Biology subjects

Kan, J.

Publications and source records attributed to Kan, J..

8 recordsLinked to original sources

bioRxiv2026

Rate of meristem initiation driven by the MADS-WUS axis contributes to floral survival and inflorescence evolution in grasses

Crop domestication has repeatedly shaped inflorescence architecture to improve floral production, but mechanisms coordinating the rate of floral initiation, maturation and survival remain unclear. Combining morphometry, modelling and molecular genetic analyses, we show that floral production in the indeterminate barley (Hordeum vulgare L.) inflorescence follows an "initiate fast-die young" strategy orchestrated by a main MADS-box gene, SPIKELET INITIATION AND FERTILITY (SIF). SIF accomplishes this duality by coordinately terminating the inflorescence meristem via WUSCHEL and activating the floral meristem via APETALA1 (Vrn-H1). Hereby, the ancestral SIF "slow" allele promotes a timely commitment to floral maturation, whereas the derived "fast" allele permits more floral initiations. Postdomestication selection of SIF alleles thus enables diversified reproductive strategies in barley populations to maintain yield traits in the field. Finally, we show that a lineage-specific SIF duplication contributed to meristem fate transition and inflorescence evolution during Triticeae cold adaptation. Our results establish developmental rate as a key driver of architectural innovation and reproductive success.

plant biology↗

bioRxiv2025

Soil to human health continuum: Exploring ergothioneine and mycorrhizal fungi in shaping the wheat microbiome

BackgroundThe association between plants and soil microbes is critical for both soil and plant health. Studies have shown that introducing beneficial microbial inoculants can shape the soil microbiome community for plant health. Among these microbes, mycorrhizal fungi play a well-documented role in enhancing nutrient uptake in plants. Ergothioneine (ERGO), a compound well-known for its anti-inflammatory and antioxidant properties, has been linked to increased longevity in various model systems and its significance for human health. However, neither animals nor plants contain ERGO biosynthetic pathways, which are limited to fungi, including and some species of bacteria, including Actinomyceota, Cyanobacteria, and Methylobacteria. Though the leading dietary sources of ERGO for humans are fungi in the form of mushrooms or fermented foods, biofortification of crops by promoting the production and uptake of ERGO from microbial sources in the soil has promise for enhancing nutritional quality and public health outcomes. ResultsThis study explores the of interaction between soil ERGO application and arbuscular mycorrhizal fungi (AMF) in plant-symbiotic relationships to increase the ERGO content in the staple crop wheat (Triticum aestivum). We investigate how ERGO supplementation, both alone and in combination with AMF, influences the wheat root and soil microbiome in a greenhouse experiments. Our data shows that plants can take up ERGO in absence of AMF fungi. In addition, treatment with pure ERGO and ERGO in combination with AMF altered microbial diversity and community structure in both the rhizosphere and rhizoplane regions of wheat roots. ConclusionsOverall, our work reveals that plants can readily take up ERGO from soil, both with and without AMF presence, highlighting a broader role of ERGO in connecting soil health to human health, a connection that warrants further investigation.

plant biology↗

bioRxiv2025

Streptomyces coelicolor-plant association facilitates ergothioneine (EGT) uptake in Triticum aestivum

The growing market of agricultural biologicals as alternatives to synthetic crop chemicals is driven by their ability to improve soil health, reduce carbon footprints, enhance crop yield and quality, and help counter declining protein levels in cereal crops linked to climate change and soil degradation. Ergothioneine (EGT), an amino acid with recognized nutraceutical and micronutrient properties, has gained popularity for its anti-inflammatory and antimicrobial properties on human health. While plants and humans cannot biosynthesize EGT, its production by Streptomyces coelicolor presents as a promising bio-stimulant to support overall plant health and human health. Our study investigates the potential for Streptomyces coelicolor M145 to enhance EGT levels in spring wheat (Triticum aestivum). Results confirmed successful EGT extraction from bacterial cell extracts and plant tissues. Additionally, a fluorescent confocal microscopy staining and imaging protocol showed bacterial colonization on T. aestivum and its potential as a root endophyte. Following root inoculation, S. coelicolor was observed inhabiting roots, shoots, and internodes of T. aestivum, suggesting its potential endophytic lifestyle on host plants. Our data showed that S. coelicolor-associated wheat plants produce EGT in planta. Overall, our findings establish a direct link between soil and human health through rhizosphere colonization by S. coelicolor and in planta production of EGT, suggesting an alternate route to enhance protein concentration in crop plants.

plant biology↗

bioRxiv2024

Oxydifficidin, a potent Neisseria gonorrhoeae antibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity

Gonorrhea, which is caused by Neisseria gonorrhoeae, is the second most reported sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potent N. gonorrhoeae antibiotic through the observation of a Bacillus amyloliquefaciens contaminant in a lawn of N. gonorrhoeae. Oxydifficidin is active against both wild- type and multidrug-resistant N. gonorrhoeae. Its potent activity results from a combination of DedA- assisted uptake into the cytoplasm and the presence of an oxydifficidin-sensitive ribosomal protein L7/L12 (RplL). Our data indicates that oxydifficidin binds to the ribosome at a site that is distinct from other antibiotics and that L7/L12 is uniquely associated with its mode of action. This study opens a potential new avenue for addressing antibiotic resistant gonorrhea and underscores the possibility of identifying overlooked natural products from cultured bacteria, particularly those with activity against previously understudied pathogens.

microbiology↗

bioRxiv2023

Unraveling the dynamic transcriptomic changes during the dimorphic transition of Talaromyces marneffei through time-course analysis

Systemic dimorphic fungi pose a significant public health challenge, causing over one million new infections annually. The dimorphic transition between saprophytic mycelia and pathogenic yeasts is strongly associated with the pathogenesis of dimorphic fungi. However, despite the dynamic nature of dimorphic transition, the current omics studies focused on dimorphic transition primarily employ static strategies, partly due to the lack of suitable dynamic analytical methods. Here, we firstly conducted time-course transcriptional profiling during the dimorphic transition of Talaromyces marneffei, a model organism for thermally dimorphic fungi. Then, we identified 5,223 dimorphic transition induced genes (DTIGs) by developing DyGAM-NS (dynamic optimized generalized additive model with natural cubic smoothing), a model that enables the capture of non-uniform and nonlinear transcriptional changes during intricate biological processes. Notably, the DyGAM-NS outperformed other commonly used models, achieving the highest F1-score in DTIGs identification. The cluster analysis of DTIGs suggests differential functional involvement of genes at distinct stages of dimorphic transition. Moreover, we observed divergent gene expression patterns between mycelium-to-yeast and yeast-to-mycelium transitions, indicating the asymmetrical nature of two transition directions. Additionally, leveraging the identified DTIGs, we constructed a regulatory network for the dimorphic transition and identified two zinc finger-containing transcription factors that potentially regulate dimorphic transition in T. marneffei. In summary, our study not only elucidates the dynamic changes in transcriptional profiles during the dimorphic transition of T. marneffei but also provides a novel perspective for unraveling the underlying mechanisms of fungal dimorphism. IMPORTANCEThe dimorphic transition, i.e., morphological switch between saprophytic mycelia and pathogenic yeasts, plays a pivotal role in the pathogenesis of dimorphic fungi. However, the underlying mechanisms of dimorphic transition remain poorly understood, partly due to the lack of dynamic analytical methods suitable for its intricate nature. In the current study, we dissected the dynamic transcriptional profiles of dimorphic transition with a model thermally dimorphic fungus, T. marneffei, by developing a novel analytical method, DyGAM-NS. We proved that DyGAM-NS was more powerful in capturing the non-uniform and nonlinear gene expression variations during the dimorphic transition. With DyGAM-NS, we identified a repertoire of genes associated with dimorphic transition, and comprehensively unraveled distinct functions and expression patterns at different transition stages of T. marneffei, which offers novel perspectives regarding the mechanistic underpinnings of fungal dimorphism.

microbiology↗

bioRxiv2021

Spatial Variability in Streambed Microbial Community Structure Across Two Watersheds

The spatial patterns of microbial communities are largely unknown compared to those of macro-fauna and flora. We investigated patterns of microbial community structure on streambed sediments from two watersheds across spatial scales spanning < 1m within a single stream to several hundred km between watersheds. Analyses of phospholipid fatty acids (PLFA) profiles indicated that the variations in microbial community structure were driven by increases in the relative abundance of microeukaryotic photoautotrophs and their contribution to total microbial biomass. Furthermore, streams within watersheds had similar microbial community structure, underscoring within-watershed controls of microbial communities. Moreover, bacterial community structure assayed as either polymerase chain reaction-denaturing gradient gelelectrophoresis (PCR-DGGE) fingerprints or PLFA profiles edited to remove microeukaryotes indicated a distinct watershed-level biogeography. No distinct stream order-level distributions were identified although DGGE analysis clearly indicated that there was greater variability in community structure among 1st-order streams compared to 2nd- and 3rd-order streams into which they flowed. Longitudinal gradients in microbial biomass and structure showed that the greatest variations were associated with 1st order streams within a watershed and 68% of the variation in total microbial biomass was explained by sediment C:N mass ratio, percent Carbon, sediment surface area, and percent water content. This study confirms a distinct microbial biogeography for headwater stream communities driven by environmental heterogeneity across distant watersheds and suggests that eukaryotic photoautotrophs play a key role in structuring sediment microbial communities. IMPORTANCEMicroorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow, yet the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds; Neversink River (New York) and White Clay Creek (Pennsylvania) watersheds and measured microbial biomass, total microbial and bacterial community structures using phospholipid and molecular methods. Microbial and bacterial community structures displayed a distinct watershed-level biogeography. The smallest headwater streams within a watershed showed the greatest variation in microbial biomass, and C:N ratio, percent carbon, sediment surface area and percent water content explained 68% of the variations in microbial biomass. This study indicates a non-random distribution of microbial communities in streambeds, and that microeukaryotic photoautotrophs, environmental heterogeneity and geographical distance influence microbial composition and spatial distribution.

microbiology↗

bioRxiv2019

A bifunctional ATPase drives tad pilus extension and retraction

Molecular motors convert chemical energy directly into mechanical work1 and are found in all domains of life2. These motors are critical to intracellular transport3, motility4,5, macromolecular protein assembly3,6, and many essential processes7. A wide-spread class of related bacterial motors drive the dynamic activity of extracellular fibers, such as type IV pili (T4P), that are extended and retracted using so-called secretion motor ATPases. Among these, the tight adherence (tad) pili are critical for surface sensing, surface attachment, and biofilm formation8-10. How tad pili undergo dynamic cycles of extension and retraction8 despite lacking a dedicated retraction motor ATPase has remained a mystery. Here we find that a bifunctional pilus motor ATPase, CpaF, drives both activities through ATP hydrolysis. Specifically, we show that mutations within the ATP hydrolysis active site of Caulobacter crescentus CpaF result in a correlated reduction in the rates of extension and retraction. Moreover, a decrease in the rate of ATP hydrolysis directly scales with a decrease in the force of retraction and reduced dynamics in these CpaF mutants. This mechanism of motor protein bifunctionality extends to another genus of tad-bearing bacteria. In contrast, the T4aP subclass of pili possess dedicated extension and retraction motor ATPase paralogs. We show that these processes are uncoupled using a slow ATP hydrolysis mutation in the extension ATPase of competence T4aP of Vibrio cholerae that decreases the rate of extension but has no effect on the rate of retraction. Thus, a single motor ATPase is able to drive the bidirectional processes of pilus fiber extension and retraction.

microbiology↗

bioRxiv2017

Obstruction of pilus retraction stimulates bacterial surface sensing

Surface association provides numerous fitness advantages to bacteria. Thus, it is critical for bacteria to recognize surface contact and to consequently initiate physiological changes required for a surface-associated lifestyle (1). Ubiquitous microbial appendages called pili are involved in sensing surfaces and mediating downstream surface-associated behaviors (2-6). The mechanism by which pili mediate surface sensing remains unknown, largely due to the difficulty to visualize their dynamic nature and to directly modulate their activity without genetic modification. Here, we show that Caulobacter crescentus pili undergo dynamic cycles of extension and retraction that cease within seconds of surface contact, and this arrest of pilus activity coincides with surface-stimulated holdfast synthesis. By physically blocking pili, we show that imposing resistance to pilus retraction is sufficient to stimulate holdfast synthesis in the absence of surface contact. Thus, resistance to type IV pilus retraction upon surface attachment is used for surface sensing.\n\nOne Sentence SummaryBacteria use the tension imparted on retracting pilus fibers upon their binding to a surface for surface sensing.

microbiology↗