown to be caused by Mycobacterium avium subsp. paratuberculosis, the likeliness of mycobacteria as a causative factor of Crohn's disease is still heavily debated. In this review, we summarize the advances in research that could be used to further investigate the role of mycobacteria in intestinal diseases and to give better estimations about which mycobacterial species are most probably hazards for health. New advances in molecular, genetic and imaging methods give hope for better diagnostics, disease prevention, and development of new therapeutics. In addition, these techniques offer researchers a toolbox and general model systems for better understanding the mechanisms of intestinal diseases caused by mycobacteria and the role of the microbiome in the control of disease progression.
AbstractHost–pathogen interactions frequently depend on key components of the bacterial cell surface, such as capsules and lipopolysaccharides in Gram-negative bacteria. The first step in the synthesis of lipid-linked polysaccharides is the substitution of a uridine diphosphate (UDP)-sugar by a lipid monophosphate catalysed by a phosphoglycosyl transferase (PGT). We report the 3.0 Å cryo-electron microscopy apo-structure of the PGT enzyme WbaP from Escherichia coli, a UDP-galactose:undecaprenolphosphate galactose-1-phosphoryl transferase. The structure is a dimer with each monomer formed of four N-terminal transmembrane helices, a small α/β domain with a distinctive β-hairpin that inserts into the other monomer, and a catalytic domain, which sits perpendicular to the transmembrane domain. A complex of WbaP with the UDP-galactose substrate shows binding of the UDP moiety by R319 and R377. Mutations of R319 and R377, along with K331 and R401, highlighted the essential nature of these residues for the catalytic activity of the protein, as confirmed by an in vivo functional assay. Our results provide new insights into the PGT family of enzymes.
AbstractStress granules form in response to diverse cellular perturbations to sequester translation components until the stress is resolved. Stress granules are composed of RNA–protein assemblies in membrane-delimited structures and must be rapidly disassembled to release components to allow translation to resume. Disassembly of stress granules formed in response to heat stress is dependent on ubiquitylation of stress granule components such as G3BP1. Ubiquitylation of stress granule proteins recruits the AAA-ATPase p97 (also known as VCP) to enable ubiquitin-dependent disassembly of these structures. Loss of p97 activity leads to the persistence of stress granules and is implicated in several age-related neurodegenerative diseases. Here, we show that p97 recruitment to stress granules is dependent on its ubiquitin-binding co-factor p47. p47 translocates to stress granules in response to a variety of cellular stressors and is required for the recruitment of p97 to stress granules. Loss of p47 leads to an inhibition in stress granule disassembly. We further show that p47 associates with G3BP1 in response to heat stress in a ubiquitin-dependent manner. Taken together, our data add to the growing list of p97 adaptors that are implicated in the recruitment of p97 for the dissolution of stress granules.
Intestinal epithelial cells play a crucial role in teleost defence against complex aquatic environments. However, the study of intestinal mucosal immunity in teleosts has been hindered by the lack of reliable and specific marker genes to distinguish between different cell types. In this study, single-cell RNA-seq analysis of the intestinal epithelial cells from healthy and infected Sebastes schlegeli was performed to investigate the heterogeneity of teleost intestinal epithelial cells. Immune cells, including T cells, B cells, non-specific cytotoxic cells (NCCs) and myeloid cells, and non-immune cells including enterocyte, erythrocyte, BEST4+ cell, goblet cell and enteroendocrine cell, were identified. Several notable cell populations, including early myeloid cells, lysosome-rich enterocytes, enterocyte progenitors and BEST4+ cells, were characterized in detail. Additionally, significant changes in the expression of actin polymerization-related genes were observed in various intestinal mucosal cell types following Edwardsiella piscicida infection, suggesting a mechanism of invasion with E. piscicida. These findings enhance our understanding of teleost intestinal cellular composition and provide valuable insights for the development of therapeutic strategies against E. piscicida.
Feeding behaviour is not solely governed by metabolic need, but emerges from the integration of internal state, sensory input, competing motivational demands and prior experience. In this review, we synthesize current understanding of the neural and physiological mechanisms that shape feeding-related decision-making across species, with a focus on rodents. We first outline core homeostatic circuits that regulate energy balance and then consider how interoceptive and exteroceptive sensory signals inform feeding behaviour. We next examine appetitive influences, including reward and palatability, alongside aversive competing inputs, such as threat and stress. We then discuss how learning and memory shape feeding through experience-dependent processes, before considering how all of these signals converge in cortical valuation and integration circuits to guide food-related choices. Finally, we address how disruptions in these systems contribute to disorders, such as obesity, anorexia nervosa and binge-eating disorder, and evaluate how rodent models can be used to study underlying mechanisms while highlighting their limitations. Together, this framework positions feeding as a context-dependent decision-making process and highlights the need for integrative approaches to understand its dysregulation in disease.
The presence of lipopolysaccharide (LPS) contaminant from the vector expression bacteria Escherichia coli was described as a factor responsible for accelerating the in vitro fibrillation of recombinant α-synuclein (αS), a key protein involved in the neuropathogenesis of Parkinson's disease. Herein, we describe an efficient protocol for the removal of LPS from αS samples based on phase separation using Triton X-114. Importantly, this method was more feasible, faster and cheaper in eliminating LPS than the commercially available protocol using an affinity matrix of modified polymyxin B. Endotoxin-free αS (αSLPS-free) and the protein purified by a commonly used method (αSc) were evaluated in terms of the kinetics of fibrillation, the microstructure of the aggregates and their susceptibility to certain inhibitors of fibrillation. Monomeric αSc and αSLPS-free exhibit quite different susceptibility to modulators of the fibrillation process, despite their fibrils having similar morphologies and thickness according to the atomic force microscopy analysis. Unlike αSc, the fibrillation of αSLPS-free was poorly inhibited to low concentrations of rosmarinic acid or baicalein. On the other hand, αSLPS-free, but not αSc, had its fibrillation accelerated by harman and rifampicin. Collectively, these results highlight that the presence of LPS might generate artefacts regarding the in vitro screening of fibrillation modulators.
AbstractCancer remains a leading cause of death globally, with nearly 10 million deaths in 2020. Advances in genomic technologies have revolutionized cancer research, shifting focus towards precision medicine based on comprehensive tumour genomic profiling. Concurrently, deep learning (DL) has emerged as a powerful paradigm for complex biological data. This review critically assesses recent advances in DL applications for tumour genomics, emphasizing four key domains: DNA sequencing analysis for mutation detection, gene expression profiling for cancer subtype classification, methylation function prediction for epigenetic characterization and integrative multi-omics approaches for comprehensive tumour profiling. We systematically analyse how different DL architectures—including convolutional neural networks, recurrent neural networks, graph neural networks, autoencoders and transformers—address specific challenges in cancer genomics. Our review highlights how these approaches significantly enhance detection sensitivity for genomic alterations, improve cancer subtype stratification, identify novel biomarkers and optimize therapeutic target selection. We examine technical challenges in DL implementation, including model interpretability, data scarcity, computational requirements and integration issues, alongside emerging solutions such as explainable AI, federated learning, and multi-modal frameworks. By synthesizing methodological innovations and identifying research directions, this review provides bioinformaticians and cancer researchers with a roadmap for leveraging DL to advance precision oncology.
AbstractGonadotropin-releasing hormone (GnRH) is a peptide hormone forming a central component of the hypothalamic–pituitary–gonadal axis and is critical for controlling reproductive functions. Dysregulated GnRH is implicated in many steroid hormone-dependent diseases, and its receptor, GnRHR, is an attractive and clinically exploited therapeutic target. Mounting evidence suggests that beyond the hypothalamus and pituitary, GnRH and GnRHR are expressed in reproductive and non-reproductive, healthy and malignant peripheral tissues, where they act in an autocrine and paracrine manner. This review provides an updated overview of GnRH and GnRHR signalling with a focus on extrapituitary autocrine and paracrine roles in female reproductive health. We examine the molecular and cellular mechanisms of extrapituitary GnRHR signalling, including G-protein coupling profiles, and alternative cell-specific mechanisms that differ from pituitary signalling. We highlight recent data surrounding the (patho) physiological functions of local GnRH systems, including in the endometrium, ovary, placenta and breast, and their implications for hormone-dependent gynaecological conditions and cancers. Finally, we consider implications of peripheral GnRH/GnRHR systems for therapeutic innovation, including avenues for targeted or biased GnRH-based therapeutics, GnRH/GnRHR-mediated ‘off target’ effects of GnRH analogues, and explore future translational avenues for the treatment of both hormone-dependent and hormone-refractory diseases.
AbstractNeuropeptides derived from larger precursor proteins are neuronal signalling molecules that regulate physiological processes and behaviour. Some precursors, particularly in invertebrates, give rise to ‘cocktails’ of structurally related neuropeptides, but the functional significance of this phenomenon is poorly understood. Here, we investigate this by analysing the evolution and receptor pharmacology of SALMFamide-type neuropeptides in starfish (class Asteroidea, phylum Echinodermata). Two types of SALMFamide precursors occur in echinoderms: L-type and F-type, which contain neuropeptides that typically have C-terminal LxF-NH2 and FxF-NH2 motifs (x is variable), respectively. In starfish, L-type and F-type precursors typically contain seven and nine neuropeptides, respectively, but taxon-specific loss/gain of neuropeptides has occurred. Experimental tests revealed that most neuropeptides derived from L-type and F-type precursors in the starfish Asterias rubens exhibit similar potency/efficacy as ligands for their kisspeptin-type receptors, ArKPR7 and ArKPR6, respectively. However, the N-terminally positioned neuropeptide in each precursor has lower potency/efficacy. Furthermore, one neuropeptide derived from the F-type precursor exhibits convergent similarity with L-type precursor-derived neuropeptides, but it has low potency as a ligand for ArKPR7. Our findings indicate that structurally related neuropeptides derived from the same precursor are functionally redundant as receptor ligands; therefore, loss of neuropeptides and/or neuropeptide bioactivity can occur.
Stress granules form in response to diverse cellular perturbations to sequester translation components until the stress is resolved. Stress granules are composed of RNA-protein assemblies in membrane-delimited structures and must be rapidly disassembled to release components to allow translation to resume. Disassembly of stress granules formed in response to heat stress is dependent on ubiquitylation of stress granule components such as G3BP1. Ubiquitylation of stress granule proteins recruits the AAA-ATPase p97 (also known as VCP) to enable ubiquitin-dependent disassembly of these structures. Loss of p97 activity leads to the persistence of stress granules and is implicated in several age-related neurodegenerative diseases. Here, we show that p97 recruitment to stress granules is dependent on its ubiquitin-binding co-factor p47. p47 translocates to stress granules in response to a variety of cellular stressors and is required for the recruitment of p97 to stress granules. Loss of p47 leads to an inhibition in stress granule disassembly. We further show that p47 associates with G3BP1 in response to heat stress in a ubiquitin-dependent manner. Taken together, our data add to the growing list of p97 adaptors that are implicated in the recruitment of p97 for the dissolution of stress granules.
AbstractInsulin-related hormones regulate key life processes in the animal kingdom, from metabolism to growth, lifespan and ageing, through an evolutionarily conserved insulin and insulin-like hormones signalling axis (IIS). In humans, the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. In Drosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR) that follows the blueprint of hIR/hIGF-1R. This report describes two cryo-EM structures of the dmIR ectodomain (dmIR-ECD) in complex with DILP2, revealing their relationship to other known DILP5/2/1 complexes. A high excess of DILP2 yielded two dmIR-ECD complexes in asymmetric conformations, similar to that observed in some complexes of hIR and in the dmIR-ECD:DILP5 complex. This stoichiometric and structural heterogeneity was not observed in DILP5:dmIR-ECD and DILP2 full-length dmIR assemblies. Also, in contrast to DILP5, the resistance of DILP2 to form more dmIR-ECD–saturated complexes, despite very high 40 : 1 excess of this hormone, suggests some structural bases for DILP1-7 specificities. This work expands understanding of the dmIR conformational flexibility, indicating that insect dmIR follows a more hIR:IGF-1R receptor hybrid mode of structural signal transduction pattern induced by various two-chains DILPs.
Animal models with natural variation in family structure, like the prairie vole (Microtus ochrogaster), offer valuable insight into how parental care shapes offspring behaviour. While prior studies have linked early care to long-term behavioural outcomes, the underlying brain network adaptations remain unclear. Using resting-state functional magnetic resonance imaging, we examined how monoparental (single-parent) versus biparental rearing influences brain connectivity and socio-sexual behaviour. Offspring raised by a single parent received less licking and grooming, and monoparentally reared males failed to form pair bonds after 48 h of cohabitation. Functional connectivity analysis revealed distinct networks shaped by early parental care. One network was linked specifically to monoparental upbringing, while another correlated with the amount of care received. During cohabitation, additional networks associated with prosocial behaviour and pair bonding were also modulated by early-life care. These results demonstrate that parental rearing has long-term effects on brain functional organization and social behaviour in adulthood.
AbstractAnatomists have recognized the periosteum as essential for bone growth and repair, and yet its broader physiological roles have remained underappreciated. Emerging evidence now positions the periosteum not only as a structural membrane, but also as a dynamic interface that integrates mechanical load, nutritional status, metabolic cues and systemic hormones to regulate skeletal homeostasis. In this review, we trace the historical foundations that first revealed periosteal function and synthesize modern insights into the cellular and molecular pathways that enable this tissue to sense and respond to its environment. We highlight nutrient- and energy-sensing mechanisms, alongside classical endocrine pathways. We also discuss mechanical load sensing, neural, vascular and immune signals within the periosteum. By uniting historical observations with single-cell and spatial omics datasets, we propose a modern framework in which the periosteum is reconsidered as an endocrine organ with implications for bone growth, homeostasis and regeneration.
Aeromonas species are globally significant pathogens. However, the mechanisms driving their antimicrobial resistance patterns remain unclear. This study addresses the spread of resistance genes in the Aeromonas genus through a large-scale genomic analysis of all complete Aeromonas genomes in the RefSeq database. The emergence of next-generation genomic sequencing enabled the sequencing, assembling and annotation of numerous genomes with a description and characterization of the genomic plasticity and the pan-resistome, through bioinformatics programmes, of each species in the Aeromonas genus, and revealed species-specific patterns of resistance determinants. Leveraging these genomic insights, we applied a reverse vaccinology approach with a subtractive genomic workflow to select novel in silico vaccine targets for the three main pathogens: A. veronii, A. hydrophila and A. caviae. These protein candidates offer a potential alternative to prevent the spread of antibiotic resistance genes. Our findings underscore that continuous genomic surveillance is essential for monitoring established and emerging pathogens. While further in vitro and in vivo validation is pending, this work provides a robust framework for understanding Aeromonas resistance and developing new strategies to protect public and environmental health.
AbstractAngiogenesis, the formation of new blood vessels from pre-existing vasculature, is a complex and tightly regulated biological process that plays a fundamental role in both physiological and pathological tissue remodeling by facilitating the delivery of oxygen and nutrients. Over recent decades, extensive research has identified a wide array of factors that regulate the balance between endothelial cell quiescence and activation. This review discusses the cellular events and molecular mechanisms that regulate angiogenesis within skeletal muscle, considering dynamic interactions with the extracellular matrix and highlighting the critical involvement of multiple resident and infiltrating cell types—including myofibres, satellite cells, fibro-adipogenic progenitors, immune cells and pericytes. The current understanding of these regulatory networks is examined in both healthy muscle tissue as part of the phenotype changes that occur during exercise and in pathological conditions that affect skeletal muscle angiogenesis. Particular attention is given to introduce data of emerging high-resolution techniques, especially omics-based approaches such as single-cell RNA sequencing (scRNA-seq) of skeletal muscle tissue. These methodologies hold significant promise for elucidating cell-type-specific roles and intercellular interactions that drive angiogenic processes in both physiological and disease contexts. Despite substantial progress, the precise mechanisms governing angiogenesis in skeletal muscle remain only partially understood.
AbstractAlzheimer’s disease (AD) is the leading cause of dementia and the most common neurodegenerative disorder. Understanding the molecular pathology of AD may help identify new ways to reduce neuronal damage. In the past decades, Drosophila has become a powerful tool in modelling mechanisms underlying human diseases. Here, we investigate how the expression of the human 42-residue β-amyloid (Aβ) carrying the E22G pathogenic ‘Arctic’ mutation (Aβ42Arc) affects axonal health and behaviour in Drosophila. We find that Aβ42Arc flies present aberrant neurons, with altered axonal transport of mitochondria and aberrant terminal boutons at neuromuscular junctions. We demonstrate that the motor proteins kinesin-1 and kinesin-3 are essential for the correct development of neurons in Drosophila larvae and in human induced pluripotent stem cell-derived cortical neurons. We then show that the overexpression of kinesin-1 or kinesin-3 restores the correct number and morphology of boutons in Aβ42Arc-expressing neurons and rescues neuronal function measured by negative geotaxis locomotor behavioural assay. We therefore provide new evidence towards understanding the mechanisms of axonal transport defects in AD, and our results support the idea that kinesins should be considered as potential drug targets to help reduce dementia-associated disorders.
Axonal regeneration in the central nervous system is imperative for functional restoration following spinal cord injury (SCI). Myeloid cells are key regulators of axonal regeneration, yet their roles are not fully revealed. SCI perturbs glucose metabolism; however, its precise impact on axonal regeneration remains undefined. Moreover, whether myeloid cells orchestrate glucose metabolic responses to facilitate regeneration is unclear. Here, using the zebrafish Mauthner cell axon transection model, we demonstrate that following SCI, myeloid cell deficiency leads to a late-stage glucose surge, which leads to impaired axonal regeneration. We further identify glucagon signalling as a critical molecular determinant of this metabolic dysregulation and show that targeted mutations in gcga or its receptors (gcgra, gcgrb) rescue the axonal regeneration defects caused by myeloid cell deficiency. Finally, cell-depletion experiments demonstrated that macrophages are responsible for the late-stage hyperglycemia and defective axon regeneration of Mauthner cells. These findings suggest that glucose metabolism plays a critical role in macrophage-warranted axon regeneration in the spinal cord, positioning glucose homeostasis as a potential therapeutic target for enhancing axon regeneration and recovery.
