Biology subjects

Kim, J.-E.

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

5 recordsLinked to original sources

bioRxiv2026

Transcriptome dissection of the Zeb2-associated network reveals a role for NRPS15 in zearalenone biosynthesis in Fusarium graminearum

Fungal secondary metabolites, including mycotoxins, play important roles in fungal biology and represent major concerns for food and feed safety. Zearalenone (ZEA) is an estrogenic polyketide mycotoxin produced by several Fusarium species, yet the genetic network governing its production remains poorly characterized. Here, we investigated genes associated with ZEA production in Fusarium graminearum using two complementary transcriptomic approaches. Time-resolved transcriptome analysis revealed transcriptional changes preceding detectable ZEA accumulation. Temporal clustering further revealed coordinated changes in primary metabolism, transcriptional regulation, carbohydrate utilization, and stress- and transport-associated pathways during ZEA-inducing cultivation. Genotype-based transcriptome analysis of ZEB2 deletion and overexpression strains subsequently identified Zeb2-responsive genes. Functional screening identified NRPS15, encoding a previously uncharacterized nonribosomal peptide synthetase-like protein adjacent to the ZEA biosynthetic cluster, as an important contributor to ZEA production. Deletion of NRPS15 markedly reduced ZEA production and expression of PKS4, PKS13, ZEB1, and ZEB2. NRPS15 expression did not restore ZEA production in the absence of Zeb2. NRPS15 orthologs were conserved in several ZEA-producing Fusarium species, and deletion of NRPS15 substantially reduced ZEA production in Fusarium culmorum. These findings expand the functional genetic context of ZEA production beyond the canonical four-gene biosynthetic cluster.

molecular biology↗

bioRxiv2026

High-variance phenome database reveals important roles of WD40 proteins in the plant pathogenic fungus Fusarium graminearum

WD40 is a highly conserved protein domain in eukaryotes, playing a critical role in various cellular process. We conducted genome-wide functional analysis of WD40 genes in Fusarium graminearum-a phytopathogenic fungus that causes severe yield loss and mycotoxin contamination in major cereal crops. Comprehensive phenome analysis of 119 WD40 gene deletion mutants across 22 distinct phenotypic traits revealed phenotypic divergence within the phenome, establishing a strong correlation between virulence and sexual reproduction. Notably, 21 core WD40 genes were identified, offering valuable insights into divergent biological processes. Pilot interactome studies of Fgwd101 and Fgwd133 provided further insights into their potential pathobiological functions. Our investigation contributes to broadening our knowledge of the biological mechanisms underlying fungal pathogenesis and may assist in the identification of targets for antifungal agents.

molecular biology↗

bioRxiv2024

Evolutionary unique N-glycan-dependent protein quality control system plays pivotal roles in cellular fitness and extracellular vesicle transport in Cryptococcus neoformans

A conserved N-glycan-dependent endoplasmic reticulum protein quality control (ERQC) system has evolved in eukaryotes to ensure accuracy during glycoprotein folding. The human pathogen Cryptococcus neoformans possesses a unique N-glycosylation pathway that affects microbial physiology and interactions with the infected host. To investigate the molecular features and functions of the ERQC system in C. neoformans, we characterized a set of mutants with deletion of genes coding for the ERQC sensor UDP-glucose:glycoprotein glucosyltransferase (UGG1) and putative 1,2-mannose-trimming enzymes (MNS1, MNS101, MNL1, and MNL2). The ugg1{Delta}, mns1{Delta}, mns101{Delta}, and mns1{Delta}101{Delta} mutants showed alterations in N-glycan profiles, defective cell surface organization, decreased survival in host cells, and varying degrees of reduced in vivo virulence. The ugg1{Delta} strain exhibited severely impaired extracellular secretion of capsular polysaccharides and virulence-related enzymes. Comparative transcriptome analysis showed the upregulation of protein folding, proteolysis, and cell wall remodeling genes, indicative of induced ER stress. However, no apparent changes were observed in the expression of genes involved in protein secretion or capsule biosynthesis. Additionally, extracellular vesicle (EV) analysis combined with proteomic analysis showed significant alterations in the number, size distribution, and cargo composition of EVs in ugg1{Delta}. These findings highlight the essential role of the functional ERQC system for cellular fitness under adverse conditions and proper EV-mediated transport of virulence factors, which are crucial for the full fungal pathogenicity of C. neoformans.

microbiology↗

bioRxiv2023

Comparative Interactome Analysis of α-arrestin Families in Human and Drosophila

The -arrestins form a large family of evolutionally conserved modulators that control diverse signaling pathways, including both G-protein-coupled receptor-(GPCR-) mediated and non-GPCR mediated pathways, across eukaryotes. However, unlike {beta}-arrestins, only a few -arrestin targets and functions have been characterized. Here, using affinity purification and mass spectrometry, we constructed interactomes for six human and twelve Drosophila -arrestins. The resulting high-confidence interactomes comprised 307 and 467 prey proteins in human and Drosophila, respectively. A comparative analysis of these interactomes predicted not only conserved binding partners, such as motor proteins, proteases, ubiquitin ligases, RNA splicing factors, and GTPase-activating proteins, but also those specific to mammals, such as histone modifiers and the subunits of V-type ATPase. Given the manifestation of the interaction between the human -arrestin, TXNIP, and the histone-modifying enzymes, including HDAC2, we undertook a global analysis of transcription signals and chromatin structures that were affected by TXNIP knockdown. We found that TXNIP activated targets by blocking HDAC2 recruitment to targets, a result that was validated by chromatin immunoprecipitation assays. Additionally, the interactome for an uncharacterized human -arrestin ARRDC5 uncovered multiple components in the V-type ATPase, which plays a key role in bone resorption by osteoclasts. Our study presents conserved and species-specific protein-protein interaction maps for -arrestins, which provide a valuable resource for interrogating their cellular functions for both basic and clinical research.

cell biology↗

bioRxiv2018

High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have several technical limitations such as low process throughput from laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire. TrueRepertoire provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire was demonstrated by a phage-displayed single-chain variable fragment (scFv) library targeting human hepatocyte growth factor (hHGF) protein.

bioengineering↗