Biology subjects

Song, J.-J.

Publications and source records attributed to Song, J.-J..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic Filament Assembly Regulates the Prolyl Aminopeptidase Activity of Plant Immune Protein DM3

The alpha/beta hydrolase DANGEROUS MIX 3 (DM3), a proline aminopeptidase in Arabidopsis thaliana, contributes to stress resilience through both metabolic regulation and immune signaling. Its functions are partitioned within its oligomeric structure as a trimer-of-dimers, in which the immune regulatory switch resides at the dimer interface. While the enzymatic activity of DM3 is not necessary for immune response, its activity to free prolines is critical to promote tolerance to salt and drought stress. However, how this activity is regulated has remained unclear. Here, we show that DM3 undergoes dynamic and reversible assembly into higher-order filaments in a salt-sensitive manner. The cryo-electron microscopy (EM) structure of filamentous DM3 reveals that the three-stranded helical filament arises from rearrangements of a planar hexamer into a tilted hexameric configuration. Notably, within these filaments, one of the catalytic residues is flipped out to disrupt the catalytic geometry, rendering the enzyme inactive. These findings establish filament assembly as a mechanism to sequester DM3 in an inactive state and suggest that the transition between distinct oligomeric states enables DM3 to coordinate its roles in biotic and abiotic stress responses.

plant biology↗

bioRxiv2026

Transcutaneous auricular Vagus nerve stimulation for working memory enhancement: A comparative study of electrical and ultrasound stimulation

ObjectivesTranscutaneous auricular vagus nerve stimulation (taVNS) is a non-invasive neuromodulation technique that has shown potential to enhance cognitive function, including working memory. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on working memory using a 3-back task in healthy young adults. We hypothesized that active taVNS would enhance working memory performance relative to sham, and that both stimulation modalities would engage similar neuromodulatory mechanisms. Materials and MethodsFifty-nine participants underwent a single-blind, sham-controlled, within-subject design study, with working memory performance assessed using a 3-back task before and after stimulation. Primary performance measures included correct rejection rate, error false alarm, and sensitivity (d'). Statistical analyses compared pre- and post-stimulation performance across modalities. ResultsE-taVNS significantly enhanced working memory performance through an increase in correct rejection rate and sensitivity (measured by d), alongside a reduction in error of false alarm. U-taVNS showed a similar directional trend across performance measures, although these effects did not reach statistical significance. Baseline anxiety levels significantly predicted individual responsiveness to taVNS. In terms of tolerability, a higher proportion of participants receiving E-taVNS reported skin irritation compared to those receiving U-taVNS. ConclusionsE-taVNS can acutely enhance working memory performance, while U-taVNS may offer a comparable, better tolerated alternative. Our findings highlight the potential of taVNS to support memory function, while showing the importance of further research to clarify modality-specific effects and optimize stimulation parameters.

neuroscience↗

bioRxiv2026

Comparing Electrical and Ultrasound Transcutaneous Vagus Nerve Stimulation (taVNS) on Associative Memory

Associative memory, the ability to bind and retrieve relationships between unrelated elements, is a cornerstone of human cognition and a primary target for neurorehabilitation. Vagus nerve stimulation (VNS) has emerged as a promising method to modulate the locus coeruleus-norepinephrine (LC-NE) system and hippocampal-prefrontal circuits essential for memory. However, the comparative efficacy of non-invasive modalities such as electrical (E-taVNS) and the emerging field of ultrasound (U-taVNS) remains poorly understood in the context of active recall. In this study, participants performed a crossmodal video-word associative memory task before and after receiving either E-taVNS or U-taVNS in active and sham conditions. We investigated whether these modalities enhance cued recall accuracy and retrieval reaction time. Our results revealed that neither E-taVNS nor U-taVNS significantly improved recall accuracy. However, E-taVNS significantly accelerated response times specifically for correctly recalled items. These findings suggest that while taVNS may not increase the likelihood of recalling associative memories, electrical stimulation may enhances the efficiency in which we do so. These findings suggest that electrical taVNS is a viable tool for facilitating memory search processes, though further research is required to optimize ultrasound parameters and validate mechanistic pathways through physiological monitoring.

neuroscience↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Transcutaneous auricular vagus nerve stimulation enhances emotional bias towards happiness in healthy young adults: A comparative study of electrical and ultrasound stimulation

Transcutaneous auricular vagus nerve stimulation (taVNS) is an emerging neuromodulation technique demonstrating promise in emotional regulation. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on emotional bias using a facial emotion categorization task in healthy young adults. Fifty-nine participants underwent a single-blind, sham-controlled, within-subject design, with emotional bias assessed at pre-, during-, and post-stimulation phases. Our findings revealed that both E-taVNS and U-taVNS significantly enhanced emotional bias scores, shifting the perception of neutral and ambiguous faces towards positive interpretations and reducing negative emotional bias. No significant differences in efficacy were observed between the two stimulation modalities. Furthermore, individual differences in interoceptive awareness were found to be associated with the observed taVNS effects. These results suggest that both electrical and ultrasound taVNS can acutely modulate emotional regulation, highlighting the potential of taVNS as a non-invasive, well-tolerated alternative for interventions targeting emotional bias and mood disorders. HighlightsO_LItaVNS reduces negative emotional bias toward ambiguous stimuli. C_LIO_LIBoth electrical and ultrasound taVNS shifted emotional bias toward more positive interpretations of ambiguous facial expressions. C_LIO_LIUltrasound taVNS (U-taVNS) demonstrated comparable efficacy to electrical taVNS (E-taVNS). C_LIO_LIThe subscale of the Multidimensional Assessment of Interoceptive Awareness predicted individual variability in taVNS-induced emotional bias change. C_LI

neuroscience↗

bioRxiv2024

Structure determinants of DANGEROUS MIX 3, an alpha/beta hydrolase, for triggering NLR-mediated genetic incompatibility in plants

Genetic incompatibility occurs when a mismatched pair of plant immune components mounts autoimmune responses in hybrids. Highly diversified NLR receptors are main culprits of the genetic conflict, recognizing host proteins from different origin as immune trigger. Here, we report the molecular mechanism underlying a DANGEROUS MIX (DM) autoimmunity, comprising DM2h/RPP1 NLR and its incompatible partner DM3, an alpha/beta hydrolase. Cryo-electron microscopy reveals the oligomeric nature of two natural DM3 variants in a trimer of dimer configuration. The polymorphism triggering autoimmunity is located at the dimer interface, resulting in drastic structural differences such that dimerizing helix and loop reinforcing the interface is lost and disordered. Structure-function analysis shows that integrity of the dimer interface, but neither maintenance of hexamer nor its enzymatic activity, is the key factor contributing to autoimmunity. Our finding pinpoints checkpoints embedded in the oligomeric configuration of a host enzyme that controls the switching mechanism of NLR activity.

plant biology↗

bioRxiv2024

PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation

Hearing loss is one of the most prevalent sensory disorders, but no commercial biological treatments are currently available. Here, we identified an East Asia-specific founder mutation, the homozygous c.220C>T mutation in MPZL2, that contributes to a significant proportion of hereditary deafness cases in our cohort study. We found that the disease-causing mutation could be targetable by adenine base editors (ABEs) that enable A{middle dot}T-to-G{middle dot}C base corrections without DNA double-strand breaks. To demonstrate this, we developed a humanized mouse model (hMPZL2Q74X/Q74X) that recapitulates human MPZL2 deafness and leads to progressive hearing loss. A PAM-flexible ABE variant with reduced bystander and off-target effects (ABE8eWQ-SpRY:sgRNA3) was packaged in dual adeno-associated viruses (AAVs) and injected into the inner ear of hMPZL2Q74X/Q74X mice and effectively corrected the mutation. This treatment significantly restored hearing function, improved inner ear structural integrity, and reversed altered gene expression. Base editing may hold therapeutic potential for hereditary deafness, including most cases of MPZL2 deafness.

genetics↗

bioRxiv2024

CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate histone supply

ASF1 is a major histone chaperone that regulates the supply of histone H3-H4 and facilitates nucleosome assembly to maintain chromatin structure during DNA replication and transcription. CODANIN-1 negatively regulates the function of ASF1. However, the molecular mechanism by which CODANIN-1 inhibits the ASF1-mediated histone supply remains elusive. Here, we present the electron microscopy (cryo-EM) structure of a human CODANIN-1_ASF1A complex at 3.75 [A] resolution. The structure reveals that CODANIN-1 forms a dimer where each monomer holds two ASF1 molecules, utilizing two B-domains and two histone H3 mimic helices (HMHs). The interaction of CODANIN-1 with ASF1 via the HMH and B domains inhibits the formation of an ASF1/H3-H4 complex and sequesters ASF1 in the cytoplasm. Our study provides a structural and molecular basis for the function of CODANIN-1 as a unique negative regulator that highjacks ASF1 interaction sites with histones and downstream chaperones to inhibit nucleosome assembly.

biophysics↗

bioRxiv2024

Abo1 ATPase facilitates the dissociation of FACT from chromatin.

The histone chaperone FACT is a heterodimeric complex consisting of Spt16 and Pob3, crucial for preserving nucleosome integrity during transcription and DNA replication. Loss of FACT leads to cryptic transcription and heterochromatin defects. FACT was shown to interact with Abo1, an AAA+ family histone chaperone involved in nucleosome dynamics. Depletion of Abo1 causes FACT to stall at transcription start sites (TSS) and mimics FACT mutants, indicating a functional association between Abo1 and FACT. However, the precise role of Abo1 in FACT function remains poorly understood. Here, we reveal that Abo1 directly interacts with FACT and facilitates the dissociation of FACT from chromatin. Specifically, the N-terminal region of Abo1 utilizes its FACT interacting (FIN) helix to bind to the N-terminal domain (NTD) of Spt16. In addition, using single-molecule fluorescence imaging, we discovered that Abo1 facilitates the ATP-dependent dissociation of FACT from nucleosomes. Furthermore, we demonstrate that the interaction between Abo1 and FACT is essential for maintaining heterochromatin in fission yeast. In summary, our findings suggest that Abo1 regulates FACT turnover in an ATP-dependent manner, proposing a model of histone chaperone recycling driven by inter-chaperone interactions.

biochemistry↗

bioRxiv2023

Huntingtin bundles and changes the local proteome of actin filaments in neurons

Huntingtin (HTT) is a large protein whose best-known function being the facilitation of intracellular dynamics along the microtubule network by scaffolding molecular motors complexes. Our recent finding that the defective axonal growth in HD was due to altered growth cone architecture led us to ask whether HTT also influences the cytoskeleton itself. In developing neurons, we found that a large proportion of HTT associates with F-actin in growth cones. Using cell free system and purified recombinant proteins, we observed that HTT binds directly filamentous actin (F-actin) and organizes filaments into bundles. Transmission electron microscopy shows that HTT dimers crosslink adjacent filaments 20 nm apart. We also provide evidence that HTT binding on F-actin modulates the association of other proteins to this cytoskeleton. Notably, HTT limits the association of the growth cone protein Drebrin1 with F-actin. HTT depletion leads to abnormal cytoskeletal organization, localization of Drebrin1 in growth cones, and axonal growth. HTT therefore serves a scaffolding function for the cytoskeleton itself, what might be relevant for HD pathophysiology.

cell biology↗

bioRxiv2023

AMLs harboring DNMT3A-destabilizing variants show increased intratumor DNA methylation heterogeneity at bivalent chromatin domains

The mechanistic link between the complex mutational landscape of de novo methyltransferase DNMT3A and the pathology of acute myeloid leukemia (AML) has not been clearly elucidated so far. A recent discovery on the catalogue of DNMT3A-destabilizing mutations throughout the DNMT3A gene as well as the oligomerization-dependent catalytic property of DNMT3A prompted us to investigate the common effect of DNMT3A-destabilizing mutations (DNMT3AINS) on the genomewide methylation patterns of AML cells. In this study, we describe the characteristics of DNMT3AINS AML methylomes through the comprehensive computational analyses on three independent AML cohorts. As a result, we show that methylomes of DNMT3AINS AMLs are considerably different from those of DNMT3AR882 AMLs in that they exhibit both locally disordered DNA methylation states and increased across-cell DNA methylation heterogeneity in bivalent chromatin domains. This increased epigenetic heterogeneity was functionally associated with heterogeneous expression of membrane-associated factors shaping stem cell niche, implying the diversification of the modes of leukemic stem cell-niche interactions. We also present that the level of methylation disorder at bivalent domains predicts the response of AML cells to hypomethylating agents through cell line- and patient-level analyses, which supports that the survival of AML cells depends on stochastic DNA methylations at bivalent domains. Altogether, our work provides a novel mechanistic model suggesting the genomic origin of the aberrant epigenomic heterogeneity in disease conditions.

cancer biology↗

bioRxiv2023

Caf1 regulates Ash1 histone methyltransferase activity via sensing unmodified histone H3.

Histone modifications are one of key mechanisms to regulate gene expression. Ash1 is a histone H3K36 methyltransferase and involved in gene activation. Ash1 forms a large complex with Mrg15 and Caf1/p55/Nurf55/RbAp48 (AMC complex). Ash1 subunit alone has very low activity due to the auto-inhibition and the binding of Mrg15 releases the auto-inhibition. Caf1 is a scaffolding protein commonly found in several chromatin modifying complexes. Caf1 has an ability to sense unmodified histone H3K4 residue. However, the role of Caf1 in AMC complex has not been investigated. Here, we dissected the interaction among the AMC complex subunits, revealing that Caf1 uses the histone H4 binding pocket to interact with Ash1 near the histone binding module cluster. Furthermore, we show that H3K4 methylation inhibits AMC HMTase activity via Caf1 sensing unmodified histone H3K4 to regulate the activity in an inter-nucleosomal manner, suggesting that there is a crosstalk between H3K4 and H3K36 methylations. Our work reveals a delicate regulatory mechanism of AMC histone H3K36 methyltransferase complex.

biochemistry↗

bioRxiv2022

Structure of the Human ATAD2 AAA+ Histone Chaperone Reveals Mechanism of Regulation and Inter-subunit Communication

ATAD2 is a non-canonical ATP-dependent histone chaperone and a major cancer. Despite widespread efforts to design drugs targeting the ATAD2 bromodomain, little is known about the overall structural organization and AAA+ domains of ATAD2. Here, we present the 3.1 [A] cryo-EM structure of human ATAD2 in the ATP state, showing a shallow hexameric spiral that binds a peptide substrate at the central pore. The spiral conformation is locked by an N-terminal linker domain (LD) that wedges between the seam subunits, thus limiting ATP-dependent symmetry breaking of the AAA+ ring. In contrast, a structure of the ATAD2-histone H3H4 complex shows the LD undocked from the seam, suggesting that H3H4 binding unlocks the AAA+ spiral by allosterically releasing the LD. These findings, together with the discovery of an inter-subunit signaling mechanism, reveal a unique regulatory mechanism for ATAD2 and lay the foundation for developing new ATAD2 inhibitors.

molecular biology↗

bioRxiv2022

Huntingtin turnover: Modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550

Huntingtons disease (HD) is a neurodegerative disorder caused by an inherited unstable HTT CAG repeat that expands further, thereby eliciting a disease process that may be initiated by polyglutamine-expanded huntingtin or a short polyglutamine-product. Phosphorylation of selected candidate residues is reported to mediate polyglutamine-fragment degradation and toxicity. Here to support the discovery of phospho-sites involved in the life-cycle of (full-length) huntingtin, we employed mass spectrometry-based phosphoproteomics to systematically identify sites in purified huntingtin and in the endogenous protein, by proteomic and phospho-proteomic analyses of members of an HD neuronal progenitor cell panel. Our results bring total huntingtin phospho-sites to 95, with more located in the N-HEAT domain relative to numbers in the Bridge and C-HEAT domains. Moreover, phosphorylation of C-HEAT Ser2550 by cAMP-dependent protein kinase (PKA), the top hit in kinase activity screens, was found to hasten huntingtin degradation, such that levels of the catalytic subunit (PRKACA) were inversely related to huntingtin levels. Taken together these findings highlight categories of phospho-sites that merit further study and provide a phospho-site kinase pair (pSer2550-PKA) with which to investigate the biological processes that regulate huntingtin degradation and thereby influence the steady state levels of huntingtin in HD cells.

biochemistry↗

bioRxiv2022

Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand binding specificity

Somatostatin is a peptide hormone regulating endocrine systems through binding to G-protein-coupled somatostatin receptors. somatostatin receptor 2 (SSTR2) is one of the human somatostatin receptors and highly implicated in cancers and neurological disorders. Here, we report the high resolution cryo-EM structure of full-length human SSTR2 bound to the agonist somatostatin (SST-14) complex with inhibitory G (Gi) proteins. Our structure shows that seven transmembrane helices form a deep pocket for ligand binding and that the highly conserved Trp-Lys motif of SST-14 positions at the bottom of the pocket. Furthermore, our sequence analysis combined with AlphaFold modeled structures of other SSTR isoforms provide how SSTR family proteins specifically interact with their cognate ligands. This work provides the first glimpse into the molecular recognition of somatostatin receptor and crucial resource to develop therapeutics targeting somatostatin receptors.

biophysics↗

bioRxiv2021

Dendrimer-like supramolecular assembly of proteins with a tunable size and valency through stepwise iterative growth

The assembly of proteins in a programmable manner provides insight into the underlying mechanisms of protein self-assembly in nature as well as the creation of novel functional nanomaterials for practical applications. Despite many advances, however, a rational protein assembly with an easy scalability in terms of size and valency remains a challenging task. Here, we present a simple bottom-up approach to the supramolecular protein assembly with a tunable size and valency in a programmable manner. The dendrimer-like protein assembly, called a "prodrimer," was constructed using a total of three monomeric proteins: a core and two building-block proteins. The prodrimer generations were grown by a stepwise and alternate addition of a building block using two pairs of orthogonal protein-peptide interactions, leading to a higher-generation prodrimer with a mega-dalton size and multi-valency. The valency of the prodrimers at the periphery was tunable with the generation, enabling a single-step functionalization. A second-generation prodrimer functionalized with a target-specific protein binder showed a three-order of magnitude increase in binding affinity compared to a monomeric counterpart due to the avidity. The prodrimers functionalized with a targeting moiety and a cytotoxic protein cargo exhibited a highly enhanced cellular cytotoxicity, exemplifying their utility as a protein delivery platform. The present approach can be effectively used in the creation of protein architectures with new functions for biotechnological and medical applications.

bioengineering↗

bioRxiv2020

CHD7 interacts with the nucleosome acidic patch for its efficient activity via its N-terminal region

Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental disorders, notably CHARGE syndrome. However, there is not much known about the molecular mechanism by which CHD7 remodels nucleosomes. Here, we performed integrative biophysical analysis on CHD7 chromatin remodeler using crosslinking-mass spectrometry (XL-MS), cryo-Electron Microscopy (cryo-EM) and single-molecule Forster Resonance Energy Transfer (smFRET). We uncover that N-terminal to the Chromodomain (N-CRD) interacts with nucleosome. Importantly, this region is required for efficient ATPase stimulation and nucleosome remodeling activity of CHD7. The cryo-EM analysis on the N-CRD_Chromodomain bound to nucleosome reveals that the N-CRD interacts with the acidic patch of nucleosome. Furthermore, smFRET analysis shows the mutations in the N-CRD result in slow or highly-fluctuating remodeling activity. Collectively, our results uncover the functional importance of a previously unidentified N-terminal region in CHD7 and implicate that the multiple domains in chromatin remodelers are involved in regulating their activities.

biochemistry↗

bioRxiv2020

Lipid Sponge Droplets as Programmable Synthetic Organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and non-ionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the co-localization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems. Significance statementOrganelles spatially and temporally orchestrate biochemical reactions in a cell to a degree of precision that is still unattainable in synthetic reaction systems. Additionally, organelles such as the endoplasmic reticulum (ER) contain highly interconnected and dense membrane networks that provide large reaction spaces for both transmembrane and soluble enzymes. We present lipid sponge droplets to emulate the functions of organelles such as the ER. We demonstrate that lipid sponge droplets can be programmed to internally concentrate specific proteins, host and accelerate biochemical transformations, and to rapidly and reversibly sequester and release proteins to control enzymatic reactions. The self-assembled and programmable nature of lipid sponge droplets will facilitate the integration of complex functions for bottom up synthetic biology.

synthetic biology↗