Biology subjects

Hyun, J.

Publications and source records attributed to Hyun, J..

9 recordsLinked to original sources

bioRxiv2026

Mucosally sourced complement factor B modulates the host response to colitis

Distinct host factors maintain intestinal homeostasis but are incompletely understood. The complement system is primarily liver-derived and serum-operative. However, there is growing recognition for complement-mediated host defense at mucosal surfaces. The alternative pathway, which is constitutively active at low levels and amplifies complement activation independent of antibodies, requires Complement Factor B (CFB). Despite its evolutionary conservation, the spatial, cellular, and functional roles of CFB in the intestine are poorly understood. Here, we show that CFB is produced in the human colon and is increased in patients with active inflammatory bowel disease. To isolate the role of local CFB in mucosal responses, we interrogated a mouse strain that has no circulating, liver-derived CFB but retains intact CFB expression in the gut. Global CFB-deficient mice succumb to colitis compared to these liver-specific knockout mice, suggesting that locally synthesized CFB mitigates colitis. Single-cell analyses identify enterocytes and fibroblasts as key CFB producers in the gut. Compartment-specific deletion of CFB from epithelial or stromal cells abrogates mucosal protection independent of circulating levels, which corroborates with pharmacological CFB inhibition. These findings redefine complement in the intestine as a locally regulated mucosal defense system and establish gut-derived CFB as a critical determinant of intestinal homeostasis. BRIEF SUMMARYThe role of local immune mediators in gut mucosal immune responses is still not entirely understood. In this study, we demonstrate a novel role for complement protein Factor B, a key component of the alternative pathway, which is locally sourced through epithelial and stromal cells. In vivo modeling of impaired local Factor B synthesis results in worse colitis, revealing a key role for mucosal sourced components of the alternative pathway.

immunology↗

bioRxiv2025

Cis-regulatory variation in ISOCHORISMATE SYNTHASE 1 modulates systemic salicylic acid biosynthesis and systemic acquired resistance in plants

Systemic acquired resistance (SAR) is a long-distance immune response that protects uninfected plant tissues following a localized pathogen attack. In the model plant Arabidopsis thaliana, SAR depends on the systemic accumulation of salicylic acid (SA), mediated by the transcription factor CCA1 HIKING EXPEDITION (CHE), which activates the SA biosynthetic gene ISOCHORISMATE SYNTHASE1 (ICS1). However, the conservation and functional significance of the CHE-ICS1 regulatory module across plant species remain poorly understood, particularly in the Brassicaceae, where ICS1 is the major contributor to SA biosynthesis among two known pathways: the ICS1 and PHENYLALANINE AMMONIA-LYASE (PAL) routes. Here, we identify natural variation in cis-regulatory elements within the ICS1 promoter that affects CHE binding across species. In multiple Brassicaceae species with divergent cis-element sequences, CHE fails to regulate ICS1, leading to the absence of systemic ICS1 induction and SA accumulation following pathogen infection. Despite this deficiency, SAR still occurs in these species, albeit to a lesser extent than in species with successful systemic induction of SA mediated by an intact CHE-ICS1 regulatory module. Interestingly, introducing the CHE-ICS1 module into species lacking this interaction confers systemic SA accumulation, highlighting the potential to enhance systemic immunity through cis-element modification. Our findings demonstrate that sequence variation in a cis-regulatory element underlies the interspecies diversification of SAR regulatory mechanisms and highlight the evolutionary plasticity of plant immune signaling. This study provides a molecular framework for engineering enhanced systemic immunity in crops, particularly within the Brassicaceae, through the targeted modification of cis-regulatory elements that regulate SA biosynthesis.

plant biology↗

bioRxiv2024

Journey to the center of the phage; revealing the ejectosome of Pectobacterium bacteriophage {Phi}M1

Podophages that infect gram-negative bacteria, such as Pectobacterium pathogen {Phi}M1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here we describe the ejectosome of bacteriophage {Phi}M1 to a resolution of 3.32 [A] by single particle cryo-EM. The core consists of tetrameric and octameric ejection proteins which form a [~]1.5 MDa ejectosome that must transition through the [~]30 [A] aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 [A] and 3.23 [A], and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the {Phi}M1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages. Significance StatementThis study resolves the cryo-EM structure of bacteriophage {Phi}M1, which possesses several unique and interesting structural elements, including a pair of distinct decoration proteins that are underreported in tailed DNA phages. Significantly, we also report the internal ejectosome proteins of {Phi}M1, which are highly non-conserved with previously solved proteins to date and demonstrate the structural diversity of ejection proteins. The ejectosome reveals a DNA spooling phenomenon whereby the viral genome wraps around the ejectosome within the capsid, which has never been reported before. We provide a clear, step-by-step method for the technically challenging reconstruction of ejectosomes using standard, open-source software.

microbiology↗

bioRxiv2024

Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility

Macrophages encounter a myriad of biochemical and mechanical stimuli across various tissues and pathological contexts. Notably, matrix rigidity has emerged as a pivotal regulator of macrophage activation through mechanotransduction. However, the precise mechanisms underlying the interplay between mechanical and biochemical cues within the nuclear milieu remain elusive. Here we elucidate how the increased matrix rigidity drives macrophages to amplify alternatively-activated (M2 phenotype) signalings cooperatively with biochemical cues (e.g., IL4/13) through altered nuclear mechanics. Notably, we found that reconstructed podosome-like F-actins and contractility induced nucleus deformation, opening nuclear pores, which facilitates nuclear translocation of the key transcription factor STAT6. Furthermore, the altered nuclear mechanics increased chromatin accessibility induced by H3K9 methylation, particularly of M2-associated gene promoters. These cooperative events of the mechano-chemical signaling at the cytoskeletal-to-nuclear domains facilitated M2 transcriptional activation and cellular functions. We further evidenced the rigidity-primed M2 macrophages were immunosuppressive and accumulated in stiffened tumor tissues. This study proposes a mechanism by which matrix mechanics crosstalks with biochemical signals to potentiate macrophage activation through nuclear mechanosensing and chromatin modifications, offering insights into macrophage mechanobiology and its therapeutic modulations.

bioengineering↗

bioRxiv2024

Peripheral mutations underlie promiscuous transport of quaternary ammonium antiseptics by Small Multidrug Resistance transporters

The mechanistic basis of transport promiscuity in multidrug exporters is not well understood. We examine this question using the Small Multidrug Resistance (SMR) transporters. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this new activity. Using x-ray crystallography, electrophysiology, and a novel proteoliposome-based antiseptic transport assay, we tease apart the mechanistic roles that these residues play in transport polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate, but through mutations peripheral to the binding pocket. Our new molecular insights into substrate promiscuity among the SMRs can be applied to understand multidrug export and the evolution of novel transport functions more generally.

biochemistry↗

bioRxiv2021

Hepatic miR-20b promotes nonalcoholic fatty liver disease by suppressing PPARα

BackgroundNon-alcoholic fatty liver disease (NAFLD) is characterized by excessive lipid accumulation and imbalances in lipid metabolism in the liver. Although nuclear receptors (NRs) play a crucial role in hepatic lipid metabolism, the underlying mechanisms of NR regulation in NAFLD remain largely unclear. MethodsUsing network analysis and RNA-seq to determine the correlation between NRs and microRNA in human NAFLD patients, we revealed that MIR20B specifically targets PPARA. MIR20B mimic and anti-MIR20B were administered to human HepG2 and Huh-7 cells and mouse primary hepatocytes as well as high fat diet (HFD)- or methionine-deficient diet (MCD)-fed mice to verify the specific function of MIR20B in NAFLD. We tested the inhibition of the therapeutic effect of a PPAR agonist, fenofibrate, by MIR20B and the synergic effect of combination of fenofibrate with anti-MIR20B. ResultsWe revealed that MIR20B specifically targets PPARA through miRNA regulatory network analysis of nuclear receptor genes in NAFLD. The expression of MIR20B was upregulated in free fatty acid (FA)- treated hepatocytes and the livers of both obesity-induced mice and NAFLD patients. Overexpression of MIR20B significantly increased hepatic lipid accumulation and triglyceride levels. Furthermore, MIR20B significantly reduced FA oxidation and mitochondrial biogenesis by targeting PPARA. In MIR20B-introduced mice, the effect of fenofibrate to ameliorate hepatic steatosis was significantly suppressed. Finally, inhibition of MIR20B significantly increased FA oxidation and uptake, resulting in improved insulin sensitivity and a decrease in NAFLD progression. Moreover, combination of fenofibrate and anti-MIR20B exhibited the synergic effect on improvement of NAFLD in MCD-fed mice. ConclusionsTaken together, our results demonstrate that the novel MIR20B targets PPARA, plays a significant role in hepatic lipid metabolism, and present an opportunity for the development of novel therapeutics for NAFLD. FundingThis research was funded by Korea Mouse Phenotyping Project (2016M3A9D5A01952411), the National Research Foundation of Korea (NRF) grant funded by the Korea government (2020R1F1A1061267, 2018R1A5A1024340, NRF-2021R1I1A2041463, 2020R1I1A1A01074940), and the Future-leading Project Research Fund (1.210034.01) of UNIST.

molecular biology↗

bioRxiv2020

DNA micro-disk for the management of DNA-based data storage with index and write-once-read-many (WORM) memory features

DNA-based data storage has attracted attention because of its higher physical density of the data and longer retention time than those of conventional digital data storage1-7. However, previous DNA-based data storage lacked index features and the data quality of storage after a single access is not preserved, obstructing its industrial use. Here, we propose DNA micro-disks, quick response (QR)-coded micro-sized disks that harbour data-encoded DNA molecules for the efficient management of DNA-based data storage. We demonstrate the two major features that previous DNA-based data storage studies could not achieve. One feature is accessing data items efficiently by indexing the data-encoded DNA library. Another is achieving write-once-read-many (WORM) memory through the immobilization of DNA molecules on the disk and their enrichment through in situ DNA production. Through these features, the reliability of DNA-based data storage was increased by allowing multiple accession of data-encoded DNA without data loss.

bioengineering↗

bioRxiv2018

RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction point

The cellular decision regarding whether to undergo proliferation or death is made at the restriction (R)-point, which is disrupted in nearly all tumors. The identity of the molecular mechanisms that govern the R-point decision is one of the fundamental issues in cell biology. We found that early after mitogenic stimulation, RUNX3 bound to its target loci, where it opened chromatin structure by sequential recruitment of Trithorax group proteins and cell-cycle regulators to drive cells to the R-point. Soon after, RUNX3 closed these loci by recruiting Polycomb repressor complexes, causing the cell to pass through the R-point toward S phase. If the RAS signal was constitutively activated, RUNX3 inhibited cell cycle progression by maintaining R-point-associated genes in an open structure. Our results identify RUNX3 as a pioneer factor for the R-point and reveal the molecular mechanisms by which appropriate chromatin modifiers are selectively recruited to target loci for appropriate R-point decisions.

cell biology↗

bioRxiv2017

In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes under physiological conditions.

During a proteolytically-driven maturation process, the ortho-retroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.

biochemistry↗