Biology subjects

Choi, S.-Y.

Publications and source records attributed to Choi, S.-Y..

12 recordsLinked to original sources

bioRxiv2026

Terminal Schwann Cells Regulate Presynaptic Vesicle Homeostasis but Not Neuromuscular Junction Integrity in Mice

Terminal Schwann cells (tSCs) are specialized glial cells persistently residing at the neuromuscular junction (NMJ), where they are widely postulated to participate in synaptic transmission and maintenance. However, elucidating their precise in vivo roles has been hindered by a lack of tSC-specific genetic models, as conventional tools simultaneously targeted axonal Schwann cells. Here, we identify Col20a1 as a highly specific marker for tSCs through single-cell transcriptomic analysis and establish a novel Col20a1-CreERT2 knock-in mouse model. Utilizing this model, we achieved highly specific systemic labeling and ablation of tSCs during the postnatal maturation window. Surprisingly, systemic tSC loss disrupted neither gross NMJ architecture nor overall motor behavior. Instead, electrophysiological and ultrastructural analyses revealed profound pre-synaptic defects, characterized by increased spontaneous miniature endplate potentials (mEPPs), accelerated synaptic depression during high-frequency stimulation, and significant physical depletion of pre-synaptic vesicles. Furthermore, long-term analysis revealed a robust glial repopulation that sustained prolonged neuromuscular integrity. Together, our findings establish Col20a1 as a definitive genetic handle for tSC research, delineating that while tSCs are dispensable for macroscopic synaptic structure, they serve a precise and critical role in regulating pre-synaptic vesicle homeostasis.

neuroscience↗

bioRxiv2026

Systematic mapping of insertion-tolerant regions enables capsid engineering of the RNA phage PP7

RNA phages are attractive platforms for the design of programmable bioparticles, but their development has been constrained by limited knowledge of genomic sites that can tolerate sequence insertion. Here, we combined MuA transposase-mediated in vitro insertion mutagenesis with our established reverse genetics systems to systematically identify insertion-tolerant regions (ITRs) in the RNA phages MS2 and PP7. Screening of 4,555 MS2 and 2,228 PP7 random insertion clones identified 29 and 26 nonredundant ITRs, respectively. We further analyzed and compared these ITRs in the context of RNA genome organization and virion architecture. Both phages contained ITRs within the maturation protein (MP), whereas only PP7 tolerated insertions within the coat protein (CP). On the basis of structural location and plaque-forming capacity, an ITR situated between Gly74 and Glu75 (GGC^GAG) in the PP7 CP was selected for further study. Infectious phage particles generated from cDNA clones retained the 15-bp insertion at both the RNA and protein levels. Engineered PP7 phages carrying an RGD motif inserted into the CP at this ITR displayed enhanced in vivo clearance in a Drosophila model, despite having in vitro stability comparable to that of the wild type. These findings provide the first example of CP engineering in an RNA phage and establish a framework for engineering RNA phages for biological and biotechnological applications. IMPORTANCEA major obstacle to developing RNA phages as synthetic biology platforms is the lack of design principles for genomic insertion. Here, we address this limitation by establishing a mutagenesis-and-recovery workflow that systematically identifies insertion-tolerant regions (ITRs) in the RNA phages MS2 and PP7. The resulting maps reveal distinct structural constraints in the two phages and enable rational engineering of a peptide-display site in the PP7 capsid. Using this approach, we generated an engineered infectious phage with a modified capsid, thereby providing the first demonstration of capsid engineering in an RNA phage. This study lays the groundwork for the rational design of RNA phage virions as tractable and engineerable scaffolds for future biological and biotechnological applications.

microbiology↗

bioRxiv2026

cDNA-guided functional selection uncovers selective defense systems against RNA phages

Bacteria encode diverse antiphage defense systems, yet mechanisms that target RNA phages remain comparatively underexplored. Here, we used a cDNA-based functional selection strategy to systematically identify genes that confer resistance to RNA phage infection independently of receptor variation in Pseudomonas aeruginosa. This approach uncovered previously uncharacterized antiphage defense systems, most of which are located within genomic islands, consistent with their being bona fide components of bacterial immune systems. Several systems conferred selective resistance to RNA phages and their carriage was associated with pilin variability, suggesting layered anti-phage immunity. Among these systems, Zws is the most prevalent RNA phage defense system and functions as a multidomain effector. Structural modeling and in vitro cleavage assays showed that ZwsA is an RNA endonuclease that selectively cleaves RNA phage genomes through a predicted NERD domain. Together, these findings expand the current framework of bacterial antiphage immunity and highlight the power of functional genomics to uncover cryptic components of the bacterial antiviral arsenal. IMPORTANCEBacteria harbor a broad repertoire of antiphage defense systems, but our understanding of mechanisms that target RNA phages remains limited, being heavily biased toward defenses against DNA phages. By applying a cDNA-based functional selection strategy, this study overcomes a major obstacle in defense-gene discovery and uncovers previously uncharacterized genes that represent bona fide components of the bacterial immune arsenal against RNA phages. The identification and characterization of Zowangsin (ZwsA), a NERD-domain RNA endonuclease that selectively cleaves specific signatures within RNA phage genomes, establish targeted RNA degradation as a central principle of bacterial defense against RNA phages. More broadly, this work expands the conceptual framework of bacterial antiviral immunity and illustrates the utility of functional selection for uncovering cryptic immune systems with implications for phage biology, RNA biology, and biotechnology. HIGHLIGTHSO_LIcDNA-based functional screen identifies six defense systems that restrict RNA phages C_LIO_LIThese defense systems are enriched within genomic islands of Pseudomonas aeruginosa C_LIO_LIZws, Szs, and Mws systems confer selective defense against RNA phages C_LIO_LIZwsA is a signature-selective RNA endonuclease that targets phage genomic RNA C_LI

microbiology↗

bioRxiv2025

Cereblon-related mild intellectual disability disrupts response inhibition and uniformity of group--individual strategies

Temporal processing, including duration, is essential for survival and communication across species. Intellectual disability (ID), which has diverse causes, including Cereblon (CRBN), impairs duration discrimination. CRBN-related ID, link to abnormal cognitive behaviors, may disrupt both perception and behavior during duration discrimination. However, cross-species behavioral strategies, their variation with ID, and associated behavioral indices remain unclear. Here, humans and wild-type (WT) mice with typical intelligence, and CRBN knockout (KO) mice with ID, performed an auditory duration discrimination task with Long (10 s) and Short (2 s) cues. All groups distinguished stimulus durations, but latency-based strategies diverged. KO mice showed impulsivity and divergent responses at both individual and group levels, whereas WT mice and humans consistently delayed their responses by [~]2 s to the Short cue length, reflecting inhibition and convergent responses. In typical intelligence models, latencies for both stimuli clustered between 2-5 s, while in ID model depended on stimulus duration. Duration perception is a conserved cross-species capacity, while task-specific cognitive strategies are intrinsically preserved though variation emerges with ID. We suggest that latency indices dissociated inhibition from impulsivity, and convergence from divergence. We further suggest that CRBN-related ID preserves perceptual understanding but disrupts the shared behavioral language of typical intelligence.

neuroscience↗

bioRxiv2025

Linking Kinetochore Attachment to Checkpoint Control: The Role of Aurora B in BubR1 Acetylation

We report here that Aurora B kinase is critical in BubR1 acetylation at K250, transducing kinetochore attachment status to spindle assembly checkpoint (SAC) activity. Aurora B phosphorylates BubR1 at serines 16 and 39 in an unattachment-dependent manner, which is a prerequisite for BubR1 acetylation at lysine 250 (K250). Utilizing a novel anti-AcK250 monoclonal antibody in structured illumination microscopy (SIM), we reveal that BubR1 acetylation is associated with kinetochore expansion, evidenced by crescent-shaped volume increase of ZW10 and Mad2 surrounding the kinetochore. Furthermore, K250-BubR1 acetylation enhances its interaction with CENP-E, a kinesin crucial for chromosome alignment through facilitating end-on attachment. Disrupting Aurora B-mediated phosphorylation of Ser16/39 impaired K250 acetylation, compromising both fibrous corona polymerization and mitotic checkpoint complex (MCC) maintenance. Conversely, introducing K250 acetylation mimetic form rescued MCC and fibrous corona in cells expressing phosphorylation-deficient S16A/S39A mutants. Our findings reveal Aurora B-BubR1 acetylation axis as a critical SAC signaling pathway, interlinking unattachment sensing with kinetochore expansion and SAC activity. We propose that this stepwise phosphorylation-acetylation on BubR1 constitutes a crucial part of SAC signaling code, transducing unattachment signal to fibrous corona polymerization and SAC activity. This phosphorylation-acetylation cascade in BubR1 offers potential therapeutic targets in treating cancers of chromosome instability.

cell biology↗

bioRxiv2025

Structural mechanism of insulin receptor activation by a dimeric aptamer agonist

Insulin binding to the insulin receptor (IR) triggers signaling pathways that regulate glucose uptake and cell growth. In previous work, we identified a DNA aptamer, A62, which partially activates the IR. During engineering aptamers for improved in vivo stability, we discovered that crosslinking two A62 aptamers with linkers of varying lengths led to full phosphorylation of the IR, though activation remained selective to the AKT pathway. To elucidate the mechanism behind this aptamer-induced full activation of the IR, we determined the structure of the IR in complex with a dimeric form of A62 (A62D) linked by an 8-nucleotide connector. We identified three distinct conformations of the IR: arrowhead-shaped, pseudo-arrowhead-shaped, and pseudo-gamma-shaped. The pseudo-gamma-shaped conformation closely resembles the structure of a fully active IR bound by a single insulin molecule. In these configurations, only one A62 monomer (A62M) within the A62D dimer binds to the IR dimer. This binding brings the IR monomers into close proximity, promoting intermolecular trans-phosphorylation. Our findings provide valuable structural insights for the development of novel therapeutic strategies targeting the IR.

biochemistry↗

bioRxiv2024

A bacterial site 2 protease contributes to RNA phage resistance by targeting phage lysis protein

Lytic phages culminate their lifecycle by causing lysis of the infected host cell. Despite extensive research on the molecular mechanisms of phage lysis, our understanding of anti-phage resistance mechanisms during the lysis stage remains less understood. Here, we demonstrated that MucP, a site 2 protease of Pseudomonas aeruginosa (PA), mitigates the activity of the RNA phage PP7 lysis protein (LP), which contains a transmembrane (TM) helix, suggesting that MucP act as a resistance mechanism against PP7-induced lysis. We identified an LP variant (LP*) having enhanced helical propensity due to P26L and S40L mutations, which was unaffected by MucP and exhibited killing activity against PA strains that are resistant to the wild type LP, with an inverse correlation between MucP activity and LP susceptibility. A PP7 mutant with LP* exhibited MucP-escaper phenotype such as discernable plaque formation on MucP-expressing cells. These results suggest that MucP targets the RNA phage LP at the TM helix in certain strains, providing a resistance function compromising phage lysis by utilizing an existing bacterial enzyme in PA. IMPORTANCEDespite the importance of cell lysis as the last stage of phage lifecycle, the factors influencing coordinated lysis remain elusive in the context of phage-bacteria interactions. Our study identifies MucP, a membrane protease in Pseudomonas aeruginosa (PA), as a resistance factor against the RNA phage PP7 by destabilizing its lysis protein (LP), with lower helical tendency at transmembrane (TM) domain. An LP variant with higher helical tendency exhibits strong killing activity against PA isolates, revealing an inverse correlation between MucP activity and LP susceptibility. Since MucP is a conserved protease in mucoid conversion of PA, we propose that MucP offers an intrinsic or passive defense or resistance mechanism against the RNA phage, whose activities vary among the diverse PA isolates.

microbiology↗

bioRxiv2023

Depletion of SMN Protein in Mesenchymal Progenitors Impairs the Development of Bone and Neuromuscular Junction in Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterized by the deficiency of the survival motor neuron (SMN) protein, which leads to motor neuron dysfunction and muscle atrophy. In addition to the requirement for SMN in motor neurons, recent studies suggest that SMN deficiency in peripheral tissues plays a key role in the pathogenesis of SMA. Using limb mesenchymal progenitor cells (MPCs)-specific SMN-depleted mouse models, we reveal that SMN reduction in chondrocytes and fibro-adipogenic progenitors (FAPs) derived from limb MPCs causes defects in the development of bone and neuromuscular junction (NMJ), respectively. We showed that impaired growth plate homeostasis, which causes skeletal growth defects in SMA, is due to reduced IGF signaling from chondrocytes rather than the liver. Furthermore, the reduction of SMN in FAPs resulted in abnormal NMJ maturation, altered release of neurotransmitters, and NMJ morphological defects. Transplantation of healthy FAPs rescued the morphological deterioration. Our findings highlight the significance of mesenchymal SMN in neuromusculoskeletal pathogenesis in SMA and provide insights into potential therapeutic strategies targeting mesenchymal cells for the treatment of SMA.

neuroscience↗

bioRxiv2020

Human spinal cord organoids exhibiting neural tube morphogenesis for a quantifiable drug screening system of neural tube defects

The human spinal cord forms well-organized neural circuits for environment sensing and motor behavior. The three-dimensional (3D) induction of the spinal cord-like tissue from human pluripotent stem cells has been reported, but they often do not mimic morphological features of neurulation and their maturity is limited. Here, we report an advanced 3D culture system for the production of human spinal cord-like organoids (hSCOs) suitable for the scale-up and quantitative studies. The hSCOs exhibited many aspects of spinal cord development, including neurulation-like tube-forming morphogenesis, differentiation of the major spinal cord neurons and glial cells, and mature synaptic functional activities. We further demonstrated that hSCOs platform allowed quantitative and systematic high-throughput examination of the potential risk of neural tube defects induced by antiepileptic drugs. Thus, hSCOs can be used for understanding human spinal cord development, disease modeling, and toxicology screening.

cell biology↗

bioRxiv2020

Calsyntenin-3 directly interacts with neurexins to orchestrate excitatory synapse development in the hippocampus

Calsyntenin-3 (Clstn3) is a postsynaptic adhesion molecule that induces presynaptic differentiation via presynaptic neurexins (Nrxns), but whether Nrxns directly bind to Clstn3 has been a matter of debate. Here, we show that {beta}-Nrxns directly interact via their LNS domain with Clstn3 and Clstn3 cadherin domains. Expression of splice site 4 (SS4) insert-positive {beta}-Nrxn variants, but not insert-negative variants, reversed the impaired Clstn3 synaptogenic activity observed in Nrxn-deficient neurons. Consistently, Clstn3 selectively formed complexes with SS4-positive Nrxns in vivo. Neuron-specific Clstn3 deletion caused significant reductions in number of excitatory synaptic inputs, and moderate impairment of light-induced anxiety-like behaviors in mice. Moreover, expression of Clstn3 cadherin domains in CA1 neurons of Clstn3 conditional knockout mice rescued structural deficits in excitatory synapses, especially within the stratum radiatum layer. Collectively, our results suggest that Clstn3 links to SS4-positive Nrxns to induce presynaptic differentiation and orchestrate excitatory synapse development in specific hippocampal neural circuits.

neuroscience↗

bioRxiv2019

Albumin inhibits the activation of hepatic stellate cells by suppressing TGF-β/Smad3 signaling via IL-1β

Activated hepatic stellate cells (HSCs) play a key role in liver fibrosis and inactivating HSCs has been considered a promising therapeutic approach. We previously showed that albumin and its derivative, retinol binding protein (RBP)-albumin domain III fusion protein (named R-III), inhibit HSC activation. Here, we investigate the mode of action of albumin and R-III. NF-{kappa}B in activated HSCs was evenly distributed in the cytoplasm, but albumin expression and R-III treatment (albumin/R-III) induced NF-{kappa}B nuclear translocation via retinoic acid (RA) sequestration, resulting in increased expression of interleukin-1{beta} (IL-1{beta}). In an IL-1{beta} dependent manner, albumin/R-III inhibited Smad3 nuclear translocation via TAK1-, JNK-mediated Smad3 linker phosphorylation and decreased expression of Smad3 target genes, such as -smooth muscle actin and collagen type I. Mutation of the Smad3 linker phosphorylation sites abolished R-III effects on Smad3. In conclusion, our data suggest that the anti-fibrotic effects of albumin/R-III are due to RA sequestration which downregulates RAR-mediated signaling and also TGF-{beta}/Smad3 signaling. This mechanistic elucidation of albumin function in HSCs provides clues to understanding the frequent albumin mutations found in hepatocellular carcinoma.

molecular biology↗

bioRxiv2017

LARGE, an AMPA receptor interactor, plays a large role in long-term memory formation by driving homeostatic scaling-down

Dynamic trafficking of AMPA-type glutamate receptor (AMPA-R) in neuronal cells is a key cellular mechanism for learning and memory in the brain, which is regulated by AMPA-R interacting proteins. LARGE, a protein associated with intellectual disability, was found to be a novel component of the AMPA-R protein complex in our proteomic study. Here, our functional study of LARGE showed that during homeostatic scaling-down, increased LARGE expression at the Golgi apparatus (Golgi) negatively controlled AMPA-R trafficking from the Golgi to the plasma membrane, leading to downregulated surface and synaptic AMPA-R targeting. In LARGE knockdown mice, long-term potentiation (LTP) was occluded by synaptic AMPA-R overloading, resulting in impaired long-term memory formation. These findings indicate that the fine-tuning of AMPA-R trafficking by LARGE at the Golgi is critical for memory stability in the brain. Our study thus provides novel insights into the pathophysiology of brain disorders associated with intellectual disability.

neuroscience↗