Biology subjects

Yu, J.-H.

Publications and source records attributed to Yu, J.-H..

13 recordsLinked to original sources

bioRxiv2025

Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae

The genomic signatures of microbial domestication remain poorly understood within the context of natural population variation. Here, we demonstrate that Aspergillus oryzae, the filamentous fungus used in soy sauce production, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of Aspergillus flavus (population C). Strikingly, A. oryzae isolates also overlap with the recently described, clinically enriched A. flavus population D, suggesting the possibility of multiple domestication events. Although A. oryzae exhibits reduced virulence compared to A. flavus, all isolates tested retained pathogenicity in a zebrafish infection model. At the transcriptomic level, Aspergillus populations are significantly differentiated, with distinct responses to population density, indicating that population-specific transcriptomes adapt differently to ecological conditions. These differences extend beyond gene content and are not always explained by phylogenetic relationships, suggesting that phenotypic diversification occurs through the rapid reorganization of transcriptomic architectures. For example, A. oryzae displays significantly elevated expression of a module enriched for carbohydrate metabolism. Population-specific variation is also evident among secondary metabolite (SM) gene clusters. While A. oryzae shows markedly reduced expression of specific SM genes, particularly those involved in aflatoxin biosynthesis, this trend does not extend across the entire secondary metabolome. Using machine- learning-based gene regulatory network inference, we identified population-specific transcriptomic differences linked to distinct transcription factors, with evidence for both cis- and trans-acting regulatory divergence, but no changes in global regulators such as laeA. Together, these findings provide new insights into the domestication of A. oryzae, its global significance, and the microevolution of fungal secondary metabolic pathways. Significance StatementAspergillus flavus poses a significant threat to global agriculture by infecting crops and producing aflatoxin, a potent carcinogen that undermines food safety and international trade. The species is also a major human pathogen causing invasive fungal infections. Here, we demonstrate that A. flavus populations exhibit not only variations in their capacity to produce toxins but also in the way they regulate gene expression in response to environmental cues. These regulatory differences played a key role in the domestication of Aspergillus oryzae, a non-aflatoxigenic relative that has been safely used in food fermentation for centuries. Notably, while A. oryzae exhibits reduced aflatoxin biosynthetic gene expression, it expresses other secondary metabolite genes and retains limited opportunistic pathogenic potential. By revealing how transcriptomic rewiring drives population-level divergence, this work provides new insights into the evolution of toxin production, with broad implications for microbial domestication, crop protection, and global food security.

microbiology↗

bioRxiv2025

Neuronal detection of social actions directs collective escape behavior

Animals in groups obtain information from their social partners to engage in collective behavior1-4. Social information transmission has been observed amongst individuals in fish schools5-8, bird flocks9,10, and human groups11,12, but the neural mechanisms for detecting socially transmitted information are poorly understood4,13-15. By studying the schooling glassfish Danionella cerebrum16-18, here we demonstrate that escape from danger is enhanced by visual perception of other escaping fish. We found that neural populations in the midbrain optic tectum19-21 and dorsal thalamus22,23 are activated by the rapid escape of social partners. These neurons are also driven by the sudden disappearance of virtual social partners, yet unaffected by disappearing stimuli without social relevance. Virtual fish schools that escape or disappear were sufficient to cause observers to escape, even in the absence of direct threats. These results demonstrate that rapid "social-off" detection in visual circuits enables the detection of socially transmitted threat information, which may be a particularly effective strategy for animals capable of rapid movement but limited visual range17,24. These results show how neural computations in individuals enables rapid information sharing in animal collectives4,15.

neuroscience↗

bioRxiv2025

Divergent Volatile Metabolomes and Flavor Attributes in Rice Fermented by Aspergillus oryzae and Aspergillus flavus

The generally recognized as safe (GRAS) fungus Aspergillus oryzae has been used for millennia in the production of traditional Asian fermented foods and beverages. This prolonged domestication has led to phenotypic adaptations that distinguish A. oryzae from its wild relative, Aspergillus flavus. While genomic and phenotypic differences between these species have been partially characterized, their comparative production of volatile compounds during food fermentation remains poorly understood. Here, we evaluated alpha-amylase activity, aflatoxin production, taste attributes (via electronic tongue), and volatile profiles (via dynamic headspace gas chromatography-mass spectrometry) of the food-grade strain A. oryzae RIB40 and two wild A. flavus strains, NPK13tox and AflaGuard. A. oryzae RIB40 exhibited significantly higher alpha-amylase activity during rice fermentation, and only A. flavus NPK13tox produced aflatoxin. Sensory analysis revealed that rice fermented by A. oryzae RIB40 exhibited more favorable taste attributes, including significantly lower astringency, aftertaste, and bitterness, as well as significantly higher richness (defined as umami aftertaste). Additionally, A. oryzae RIB40 produced a greater number and higher concentrations of volatile compounds, with 20 compounds significantly elevated compared to rice fermented by A. flavus. Many of these volatiles, including 2-methyl-3-buten-2-ol, 3-octen-2-one, 2-methyl-butanal, and 3-methyl-butanal, are associated with pleasant sensory attributes and have previously been linked to A. oryzae-fermented foods. These findings suggest that the volatilome of A. oryzae RIB40 has been shaped by domestication to produce a more desirable sensory profile, enriched in alcohols, aldehydes, ketones, and heterocyclic compounds contributing fruity, umami, and malty notes.

evolutionary biology↗

bioRxiv2024

Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides

Plant long-distance signaling peptides travel through the vascular system to coordinate development and respond to environmental cues, yet their precursor genes and expression origins remain elusive. We characterized 4,804 sap peptide precursor genes in Populus trichocarpa using an integrated approach that combined liquid chromatography tandem mass spectrometry (LC-MS/MS) peptidomics, transcriptomics, and comparative genomics. This study expands the known precursor families from approximately 50 to thousands, the majority of which are conserved across angiosperms. Transcriptome analysis across xylem developmental stages revealed that living xylem cells, typically viewed as precursors to non-living structures, predominantly express these specifically at transitions between primary and secondary growth stages, indicating an active role in plant-wide signaling coordination. The precursor genes show conservation at the transcriptome level and are under strong purifying selection. Our findings provide a comprehensive overview of the gene families encoding sap peptides, redefining xylem as an active participant in plant communication and adaptation.

plant biology↗

bioRxiv2024

A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity

Signaling peptides act as hormones to deliver short- or long-distance intercellular signals to govern complex developmental processes. Identifying endogenous signaling peptides is challenging due to their low abundance and the unknown cleavage sites required for release from precursor proteins, not to mention the investigation of their evolutionary roles across species. Consequently, very few peptides were evolutionarily characterized in vivo, especially long-distance signaling peptides. Here we present current largest peptidomic datasets from six species (maize, camphor tree, tomato, rose gum, soybean and poplar), totaling 12,242 peptides, selected from all representative evolutionary clades of angiosperms, including monocots, magnoliids, rosid eudicots, and asterid eudicots. A sap peptide was found to be identical across all six species and named as ASAP (angiosperm sap peptide), emerging as the most conserved peptide family discovered thus far. ASAP rapidly induces a series of protein phosphorylation involved in a signaling cascade previously reported to regulate lignin biosynthesis, plant growth and plant immunity. Functional assays on ASAP activity demonstrated its capability on the induction of monolignol biosynthesis and lignin deposition. High-throughput phenomic analyses showed that ASAP significantly increased plant above- and below-ground biomass. In addition, ASAP treatment enhanced plant immunity and reduced the number of galls and egg masses against nematode invasion. This study provides insights into the conservation and functional significance of plant long-distance mobile signaling peptides, offering potential applications in crop improvement and disease management strategies.

plant biology↗

bioRxiv2023

Development of neural circuits for social motion perception in schooling fish

Many animals move in groups, where collective behavior emerges from the interactions amongst individuals. These social interactions produce the coordinated movements of bird flocks and fish schools, but little is known about their developmental emergence and neurobiological foundations. By characterizing the visually-based schooling behavior of the micro glassfish Danionella cerebrum, here we found that social development progresses sequentially, with animals first acquiring the ability to aggregate, followed by postural alignment with social partners. This social maturation was accompanied by the development of neural populations in the midbrain and forebrain that were preferentially driven by visual stimuli that resemble the shape and movements of schooling fish. The development of these neural circuits enables the social coordination required for collective movement. One-Sentence SummaryThe collective behavior of schooling fish emerges with the development of neural populations selective to social motion.

neuroscience↗

bioRxiv2023

Population genomics of Aspergillus sojae is shaped by the food environment

Traditional fermented foods often contain specialized microorganisms adapted to the unique food environment. For example, the filamentous mold Aspergillus oryzae, used in sake fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae is used in soybean-based food fermentations (e.g. miso and shochu) and is closely related to Aspergillus parasiticus. Here, we investigated the impact of long-term A. sojae usage in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 12 A. sojae and 10 A. parasiticus genomes, along with phenotypic characteristics of 15 isolates. Our results revealed that A. sojae isolates formed a distinct population separate from A. parasiticus and displayed remarkably low levels of genetic diversity, indicative of a recent clonal expansion. Genome comparisons revealed numerous loss-of-function mutations in A. sojae, notably in genes responsible for secondary metabolite production, including genes in the aflatoxin encoding gene cluster. Consequently, A. sojae lacked aflatoxin production, while it varied among A. parasiticus isolates. No other significant differences were observed in growth rates or other measured phenotypic traits between A. sojae and A. parasiticus. These findings suggest that A. sojae may have evolved from a population of A. parasiticus and lost the ability to produce some secondary metabolites. To elucidate the phenotypic differences between A. sojae and A. parasiticus, future work should focus on the influence of wild and food-associated strains on the sensory aspects and microbial community dynamics of fermented soy products. Significance StatementLike plants and animals, microbes were also domesticated by humans, however relatively little is known about how the process of domestication shapes microbial genomes and traits. We found that isolates of Aspergillus sojae, a mold used in the production of miso and soy sauce, makeup a less toxic group that is genetically distinct from its closely related wild ancestor Aspergillus parasiticus. Our analyses shed new light on commonalities observed across filamentous molds adapted to the food environment.

evolutionary biology↗

bioRxiv2023

The novel spore-specific regulator SscA governs Aspergillus conidiogenesis.

A major group of fungi produces asexual spores (conidia) for propagation and infection. Despite the critical role of conidia, the underlying mechanism of spore formation, integrity, and viability is not fully elucidated. In this study, we have identified and investigated the role of the spore-specific transcription factor (TF) SscA in three representative Aspergillus species. Comparative transcriptomic analyses have revealed that 25 TF encoding genes showed higher mRNA levels in conidia than in hyphae in three species. Functional and transcriptomic analyses of the 25 genes have identified SscA as a key TF for conidial formation, maturation, germination, integrity, amino acid production, and secondary metabolism in Aspergillus nidulans conidia. Importantly, the roles of SscA are conserved in other Aspergillus species. Altogether, our study demonstrates that SscA is a novel spore-specific TF that governs production of intact and functional conidial formation in Aspergillus species. ImportanceFilamentous fungi produce myriads of asexual spores are main reproductive particles and act as infectious or allergenic agents. Although the serial of asexual sporogenesis is coordinated by various genetic regulators, there remain uncharacterized transcription factors in Aspergillus. To understand the underlying mechanism of spore formation, integrity, and viability, we have performed comparative transcriptomic analyses on three representative Aspergillus species and found a novel spore-specific transcription factor, SscA. SscA has a major role in conidial formation, maturation and dormancy, and germination in Aspergillus nidulans. Transcriptomic data indicate that SscA coordinates conidial wall integrity, amino acid production, and secondary metabolism in A. nidulans conidia. Furthermore, the roles of SscA are conserved in other Aspergillus species. Our findings that the novel SscA has broad functions in Aspergillus conidia will help to understand conidiogenesis of Aspergillus species.

microbiology↗

bioRxiv2022

Environmental luminance impairs socio-sexual recognition memory through a succinct retina to supraoptic nucleus circuit

Social memory between the same gender or even different gender is a complex and heavily modulated process in the nervous system. It is important for an individual to form social memory between the opposite sex to either increase mating opportunities with multiple partners or form monogamous pair bonding. Therefore, a specific neuronal circuit to regulate social sexual memory may enhance the mating opportunity for an individual. It has been shown that both the auditory and somatosensory systems could increase the activity of oxytocin neurons in the paraventricular nucleus to regulate social behaviors. Although light exposure could influence various forms of memory, such as fear and object memory, how luminance signals modulate social recognition memory remains unclear. Here, we show that acute light exposure could impair the socio-sexual recognition memory (SSRM) in male mice. Contrary to sound and touch, light stimulation could inhibit oxytocin neurons in the SON (SONOT) through M1 SON-projecting ipRGCs and GABAergic neurons in the peri-SON (pSONGABA). Optogenetic activation of SONOT neurons with channelrhodopsin is sufficient to enhance the SSRM performance in male mice, even under light conditions. Our results show that the visual system could modulate SSRM through a succinct ipRGCs-pSONGABA-SONOT neuronal circuitry. Together, we demonstrate a dedicated neuronal circuit of how luminance affects memory formation for an individual toward different sex through the oxytocin system, a powerful modulatory neurohormone in the central nervous system.

neuroscience↗

bioRxiv2021

Single-cell transcriptomics unveils xylem cell development and evolution

As the most abundant tissue on Earth1, xylem is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells2. In most angiosperms, fusiform cells are a combination of vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed together by tracheids in other vascular plants2. However, little is known about the developmental programs and evolutionary relationships of these xylem cell types. Through both single-cell and laser-capture microdissection transcriptomic profiling, here we demonstrate the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Cross-species analyses of single-cell trajectories reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character3, 4, exhibit strong transcriptomic similarity to vessel elements but not libriform fibers, suggesting that water transportation, instead of mechanical support, is the major feature. We also found that the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. This evo-developmental framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history5.

plant biology↗

bioRxiv2020

Transcriptomic, protein-DNA interaction, and metabolomic studies of VosA, VelB, and WetA in Aspergillus nidulans asexual spores

In filamentous fungi, asexual development involves morphological differentiation and metabolic changes leading to the formation of asexual spores. The process of asexual spore formation in Aspergillus is precisely regulated by multiple transcription factors (TFs), including VosA, VelB, and WetA, and these three TFs are key regulators of the formation and maturation of asexual spores (conidia) in Aspergillus including the model fungus Aspergillus nidulans. To gain a mechanistic insight on the complex regulatory roles of these TFs in asexual spores, we conducted genome-wide studies on the expression, protein-DNA interactions, and primary and secondary metabolism employing A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation-sequencing data have revealed that the three TFs directly or indirectly regulate the expression of genes associated with spore-wall formation/integrity, asexual development, and secondary metabolism. In addition, metabolomics analyses of wild-type and mutant conidia indicate that these three TFs regulate a diverse array of primary and secondary metabolism. In summary, WetA, VosA, and VelB play inter-dependent and distinct roles governing morphological development and primary/secondary metabolic remodeling in Aspergillus conidia. ImportanceFilamentous fungi produce a vast number of asexual spores that act as reproductive and propagator cells. These spores affect humans, due to the infectious or allergenic nature of the propagule. Aspergillus species produce asexual spores called conidia and their formation involves morphological development and metabolic changes, and the associated regulatory systems are coordinated by spore-specific transcription factors. To understand the underlying global regulatory programs and cellular outcomes associated with conidia formation, functional genomic and metabolomic analyses were performed in the model fungus Aspergillus nidulans. Our results show that the fungus specific WetA/VosA/VelB transcription factors govern the coordination of morphological and chemical developments during sporogenesis. The results of this study provide insights into the genetic regulatory networks about how morphological developments and metabolic changes are coordinated in fungi. The findings are relevant for other Aspergillus species such as the major human pathogen Aspergillus fumigatus and the aflatoxin-producer Aspergillus flavus.

microbiology↗

bioRxiv2018

Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi

Asexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In Aspergillus, the production of asexual spores is primarily governed by the BrlA[->]AbaA[->]WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and not only governs the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genus Aspergillus, the structure and degree of conservation of the wetA gene regulatory network (GRN) remains largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type asexual spores in three representative species spanning the diversity of the genus Aspergillus: A. nidulans, A. flavus, and A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascades first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA[->]AbaA[->]WetA cascades regulatory role in cellular and chemical asexual spore development is functionally conserved, but that the wetA-associated GRN has diverged during Aspergillus evolution.

microbiology↗

bioRxiv2017

NINJA-Associated ERF19 Negatively Regulates Arabidopsis Pattern-Triggered Immunity

Recognition of microbe-associated molecular patterns (MAMPs) derived from invading pathogens by plant pattern recognition receptors (PRRs) initiates defense responses known as pattern-triggered immunity (PTI). Transcription factors (TFs) orchestrate the onset of PTI through complex signaling networks. Here, we characterize the function of ERF19, a member of the Arabidopsis thaliana ethylene response factor (ERF) family. ERF19 was found to act as a negative regulator of PTI against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 (Pst). Notably, overexpression of ERF19 increased plant susceptibility to these pathogens and repressed MAMP-induced PTI outputs. In contrast, expression of the chimeric dominant repressor ERF19-SRDX boosted PTI activation, conferred increased resistance to B. cinerea, and enhanced elf18-triggered immunity against Pst. Consistent with a negative role of ERF19 in PTI, MAMP-mediated growth inhibition was respectively weakened or augmented in lines overexpressing ERF19 or expressing ERF19-SRDX. Moreover, we demonstrate that the transcriptional repressor Novel INteractor of JAZ (NINJA) associates with and represses the function of ERF19. Our work reveals ERF19 as a key player in a buffering mechanism to avoid defects imposed by over-activation of PTI and a potential role for NINJA in fine-tuning ERF19-mediated regulation.

plant biology↗