Structural insights into the activation mechanism of antimicrobial GBP1.

The dynamin-related human guanylate-binding protein 1 (GBP1) mediates host defenses against microbial pathogens. Upon GTP binding and hydrolysis, auto-inhibited GBP1 monomers dimerize and assemble into soluble and membrane-bound oligomers, which are crucial for innate immune responses. How higher-order GBP1 oligomers are built from dimers, and how assembly is coordinated with nucleotide-dependent conformational changes, has remained elusive. Here, we present cryo-electron microscopy-based structural data of soluble and membrane-bound GBP1 oligomers, which show that GBP1 assembles in an outstretched dimeric conformation. We identify a surface-exposed helix in the large GTPase domain that contributes to the oligomerization interface, and we probe its nucleotide- and dimerization-dependent movements that facilitate the formation of an antimicrobial protein coat on a gram-negative bacterial pathogen. Our results reveal a sophisticated activation mechanism for GBP1, in which nucleotide-dependent structural changes coordinate dimerization, oligomerization, and membrane binding to allow encapsulation of pathogens within an antimicrobial protein coat.

Structure of tetrameric forms of the serotonin-gated 5-HT3A receptor ion channel.

Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of many fully assembled channel structures, our understanding of assembly intermediates, multimer assembly mechanisms, and potential functions of non-standard assemblies is limited. We demonstrate that the pentameric ligand-gated serotonin 5-HT3A receptor (5-HT3AR) can assemble to tetrameric forms and report the structures of the tetramers in plasma membranes of cell-derived microvesicles and in membrane memetics using cryo-electron microscopy and tomography. The tetrameric structures have near-symmetric transmembrane domains, and asymmetric extracellular domains, and can bind serotonin molecules. Computer simulations, based on our cryo-EM structures, were used to decipher the assembly pathway of pentameric 5-HT3R and suggest a potential functional role for the tetrameric receptors.

Annealing synchronizes the 70S ribosome into a minimum-energy conformation.

Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70S ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.

USP33 promotes nonalcoholic fatty acid disease-associated fibrosis in gerbils via the c-myc signaling.

Nonalcoholic fatty acid disease (NAFLD) is a common complication of obesity associated with liver fibrosis. The underlying molecular mechanisms involved in the progression from normal to fibrosis remain unclear. Liver tissues from the liver fibrosis model identified the USP33 gene as a key gene in NAFLD-associated fibrosis. USP33 knockdown inhibited hepatic stellate cell activation and glycolysis in gerbils with NAFLD-associated fibrosis. Conversely, overexpression of USP33 caused a contrast function on hepatic stellate cell activation and glycolysis activation, which was inhibited by c-Myc inhibitor 10058-F4. The copy number of short-chain fatty acids-producing bacterium Alistipes sp. AL-1, Mucispirillum schaedleri, Helicobacter hepaticus in the feces, and the total bile acid level in serum were higher in gerbils with NAFLD-associated fibrosis. Bile acid promoted USP33 expression and inhibiting its receptor reversed hepatic stellate cell activation in gerbils with NAFLD-associated fibrosis. These results suggest that the expression of USP33, an important deubiquitinating enzyme, is increased in NAFLD fibrosis. These data also point to hepatic stellate cells as a key cell type that may respond to liver fibrosis via USP33-induced cell activation and glycolysis.

Gentle ions for cryo-FIB milling.

Cryo-EM imaging of vitreous samples is limited to a few hundred nanometers in thickness. Focused ion beams can mill windows into cells and tissues for imaging, but they damage biological samples. In this issue of Structure, Yang et al. (2023) quantitatively describe this damage and suggest ways to minimize it.

Zbtb14 Promotes Non-Alcoholic Fatty Liver Disease-Associated Fibrosis in Gerbils via the ß-Catenin Pathway.

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is a popular chronic liver disorder with high morbidity and with no approved therapeutic drugs. Fibrosis is a crucial drug efficacy indicator for NAFLD. Thus, investigating the mechanisms of NAFLD-associated fibrosis and exploring effective therapeutic targets is imperative. METHODS: Gerbil NAFLD-associated fibrosis model was constructed by feeding a high-fat and high-cholesterol diet. The hematoxylin and eosin staining and the alanine transaminase (ALT) and aspartate transaminase (AST) assays were used to determine liver tissue injury. Masson staining and hydroxyproline (Hyp) level determination were used to assess liver fibrosis. High-throughput mRNA sequencing was used to screen differentially expressed genes in the NAFLD-associated fibrosis model. Cell Counting Kit-8 was utilized to test cell viability. RESULTS: Liver injury and fibrosis were observed in the gerbil NAFLD-associated fibrosis model with increased ALT, AST, and Hyp levels. The screened differentially expressed genes were mainly enriched in "negative regulation of hemopoiesis", "response to interleukin-1", and "granulocyte migration". Zinc Finger and BTB Domain Containing 14 (Zbtb14) was upregulated in liver tissues of the gerbil NAFLD-associated fibrosis model, patients with liver fibrosis, and hepatic stellate cells (HSCs). Additionally, Zbtb14 regulated primary HSCs activation via the ß-catenin pathway. CONCLUSIONS: Zbtb14 regulated NAFLD-associated fibrosis via the ß-catenin pathway, for the first time, and it serves as the probable target for NAFLD therapy.

Mining host candidate regulators of schistosomiasis-induced liver fibrosis in response to artesunate therapy through transcriptomics approach.

BACKGROUND: Artesunate (ART) has been reported to have an antifibrotic effect in various organs. The underlying mechanism has not been systematically elucidated. We aimed to clarify the effect of ART on liver fibrosis induced by Schistosoma japonicum (S. japonicum) in an experimentally infected rodent model and the potential underlying mechanisms. METHODS: The effect of ART on hepatic stellate cells (HSCs) was assessed using CCK-8 and Annexin V-FITC/PI staining assays. The experimental model of liver fibrosis was established in the Mongolian gerbil model infected with S. japonicum cercariae and then treated with 20 mg/kg or 40 mg/kg ART. The hydroxyproline (Hyp) content, malondialdehyde (MDA) content, superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities in liver tissue were measured and histopathological changes of liver tissues were observed. Whole-transcriptome RNA sequencing (RNA-seq) of the liver tissues was performed. Differentially expressed genes (DEGs) were identified using bioinformatic analysis and verified by quantitative PCR (qPCR) and western blot assay. RESULTS: ART significantly inhibited the proliferation and induce the apoptosis of HSCs in a dose-dependent manner. In vivo, Hyp content decreased significantly in the ART-H group compared to the model (MOD) group and GPX activity was significantly higher in the ART-H group than in the MOD group. Besides, ART treatment significantly reduced collagen production (p <0.05). A total of 158 DEGs and 44 differentially expressed miRNAs related to ART-induced anti-schistosomiasis liver fibrosis were identified. The qPCR and western blot results of selected DEGs were consistent with the sequencing results. These DEGs were implicated in key pathways such as immune and inflammatory response, integrin-mediated signaling and toll-like receptor signaling pathways. CONCLUSION: ART is effective against liver fibrosis using Mongolian gerbil model induced by S. japonicum infection. We identified host candidate regulators of schistosomiasis-induced liver fibrosis in response to ART through transcriptomics approach.

Modeling of Permeability Coefficient Calculations Based on the Mesostructure Parameters of Tailings.

The permeability coefficient of tailings in tailings ponds, which can affect the release and migration of heavy metals in tailings, also affects the stability of dams by affecting the variation of the height of the saturation line. In this paper, tailings at different levels in a tailings pond were taken as research objects to measure the particle size and permeability coefficient of the tailings. At the same time, CT scanning technology and three-dimensional reconstruction were used to establish the three-dimensional model of the tailings, and the permeability coefficient of the tailings was analyzed from a mesostructural point of view. The results show the following: (1) The particle size of the tailings in the tailings pond decreased rapidly with the increase of distance from the discharge port. When the distance exceeded 8 m, a sudden change occurred, and the decreasing trend obviously slowed down. The particle size of tailings decreased, the compactness increased, and the permeability coefficient decreased gradually. (2) Statistics and analysis of the mesostructure affecting the permeability coefficient of tailings: the error between the calculated value and the measured value of the particle size and porosity of the three-dimensional reconstruction model was small, which proved that the model had high reliability. The porosity, sphericity, and particle size of the tailings were consistent and decreased with the increase of distance from the discharge port. The number of pore branches and nodes of the tailings increased with the increase of the distance from the discharge port, while the average radius and length of the pores decreased. The fragmentation index can characterize the pore channel connectivity of the tailings, which has a high negative linear correlation with the number of pore branches and a positive quadratic curve correlation with the average branch length of the pores. (3) Based on the Kozeny-Carman equation and data regression analysis method and combined with the results of permeability coefficient measurements, the fragmentation index was introduced into the Kozeny-Carman equation. Also, a modified model for calculating the permeability coefficient of the tailings was established based on the mesostructure parameters. By comparing the measured values of the tailings' permeability coefficient, the error range was 1.91-13.24%. The research results have important theoretical significance for the prevention and control of heavy metal pollution and the stability of tailings ponds.

Mesoscopic Seepage Simulation and Analysis of Unclassified Tailings Pores Based on 3D Reconstruction Technology.

Taking the unclassified tailings as the research object, the three-dimensional (3D) pore model was established using computed tomography (CT) scanning technology, image processing, and the 3D reconstruction method. The model was imported into Flac3D software for mesoscopic seepage simulation and analysis. Combined with the laboratory seepage experiment, the influence of tailings' mesoscopic parameters on permeability was explored. The results show that there is a high correlation between the fractal dimension and fragmentation index of tailings pores and the mesoscopic seepage coefficient, with correlation coefficients of 0.987 and 0.973, respectively. When the porosity difference of the pore model is small, the permeability is mainly affected by pore connectivity. The mathematical model between the permeability coefficient and the fragmentation index of tailings is established. The average error between the permeability coefficient calculated by the model and the measured value is reduced to 4.98%, which proves that the mathematical model has guaranteed reliability.

Structure and assembly of double-headed Sendai virus nucleocapsids.

Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.

A nonalcoholic fatty liver disease cirrhosis model in gerbil: the dynamic relationship between hepatic lipid metabolism and cirrhosis.

Nonalcoholic fatty liver disease (NAFLD) usually takes decades to develop into cirrhosis, which limits the longitudinal study of NAFLD. This work aims at developing a NAFLD-caused cirrhosis model in gerbil and examining the dynamic relationship between hepatic lipid metabolism and cirrhosis. We fed gerbil a high-fat and high-cholesterol diet (HFHCD) for 24 weeks, and recorded the gerbil's phenotype at 3, 6, 9, 12, 15, 18, 21, 24 weeks. The model's pathological process, lipid metabolism, oxidative stress, liver collagen deposition and presence of relevant cytokines were tested and evaluated during the full-time frame of disease onset. The gerbil model can induce non-alcoholic steatohepatitis (NASH) within 9 weeks, and can develop cirrhosis after 21 weeks induction. The model's lipids metabolism disorder is accompanied with the liver damage development. During the NAFLD progression, triglycerides (TG) and free fatty acids (FFA) have presented distinct rise and fall tendency, and the turning points are at the fibrosis stage. Besides that, the ratios of total cholesterol (CHO) to high-density lipoprotein cholesterol (HDL-C) exhibited constant growth tendency, and have a good linear relationship with hepatic stellate cells (HSC) (R2 = 0.802, P < 0.001). The gerbil NAFLD cirrhosis model has been developed and possesses positive correlation between lipids metabolism and cirrhosis. The compelling rise and fall tendency of TG and FFA indicated that the fibrosis progression can lead to impairment in lipoprotein synthesis and engender decreased TG level. CHO/HDL-C ratios can imply the fibrosis progress and be used as a blood indicator for disease prediction and prevention.

[Histological study on sciatic nerve repair at different angles in rats].

OBJECTIVE: To discuss the effect of sciatic nerve repair at different angles on the neural regeneration in rats. METHODS: Seventy-two male Sprague Dawley rats were randomly divided into groups A, B, C, and D with 18 rats in each group. The right sciatic nerve was transected at 30, 45, 60, and 90 degrees in groups A, B, C, and D, respectively, and then was repaired. The morphologic assessment of nerve regeneration was performed by gross observation, the wet weight recovery rate of gastrocnemius, histological and ultrastructural observations at 1, 2, and 3 months after operation. RESULTS: Three months later, the wet weight recovery rate of gastrocnemius, motor nerve conduction velocity and action potential of sciatic nerve, axonal diameter, medullary sheath thickness, and medullated nerve fiber counting in groups A and B were significantly better than those in groups C and D (P < 0.01); but no significant difference was found between group A and group B (P > 0.05), and between group C and group D (P > 0.05). CONCLUSION: End-to-end neurorrhaphy at 30-45 degrees can effectively promote the sciatic nerve regeneration in rats.