DNA methylation dynamics in response to abiotic and pathogen stress in plants

Characterization of the molecular role that ST3GAL1 plays in porcine susceptibility to E. coli F18 infection

Escherichia coli F18 (E. coli F18) is the main cause of bacterial diarrhea in piglets. Previous transcriptome reported that ST3GAL1 was associated to E. coli F18 infection. However, its role in mediating the resistance to E. coli F18 remains elusive. Here, we revealed that the downregulation of ST3GAL1 expression contributed to the enhancement of E. coli F18 resistance in IPEC-J2 cells. Bisulfite sequencing identified 26 methylated CpG sites in the ST3GAL1 core promoter. Among these, the ST3GAL1 mRNA levels significantly correlated with methylation levels of the mC-8 site in the specificity protein 1 (SP1) transcription factor (P < 0.01). Interestingly, ST3GAL1 expression may enhances the immune response by activating TLRs signaling, meanwhile decreases the production of the E. coli F18 receptor by inhibiting glycosphingolipid biosynthesis signaling, thereby leading to enhance the resistance to E. coli F18 infection. Besides, low ST3GAL1 expression may increase E. coli resistance by reducing sialylation. Together, these results support the status of ST3GAL1 as a viable target for efforts to modulate E. coli F18 susceptibility, offering a theoretical foundation for the use of this gene as a key biomarker for molecular breeding to improve porcine disease resistance.

Crosstalk between RNA m6A modification and epigenetic factors in plant gene regulation

N6-methyladenosine (m6A) is the most abundant modification observed in eukaryotic mRNAs. Advances in transcriptome-wide m6A mapping and sequencing technologies have enabled the identification of several conserved motifs in plants, including the RRACH (R = A/G and H = A/C/U) and UGUAW (W = U or A) motifs. However, the mechanisms underlying deposition of m6A marks at specific positions in the conserved motifs of individual transcripts remain to be clarified. Evidence from plant and animal studies suggests that m6A writer or eraser components are recruited to specific genomic loci through interactions with particular transcription factors, 5-methylcytosine DNA methylation marks, and histone marks. In addition, recent studies in animal cells have shown that microRNAs play a role in depositing m6A marks at specific sites in transcripts through a base-pairing mechanism. m6A also affects the biogenesis and function of chromatin-associated regulatory RNAs and long noncoding RNAs. Although we have less of an understanding of the link between m6A modification and epigenetic factors in plants than in animals, recent progress in identifying the proteins that interact with m6A writer or eraser components has provided insights into the crosstalk between m6A modification and epigenetic factors, which plays a crucial role in transcript-specific methylation and regulation of m6A in plants.

Abscisic Acid Induces DNA Methylation Alteration in Genes Related to Berry Ripening and Stress Response in Grape (Vitis vinifera L)

Abscisic acid (ABA) is a major regulator of nonclimacteric fruit ripening, with its processes involving epigenetic mechanisms. It remains unclear whether DNA methylation is associated with ABA-regulated ripening. In this study, we investigated the patterns of DNA methylation and gene expression following ABA treatment in grape berries by using whole-genome bisulfite sequencing and RNA-sequencing. ABA application changed global DNA methylation in grapes. The hyper-/hypo-differently methylated regions were enriched in defense-related metabolism, degreening processes, or ripening-related metabolic pathways. Many differentially expressed genes showed an alteration in DNA methylation after ABA treatment. Specifically, ten downregulated genes with hypermethylation in promoters were involved in the ripening process, ABA homeostasis/signaling, and stress response. Nine upregulated genes exhibiting hypo-methylation in promoters were related to the ripening process and stress response. These findings demonstrated ABA-induced DNA alteration of ripening related and stress-responsive genes during grape ripening, which provides new insights of the epigenetic regulation of ABA on fruit ripening.

Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase

BACKGROUND

Epigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1.

PURPOSE

Here, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system.

RESULTS

Methylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification.

CONCLUSION

Collectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.

Titanium dioxide nanoparticles alleviates polystyrene nanoplastics induced growth inhibition by modulating carbon and nitrogen metabolism via melatonin signaling in maize

BACKGROUND

Nanoplastics, are emerging pollutants, present a potential hazard to food security and human health. Titanium dioxide nanoparticles (Nano-TiO2), serving as nano-fertilizer in agriculture, may be important in alleviating polystyrene nanoplastics (PSNPs) toxicity.

RESULTS

Here, we performed transcriptomic, metabolomic and physiological analyzes to identify the role of Nano-TiO2 in regulating the metabolic processes in PSNPs-stressed maize seedlings (Zea mays L.). The growth inhibition by PSNPs stress was partially relieved by Nano-TiO2. Furthermore, when considering the outcomes obtained from RNA-seq, enzyme activity, and metabolite content analyses, it becomes evident that Nano-TiO2 significantly enhance carbon and nitrogen metabolism levels in plants. In comparison to plants that were not subjected to Nano-TiO2, plants exposed to Nano-TiO2 exhibited enhanced capabilities in maintaining higher rates of photosynthesis, sucrose synthesis, nitrogen assimilation, and protein synthesis under stressful conditions. Meanwhile, Nano-TiO2 alleviated the oxidative damage by modulating the antioxidant systems. Interestingly, we also found that Nano-TiO2 significantly enhanced the endogenous melatonin levels in maize seedlings. P-chlorophenylalanine (p-CPA, a melatonin synthesis inhibitor) declined Nano-TiO2-induced PSNPs tolerance.

CONCLUSIONS

Taken together, our data show that melatonin is involved in Nano-TiO2-induced growth promotion in maize through the regulation of carbon and nitrogen metabolism.

The complex transcriptional regulation of heat stress response in maize

As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth and reduces productivity. To mitigate the heat-induced damages and adapt to high temperature environment, plants have evolved a series of molecular mechanisms to sense, respond and adapt high temperatures and heat stress. In this review, we summarized recent advances in molecular regulations underlying high temperature sensing, heat stress response and memory in maize, especially focusing on several important pathways and signals in high temperature sensing, and the complex transcriptional regulation of ZmHSFs (Heat Shock Factors) in heat stress response. In addition, we highlighted interactions between ZmHSFs and several epigenetic regulation factors in coordinately regulating heat stress response and memory. Finally, we laid out strategies to systematically elucidate the regulatory network of maize heat stress response, and discussed approaches for breeding future heat-tolerance maize.

Methionine inducing carbohydrate esterase secretion of Trichoderma harzianum enhances the accessibility of substrate glycosidic bonds

BACKGROUND

The conversion of plant biomass into biochemicals is a promising way to alleviate energy shortage, which depends on efficient microbial saccharification and cellular metabolism. Trichoderma spp. have plentiful CAZymes systems that can utilize all-components of lignocellulose. Acetylation of polysaccharides causes nanostructure densification and hydrophobicity enhancement, which is an obstacle for glycoside hydrolases to hydrolyze glycosidic bonds. The improvement of deacetylation ability can effectively release the potential for polysaccharide degradation.

RESULTS

Ammonium sulfate addition facilitated the deacetylation of xylan by inducing the up-regulation of multiple carbohydrate esterases (CE3/CE4/CE15/CE16) of Trichoderma harzianum. Mainly, the pathway of ammonium-sulfate's cellular assimilates inducing up-regulation of the deacetylase gene (Thce3) was revealed. The intracellular metabolite changes were revealed through metabonomic analysis. Whole genome bisulfite sequencing identified a novel differentially methylated region (DMR) that existed in the ThgsfR2 promoter, and the DMR was closely related to lignocellulolytic response. ThGsfR2 was identified as a negative regulatory factor of Thce3, and methylation in ThgsfR2 promoter released the expression of Thce3. The up-regulation of CEs facilitated the substrate deacetylation.

CONCLUSION

Ammonium sulfate increased the polysaccharide deacetylation capacity by inducing the up-regulation of multiple carbohydrate esterases of T. harzianum, which removed the spatial barrier of the glycosidic bond and improved hydrophilicity, and ultimately increased the accessibility of glycosidic bond to glycoside hydrolases.

Inheritance of epigenetic transcriptional memory

Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.

Integrated transcriptome and DNA methylome analysis reveal the biological base of increased resistance to gray leaf spot and growth inhibition in interspecific grafted tomato scions

BACKGROUND

Grafting is widely used as an important agronomic approach to deal with environmental stresses. However, the molecular mechanism of grafted tomato scions in response to biotic stress and growth regulation has yet to be fully understood.

RESULTS

This study investigated the resistance and growth performance of tomato scions grafted onto various rootstocks. A scion from a gray leaf spot-susceptible tomato cultivar was grafted onto tomato, eggplant, and pepper rootstocks, creating three grafting combinations: one self-grafting of tomato/tomato (TT), and two interspecific graftings, namely tomato/eggplant (TE) and tomato/pepper (TP). The study utilized transcriptome and DNA methylome analyses to explore the regulatory mechanisms behind the resistance and growth traits in the interspecific graftings. Results indicated that interspecific grafting significantly enhanced resistance to gray leaf spot and improved fruit quality, though fruit yield was decreased compared to self-grafting. Transcriptome analysis demonstrated that, compared to self-grafting, interspecific graftings triggered stronger wounding response and endogenous immune pathways, while restricting genes related to cell cycle pathways, especially in the TP grafting. Methylome data revealed that the TP grafting had more hypermethylated regions at CHG (H = A, C, or T) and CHH sites than the TT grafting. Furthermore, the TP grafting exhibited increased methylation levels in cell cycle related genes, such as DNA primase and ligase, while several genes related to defense kinases showed decreased methylation levels. Notably, several kinase transcripts were also confirmed among the rootstock-specific mobile transcripts.

CONCLUSIONS

The study concludes that interspecific grafting alters gene methylation patterns, thereby activating defense responses and inhibiting the cell cycle in tomato scions. This mechanism is crucial in enhancing resistance to gray leaf spot and reducing growth in grafted tomato scions. These findings offer new insights into the genetic and epigenetic contributions to agronomic trait improvements through interspecific grafting.

Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications

Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.

Characterization of gene expression patterns in response to an orthotospovirus infection between two diploid peanut species and their hybrid

Tomato spotted wilt orthotospovirus (TSWV) transmitted by thrips causes significant yield loss in peanut (Arachis hypogaea L.) production. Use of peanut cultivars with moderate field resistance has been critical for TSWV management. However, current TSWV resistance is often not adequate, and the availability of sources of tetraploid resistance to TSWV is very limited. Allotetraploids derived by crossing wild diploid species could help introgress alleles that confer TSWV resistance into cultivated peanut. Thrips-mediated TSWV screening identified two diploids and their allotetraploid possessing the AA, BB, and AABB genomes Arachis stenosperma V10309, Arachis valida GK30011, and [A. stenosperma × A. valida]4x (ValSten1), respectively. These genotypes had reduced TSWV infection and accumulation in comparison with peanut of pure cultivated pedigree. Transcriptomes from TSWV-infected and non-infected samples from A. stenosperma, A. valida, and ValSten1 were assembled, and differentially expressed genes (DEGs) following TSWV infection were assessed. There were 3,196, 8,380, and 1,312 significant DEGs in A. stenosperma, A. valida, and ValSten1, respectively. A higher proportion of genes decreased in expression following TSWV infection for A. stenosperma and ValSten1, whereas a higher proportion of genes increased in expression following infection in A. valida. The number of DEGs previously annotated as defense-related in relation to abiotic and biotic stress was highest in A. valida followed by ValSten1 and A. stenosperma. Plant phytohormone and photosynthesis genes also were differentially expressed in greater numbers in A. valida followed by ValSten1 and A. stenosperma, with over half of those exhibiting decreases in expression.

Integrative transcriptome and whole-genome bisulfite sequencing analyses of a temperature-sensitive albino tea plant cultivar

Green tea made from albino buds and leaves has a strong umami taste and aroma. The cultivar 'Zhonghuang 2' (ZH2, Camellia sinensis) is a natural mutant with young shoots that are yellow in spring and green or yellow-green in summer. However, the mechanism of leaf color change remains unclear. Here, we found that young shoots of ZH2 were yellow at low temperature (LT) and green at high temperature (HT), indicating that ZH2 is a temperature-sensitive cultivar. Transmission electron microscopy analysis showed that the grana in the chloroplasts of young shoots grown at LT were poorly stacked, which caused a lack of photoreactions and chlorophyll. RNA-seq results showed 1279 genes differentially expressed in the young shoots grown at LT compared with those at HT, including genes related to cytochrome synthesis, chloroplast development, photosynthesis, and DNA methylation. A whole-genome bisulfite sequencing assay revealed that the dynamics of DNA methylation levels in the CG, CHG, and CHH contexts decreased under LT, and the change was most obvious in the CHH context. Furthermore, 72 genes showed significant changes in both expression and DNA methylation levels, and most of them were related to cytochrome synthesis, chloroplast development, photosynthesis, transcription factors, and signaling pathways. These results demonstrate that DNA methylation is involved in the LT-regulated albino processes of ZH2. Changes in DNA methylation levels were associated with changes in gene expression levels, affecting the structure and function of chloroplasts, which may have a phenotypic impact on shoot and leaf color.

Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula

The new variety Betula pendula 'Dalecarlica', selected from Betula pendula, shows high ornamental value owing to its lobed leaf shape. In this study, to identify the genetic components of leaf shape formation, we performed bulked segregant analysis and molecular marker-based fine mapping to identify the causal gene responsible for lobed leaves in B. pendula 'Dalecarlica'. The most significant variations associated with leaf shape were identified within the gene BpPIN1 encoding a member of the PIN-FORMED family, responsible for the auxin efflux carrier. We further confirmed the hypomethylation at the promoter region promoting the expression level of BpPIN1, which causes stronger and longer veins and lobed leaf shape in B. pendula 'Dalecarlica'. These results indicated that DNA methylation at the BpPIN1 promoter region is associated with leaf shapes in B. pendula. Our findings revealed an epigenetic mechanism of BpPIN1 in the regulation of leaf shape in Betula  Linn. (birch), which could help in the molecular breeding of ornamental traits.

Seed Priming with Salicylic Acid Alleviates Salt Stress Toxicity in Barley by Suppressing ROS Accumulation and Improving Antioxidant Defense Systems, Compared to Halo- and Gibberellin Priming

Plants are highly sensitive to various environmental stresses, which can hinder their growth and reduce yields. In this study, we investigated the potential of seed priming with salicylic acid (SA), gibberellic acid (GA3), and sodium chloride (NaCl) to mitigate the adverse effects of salinity stress in Hordeum vulgare at the germination and early seedling stages. Exposing H. vulgare seeds to salt stress reduced the final germination percentage and seedling shoot and root growth. Interestingly, all seed treatments significantly improved salt-induced responses, with GA3 being more effective in terms of germination performance, plant growth, and photosynthesis. SA priming exhibited promising effects on antioxidant defense mechanisms, proline, sugar, and ascorbic acid production. Notably, SA priming also suppressed reactive oxygen species accumulation and prevented lipid peroxidation. These findings highlight the ability of SA to manage crosstalk within the seed, coordinating many regulatory processes to support plant adaptation to salinity stress.

Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis

Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.

Geographical Parthenogenesis in Alpine and Arctic Plants

The term "Geographical parthenogenesis" describes the phenomenon that asexual organisms usually occupy larger and more northern distribution areas than their sexual relatives, and tend to colonize previously glaciated areas. Several case studies on alpine and arctic plants confirm the geographical pattern, but the causal factors behind the phenomenon are still unclear. Research of the last decade in several plant families has shed light on the question and evaluated some of the classical evolutionary theories. Results confirmed, in general, that the advantages of uniparental reproduction enable apomictic plants to re-colonize faster in larger and more northern distribution areas. Associated factors like polyploidy seem to contribute mainly to the spatial separation of sexual and asexual cytotypes. Ecological studies suggest a better tolerance of apomicts to colder climates and temperate extremes, whereby epigenetic flexibility and phenotypic plasticity play an important role in occupying ecological niches under harsh conditions. Genotypic diversity appears to be of lesser importance for the distributional success of asexual plants. Classical evolutionary theories like a reduced pressure of biotic interactions in colder climates and hence an advantage to asexuals (Red Queen hypothesis) did not gain support from studies on plants. However, it is also still enigmatic why sexual outcrossing remains the predominant mode of reproduction also in alpine floras. Constraints for the origin of apomixis might play a role. Interestingly, some studies suggest an association of sexuality with abiotic stresses. Light stress in high elevations might explain why most alpine plants retain sexual reproduction despite other environmental factors that would favor apomixis. Directions for future research will be given.

Active DNA demethylation in plants: 20 years of discovery and beyond

Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.