Biology subjects

Lee, E.-J.

Publications and source records attributed to Lee, E.-J..

7 recordsLinked to original sources

bioRxiv2026

Atf6-/- mouse photoreceptors exhibit novel ciliary rootlet defect

ATF6 is a regulator of the Unfolded Protein Response that maintains cellular homeostasis during ER stress. In patients, ATF6 mutations cause photoreceptor dystrophy and sensorineural hearing loss. Atf6-/- mice develop progressive hearing loss with stereocilia disorganization and mild retinal dysfunction, suggesting that ATF6 loss may impair the structural integrity of sensory cells. To test this possibility, we analyzed the retinal ultrastructure of Atf6-/- mouse photoreceptors using transmission electron microscopy and identified a novel defect in which the ciliary rootlet is unbundled, disorganized, and possibly detached from the basal body. These findings demonstrate that ATF6 is essential for maintaining the structural organization of the photoreceptor ciliary apparatus, linking ER proteostasis to cytoskeletal integrity and providing a potential mechanistic basis for the progressive degeneration of photoreceptor outer segments and stereocilia observed in ATF6-deficient patients.

cell biology↗

bioRxiv2025

Bioinformatics classification of the MgtE Mg2+ channel and de novo protein design for the stabilization of its novel subclass

MgtE channels play crucial roles in Mg{superscript 2} homeostasis and are implicated in bacterial survival under antibiotic exposure. Previous structural and biophysical studies have predominantly focused on the Thermus thermophilus MgtE, leaving the structural and mechanistic diversity of MgtE family proteins largely unexplored. In this study, using a genome mining approach, we identified diverse MgtE homologs, including a novel subclass termed the "mini-N type," which lacks the canonical cytoplasmic N and CBS domains but possesses a unique small N-like domain. Despite extensive expression screening, mini-N type homologs could not be stably purified. To address this issue, we designed a series of de novo proteins and determined their crystal structures. A selected de novo protein was fused to a mini-N type MgtE, enabling successful purification and preliminary cryo-EM imaging. Our findings demonstrate that de novo designed protein fusions can serve as powerful tools for stabilizing and purifying otherwise unstable membrane proteins, opening new avenues for the structural and functional studies of otherwise inaccessible membrane proteins.

biophysics↗

bioRxiv2025

A Salmonella type I toxin promotes systemic infection by inhibiting FoF1 ATP synthase

Intracellular pathogens including Salmonella Typhimurium survive within macrophage phagosomes by forming non-replicating persisters. Toxins from toxin-antitoxin systems have been implicated in persister formation as key contributors, although the biological targets of toxins remain largely unknown. Here, we report that Salmonella IbsA, a 19-amino-acid-long type I toxin, induces growth arrest and decreases intracellular ATP levels. An unbiased large-scale bacterial two-hybrid screen identified 54 IbsA-interacting targets, including proteins involved in oxidative phosphorylation and cell division. Among these, IbsA toxin specifically targets two subunits of the bacterial FoF1 ATP synthase. IbsA interacts with the a and b subunits in the membrane-bound Fo sector and inhibits proton translocation, thereby decreasing ATP levels. In turn, this IbsA-mediated decrease facilitates Salmonella spread between macrophages, promoting systemic infection. Accordingly, ibsA deletion decreases bacterial burden in organs and attenuates mouse virulence. Therefore, unlike other bacterial toxins, the IbsA toxin enhances Salmonella pathogenicity by decreasing the bacteriums ATP levels.

microbiology↗

bioRxiv2024

Elongation factor P controls ribosomal frameshift of a Salmonella antimicrobial resistance gene

Ribosomes translate mRNAs by matching every 3-nucleotide sequence in mRNA, producing the corresponding proteins. As the amino acid sequence directly dictates the activity of the protein, frameshifts often lead to unexpected effects. Here, ribosome profiling reveals that the intracellular pathogen Salmonella Typhimurium suppresses frameshift in the ugtL antimicrobial resistance gene during translation. This suppression of frameshift is mediated by a ribosome pause occurring in a newly-identified overlapping gene, serving as a non-slip bump. Given that the pause site contains a poly-proline motif and can be resolved by elongation factor P, the removal of the ribosome pause by substituting the motif induces ribosome slippage in ugtL, resulting in UgtL frameshifted protein production. This renders Salmonella sensitive to antimicrobial peptides but, in turn, protects the MgtC virulence factor from the FtsH-mediated proteolysis, indicating that elongation factor P-dependent ribosome pause is required for controlling both full antimicrobial resistance and mouse virulence. These findings reveal a new regulatory mechanism in which ribosome pause controls the production of two different protein isoforms by suppressing ribosome slippage-mediated frameshift.

microbiology↗

bioRxiv2024

A HigB-like toxin promotes non-replicating Salmonella inside macrophages by inhibiting ribonuclease III

Many bacteria are often resistant to antibiotic treatment because they can slow down their growth rate, thereby attenuating the drugs effectiveness. A similar growth-rate control is observed in pathogens that infect and persist inside their hosts. The bacterial toxin-antitoxin (TA) system serves as a non-heritable phenotypic switch by slowing down growth through the expression of a toxin component. Here, we investigated a HigB-like type II toxin from the intracellular bacterial pathogen Salmonella Typhimurium. Unlike other HigB-like toxins that cleave ribosome-bound mRNAs, it does not exhibit endoribonuclease activity. Instead, it inhibits ribonuclease III, which mediates the initial cleavage for rRNA processing, by directly binding to the dsRNA-binding domain of RNase III, thereby decreasing ribosome assembly and bacterial growth. Given that the formation of HigB-like toxin-mediated non-replicating Salmonella within macrophages is RNase III-dependent, persister formation by inhibiting RNase III is a newly identified strategy for pathogens to survive within host cells.

microbiology↗

bioRxiv2024

Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo approach

Genome-wide identification of binding profiles for DNA-binding proteins in Salmonella Typhimurium within macrophages is crucial for understanding virulence gene expression and cellular processes. However, this task remains challenging due to the limited amount of intracellular bacterial cells. Here, we present ChIP-mini, a low-input ChIP-exo utilizing 5,000-fold reduced number of initial bacterial cells and analysis pipeline (DiffExo), to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular S. Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, with near-base pair resolution, elucidating their roles in transcriptional initiation. Post-infection, we observed 21 significant reductions in H-NS binding at intergenic regions, exposing the promoter region of virulence genes, such that those in Salmonella pathogenicity islands-2, 3 and effectors, facilitating RpoD binding for transcription initiation. Furthermore, we identified 24 novel RpoD binding sites and 19 significantly increased RpoD bindings at the transcription start sites of virulence genes. These findings substantially enhance our understanding of how H-NS and RpoD simultaneously coordinate the transcription initiation of virulence genes within macrophages. Collectively, this optimized method demonstrates a tool that can be broadly adapted to elucidate transcriptional regulatory networks of host-infected pathogens, revealing critical interactions between host and microbe.

systems biology↗

bioRxiv2020

The RNA binding protein hnRNP-U is required for physiological hypertrophy of skeletal muscle

Skeletal muscle has the remarkable ability to modulate its mass in response to physiological changes associated with nutritional input, functional utilization, systemic disease, and age. A decreased responsiveness to anabolic stimuli is thought to contribute significantly to the loss of skeletal muscle mass and strength associated with sarcopenia, however the molecular mechanisms precipitating this are unclear. The signal transduction pathways that control the relative balance between anabolic and catabolic processes are tightly regulated at the transcriptional and post-transcriptional levels. Alternative splicing produces multiple protein isoforms from a single gene in a cell-type-specific manner and in response to environmental cues. We show that sustained activation of Akt1 in Hnrnpu deficient mice leads to premature muscle wasting, in part, through impaired autophagy while providing mechanistic insights into the development of anabolic resistance.

cell biology↗