Biology subjects

Lee, K.-T.

Publications and source records attributed to Lee, K.-T..

14 recordsLinked to original sources

bioRxiv2026

A convergent proline biosynthetic step couples cell wall integrity to virulence in Cryptococcus neoformans

Metabolic adaptation is essential for the pathogenicity of the opportunistic fungus Cryptococcus neoformans. Although amino acid biosynthesis pathways are critical fitness determinants in fungal pathogens, the physiological contributions of proline biosynthesis remain incompletely understood, with most studies focusing on proline catabolism. Here, we characterized the proline biosynthetic enzymes Pro1, Pro2, and Pro3 in C. neoformans. Proline is produced by two routes that converge on {Delta}1-pyrroline-5-carboxylate (P5C): a de novo pathway from glutamate via Pro1 and Pro2, and an arginine-derived bypass via Car1 and Car2--both requiring Pro3 for the final reduction of P5C to proline. Although all biosynthetic mutants were strictly auxotrophic for proline, their requirements for virulence differed markedly: in a murine infection model, pro1{Delta} and pro2{Delta} mutants retained full virulence, whereas pro3{Delta} exhibited significantly attenuated virulence accompanied by growth defects and impaired cell wall integrity. Genetic disruption of P5C-generating routes partially restored distinct pro3{Delta} phenotypes, with PRO2 deletion alleviating delayed growth and combined PRO2 and CAR2 deletion partially restoring cell size, while cell wall defects remained unresolved. This dissociation indicates that growth requires proper balance of P5C-generating metabolic flux, whereas cell wall integrity depends on a distinct mechanism that is not resolved by blocking P5C production. Together, these findings identify Pro3 as a metabolic gatekeeper coupling proline biosynthesis to cell wall homeostasis, establishing the biosynthetic branch of proline metabolism as a previously unappreciated determinant of fungal pathobiology.

microbiology↗

bioRxiv2026

Systematic histone mutagenesis reveals nucleosome-dependent maintenance of three-dimensional chromosome architecture and virulence in Cryptococcus neoformans

BackgroundGenomic stability is maintained through the coordinated regulation of DNA repair, dNTP pool balance, and histone dynamics--the three pillars of the DNA damage response. Because histones constitute the fundamental 3D physical scaffold of the genome, their precise regulation is essential for the spatial organization that dictates environmental fitness. In the radiotolerant pathogen Cryptococcus neoformans, the Rad53-Bdr1 pathway is a central DDR mediator; however, the mechanisms linking this checkpoint to histone dynamics remain poorly understood. Because conventional one-dimensional analyses cannot capture how spatial chromatin folding shapes transcriptional reprogramming, we integrated high-throughput chromosome conformation capture (Hi-C) with transcriptomic profiling to address this gap. ResultsWe demonstrate that HTA1 and HTB1, encoding H2A and H2B, are essential for viability, whereas H3 and H4 paralogs exhibit functional redundancy. Although most core histones are regulated by Rad53, HHT1 and variant HTZ1 are expressed independently of the Rad53. Notably, loss of the H3 paralog HHT2 induces growth defects under diverse stress conditions. Integrated RNA sequencing and Hi-C analyses reveal that HHT2 deletion drives transcriptional reprogramming of stress-responsive genes, coinciding with large-scale chromatin rearrangements such as A/B compartment switching and topologically associating domain boundary shifts. Furthermore, HHT2 loss impairs virulence factor formation and attenuates virulence. ConclusionOur findings identify core histones as essential architects of the 3D genome in C. neoformans. By establishing a causal link between chromatin structural collapse and transcriptional reprogramming, this study highlights 3D genome architecture as a decisive physical switch linking nucleosome-level dynamics to global transcriptional programs required for environmental survival.

microbiology↗

bioRxiv2026

Systematic profiling of WD40 proteins reveals Wcp1, a cyclophilin linking CO2/heat tolerance to acidic pH adaptation in Cryptococcus neoformans

WD40 domains are major protein-protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional knockdown and sporulation identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We identified Wcp1, a dual-domain protein whose WD40-repeat and cyclophilin domains are required for growth at 37{degrees}C under 5% CO2. Its WD40 scaffold and PPIase domain supported CO2/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1{Delta} failed to grow under elevated temperature and CO2 at acidic pH, exhibited enhanced intracellular acidification, reduced macrophage survival and attenuated virulence in Drosophila and mice. Integrated transcriptomic and proteomic analyses place Wcp1 at the centre of intracellular pH homeostasis, coordinating proton transport, metabolic adaptation and stress-buffering networks.

microbiology↗

bioRxiv2026

Systematic Profiling of Essential Fungal Transcription Factors Uncovers Ezt1 as a Central Pathobiological and Morphogenic Regulator in Cryptococcus neoformans

Cryptococcus neoformans is a global fungal pathogen that causes fatal cryptococcosis, and the limitations of current antifungals underscore the urgent need for new therapeutics. Here we systematically investigate essential transcriptional regulators in C. neoformans as potential antifungal targets, developing experimental pipelines that assess growth requirement, essentiality and function through conditional gene expression, constitutive overexpression, and meiotic spore analysis. We identify one quasi-essential (growth-required but non-essential) transcription factor, Fhl1, and 13 essential transcriptional regulators, three of which are transcription factors (Ezt1, Ezt2 and Cbf1) highly divergent from counterparts in other eukaryotes. Notably, Ezt1 modulates the expression of more than 1,200 genes, controlling growth, antifungal drug and stress responses, sexual development and virulence. Our findings define the essential transcriptional regulator landscape of C. neoformans and provide a framework for prioritising divergent essential regulators, particularly Ezt1, for antifungal target discovery.

microbiology↗

bioRxiv2026

Mitochondrial metabolic remodeling drives innate immune activation in Drosophila hemocytes

Innate immune cells rapidly reprogram their metabolism upon activation, yet the metabolic basis of this flexibility in invertebrate systems remains largely unexplored. Here, we investigate the metabolic landscape of Drosophila larval hemocytes, functional analogs of vertebrate myeloid cells, across developmental stages, genotypes, and immune activation states, by combining metabolic flux measurements with single-cell transcriptomics. Under homeostatic conditions, hemocytes rely predominantly on mitochondrial oxidative phosphorylation for ATP production, with minimal glycolytic contribution. Immune activation, particularly lamellocyte differentiation, drives enhanced mitochondrial respiration and metabolic flexibility, accompanied by structural remodeling of the mitochondrial network. Mechanistically, functional lamellocytes require Drp1-mediated mitochondrial fission and utilize glucose and trehalose as primary carbon sources to sustain mitochondrial respiration, which is essential for effective immune responses. Overall, these findings establish that mitochondrial metabolic reprogramming is a conserved feature of innate immune activation in myeloid-like immune cells and reveal an evolutionarily ancient link between mitochondrial dynamics and immune cell activation, with implications for understanding metabolic regulation of innate immunity in invertebrate models and beyond.

developmental biology↗

bioRxiv2025

The protein phosphatase 2C domain contributes to the pathobiological function of adenylyl cyclase in Cryptococcus neoformans

Adenylyl cyclase produces cyclic adenosine monophosphate, a signalling molecule that controls fungal development and virulence. Fungal adenylyl cyclases are distinguished by the presence of a conserved protein phosphatase 2C domain, whose function remains unknown. Here we show that the protein phosphatase 2C domain of Cac1, the adenylyl cyclase of the human pathogen Cryptococcus neoformans, has an unusual structure but functions as a metal-dependent serine/threonine phosphatase. Deletion of this domain or the adenylyl cyclase catalytic domain demonstrated that the protein phosphatase 2C domain is required for full Cac1 activity, influencing melanin and capsule synthesis, sexual differentiation, titan cell formation, and cell wall integrity. Notably, loss of the protein phosphatase 2C domain induces type 2 helper T-cell-biased immunity and extensive pulmonary damage yet does not cause mortality in mice. Integrated transcriptomic and phosphoproteomic analyses further revealed shared and domain-specific signalling outputs. Together, these findings define a pivotal role for the adenylyl cyclase-linked protein phosphatase 2C domain in C. neoformans pathobiology.

microbiology↗

bioRxiv2025

A hydrophobic core in the coiled-coil domain essential for NRC resistosome function

The nucleotide-binding leucine-rich repeat protein (NLR) required for cell death (NRC) family represents a group of helper NLRs that are required by sensor NLRs to execute hypersensitive cell death during pathogen infection. NRCs contain an N-terminal coiled-coil (CC) domain essential for their function, yet our knowledge of how this domain contributes to NRC function remains limited. Here, we identified a novel hydrophobic feature within the CC domain that contributes to NRC-mediated immunity. We screened for conserved hydrophobic residues among NRCs and identified seven required for NRC4-mediated cell death. Structural analysis revealed that four of these residues form a hydrophobic core in the CC domain. This hydrophobic core is important for NRC4 subcellular localization, oligomerization, and phospholipid association, but not for NRC4 focal accumulation at the extrahaustorial membrane during Phytophthora infestans infection. Sequence analysis and functional assays revealed this core is highly conserved in NRCs and some singleton NLRs but has degenerated in NRC-dependent sensor NLRs. Our study identifies a novel hydrophobic feature in the CC domain of NRCs and reveals its contribution to NLR-mediated immunity.

plant biology↗

bioRxiv2025

The calcineurin pathway regulates extreme thermotolerance, cell membrane and wall integrity, antifungal resistance, and virulence in Candida auris

Candida auris, an emerging fungal pathogen characterized by its multidrug resistance and high mortality rates, poses a significant public health challenge. Despite its importance, the signaling pathways governing virulence and antifungal resistance in C. auris remain poorly understood. This study investigates the calcineurin pathway in C. auris, critical for virulence and antifungal resistance in other fungal pathogens. Calcineurin, a calcium/calmodulin-dependent protein phosphatase, comprises a catalytic subunit (Cna1) and a regulatory subunit (Cnb1) in C. auris. Our findings reveal that deletion of CNA1 or CNB1 disrupts extreme thermotolerance and cell membrane and wall integrity, leading to increased susceptibility to azoles and echinocandins. Moreover, we identified a downstream transcription factor, Crz1, which plays a central role in this pathway in other fungal species. Deletion of CRZ1 resulted in similar membrane integrity defects observed in the cna1{Delta} and cnb1{Delta} mutants and increased susceptibility to azole drugs. Supporting it, fluconazole treatment induced Crz1 nuclear translocation in a Cna1-dependent manner. However, unlike cna1{Delta} and cnb1{Delta} mutants, the crz1{Delta} mutant displayed increased resistance to echinocandins, suggesting the opposing roles for Crz1 in regulating cell wall integrity. Nevertheless, echinocandins also promoted Crz1 nuclear translocation via Cna1, underscoring the complex regulatory mechanisms at play. Cna1 was found to be required for virulence in both the Drosophila systemic infection model and the murine skin infection model. However, in a systemic murine infection model, both calcineurin and Crz1 appeared dispensable for C. auris virulence. Our findings highlight that the evolutionarily conserved calcineurin pathway employs distinct regulatory mechanisms to perform divergent roles in regulating cell wall and membrane integrity, antifungal drug resistance, and virulence in C. auris. Author SummaryThe fungal pathogen Candida auris presents a global health threat due to its multidrug resistance and high mortality rates. Despite its clinical significance, the molecular mechanisms underlying its virulence and antifungal resistance remain poorly understood. This study investigates the complex role of the calcineurin signaling pathway in C. auris pathogenicity. Deletion of the calcineurin complex impairs extreme thermotolerance and compromises cell membrane and wall integrity, leading to increased susceptibility to azoles and echinocandins, antifungal agents targeting the cell membrane and wall, respectively. We also identified the Crz1 transcription factor as a downstream target of calcineurin signaling. Interestingly, unlike calcineurin mutants, Crz1 mutants are susceptible only to cell-membrane-targeting azoles but surprisingly exhibit increased resistance to cell-wall-targeting echinocandins, suggesting that the calcineurin pathway may regulate multiple transcription factors, including Crz1. Additionally, calcineurin was found to be essential for virulence in vivo, using two different animal infection models, Drosophila and mice. These findings highlight the essential role of the calcineurin pathway in C. auris virulence, offering novel insights into its role in antifungal resistance and virulence, and paving the way for targeted therapies.

microbiology↗

bioRxiv2024

Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants

Agroinfiltration, a method utilizing agrobacteria to transfer DNA into plant cells, is widely used for transient gene expression in plants. Besides the commonly used Agrobacterium strains, Rhizobium rhizogenes can also introduce foreign DNA into host plants for gene expression. While many R. rhizogenes strains have been known for inducing hairy root symptoms, their use for transient expression has not been fully explored. Here, we showed that R. rhizogenes A4 outperformed all other tested agrobacterial strains in agroinfiltration experiments on leaves of Nicotiana benthamiana and other solanaceous plants. By conducting an agroinfiltration screening in N. benthamiana leaves using various agrobacterial strains carrying the RUBY reporter gene cassette, we discovered that A4 mediates the strongest and fastest transient expression. Utilizing the genomic information, we developed a collection of disarmed and modified strains derived from A4. By performing vacuum infiltration assays, we demonstrated that these A4-derived strains efficiently transiently transform 6-week-old N. benthamiana leaves, showing less sensitivity to the age of plants compared to the laboratory strain GV3101. Furthermore, we performed agroinfiltration using AS109, an A4-derived disarmed strain, on the leaves of tomato, pepper, and eggplant. Remarkably, AS109 mediated transient gene expression on tested solanaceous plants more effectively than all the tested commonly used agrobacterial strains. This discovery paves the way for establishing R. rhizogenes A4-derived strains as a new option for enhancing transient expression in N. benthamiana and facilitating the functional study of plant genes in other solanaceous species.

plant biology↗

bioRxiv2024

The amino acid permease Byc1 is involved in calcineurin-dependent thermos-tolerance in Cryptococcus neoformans

Cryptococcosis is one of the most serious infectious fungal diseases. It is known to infect the human respiratory tract and central nervous system and cause meningitis and encephalitis, especially in patients with AIDS. In the sub-Saharan area, cryptococcosis causes more mortality than tuberculosis. Cryptococcus neoformans is the etiological agent. There has been a growing number of reports of antifungal resistance in C. neoformans, and this fungus is also primarily resistant to the newest antifungal drug class, the echinocandins. Despite advances in modern medicine, the morbidity and mortality of C. neoformans infections remain unacceptably high. In C. neoformans, calcineurin, a serine/threonine phosphatase, is required for growth at the human host temperature, and calcineurin mutants are not virulent in murine models of cryptococcal meningitis. Therefore, calcineurin has long been considered an antifungal target. However, calcineurin is highly conserved in fungi and humans, and thus direct pharmacological inhibition of calcineurin can risk lowering host immunity as the human calcineurin is required for T-cell responses. A previous study demonstrated that there is a link between calcineurin, an amino acid permease, and protein kinase As in Mucorales. In this study, we further reveal the existence of a novel link between calcineurin and an amino acid permease, Byc1, for a thermo-tolerance phenotype in this fungus. We found that calcineurin negatively regulates the expression of the BYC1 gene and that byc1{Delta} mutants are partially resistant to FK506. Moreover, we revealed that overexpression of the BYC1 gene recapitulates the calcineurin mutants thermos-sensitive phenotypes, including FK506 sensitivity and lowered virulence in a murine infection model. We also found that protein kinase A (Pka1) mutants are also partially resistant to FK506. These results support the link between calcineurin, Byc1, and Pka1 in C. neoformans and will serve as a platform for developing novel antifungal drugs against the calcineurin pathway without directly targeting the phosphatase.

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↗

bioRxiv2022

Bub1 kinase acts as a signalling hub for the entire Cryptococcus neoformans spindle assembly checkpoint pathway

Cryptococcus neoformans (Cn) is an important human pathogen and a model system for basidiomycetes. Here we carry out a dissection of its spindle assembly checkpoint (SAC), focusing on Bub1 and Bub3. In many eukaryotes, including humans, Saccharomyces cerevisiae and Schizosaccharomyces pombe, Bub1 underwent gene duplication, generating paralogues referred to as Bub1 and BubR1 (or Mad3). Bub1 has upstream signalling functions at kinetochores, whilst BubR1/Mad3 is a component of the downstream mitotic checkpoint complex (MCC) that delays anaphase onset until all chromosomes are correctly attached. Here we demonstrate that the single CnBub1 protein carries out all the checkpoint roles of both Bub1 kinase and Mad3/BubR1. Proteomic analysis reveals kinetochore targeting via Spc105KNL1 and interactions with all downstream SAC components and effectors (Cdc20 and the anaphase promoting complex/cyclosome). We demonstrate that CnBub1 kinase activity is required to maintain prolonged checkpoint arrest. Thus CnBub1 acts as a SAC signalling hub and is a future target for anti-mitotic drugs.

cell biology↗

bioRxiv2017

Whole genome hybrid assembly and protein-coding gene annotation of the entirely black native Korean chicken breed Yeonsan Ogye

Yeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 551 structural variations including the Fibromelanosis (FM) locus duplication, compared to galGal4 and 5. The completeness (97.6%) of the draft genome (Ogye_1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were expressed in the tissue-specific manner, closely related with the DNA methylation pattern in the promoter regions.

genomics↗

bioRxiv2017

Non-coding Transcriptome Maps Across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

The Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

bioinformatics↗