Structural basis of negative regulation of CRISPR-Cas7-11 by TPR-CHAT.

CRISPR‒Cas7-11 is a Type III-E CRISPR-associated nuclease that functions as a potent RNA editing tool. Tetratrico-peptide repeat fused with Cas/HEF1-associated signal transducer (TPR-CHAT) acts as a regulatory protein that interacts with CRISPR RNA (crRNA)-bound Cas7-11 to form a CRISPR-guided caspase complex (Craspase). However, the precise modulation of Cas7-11's nuclease activity by TPR-CHAT to enhance its utility requires further study. Here, we report cryo-electron microscopy (cryo-EM) structures of Desulfonema ishimotonii (Di) Cas7-11-crRNA, complexed with or without the full length or the N-terminus of TPR-CHAT. These structures unveil the molecular features of the Craspase complex. Structural analysis, combined with in vitro nuclease assay and electrophoretic mobility shift assay, reveals that DiTPR-CHAT negatively regulates the activity of DiCas7-11 by preventing target RNA from binding through the N-terminal 65 amino acids of DiTPR-CHAT (DiTPR-CHATNTD). Our work demonstrates that DiTPR-CHATNTD can function as a small unit of DiCas7-11 regulator, potentially enabling safe applications to prevent overcutting and off-target effects of the CRISPR‒Cas7-11 system.

Structure and activity of the septal peptidoglycan hydrolysis machinery crucial for bacterial cell division.

The peptidoglycan (PG) layer is a critical component of the bacterial cell wall and serves as an important target for antibiotics in both gram-negative and gram-positive bacteria. The hydrolysis of septal PG (sPG) is a crucial step of bacterial cell division, facilitated by FtsEX through an amidase activation system. In this study, we present the cryo-EM structures of Escherichia coli FtsEX and FtsEX-EnvC in the ATP-bound state at resolutions of 3.05 Å and 3.11 Å, respectively. Our PG degradation assays in E. coli reveal that the ATP-bound conformation of FtsEX activates sPG hydrolysis of EnvC-AmiB, whereas EnvC-AmiB alone exhibits autoinhibition. Structural analyses indicate that ATP binding induces conformational changes in FtsEX-EnvC, leading to significant differences from the apo state. Furthermore, PG degradation assays of AmiB mutants confirm that the regulation of AmiB by FtsEX-EnvC is achieved through the interaction between EnvC-AmiB. These findings not only provide structural insight into the mechanism of sPG hydrolysis and bacterial cell division, but also have implications for the development of novel therapeutics targeting drug-resistant bacteria.

A chimeric adenovirus-vectored vaccine based on Beta spike and Delta RBD confers a broad-spectrum neutralization against Omicron-included SARS-CoV-2 variants.

Urgent research into innovative severe acute respiratory coronavirus-2 (SARS-CoV-2) vaccines that may successfully prevent various emerging emerged variants, particularly the Omicron variant and its subvariants, is necessary. Here, we designed a chimeric adenovirus-vectored vaccine named Ad5-Beta/Delta. This vaccine was created by incorporating the receptor-binding domain from the Delta variant, which has the L452R and T478K mutations, into the complete spike protein of the Beta variant. Both intramuscular (IM) and intranasal (IN) vaccination with Ad5-Beta/Deta vaccine induced robust broad-spectrum neutralization against Omicron BA.5-included variants. IN immunization with Ad5-Beta/Delta vaccine exhibited superior mucosal immunity, manifested by higher secretory IgA antibodies and more tissue-resident memory T cells (TRM) in respiratory tract. The combination of IM and IN delivery of the Ad5-Beta/Delta vaccine was capable of synergically eliciting stronger systemic and mucosal immune responses. Furthermore, the Ad5-Beta/Delta vaccination demonstrated more effective boosting implications after two dosages of mRNA or subunit recombinant protein vaccine, indicating its capacity for utilization as a booster shot in the heterologous vaccination. These outcomes quantified Ad5-Beta/Delta vaccine as a favorable vaccine can provide protective immunity versus SARS-CoV-2 pre-Omicron variants of concern and BA.5-included Omicron subvariants.

The severity of addiction mediates loneliness and cortical volume in internet gaming disorder.

Internet gaming disorder (IGD) subjects reported higher loneliness scores than healthy controls. However, the neural correlates underlying the association between loneliness and IGD remain unclear. Thus, the aim of this study was to explore the relationship between loneliness, online gaming addiction and brain structure. In the current study, structural MRI data were acquired from 84 IGD subjects and 103 matched recreational game users (RGUs). We assessed and compared their addiction severity, loneliness scores, and cortical volumes and analyzed the correlations among these values. Significant correlations were found between loneliness scores and brain volumes in the postcentral cortex, the medial orbitofrontal cortex, the rostral anterior cingulate cortex, and the temporal cortex. In addition, the addiction severity scores partly mediated the relationship between loneliness score and cortical volume in IGD. The results showed that participants with extreme loneliness had significant correlations with brain regions responsible for executive control, social threat surveillance and avoidance. More importantly, the severity of addiction mediates loneliness and cortical volume. The findings shed new insight into the neural mechanisms of loneliness and IGD and have implications for potential treatment.

Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization.

The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and profound immune-escape capacity makes it an urgent need to develop broad-spectrum therapeutics. Nanobodies have recently attracted extensive attentions due to their excellent biochemical and binding properties. Here, we report two high-affinity nanobodies (Nb-015 and Nb-021) that target non-overlapping epitopes in SARS-CoV-2 S-RBD. Both nanobodies could efficiently neutralize diverse viruses of SARS-CoV-2. The neutralizing mechanisms for the two nanobodies are further delineated by high-resolution nanobody/S-RBD complex structures. In addition, an Fc-based tetravalent nanobody format is constructed by combining Nb-015 and Nb-021. The resultant nanobody conjugate, designated as Nb-X2-Fc, exhibits significantly enhanced breadth and potency against all-tested SARS-CoV-2 variants, including Omicron sub-lineages. These data demonstrate that Nb-X2-Fc could serve as an effective drug candidate for the treatment of SARS-CoV-2 infection, deserving further in-vivo evaluations in the future.

Structural and functional basis of low-affinity SAM/SAH-binding in the conserved MTase of the multi-segmented Alongshan virus distantly related to canonical unsegmented flaviviruses.

Alongshan virus (ALSV), a newly discovered member of unclassified Flaviviridae family, is able to infect humans. ALSV has a multi-segmented genome organization and is evolutionarily distant from canonical mono-segmented flaviviruses. The virus-encoded methyltransferase (MTase) plays an important role in viral replication. Here we show that ALSV MTase readily binds S-adenosyl-L-methionine (SAM) and S-adenosyl-L-homocysteine (SAH) but exhibits significantly lower affinities than canonical flaviviral MTases. Structures of ALSV MTase in the free and SAM/SAH-bound forms reveal that the viral enzyme possesses a unique loop-element lining side-wall of the SAM/SAH-binding pocket. While the equivalent loop in flaviviral MTases half-covers SAM/SAH, contributing multiple hydrogen-bond interactions; the pocket-lining loop of ALSV MTase is of short-length and high-flexibility, devoid of any physical contacts with SAM/SAH. Subsequent mutagenesis data further corroborate such structural difference affecting SAM/SAH-binding. Finally, we also report the structure of ALSV MTase bound with sinefungin, an SAM-analogue MTase inhibitor. These data have delineated the basis for the low-affinity interaction between ALSV MTase and SAM/SAH and should inform on antiviral drug design.

Cryo-EM structures of human GPR34 enable the identification of selective antagonists.

GPR34 is a functional G-protein-coupled receptor of Lysophosphatidylserine (LysoPS), and has pathogenic roles in numerous diseases, yet remains poorly targeted. We herein report a cryo-electron microscopy (cryo-EM) structure of GPR34 bound with LysoPS (18:1) and Gi protein, revealing a unique ligand recognition mode with the negatively charged head group of LysoPS occupying a polar cavity formed by TM3, 6 and 7, and the hydrophobic tail of LysoPS residing in a lateral open hydrophobic groove formed by TM3-5. Virtual screening and subsequent structural optimization led to the identification of a highly potent and selective antagonist (YL-365). Design of fusion proteins allowed successful determination of the challenging cryo-EM structure of the inactive GPR34 complexed with YL-365, which revealed the competitive binding of YL-365 in a portion of the orthosteric binding pocket of GPR34 and the antagonist-binding-induced allostery in the receptor, implicating the inhibition mechanism of YL-365. Moreover, YL-365 displayed excellent activity in a neuropathic pain model without obvious toxicity. Collectively, this study offers mechanistic insights into the endogenous agonist recognition and antagonist inhibition of GPR34, and provides proof of concept that targeting GPR34 represents a promising strategy for disease treatment.

Lipid-Polymer Hybrid Nanoparticles with Both PD-L1 Knockdown and Mild Photothermal Effect for Tumor Photothermal Immunotherapy.

In developing countries, the incidence of colorectal cancer (CRC) is on the rise. The combination of programmed cell death ligand-1 (PD-L1) siRNA (siPD-L1) and mild photothermal therapy (PTT) is a promising strategy for CRC treatment. In this study, dopamine-modified polyethylenimine (PEI) was prepared to fabricate an IR780 and siPD-L1 codelivery lipid-polymer hybrid nanoparticle (lip@PSD-siP) for the photothermal immunotherapy of CRC. The modification of dopamine can significantly reduce the cytotoxicity of PEI. lip@PSD-siP can be effectively taken up by CT26 cells and successfully escaped from lysosomes after entering the cells for 4 h. After CT26 cells were transfected with lip@PSD-siP, the PD-L1 positive cell rate decreased by 82.4%, and its PD-L1 knockdown effect was significantly stronger than the positive control Lipo3000-siP. In vivo studies showed that lip@PSD-siP-mediated mild PTT and efficient PD-L1 knockdown exhibited primary and distal tumor inhibition, metastasis delay, and rechallenged tumor inhibition. The treatment with lip@PSD-siP significantly promoted the maturation of dendritic cells in lymph nodes. The amount of T cell infiltration in the tumor tissues increased significantly, and the frequency of CD8+ T cells and CD4+ T cells was significantly higher than that of other groups. The percentage of immunosuppressive regulatory cells (Tregs) in the tumor tissue on the treatment side decreased by 88% compared to the PBS group, and the proportion of CD8+CD69+ T cells in the distal tumor tissue was 2.8 times that of the PBS group. The memory T cells of mice in the long-term antitumor model were analyzed. The results showed that after treatment with lip@PSD-siP, the frequency of effector memory T cells (Tem cells) significantly increased, suggesting the formation of immune memory.

Cryo-EM structure of the nucleocapsid-like assembly of respiratory syncytial virus.

Respiratory syncytial virus (RSV) is a nonsegmented, negative strand RNA virus that has caused severe lower respiratory tract infections of high mortality rates in infants and the elderly, yet no effective vaccine or antiviral therapy is available. The RSV genome encodes the nucleoprotein (N) that forms helical assembly to encapsulate and protect the RNA genome from degradation, and to serve as a template for transcription and replication. Previous crystal structure revealed a decameric ring architecture of N in complex with the cellular RNA (N-RNA) of 70 nucleotides (70-nt), whereas cryo-ET reconstruction revealed a low-resolution left-handed filament, in which the crystal monomer structure was docked with the helical symmetry applied to simulate a nucleocapsid-like assembly of RSV. However, the molecular details of RSV nucleocapsid assembly remain unknown, which continue to limit our complete understanding of the critical interactions involved in the nucleocapsid and antiviral development that may target this essential process during the viral life cycle. Here we resolve the near-atomic cryo-EM structure of RSV N-RNA that represents roughly one turn of the helical assembly that unveils critical interaction interfaces of RSV nucleocapsid and may facilitate development of RSV antiviral therapy.

Structural basis of BAM-mediated outer membrane ß-barrel protein assembly.

The outer membrane structure is common in Gram-negative bacteria, mitochondria and chloroplasts, and contains outer membrane ß-barrel proteins (OMPs) that are essential interchange portals of materials1-3. All known OMPs share the antiparallel ß-strand topology4, implicating a common evolutionary origin and conserved folding mechanism. Models have been proposed for bacterial ß-barrel assembly machinery (BAM) to initiate OMP folding5,6; however, mechanisms by which BAM proceeds to complete OMP assembly remain unclear. Here we report intermediate structures of BAM assembling an OMP substrate, EspP, demonstrating sequential conformational dynamics of BAM during the late stages of OMP assembly, which is further supported by molecular dynamics simulations. Mutagenic in vitro and in vivo assembly assays reveal functional residues of BamA and EspP for barrel hybridization, closure and release. Our work provides novel insights into the common mechanism of OMP assembly.

Deficient dynamics of prefrontal-striatal and striatal-default mode network (DMN) neural circuits in internet gaming disorder.

BACKGROUND: Studies have proven that individuals with internet gaming disorder (IGD) show impaired cognitive control over game craving; however, the neural mechanism underlying this process remains unclear. Accordingly, the present study aimed to investigate the dynamic features of brain functional networks of individuals with IGD during rest, which have barely been understood until now. METHODS: Resting-state fMRI data were collected from 333 subjects (123 subjects with IGD (males/females: 73/50) and 210 healthy controls (males/females: 135/75)). First, the data-driven methodology, named co-activation pattern analysis, was applied to investigate the dynamic features of nucleus accumbens (the core region involved in craving/reward processing and addiction)-centered brain networks in IGD. Further, machine learning analysis was conducted to investigate the prediction effect of the dynamic features on participants' addiction severity. RESULTS: Compared to controls, subjects in the IGD group showed decreased resilience, betweenness centrality and occurrence in the prefrontal-striatal neural circuit, and decreased in-degree in the striatal-default mode network (DMN) circuit. Moreover, these decreased dynamic features could significantly predict participants' addiction severity. LIMITATIONS: The causal relationship between IGD and the abnormal dynamic features cannot be identified in this study. All the subjects were university students. CONCLUSIONS: The present results revealed the underlying brain networks of uncontrollable craving and game-seeking behaviors in individuals with IGD during rest. The decreased dynamics of the prefrontal-striatal and striatal-DMN neural circuits might be potential biomarkers for predicting the addiction severity of IGD and potential targets for effective interventions to reduce game craving of this disorder.

Gender difference in network relationship between inter-temporal decisions and prefrontal activation levels in internet gaming disorder.

Background: Impulsivity and decision-making are key factors in addiction. However, little is known about how gender and time sensitivity affect impulsivity in internet gaming disorder (IGD). Objective: To investigate the gender difference of impulsive decision-making and relevant brain responses in IGD. Methods: We conducted a functional magnetic resonance imaging (fMRI) study with 123 participants, including 59 IGD individuals (26 females) and 64 matched recreational game users (RGUs, 23 females). Participants performed a delay-discounting task during fMRI scanning. We examined gender-by-group effects on behavioral and neural measures to explore the preference for immediate over delayed rewards and the associated brain activity. We also investigated the network correlations between addiction severity and behavioral and neural measures, and analyzed the mediating role of brain activity in the link between delay discounting parameters and IGD severity. Results: We found significant gender-by-group interactions. The imaging results revealed gender-by-group interactions in the dorsolateral prefrontal cortex, medial frontal gyrus, and inferior frontal gyrus (IFG). Post hoc analysis indicated that, for females, RGUs showed higher activity than IGD individuals in these brain regions, while for males IGD individuals exhibited higher activity than RGUs. The activation in the left IFG mediated the relation between Internet Addiction Test score and discount rate in females. In males, the activation in the right dlPFC mediated the relation between IAT score and time sensitivity. Discussion: Our findings imply that male IGD participants demonstrate impaired intertemporal decisions associated with neural dysfunction. Influencing factors for impulsive decision-making in IGD diverge between males (time sensitivity) and females (discount rate). These findings augment our comprehension of the neural underpinnings of gender differences in IGD and bear significant implications for devising effective intervention strategies for treating people with IGD.

Uncovering lipopolysaccharide regulation in bacteria via the critical lipid binding tunnel of YciS/YciM.

Gram-negative bacteria contain an asymmetric outer membrane, in which the outer leaflet is composed of lipopolysaccharide (LPS). LPS, a drug target of polymyxin, plays an essential role in drug resistance, biofilm formation, and pathogenesis. An important inner membrane protein, YciM, may be responsible for the regulation of LPS biosynthesis and transport. Here, we report the crystal structure of YciM from Salmonella typhimurium in a complex with a non-specifically bond molecule, an ethylene glycol, which identified a tunnel that could bind lipids. Our in vitro assays showed that YciM could bind lipid molecules with affinity in the micromolar range, while mutagenic and functional studies confirmed that lipid-binding residues are critical for the function of YciM. Additionally, our data also showed that YciM accurately regulates LPS biosynthesis and transport with YciS, which could help to better understand the regulation mechanism of LPS.

Predicting the severity of internet gaming disorder with resting-state brain features: A multi-voxel pattern analysis.

BACKGROUND: Internet gaming disorder (IGD) has become a worldwide mental health concern; however, the neural mechanism underlying this disorder remains unclear. Multivoxel pattern analysis (MVPA), a newly developed data-driven approach, can be used to investigate the neural features of IGD based on massive neural data. METHODS: Resting-state fMRI data from four hundred and two participants with varying levels of IGD severity were recruited. Regional homogeneity (ReHo) and the amplitude of low-frequency fluctuation (ALFF) were calculated and subsequently decoded by applying MVPA. The highly weighted regions in both predictive models were selected as regions of interest for further graph theory and Granger causality analysis (GCA) to explore how they affect IGD severity. RESULTS: The results revealed that the neural patterns of ReHo and ALFF can independently and significantly predict IGD severity. The highly weighted regions that contributed to both predictive models were the right precentral gyrus and left postcentral gyrus. Moreover, topological properties of the right precentral gyrus were significantly correlated with IGD severity; further GCA revealed effective connectivity from the right precentral gyrus to left precentral gyrus and dorsal anterior cingulate cortex, both of which were significantly associated with IGD severity. CONCLUSIONS: The present study demonstrated that IGD has distinctive neural patterns, and this pattern could be found by machine learning. In addition, the neural features in the right precentral gyrus play a key role in predicting IGD severity. The current study revealed the neural features of IGD and provided a potential target for IGD interventions using brain modulation.

The unbalanced behavioral activation and inhibition system sensitivity in internet gaming disorder: Evidence from resting-state Granger causal connectivity analysis.

BACKGROUND: Patients with behavioral or substance addiction show an unbalanced behavioral activation system (BAS) and behavioral inhibition system (BIS) sensitivity. However, the relationship between internet gaming disorder (IGD) and BAS/BIS is obscure and the neurobiological mechanism underlying this relationship remains unclear. METHODS: We recruited 154 IGDs and 229 recreational game users (RGUs) in the current study. First, we explored the relationship between BAS/BIS and IGD. Second, subjects were subdivided into subgroups by BAS/BIS sensitivity. Third, whole-brain Granger causal connectivity (GCC) of striatum and amygdala subdivisions was estimated for the subgroup. Fourth, mediation analysis was performed to explore the role of connectivity in the relationship between IGD and BAS/BIS sensitivity. RESULTS: We found the IGD group scored higher than the RGU on BIS and BASf (fun-seeking) sensitivity. Then, we identified 4 (2*2) subgroups: low/high risk of IGD with low/high BAS/BIS sensitivity groups. Two-way ANCOVA main results of interaction effects showed that in the high BAS/BIS group, the RGU exhibited increased strength in the GCC from the left putamen to the right cuneus, and the IGD exhibited decreased strength in the GCC from the right medial frontal gyrus to the caudate, from the left superior frontal gyrus to the centromedial amygdala, and from the right superior parietal lobule to the left laterobasal amygdala. Moreover, the GCC from the centromedial amygdala to the middle frontal gyrus mediated the directional relationship between BIS and IAT (Young's internet addiction test) scores. CONCLUSIONS: The IGD individuals exhibited higher BIS and BAS-fun seeking sensitivity. Moreover, IGD with unbalanced BAS/BIS sensitivity exhibited alternative connectivity patterns involving amygdala and striatum subdivisions. These findings suggest a neurobiological mechanism for an alternation between IGD and RGU with different BAS/BIS sensitivity.

A Potent Neutralizing Nanobody Targeting the Spike Receptor-Binding Domain of SARS-CoV-2 and the Structural Basis of Its Intimate Binding.

The continuous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) around the world has raised unprecedented challenges to the human society. Antibodies and nanobodies possessing neutralization activity represent promising drug candidates. In this study, we report the identification and characterization of a potent SARS-CoV-2 neutralizing nanobody that targets the viral spike receptor-binding domain (S-RBD). The nanobody, termed as Nb-007, engages SARS-CoV-2 S-RBD with the two-digit picomolar binding affinity and shows outstanding virus entry-inhibition activity. The complex structure of Nb-007 bound to SARS-CoV-2 S-RBD reveals an epitope that is partially overlapping with the binding site for the human receptor of angiotensin-converting enzyme 2 (ACE2). The nanobody therefore exerts neutralization by competing with ACE2 for S-RBD binding, which is further ascertained by our in-vitro biochemical analyses. Finally, we also show that Nb-007 reserves promising, though compromised, neutralization activity against the currently-circulating Delta variant and that fusion of the nanobody with Fc dramatically increases its entry-inhibition capacity. Taken together, these data have paved the way of developing Nb-007 as a drug-reserve for potential treatment of SARS-CoV-2 related diseases.

An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related sarbecoviruses enter host cells by receptor-recognition and membrane-fusion. An indispensable step in fusion is the formation of 6-helix bundle by viral spike heptad repeats 1 and 2 (HR1 and HR2). Here, we report the construction of 5-helix bundle (5HB) proteins for virus infection inhibition. The optimal construct inhibits SARS-CoV-2 pseudovirus entry with sub-micromolar IC50. Unlike HR2-based peptides that cannot bind spike in the pre-fusion conformation, 5HB features with the capability of binding to pre-fusion spike. Furthermore, 5HB binds viral HR2 at both serological- and endosomal-pH, highlighting its entry-inhibition capacity when SARS-CoV-2 enters via either cell membrane fusion or endosomal route. Finally, we show that 5HB could neutralize S-mediated entry of the predominant SARS-CoV-2 variants and a wide spectrum of sarbecoviruses. These data provide proof-of-concept evidence that 5HB might be developed for the prevention and treatment of SARS-CoV-2 and other emerging sarbecovirus infections.