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DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns—characterized by spatial-temporal dysregulation and stochastic molecular noise—serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation.

The functionalities of porous materials could be significantly enhanced if the materials themselves were in single-crystal form, which, owing to structural coherence, would reduce electronic and optical scattering effects. However, growing macroporous single crystals remains a fundamental challenge, let alone manufacturing crystals large enough to be of practical use. Here we demonstrate a straightforward, inexpensive, versatile method for creating macroporous gallium nitride single crystals on a centimetre scale. The synthetic strategy is built upon a disruptive crystal growth mechanism that utilises direct nitridation of a parent LiGaO 2 single crystal rendering an inward epitaxial growth process. Strikingly, the resulting single crystals exhibit electron mobility comparable to that for bulk crystals grown by the conventional sodium flux method. This approach not only affords control of both crystal and pore size through synthetic modification, but proves generic, thus opening up the possibility of designing macroporous crystals in a wealth of other materials. Porous single crystals are desirable for optoelectronic applications, but their fabrication remains challenging. Here the authors produce centimetre-sized macroporous GaN single crystals with electron mobility comparable to that of bulk crystals via in situ inward epitaxial growth on parent LiGaO 2 crystals.

The TFIIIA-type zinc finger transcription factors are involved in plant development and abiotic stress responses. Most TFIIIA-type zinc finger proteins are transcription repressors due to existence of an EAR-motif in their amino acid sequences. In this work, we found that ZFP182, a TFIIIA-type zinc finger protein, forms a homodimer in the nucleus and exhibits trans-activation activity in yeast cells. The deletion analysis indicated that a Leu-rich region at C-terminus is required for the trans-activation. Overexpression of ZFP182 significantly enhanced multiple abiotic stress tolerances, including salt, cold and drought tolerances in transgenic rice. Overexpression of ZFP182 promotes accumulation of compatible osmolytes, such as free proline and soluble sugars, in transgenic rice. ZFP182 activates the expression of OsP5CS encoding pyrroline-5-carboxylate synthetase and OsLEA3 under stress conditions, while OsDREB1A and OsDREB1B were regulated by ZFP182 under both normal and stress conditions. Interestingly, site-directed mutagenesis assay showed that DRE-like elements in ZFP182 promoter are involved in dehydration-induced expression of ZFP182 . The yeast two-hybrid assay revealed that ZFP182 interacted with several ribosomal proteins including ZIURP1, an ubiquitin fused to ribosomal protein L40. The in vivo and in vitro interactions of ZFP182 and ZIURP1 were further confirmed by bimolecular fluorescence complementation and His pull-down assays. Our studies provide new clues in the understanding of the mechanisms for TFIIIA-type zinc finger transcription factor mediated stress tolerance and a candidate gene for improving stress tolerance in crops.

Background The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relationship with the cultivation cycle as well as the agronomic traits and yields of fruiting bodies. Results In all of the samples from cultivation bags of Hypsizygus marmoreus , 34 bacterial phyla were detected. Firmicutes was the most abundant bacterial phylum (78.85%). The genus Serratia showed an exponential increase in abundance in samples collected from the cultivation bags in the mature period, reaching a peak abundance of 55.74% and the dominant symbiotic flora. The most predominant strain was Serratia odorifera HZSO-1, and its abundance increased with the amount of hyphae of H. marmoreus . Serratia odorifera HZSO-1 could reside in the hyphae of H. marmoreus , promote growth and development, shorten the fruiting cycle by 3–4 days, and further increase the fruiting body yield by 12%. Conclusions This study is a pioneering demonstration of the community structure of the symbiotic microbiota and bacteria-mushroom interaction in the growth and development of edible fungi. This work lays a theoretical foundation to improve the industrial production of mushrooms with symbiotic bacteria as assisting agents.

Liquid inoculum is widely adopted in the mushroom industry, yet preparing Tremella fuciformis liquid inoculum remains challenging due to its complex microbial community and dimorphic growth. This study aimed to establish a reliable protocol for T. fuciformis liquid inoculum and assess its practical application. Initially, liquefied spawn was produced by liquefying solid spawn. The application of standard liquefied spawn increased fruiting body yield by 8.2% (502.4 g/kg dry substrate) compared to solid spawn, but exhibited substantial batch-to-batch variation due to unstable microbial communities and low Tremellomycetes abundance. To address these limitations, liquid spawn was developed via pre-culture of pure T. fuciformis and Annulohypoxylon stygium mycelia. Cultivation tests demonstrated significantly enhanced performance with 608.2 g of fruiting bodies, which represented 11.1% improvement compared to solid spawn. Moreover, consistent yields could be observed across multiple batches. This stability was attributed to stable microbial community structure and the dominance of Tremellomycetes (abundance > 50%) in the fungal community. These results confirm the cultivation performance of T. fuciformis liquid spawn, highlighting its potential as an effective alternative to solid spawn for T. fuciformis industrial production.

Background As the prevalence of metabolic syndrome (MetS) rises among older adults, the associated risks of cardiovascular diseases and diabetes significantly increase, and it is closely linked to various metabolic processes in the body. Dysregulation of tryptophan (TRP) metabolism, particularly alterations in the kynurenine (KYN) and serotonin pathways, has been linked to the onset of chronic inflammation, oxidative stress, and insulin resistance, key contributors to the development of MetS. We aim to investigate the relationship between the TRP metabolites and the risk of MetS in older adults. Methods Ultra-performance liquid chromatography tandem mass spectrometry was used to detect TRP and its seven metabolites in a study involving 986 participants. Physical examination included the following indicators: blood pressure, body mass index, triglyceride levels, and high-density lipoprotein cholesterol (HDL-C) levels. Multiple linear regression, restricted cubic spline curve, binary logistic analysis, and sex-stratified analysis were used to explore the relationship between the metabolites and the risk of MetS in older adults. Results The results indicated that, after adjusting for covariates, higher levels of TRP, KYN, kynurenic acid (KA), and xanthurenic acid (XA) were risk factors for MetS ( P for trend < 0.05). By contrast, higher ratios of 5-hydroxytryptamine to TRP and indole-3-propionic acid to TRP were protective factors against MetS ( P for trend < 0.05). Conclusions TRP and its metabolites may serve as potential indicators for assessing and managing MetS in older adults, complementing existing biomarkers. Clinical trial number Not applicable.

In this study, fresh Lyophyllum decastes was dried using hot air drying (HAD), hot air combined with vacuum drying (HAVD), and vacuum freeze drying (VFD). Additionally, the quality and volatile compounds were analyzed. VFD achieved the best color retention, the highest rehydration capacity, and the slightest damaged tissue structure; however, it recorded the longest drying time and the highest energy consumption. HAD was the most energy-efficient of the three methods. Furthermore, the products with more hardness and elasticity were obtained by HAD and HAVD—this finding was convenient for transportation. In addition, GC-IMS demonstrated that the flavor components had significantly changed after drying. A total of 57 volatile flavor compounds was identified, and the aldehyde, alcohol, and ketone compounds were the primary ingredient of the L. decastes flavor component, whereby the relative content of the HAD sample was apparently higher than HAVD and VFD. Taken together, VFD was better at preserving the color and shape of fresh L. decastes, but HAD was more appropriate for drying L. decastes because of the lower energy consumption, and was more economical. Meanwhile, HAD could be used to produce a more intense aroma.

Tremella fuciformis Berk., also known as white fungus and snow fungus, is one of the important edible and medicinal mushrooms in China. The quality characteristics and metabolites of different T. fuciformis varieties directly affect the stability of their processed products. In this study, two new varieties of Tremella fuciformis, namely ’TYH-SD1’ (yellow) and ’TWH-SD2’ (white), which were obtained by the team through single-spore crossbreeding and its control varieties Tr21 (yellow) and Tr01 (white), were used as test materials. The characteristics and nutritional quality of the four varieties of substrates were comparatively analyzed, while metabolomics was employed to investigate the differences in flavor substances. The results demonstrate that TYH-SD1 and TWH-SD2 had a higher rehydration rate and faster rehydration speed compared with the control strains Tr21 and Tr01, with a smaller stem and higher yield. Notably, TWH-SD2 had a 29.06% increase in its rehydration rate and it had higher contents of crude polysaccharide and vitamin D3. The surface of TYH-SD1 ear pieces exhibited a porous structure with a larger pore size and the surface of TWH-SD2 ear pieces displayed a surface characterized by connected gully-like protrusions and fewer indentations, which were significantly different from that of Tr21 and Tr01 ear pieces. The textural analysis shows that TYH-SD1 and TWH-SD2 ear pieces were softer and more elastic, with greater cohesion and recovery, indicating that they had high tensile and deformation recovery ability. Metabolomics analysis revealed that the relative content of aldehydes in the volatile flavor substances TYH-SD1 and TWH-SD2 was high in n-alpha-aldehyde, nonanaldehyde, and n-pentanal. The relative content of alkanes in TYH-SD1 was second only to that of aldehydes, with decane having the highest content, contributing to its more almond aroma, fruity aroma, and fat aroma. TWH-SD2 exhibited the highest concentration of alcohols, accounting for 43.57%, which may result in a clear, mushroom, and lipid odor. The above results will provide theoretical basis for the further production, processing, and application of the new varieties.

In this study, a novel laccase gene (Lcc1) from Ganoderma tsugae was isolated and its functions were characterized in detail. The results showed that Lcc1 has the highest expression activity during mycelium development and fruit body maturation based on the analysis of Lcc1 RNA transcripts at different developmental stages of G. tsugae. To investigate the exact contribution of Lcc1 to mycelium and fruit body development in G. tsugae, Lcc1 transgenic strains were constructed by targeted gene replacement and over-expression approaches. The results showed that the lignin degradation rate in Lcc1 deletion mutant was much lower than the degradation efficiency of the wild-type (WT), over-expression and rescue strains. The lignin degradation activity of G. tsugae is dependent on Lcc1 and the deletion of Lcc1 exerted detrimental influences on the development of mycelium branch. Furthermore, the study uncovered that Lcc1 deletion mutants generated much shorter pale grey fruit bodies, suggesting that Lcc1 contributes directly to pigmentation and stipe elongation during fruit body development in G. tsugae. The information obtained in this study provides a novel and mechanistic insight into the specific role of Lcc1 during growth and development of G. tsugae.

Hypsizygus marmoreus has become one of the most popular edible mushrooms due to its high nutritional and economic value. Previous researchers found that Serratia odorifera could promote the growth of H. marmoreus by producing and secreting some of its inducers. However, the specific mechanism of action was still unclear. In this study, we found that the exogenous addition of sterile fermentation filtrate (HZSO-1), quorum sensing (QS) signaling molecules, 3-oxo-C6-HSL, cyclo(Pro-Leu), and cyclo(Tyr-Leu) could significantly promote the growth of H. marmoreus, increase the number of clamp junctions, and the diameter of mycelium (p < 0.05). In addition, non-targeted metabolomic analysis revealed that 706 metabolites were detected in the treated group. Of these, 307 metabolites were significantly different (p < 0.05). Compared with the control, 54 and 86 metabolites were significantly increased and decreased in the HZSO-1 group, respectively (p < 0.05). We speculate that the sterile fermentation filtrate of S. odorifera could mediate the carbohydrate and amino acid metabolism of H. marmoreus by influencing the pentose phosphate pathway (PPP) to increase the energy supply for the growth and development of the mycelium. The above results will further reveal the growth-promoting mechanism of S. odorifera on H. marmoreus.