Biology subjects

Suzuki, S.

Publications and source records attributed to Suzuki, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity

The global circulation of SARS-CoV-2 in human populations has driven the emergence of Omicron subvariants, which have become highly diversified through recombination. In late 2024, SARS-CoV-2 Omicron XEC variant emerged from the recombination of two JN.1 progeny, KS.1.1 and KP.3.3, and became predominant worldwide. Here, we investigated virological features of the XEC variant. Epidemic dynamics modeling suggested that spike substitutions in XEC mainly contribute to its increased viral fitness. Additionally, four licensed antivirals were effective against XEC. Although the fusogenicity of XEC spike is comparable to that of the JN.1 spike, the intrinsic pathogenicity of XEC in hamsters was significantly higher than that of JN.1. Notably, we found that the nucleocapsid R204P mutation of XEC enhanced inflammation through NF-{kappa}B activation. Recent studies suggest that the evolutionary potential of spike protein is reaching its limit. Indeed, our findings highlight the critical role of non-spike mutations in the future evolution of SARS-CoV-2.

microbiology↗

bioRxiv2025

Whom Do We Prefer to Learn From in Observational Reinforcement Learning?

Learning by observing others experiences is a hallmark of human intelligence. While the neurocomputational mechanisms underlying observational learning are well understood, less is known about whom people prefer to learn from in the context of observational learning. One hypothesis posits that learners prefer individuals who exhibit a high degree of decision noise (randomness in action selection), free riding on the costly exploration of others. An alternative hypothesis suggests that learners prefer individuals with low decision noise, and imitate consistent and reliable behavior. In a preregistered experiment, we found that most participants preferred to learn from low-noise individuals. Furthermore, exploratory analyses revealed that participants who preferred lownoise individuals tended to rely on imitation of others actions, whereas those who preferred high-noise individuals relied more on learning from others reward outcomes. These findings offer a potential computational account of how learning styles shape partner selection in social learning. Author SummaryIn our daily lives, we often learn by watching others. For example, when starting a new job, we might watch an experienced colleague to learn effective strategies, or an inexperienced coworker to avoid common mistakes. While previous studies have examined how people learn by observing others, less is known about how we decide whom to observe. This study explored whether people prefer to learn from individuals who make consistent choices or those who behave more randomly. At first glance, the answer seems obvious: we would naturally prefer to learn from those who make consistent, reliable decisions. However, there can also be value in learning from someone who behaves unpredictably. For example, when searching for a good restaurant, observing an adventurous friend who tries unfamiliar places might help us discover hidden gems. Despite this potential advantage, we found that most participants preferred consistent decision-makers. Further analysis revealed that participants who favored reliable partners tended to imitate their actions, while those who chose more exploratory partners focused more on outcomes. Our findings suggest that personal learning styles shape partner preferences. These insights could help us understand how people choose whom to learn from in everyday settings like classrooms, or workplaces.

animal behavior and cognition↗

bioRxiv2025

IL-18 produced by pregnant uterus promotes essential inflammatory responses and fetoplacental growth

Placental insufficiency affects fetomaternal health throughout life. Although the interaction between the maternal uterine immune milieu and fetal-derived cells plays a crucial role in placental formation, several aspects remain unclear. Therefore, we conducted this study to investigate the effects of interleukin (IL)- 18, a unique cytokine with both proinflammatory and anti-inflammatory properties, on the uterine immune milieu and placental development. Our results identified pregnant uterine smooth muscle cells as an important source of IL-18, which supports homeostatic type 1 immune responses. IL-18 facilitates appropriate placental development through uterine vascular remodeling and placental angiogenesis. Smooth muscle cell-specific Il18-knockout dam mice exhibited impaired fetoplacental growth and elevated maternal blood pressure, reflecting preeclampsia-like phenotypes. Their offspring demonstrated a tendency toward excessive weight gain and delayed neurodevelopment. Overall, this study emphasizes the essential role of IL-18 in placental formation and its wider implications for fetomaternal health. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/649615v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@27862eorg.highwire.dtl.DTLVardef@da4786org.highwire.dtl.DTLVardef@8dd7e2org.highwire.dtl.DTLVardef@584c41_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISmooth muscle cells in the pregnant uterine myometrium sufficiently produce IL-18 C_LIO_LIIL-18 induces type 1 immune responses in the uterine immune milieu C_LIO_LIIL-18 promotes maternal uterine vascular remodeling and placental angiogenesis C_LIO_LIIL-18-signaling deficiency in the mouse model shows the preeclampsia-like clinical course C_LI

immunology↗

bioRxiv2025

Evolution of BA.2.86 to JN.1 reveals functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), is still circulating among humans, leading to the continuous evolution. SARS-CoV-2 Omicron JN.1 evolved from a distinct SARS-CoV-2 lineage, BA.2.86, spread rapidly worldwide. It is unclear why BA.2.86 did not become dominant and was quickly replaced by JN.1, which possesses one amino acid substitution in the spike protein (S:L455S) and two in the non-spike proteins NSP6 and ORF7b (NSP6:R252K and ORF7b:F19L) compared to BA.2.86. Here, we utilized recombinant viruses to elucidate the impact of these mutations on the virological characteristics of JN.1. We found that the mutation in the spike attenuated viral replication, but the non-spike mutations enhanced replication, suggesting the mutations in the non-spike proteins compensate for the one in the spike to improve viral fitness, as the mutations in the spike contribute to further immune evasion. Our findings suggest that functional changes in both the spike and non-spike proteins are necessary in the evolution of SARS-CoV-2 to enable evasion of adaptive immunity within the human population while sustaining replication. IMPORTANCEBecause the spike protein is strongly associated with certain virological properties of SARS-CoV-2, such as immune evasion and infectivity, most previous studies on SARS-CoV-2 variants have focused on spike protein mutations. However, the non-spike proteins also contribute to infectivity, as observed throughout the evolution of Omicron subvariants. In this study, we demonstrate a "trade-off" strategy in SARS-CoV-2 Omicron JN.1 in which the reduced infectivity caused by spike mutation is compensated by non-spike mutations. Our results provide insight into the evolutionary scenario of the emerging virus in the human population.

microbiology↗

bioRxiv2025

Temperature vaulting: A method for screening selective, slow- and tight-binding inhibitors targeting kinases in their non-native state

A polypeptide folds into its protein tertiary structure in the native state through a folding intermediate in the non-native state. The transition between these states is thermodynamically driven. A folding intermediate of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) autophosphorylates intramolecularly, whereas DYRK1A in the native state no longer catalyzes this reaction. The alteration in substrate specificity suggests a conformational transition of DYRK1A during its folding process. Consistent with this hypothesis, we identified FINDY (1), which inhibits the intramolecular autophosphorylation but not the intermolecular phosphorylation, suggesting that the folding intermediate possesses an alternative inhibitor-binding site. Meanwhile, it remains an issue that the methods for approaching the alternative binding site require an intricate assay tailored to the individual target. Here we show a method, designated as "temperature vaulting," for screening the non-native-state-targeted inhibitors of DYRK1A. Transient heating of recombinant DYRK1A protein drove the reversible transition between the native state and the non-native state targeted by FINDY (1). At physiological temperature, FINDY (1) slowly bound to the DYRK1A protein. These results indicate that transient heating accelerates the slow-binding process by assisting the protein to overcome the high-energy barrier leading to the target non-native state. The energy barrier also slowed down the dissociation process, resulting in tight binding between DYRK1A and FINDY (1). Furthermore, this study suggests that the dissociation rate underlies the inhibition selectivity of FINDY (1) between DYRK1A and its family kinase DYRK1B. This method enables the identification of slow- and tight-binding inhibitors that have been missed in conventional assays. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/632643v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@be5661org.highwire.dtl.DTLVardef@1925beorg.highwire.dtl.DTLVardef@fceb5borg.highwire.dtl.DTLVardef@bfbf91_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSA temperature vaulting method facilitated the screening of a slow- and tight-binding inhibitor targeting DYRK1A in the non-native state. A structure-activity relationship study of FINDY (1) demonstrated that a slight alteration in chemical structure impacts the inhibition kinetics. A molecular dynamics simulation of DYRK1A revealed binding-ready conformations for FINDY (1). The dissociation rate may underlie the inhibition selectivity of FINDY (1) between DYRK1A and DYRK1B in cellular systems.

biophysics↗

bioRxiv2024

Evolutionary flexibility of ribosome biogenesis in bacteria

Ribosomes are essential for protein synthesis and require ribosome biogenesis factors (RBFs) for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed that Candidate Phyla Radiation (CPR), also known as the phylum Patescibacteria, characterized by reduced genomes and smaller ribosomes, has about half the average number of RBFs compared with non-CPR bacteria. Notably, key RBFs such as der, obgE, and rbfA, considered indispensable, are conserved in only around 20%-70% of CPR genomes. Since such repertoires were not observed in reduced genomes of other phyla, CPR presumably diverged early in bacterial evolution. We further confirmed that ribosomal structural changes correlate with reduced RBFs, evidencing co-evolution between RBFs and the ribosome. These findings suggest that ribosomal biogenesis is more flexible than recognized, and the small cell and genome sizes of CPR bacteria and their early divergence may influence the unusual repertoires of RBFs. TeaserRibosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional views of this essential process in evolution.

microbiology↗

bioRxiv2024

Involvement of Hepatitis B Core-Related Antigen in Viral Genome Integration in Patients With Prior Hepatitis B Virus Infection

BackgroundThe incidence of non-B non-C hepatocellular carcinoma (NBNC-HCC), which is negative for hepatitis B surface antigen and hepatitis C virus antibodies, is on the rise. Relatively high numbers of NBNC-HCC patients are hepatitis B core antibody (HBcAb) positive, suggesting that previous HBV infection may play a role in NBNC-HCC development, though the exact mechanisms are unclear. This study aimed to investigate whether HBV genomes are integrated into the host genome of HBcAb-positive NBNC-HCC cases and how these integrations may contribute to cancer development and progression. MethodsHBV detection PCR using HBV-specific primers on DNA extracted from HBcAb-positive NBNC-HCC tissue samples was performed. Positive samples were further examined for HBV integration sites using viral DNA-capture sequencing. Additionally, hepatitis B core-related antigen (HBcrAg) serum levels were measured to assess whether they could be predictive for HBV detection PCR results. ResultsAmong 90 HBcAb-positive NBNC-HCC samples, HBV genome amplification was detected in 18 samples, and elevated HBcrAg levels were associated with the HBV detection PCR results. Seventeen of these samples exhibited HBV integration. The HBV genome was integrated near the TERT gene in 7 samples, resulting in significantly increased TERT mRNA levels; in the KMT2B gene (2 samples); and downstream of LOC441666 (2 samples). ConclusionThe integration sites we identified in our samples have been previously reported in HBV-related HCC, suggesting that HBV integration may also contribute to hepatocarcinogenesis in HBcAb-positive NBNC-HCC. Furthermore, HBcrAg could serve as a potential, noninvasive marker for detecting HBV integration in these cases.

microbiology↗

bioRxiv2024

Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery

Modification of RNA with N6-methyladenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A, along with its associated machinery, has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. However these observational data have yet to be causally examined in vivo. For example, neither perturbation of the key m6A writers Mettl3 and Mettl14, nor the m6A readers Ythdf1 and Ythdf2 have been thoroughly mechanistically characterized in vivo as they have been in vitro. To understand the functions of these machineries, we developed mouse models and found that deleting Mettl14 led to progressive liver injury characterized by nuclear heterotypia, with changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.

molecular biology↗

bioRxiv2024

Macro-environment strongly interacts with warming in a global analysis of decomposition

Empirical studies worldwide show substantial variability in plant litter decomposition responses to warming, leaving the overall impact of climate change on this process uncertain. We conducted a meta-analysis of 109 experimental warming studies across seven continents, utilizing natural and standardized plant material, to assess the overarching effect of warming on decomposition and identify potential moderating factors. Warming influences decomposition differently across macro-environmental gradients of moisture and temperature. Negative warming effects on decomposition in warmer, low-moisture areas were counterbalanced by the positive, though not significant, warming effects in colder areas, resulting in an overall non-significant effect. We determine that at least 5.2 degrees of warming is required for a significant increase in decomposition. This is particularly relevant given the past decades global warmth in higher latitudes, holding a significant proportion of terrestrial carbon. Low-quality plant litter was more sensitive to warming. Therefore, future vegetation changes toward low-quality, temperature-sensitive plants could increase carbon release and reduce the net supply of stored organic matter in the soil by increasing the decomposition of low-quality litter with warming. Our findings emphasize the connection between warming responses, macro-environment, and litter characteristics, refining predictions of climate changes consequences on key ecosystem processes and its contextual dependencies.

ecology↗

bioRxiv2024

Human spermatogonial stem cells retain states with a foetal-like signature

Spermatogenesis involves a complex process of cellular differentiation maintained by spermatogonial stem cells (SSCs). Being critical to male reproduction, it is generally assumed that spermatogenesis starts and ends in equivalent transcriptional states in related species. Based on single-cell gene expression profiling it has been proposed that undifferentiated human spermatogonia can be sub-classified into four heterogenous subtypes, termed states 0, 0A, 0B, and 1. To increase the resolution of the undifferentiated compartment and trace the origin of the spermatogenic trajectory, we re-analysed the single-cell (sc)RNA-seq libraries of 34 post-pubescent human testes to generate an integrated atlas of germ cell differentiation. We then used this atlas to perform comparative analyses of the putative SSC transcriptome both across human development (using 28 foetal and pre-pubertal scRNA-seq libraries) and across species (including data from sheep, pig, buffalo, rhesus and cynomolgus macaque, rat and mouse). Alongside its detailed characterisation, we show that the transcriptional heterogeneity of the undifferentiated spermatogonial cell compartment varies not only between species but across development. Our findings associate state 0B with a suppressive transcriptomic program that, in adult humans, acts to functionally oppose proliferation and maintain cells in a ready-to-react state. Consistent with this conclusion, we show that human foetal germ cells - which are mitotically arrested - can be characterised solely as state 0B. While germ cells with a state 0B signature are also present in foetal mouse (and are likely conserved at this stage throughout mammals), they are not maintained into adulthood. We conjecture that in rodents, the foetal-like state 0B differentiates at birth into the renewing SSC population, whereas in humans it is maintained as a reserve population, supporting testicular homeostasis over a longer reproductive life while reducing mutagenic load. Together, these results suggest that SSCs adopt differing evolutionary strategies across species to ensure fertility and genome integrity over vastly differing life histories and reproductive timeframes.

cell biology↗

bioRxiv2024

Frontal engagement in perceptual integration under low subjective visibility

We investigated how spatiotemporal neural dynamics underlying perceptual integration changed with the degree of conscious access to a set of backward-masked pacman-shaped inducers that generated the percept of an illusory triangle. We kept the stimulus parameters at a fixed near-threshold level throughout the experiment and recorded electroencephalography from participants who reported the orientation and subjective visibility of the illusory triangle on each trial. Our multivariate pattern analysis revealed that posterior and central regions initially used dynamic neural code and later switched to stable neural code. The transition from dynamic to stable neural code in posterior region occurred increasingly later and eventually disappeared with decreasing conscious access. Anterior region primarily used stable neural code which waned with decreasing conscious access, but increased at below-median visibility and remained even when stimulus awareness was minimal. These results demonstrate differential spatiotemporal neural dynamics underlying perceptual integration depending on conscious access and emphasize a unique role of anterior region in processing integrated shape information especially under low subjective visibility.

neuroscience↗

bioRxiv2024

A Novel Support Vector Machine-Based One-Day, Single-Dose Prediction Model of Genotoxic Hepatocarcinogenicity in Rats

The development of a rapid and accurate model for determining the genotoxicity and carcinogenicity of chemicals is crucial for effective cancer risk assessment, and it also contributes to cancer prevention. This study aims to develop a one-day, single-dose model for identifying genotoxic hepatocarcinogens (GHCs) in rats. Microarray gene expression data from the livers of rats administered a single dose of 58 compounds, including 5 GHCs, was obtained from the Open TG-GATEs database and used for the identification of marker genes and the construction of a predictive classifier to identify GHCs in rats. We identified 10 gene markers commonly responsive to all 5 GHCs and used them to construct a support vector machine-based predictive classifier. This classifier effectively distinguishes GHCs from other compounds, demonstrating 100% sensitivity and over 96% specificity. To further assess the models effectiveness and reliability, we conducted multi-institutional one-day single oral administration studies on rats. These studies examined 64 compounds, including 23 GHCs, with gene expression data of the marker genes obtained via quantitative PCR (qPCR) 24 hours after a single oral administration. Our results demonstrate that qPCR analysis is an effective alternative to microarray analysis. The GHC predictive model showed high accuracy and reliability, achieving a sensitivity of 91% (21/23) and a specificity of 93% (38/41) across multiple validation studies in three institutions. In conclusion, the present one-day single oral administration model proves to be a reliable and highly sensitive tool for identifying GHCs and is anticipated to be a valuable tool in identifying and screening potential GHCs.

pharmacology and toxicology↗

bioRxiv2024

Beta-Glucanase superfamily identified by sequential, functional, and structural analyses

{beta}-1,2-Glucans are natural glucose polymers that play important physiological roles, including as symbiotic or pathogenic factors and in osmoregulation. Phylogenetically new glycoside hydrolase (GH) families have recently been identified from {beta}-1,2-glucanase (SGL) sequences from bacteria (GH144) and a fungus (GH162). In this study, we identified four phylogenetically new groups (Groups 1-4), and determined that these families, together with GH144, GH162, and GH189, a family of transglycosylase domains in cyclic {beta}-1,2-glucan synthases, form a superfamily. Biochemical analysis of six proteins in these groups revealed that the proteins in Groups 1-3 showed hydrolytic activity specific to {beta}-1,2-glucan. The kinetic parameters of the enzymes of Groups 1-3 were similar to GH144 and GH162 SGLs, indicating that these enzymes were SGLs. Optical rotation analysis revealed that the SGLs followed an anomer-inverting mechanism. Structural analysis and prediction of the proteins in Groups 1-4, GH144, GH162, and GH189 suggested that Groups 1-3 and GH144 had the same reaction mechanism. Nevertheless, Groups 1-3 were dispersed irregularly in the superfamily. Overall, we determined that Groups 1-3 were new GH families, GHxxx, GHyyy, and GHzzz, respectively, and proposed that this superfamily be called an SGL superfamily because of the phylogenetical, functional, and structural relationships within the superfamily. HighlightsWide variety of glycoside hydrolases is far beyond our understanding. Functional and structural analysis identified three new glycoside hydrolase families. Molecular evolution with irregular changes in reaction mechanism was revealed.

biochemistry↗

bioRxiv2024

Dynamic formation of a posterior-to-anterior peak-alpha-frequency gradient driven by two distinct processes

Peak-alpha frequency varies across individuals and mental states, but it also forms a negative gradient from posterior to anterior regions in association with increases in cortical thickness and connectivity reflecting the cortical hierarchy in temporal integration. Tracking the spatial standard deviation of peak-alpha frequency in scalp EEG, we observed that the posterior-to-anterior gradient dynamically formed and dissolved. Periods of high spatial standard deviation yielded robustly negative posterior-to-anterior gradients--the gradient state--while periods of low spatial standard deviation yielded globally converged peak-alpha frequency--the uniform state. Our analyses suggest that the fluctuations between the gradient and uniform states are associated with two separate variables: (1) coordinated variations in peak-alpha frequency in anterior regions and (2) coordinated variations in peak-alpha power in central regions driven by posterior regions. These variables each accounted for [~]25% of the state fluctuations, were uncorrelated with each other, and together accounted for [~]50% of the state fluctuations. These results reflect general mechanisms as they replicated while participants engaged in a variety of behavioral tasks with their eyes closed (breath focus, vigilance, working memory, mental arithmetic, and generative thinking). Overall, our results suggest that the spatial pattern of peak-alpha frequency dynamically fluctuates between the gradient state, potentially facilitating information influx and temporal integration toward anterior regions, and the uniform state, potentially facilitating global communication, with the state fluctuations controlled by at least two distinct mechanisms, an anterior mechanism that directly adjusts peak-alpha frequencies and a posterior mechanism that indirectly adjusts them by influencing synchronization.

neuroscience↗

bioRxiv2023

Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

The imprinted ZDBF2 gene is controlled by oocyte-derived DNA methylation, but its epigenetic regulation is quite different from that of other canonically imprinted genes that are dependent on DNA methylation deposited in the gametes. At the ZDBF2 locus, maternal DNA methylation in the imprinted differentially methylated region (DMR) does not persist after implantation. Instead, a transient transcript expressed in the early embryo exclusively from the unmethylated paternal allele of the DMR, known as GPR1-AS in humans and Liz in mice, contributes to establishing secondary DMRs that maintain paternal expression of ZDBF2 in the somatic lineage. While the imprinting of ZDBF2 is evident in humans and mice, whether this process is conserved in other mammals has not been addressed. Here, we show that the first exon of human GPR1-AS overlaps with that of a long terminal repeat (LTR) belonging to the MER21C subfamily of retrotransposons. Although this LTR family appears and is amplified in Boroeutherians, the magnorder of placental mammals that includes the Euarchontoglires and Laurasiatheria superorders, the MER21C insertion into the GPR1-AS orthologous region occurred specifically in the common ancestor of Euarchontoglires, a clade that includes extant primates, rodents, and rabbits. The first exon of mouse Liz does not overlap with an annotated LTR in standard repeat annotation; however, promoter activity assay and multiple sequence alignment suggests that it retains a functionally conserved relationship with the MER21C-overlapping first exon of GPR1-AS. Furthermore, directional RNA sequencing of placental tissues from rabbits and nonhuman primates also revealed GPR1-AS orthologs, with their first exon embedded within the same ancestral LTR. In contrast, allele-specific expression profiling of cow and tammar wallaby, mammals outside the Euarchontoglires group, revealed expression from both alleles in all tissues analyzed. Taken together, these observations suggest that imprinting of ZDBF2 in Euarchontoglires had its genesis in the insertion of a MER21C element in their common ancestor. Our previous studies showed that LTRs reactivated in oocytes contribute to lineage-specific imprinting during mammalian evolution. The data presented here suggest that post-fertilization activation of an ancestral LTR-derived sequence can also contribute to the lineage-specific establishment of imprinted genes.

genomics↗

bioRxiv2023

Activity-regulated micro-exon splicing programs underlie late-onset plasticity at the axon initial segment

The axon initial segment (AIS) is a specialized neuronal compartment located at the proximal end of axons and initiates action potentials. AIS undergoes plastic changes with aging, disease, and activity levels; however, the molecular mechanisms underlying their plasticity remain unclear. We discovered that depolarization induces diffuse elongation of the AIS in cerebellar granule cells over the span of days via the Ca2+-dependent ERK/MAP kinase pathway. These structural changes were accompanied by a decrease in voltage-gated Na+ channel density, resulting in a homeostatic attenuation in neuronal excitability. Notably, we found that the late-onset AIS plasticity is associated with depolarization-induced alternative splicing of smaller exons (<100 nt) of transcripts encoding AIS-enriched proteins. In addition, depolarization-induced the skipping of the 53-nt exon19 from the transcript of the splicing protein Rbfox1. CRISPR-mediated removal of exon 19 from Rbfox1 promoted its nuclear localization and sequentially induced a series of downstream micro-exon splicing changes in several AIS proteins, recapitulating cerebellar AIS plasticity. In a Rbfox1-independent mechanism, depolarization-induced insertion of the developmentally regulated micro-exon 34 into the key AIS scaffolding protein Ankyrin G (AnkG). The constitutive insertion of exon 34 into AnkG disrupted its interaction with the AIS cytoskeletal protein {beta}IV spectrin and induced plastic changes in the AIS. Our findings provide fundamental mechanistic insights into the activity-mediated late-onset plasticity of AIS, highlighting the power of micro-scale splicing events in the homeostatic regulation of axonal remodeling.

neuroscience↗

bioRxiv2023

Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection

Monitoring in vivo viral dynamics can improve our understanding of pathogenicity and tissue tropism. For positive-sense, single-stranded RNA viruses, several studies have attempted to monitor viral kinetics in vivo using reporter genomes. The application of such recombinant viruses can be limited by challenges in accommodating bioluminescent reporter genes in the viral genome. Conventional luminescence also exhibits relatively low tissue permeability and thus less sensitivity for visualization in vivo. Here we show that unlike NanoLuc bioluminescence, the improved method, termed AkaBLI, allows visualization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Syrian hamsters. By successfully incorporating a codon-optimized Akaluc luciferase gene into the SARS-CoV-2 genome, we visualized in vivo infection, including the tissue-specific differences associated with particular variants. Additionally, we could evaluate the efficacy of neutralizing antibodies and mRNA vaccination by monitoring changes in Akaluc signals. Overall, AkaBLI is an effective technology for monitoring viral dynamics in live animals.

microbiology↗

bioRxiv2023

NEDD4-binding protein 1 suppresses HBV replication by degrading pgRNA

Chronic infection with hepatitis B virus (HBV) places patients at increased risk for liver cirrhosis and hepatocellular carcinoma. Although nucleos(t)ide analogs are mainly used for the treatment of HBV, they require long-term administration and may lead to the emergence of drug resistant mutants. Therefore, to identify targets for the development of novel anti-HBV drugs, we screened for HBV-suppressive host factors using a plasmid expression library of RNA-binding proteins (RBPs). We screened 132 RBPs using an expression plasmid library by measuring HBV relaxed circular DNA (rcDNA) levels in hepatocellular carcinoma. Our screen identified NEDD4-binding protein 1 (N4BP1) as having an anti-HBV effect. In hepatocellular carcinoma cell lines transfected or infected with HBV, overexpression of N4BP1 decreased rcDNA levels while knockdown or knockout of the gene encoding N4BP1 rescued rcDNA levels. N4BP1 possesses the KH-like and RNase domains and both were required for the anti-HBV effect of N4BP1. Additionally, we measured levels of HBV pregenomic RNA (pgRNA) and covalently closed circular DNA (cccDNA) in the RBP-transfected cells and confirmed that N4BP1 binds pgRNA directly and degraded both the 3.5 kb and 2.4/2.1 kb HBV RNA. In summary, N4BP1 is a newly identified host factor able to counteract HBV production by promoting the degradation of 3.5 kb and 2.1/2.4 kb HBV RNA. ImportanceThere is still a large number of HBV-infected people in the world today because of no curative treatment for HBV infection. In this study, we focused on and screened RNA-binding proteins to identify new host factors which inhibit HBV replication. As a result, we found that NEDD4-binding protein 1 (N4BP1) expression suppresses rcDNA production by promoting the degradation of pregenomic RNA, 2.4kb and 2.1kb HBV RNA. Furthermore, KH-like domain or RNase domain of N4BP1 were involved in this anti-HBV effect. In addition, the N4BP1 levels were lower in HCC resection samples of exacerbated patients, suggesting that individual N4BP1 levels might be related to HCC progression. This novel factor can potentially become a key to new HBV treatments.

microbiology↗