Communications Biology最新文献

The Sec pathway is an essential protein secretion route for all organisms. In bacteria, the SecA ATPase peripherally associates with the SecYEG channel to form the translocase that mediates preprotein export. Activation of the translocase depends strictly on the synergy of signal peptide and mature domain binding. Thus, client selectivity, translocase activation and protein secretion are coupled by one mechanism. We show here that a previously identified small molecule (HSI#6) binds SecA, modulates its intrinsic dynamics and allosterically activates the translocase in the absence of clients. By uncoupling translocase activation from preprotein binding, HSI#6 transformed the translocase into a promiscuous nanomachine that lost client selectivity and secreted unfolded pre- mature- and cytoplasmic- proteins with high efficiency in vivo or in vitro. To our knowledge, HSI#6 is the first activator of the Sec pathway and might offer unique opportunities for the discovery of new antibacterials.

Sleep deprivation (SD) disrupts systemic homeostasis, but how it drives ocular surface disease remains unclear. Using a male mouse SD model, we show that chronic SD activates the hypothalamic-pituitary-adrenal (HPA) axis, elevates corticosterone, alters gut microbiota, and depletes short-chain fatty acids (SCFAs). These alterations coincide with lacrimal gland atrophy, reduced tear secretion, and increased CD4⁺/CD8⁺ T cell infiltration, accompanied by activation of IL-17-associated inflammatory pathways. Pharmacological inhibition of glucocorticoid synthesis with metyrapone preserves lacrimal gland structure and function while attenuating immune activation. Microbiome-directed interventions, including SCFA supplementation and fecal microbiota transplantation, rebalance gut communities, suppress pro-inflammatory T cell responses, and maintain lacrimal gland homeostasis. Transcriptomic and immunohistochemical analyses further reveal that all three interventions converge on the downregulation of IL-17 signaling. Collectively, these findings establish an HPA-gut microbiome-lacrimal gland axis that links neuroendocrine stress to microbial dysbiosis and ocular inflammation, and they suggest therapeutic strategies for SD-associated lacrimal gland dysfunction.

Cells throughout physiological and pathological contexts are exposed to a broad spectrum of mechanical stimuli, triggering extensive nuclear deformation and chromatin remodeling. These mechanical cues drive the cell to dynamically adapt through coordinated structural, epigenetic, and biochemical mechanisms to withstand mechanical stress while protecting genomic integrity. However, whether such cellular adaptations are reversible or result in persistent alterations remains unresolved. In cancer metastasis, addressing this issue is critical: confined migration through narrow pores prompts chromatin condensation with heterochromatin enrichment, yet cancer cells must preserve their oncogenic potential while preparing for future deformations. Therefore, the ability of these cells to reconcile reversible chromatin remodeling and mechanical memory could be key to metastatic resilience. Here, using a custom-designed microfluidic device to monitor single-cell chromatin reorganization, we show confined migration induces partially-reversible chromatin condensation: total highly-condensed chromatin content is recovered after deformation, but the distribution of condensed chromatin clusters remains altered. Our findings highlight this duality of chromatin condensation as both a short-term adaptive response and a mechanical memory strategy, which could potentially contribute to address cancer invasiveness.

CRISPR/Cas9-mediated genome editing has expanded the possibilities for precise gene modifications; however, the efficiency of targeted insertion remains suboptimal. In this study, we describe a triple-reporter system in mouse embryonic stem cells that simultaneously tracks double-strand break (DSB) induction, homology-directed repair (knock-in), and end-joining-mediated targeted insertion (EJ-TI). Using both plasmid and adeno-associated virus (AAV) donor vectors, our results demonstrate that ataxia telangiectasia and Rad3-related kinase (ATR) activity is essential for knock-in regardless of the donor type, whereas ataxia telangiectasia mutated (ATM) inhibition exhibits a donor-dependent role. In cells receiving circular plasmid donors, ATM inhibition with AZD1390 markedly reduced the knock-in and EJ-TI efficiencies, consistent with its canonical role in DSB repair. In contrast, with linear AAV donors, ATM inhibition enhanced the knock-in efficiency by suppressing the overactivation of the ATM-p53-caspase 3 apoptotic pathway and partially suppressing classical non-homologous end-joining. These findings highlight the critical influence of donor DNA configuration on DNA damage response signaling and provide a strategy for optimizing genome editing efficiency by selectively modulating the ATM pathways, an approach that may have significant implications for gene therapy, cell engineering, and other applications.

Insect pest population control via sterile insect technique markedly benefits from separation by sex prior to release. To simplify this process, traditional genetics has been deployed to develop genetic sexing strains (GSSs) for several disease vectors and agricultural pests of vast economic significance, although very few are applied in the field due to associated fitness costs and instability. In this study, we generated a method to engineer cisgenic GSS (CGSS) in insects. We use CRISPR/Cas9-mediated homology-directed repair to seamlessly translocate a sex-specific alternatively spliced intron into a dominant phenotypic gene generating a genetically stable strain that enables sex-sorting by eye. To achieve this feat, we use Ceratitis capitata as our model and relied on the sex-specifically spliced intron of its endogenous transformer gene, which we seamlessly inserted a copy into the pupal colouration white pupae gene. This minimal modification resulted in the generation of a homozygous strain we term IMPERIAL that was genetically and phenotypically stable where all female pupae are brown while male pupae are white with overall good fitness. By minimally editing the genome, our novel CGSS approach can be applied to other pests that may aid more efficient and economically suitable pest control.

Divalent cations such as Mg²⁺ and Ca²⁺ are key modulators of chromatin architecture, yet their atomistic influence on nucleosome structure and histone tail dynamics remains elusive. Here, we present 81 microseconds of all-atom molecular dynamics (MD) simulations to dissect how these ions shape nucleosome dynamics and plasticity. We quantitively mapped the selective binding patterns of Mg²⁺ and Ca²⁺ in nucleosomes with and without histone tails, revealing distinct ion-nucleosome interactions. Notably, divalent ion binding reduces inter-gyre electrostatic repulsion, facilitates DNA gyre compaction, and increases nucleosome stiffness, as quantified by estimates of the Young's modulus and correlated motions within specific DNA regions. Importantly, ion binding weakens histone tail-DNA interactions and enhances tail mobility-particularly that of H3-potentially facilitating access by chromatin regulators and tail-mediated chromatin compaction. These findings reveal a dual role of divalent ions in modulating nucleosome plasticity while reinforcing histone tail dynamics, providing a mechanistic framework for understanding how ionic fluctuations influence gene accessibility and chromatin state.

Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar energy. Liverworts such as Marchantia polymorpha occupy an early evolutionary position among land plants and faced major challenges during terrestrial adaptation, including desiccation, strong light, and UV radiation. We reveal the cryo-electron microscopic structures of PSI-LHCI monomer and homodimer from the liverwort M. polymorpha at resolutions of 1.94 and 2.52 Å, respectively. The high-resolution map allows identification of the cofactors of the monomer and reveal differences between the liverwort and moss, another clade of bryophytes. The PSI-LHCI monomer-monomer is stabilized by PsaG and PsaH interactions on the stromal side, which causes the bending and twisting of the homodimer. PsaM interacts with PsaB tightly, indicating a key role of PsaM in mediating the dimerization.

Interleukin-6 (IL-6) drives metabolic and inflammatory processes central to disease. Current knowledge implicates epigenetic mechanisms in the regulation of these pathways, including through the methylation of CpG sites. This blood-based meta-analysis of three cohorts (n = 4,361) identifies 401 IL-6-associated CpGs enriched in regulatory regions and linked to key immunometabolic genes, including AIM2, MTOR, and IL6R. Three complementary causal inference approaches support most sites as responding to IL-6, with SOCS3 (Suppressor of Cytokine Signalling 3) methylation statistically mediating inflammatory bowel disease risk. Notably, one CpG connected to NFATC2IP (Nuclear Factor of Activated T-cells 2 Interacting Protein) plausibly influences both IL-6 production and multiple immunometabolic conditions, including body mass index and type 2 diabetes. Collectively, our results map the DNA methylation landscape surrounding circulating IL-6 levels and unveil directional effects and distinct functional relationships between epigenetics and inflammation.

The enteric nervous system (ENS) is involved in many gastrointestinal (GI) disorders and our understanding of how gut morphology is disrupted remains limited due to a lack of tools to investigate tissues at the organ scale. Here we present enGLOW (enteric network Gastrointestinal Lightsheet Optical Workflow), a workflow customized for high spatial-resolution investigation of the ENS in gastrointestinal samples. We demonstrate how enGLOW can extract quantitative data in cubic centimeters of intact tissue. In a single dataset, we quantify intestinal wall metrics in autofluorescence and labeled ENS-associated cells in centimeter-long segments of tissue using three-dimensional (3D) segmentation. With virtual tissue flattening, we separate neuronal plexuses in mouse and human samples, and observe variations in mucosal morphology and labeled signal distribution in genetically modified animals. As an optimized ready-to-use workflow, enGLOW expands the gut research toolbox to enable understanding of enteric network morphology at scales that encompass functional networks.

Single-cell RNA sequencing (scRNA-seq) in multi-condition experiments enables the systematic assessment of treatment effects. Analyzing scRNA-seq data relies on linear dimensionality reduction (DR) methods like principal component analysis (PCA). These methods decompose high-dimensional gene expression profiles into interpretable factor representations and prototypical expression patterns (components). However, integrating study covariates within linear DR frameworks remains a challenging task. We present scPCA, a flexible DR framework that jointly models cellular heterogeneity and conditioning variables, allowing it to recover an integrated factor representation and reveal transcriptional changes across conditions and components of the decomposition. We show that scPCA extracts an interpretable latent representation by analyzing unstimulated and IFNß-treated PBMCs and show its utility in mitigating batch effects. We examine age-related changes in rodent lung cell populations, uncovering a previously unreported surge in Ccl5 expression in T cells. We illustrate how scPCA may be employed to identify coordinated transcriptional changes across multiple time-points in depolarized visual cortex neurons. Finally, we show that scPCA elucidates transcriptional shifts in CRISPR-Cas9 chordin knockout zebrafish single-cell data despite large difference cell abundance across conditions. scPCA is a general method applicable beyond scRNA-seq to other high-dimensional datasets.