Communications Biology最新文献

Polar growth and cell shape determination in mycelium-forming Streptomyces bacteria depends on the function of a polarly localised multiprotein complex that directs cell wall synthesis - the polarisome. This complex assembles around the essential cell polarity determinant DivIVA, alongside other largely unknown components. We report here the discovery of a conserved hybrid histidine kinase-like protein, PsmA, that interacts and co-localises with DivIVA at the hyphal tips. Deletion of psmA affects the shape and dynamics of the polarisome, leading to aberrant cell shape and hyphal hyperbranching. PsmA is a pseudokinase that lacks the critical histidine residue in its catalytic core. Our results suggest that PsmA tunes the dynamics and properties of the DivIVA-based polar organelle in streptomycetes in parallel to but not redundantly with Scy and FilP, two coiled-coil proteins known to influence polarisome properties. In summary, PsmA interacts with DivIVA and modulates the integrity of the growth zones at hyphal tips.

Developability optimisation is an important step for successful biotherapeutic design. For monoclonal antibodies, developability is relatively well characterised. However, progress for novel biotherapeutics such as nanobodies is more limited. Differences in structural features between antibodies and nanobodies render current antibody computational methods unsuitable for direct application to nanobodies. Following the principles of the Therapeutic Antibody Profiler (TAP), we have built the Therapeutic Nanobody Profiler (TNP), an open-source computational tool for characterising nanobody developability. Tailored specifically for nanobodies, it accounts for their unique properties compared to conventional antibodies for more efficient development of this novel therapeutic format. We calibrate TNP metrics using the 36 currently available sequences from clinical-stage nanobody-based drugs. We also collected experimental developability data for 108 nanobodies expressed as IgG constructs and examine how these results are related to the TNP guidelines. TNP is available as a web application at opig.stats.ox.ac.uk/webapps/tnp.

The soil microbiome plays a vital role in maintaining soil nutrient levels and ecological stoichiometry balance. However, the relationships between rhizosphere microbiomes and soil ecological stoichiometric characteristics, including organic carbon (SC), total nitrogen (SN), total phosphorus (SP), and their ratios, remain poorly understood. Here, we used a temperate mountain ecosystem as a natural laboratory along a ~ 2190 m elevational gradient spanning a desert steppe-alpine meadow transition. We investigated rhizosphere microbiomes from 20 dominant plant populations across 17 sites by integrating environmental factors, microbial community structure, functional genes, microbial biomass, and ectorhizosphere soil stoichiometric characteristics. Ectorhizosphere soil stoichiometric characteristics were significantly associated with microbial biomass stoichiometric characteristics, rhizosphere community composition, and C-, N-, and P-cycling genes, with functional genes emerging as the strongest predictors. Structural equation modeling further identified the composition and diversity of functional genes as key drivers of soil stoichiometric characteristics. Geographic and edaphic factors exerted primarily direct effects, whereas climatic influences were indirect and mediated through the rhizosphere microbiome. These findings highlight the rhizosphere microbiome as a critical biological filter linking climate to soil nutrient stoichiometry at the root-soil interface.

Mesenchymal stem cell-derived extracellular matrix (mECM) is increasingly recognized in tissue regeneration due to its high biocompatibility, controllability, and customizability. In musculoskeletal diseases, mECM provides a 3D scaffold mimicking the natural cellular environment and contains bioactive components regulating cell behavior and fate to promote tissue regeneration and repair. This review summarizes the preparation methods and composition of mECM, its effects on regulating cell behavior, and its applications in bone, cartilage, muscle, nerve, and blood vessel repair. It also analyzes the potential mechanisms of mECM's effects and identifies key challenges to be addressed prior to clinical translation, outlining future development directions.

Pericytes, essential components of the tumor microenvironment, undergo phenotypic alterations that influence cancer progression, yet the molecular mechanisms governing these changes remain poorly understood. Here, we investigate the role of Notch3 signaling in pericyte phenotype and functions in colorectal cancer (CRC). Using lineage tracing approaches, we show that murine tumor pericytes originate from normal tissue-resident pericytes, which proliferate inside tumors. In vivo genetic manipulation reveals that Notch3 pathway activation promotes pericyte proliferation, while suppressing contractile protein expression, and leads to increased endothelial cell proliferation and reduced blood vessel integrity. In contrast, Notch3 deletion leads to decreased endothelial proliferation, blood vessel normalization, and a significant reduction in tumorigenesis in an advanced orthotopic mouse model. Single-cell RNA sequencing analysis uncovers significant pericyte heterogeneity in both mouse colitis-associated cancer and human CRC. It specifically identifies distinct subpopulations characterized by differential Notch3 activity, which is enriched in a synthetic subset and absent in a contractile subset, further supporting our in vivo findings. Our results establish Notch3 as a key regulator of pericyte phenotypic plasticity in CRC and suggest that targeting this pathway could represent a promising strategy for improving therapeutic outcomes through vascular normalization.

GPR99 holds promise as a potential therapeutic target for inflammatory diseases. GPR99 exhibits marked basal activity when coupled with the G_q protein, its activation mechanism remains elusive. In this study, we determine the high-resolution structure of the human GPR99 in complex with the heterotrimeric miniG_q in the ligand-free state using cryo-electron microscopy (cryo-EM). Our structural analysis and functional experiments reveal that the second extracellular loop (ECL2) of GPR99 occupies the orthosteric binding pocket, thereby promoting receptor self-activation. Moreover, we observe structural water molecules forming an extended polar network that connects ECL2 and the binding pocket, intricately linking these elements to the receptor's functional activity. Structure-based mutagenesis experiments further validate the critical role of ECL2 in intracellular signal transduction of GPR99, offering a structural basis for exploring its function under physiological or pathological conditions. Additionally, these findings also provide a crucial theoretical framework for the design of drugs targeting GPR99.

Atypical sensory processing is a common feature of autism, yet the neural computations that give rise to these differences, particularly in relation to biological sex and etiological origin, remain unclear. Here we examine predictive auditory processing at the single-neuron level in the inferior colliculus of two adult rat models of autism: a genetic model with a heterozygous Grin2b deletion (Grin2b + /-) and an environmental model based on prenatal valproic acid exposure. We recorded neuronal responses to an auditory oddball paradigm and a cascade control sequence across lemniscal and non-lemniscal IC divisions under high-intensity stimulation, allowing us to derive indices of repetition suppression, prediction error and neuronal mismatch. Using generalized linear mixed-effects models that accounted for animal identity, inferior colliculus division, sex, and rat model, followed by hierarchical group-level comparisons, we identified robust alterations in predictive processing in both autism-like models. These effects varied across inferior colliculus divisions and differed between sexes, revealing distinct phenotype-specific signatures. The results indicate that sex and etiology jointly modulate early auditory computations in autism. More broadly, our findings highlight the translational value of predictive coding frameworks and support the use of complementary animal models to capture neurobiological heterogeneity across the autism spectrum.

The flexibility of human vocal production is well studied, but the direct role of the auditory system in regulating vocalizations in rodents remains largely unexplored. We show that during vocalizations, a fraction of rat auditory cortex neurons shows pre-call activity and different patterns of responses during calls and playback of calls. Additionally, we classified five auditory cortical vocalization responses: pre-call activated, onset activated, onset suppressed, ramping activated and ramping suppressed neurons. Intriguingly, onset suppressed cells can predict vocalization duration and occurrence. Injecting the auditory cortex with muscimol (GABA_A receptor agonist) prolonged vocalizations, while injecting the auditory cortex with gabazine (GABA_A receptor antagonist) shortened them. Similar reductions in call duration were observed during external white-noise stimulation of the auditory cortex and/or other auditory brain structures, resembling the effects of gabazine. Together, neuronal recordings, pharmacological interference and noise induced vocal modifications indicate direct modulation of vocal productions by the rat auditory cortex.

Hepatocellular carcinoma (HCC) is a highly lethal malignancy, with epithelial-mesenchymal transition (EMT)-driven metastasis a key factor for poor prognosis. The C5a/C5a receptor (C5aR) pathway significantly facilitates HCC cell EMT, yet no approved anti-cancer drugs specifically target C5aR. LukS-PV, a component of Staphylococcus aureus-secreted Panton-Valentine leukocidin (PVL), specifically targets C5aR and exerts anti-tumor effects in hematological and solid tumors. However, its impact on HCC EMT and mechanisms remains unknown. Our study showed LukS-PV targets C5aR to inhibit HCC cell EMT, migration, invasion, and in vivo lung metastasis. Mechanistically, LukS-PV downregulates B-cell lymphoma 6 (BCL6), reducing histone deacetylase 6 (HDAC6) expression. Decreased HDAC6 increases heat shock protein 60 (HSPD1) acetylation, promoting its ubiquitin-mediated degradation and EMT inhibition. This study demonstrates LukS-PV targets C5aR to inhibit HCC EMT via the BCL6/HDAC6/HSPD1 axis, highlighting its potential as an HCC therapeutic agent. These findings provide valuable EMT regulatory insights and identify potential HCC therapeutic targets.

Numerous computational approaches have been developed to infer cell state transition trajectories from snapshot single-cell data. Most approaches first require projecting high-dimensional data onto a low-dimensional representation; however, this can distort the dynamics of the system. Using epithelial-to-mesenchymal transition (EMT) as a test system, we show that both biology-guided low-dimensional representations and trajectory simulations in high-dimensional state space, not representations obtained with brute force dimensionality-reduction methods, reveal two broad paths of TGF-β induced EMT. The paths arise from the coupling between cell cycle and EMT at either the G1 or G2/M phase, contributing to cell-cycle related EMT heterogeneity. Subsequent multi-plex immunostaining studies confirmed the multiple predicted paths at the protein level. The present study highlights the heterogeneity of EMT paths, emphasizes that caution should be taken when inferring transition dynamics from snapshot single-cell data in two- or three-dimensional representations, and shows that incorporating dynamical information can improve prediction accuracy.