Interactions between metabolism and chromatin in plant models

Multiscale chromatin dynamics and high entropy in plant iPSC ancestors

Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.

B Vitamins: An Update on Their Importance for Plant Homeostasis

B vitamins are a source of coenzymes for a vast array of enzyme reactions, particularly those of metabolism. As metabolism is the basis of decisions that drive maintenance, growth, and development, B vitamin-derived coenzymes are key components that facilitate these processes. For over a century, we have known about these essential compounds and have elucidated their pathways of biosynthesis, repair, salvage, and degradation in numerous organisms. Only now are we beginning to understand their importance for regulatory processes, which are becoming an important topic in plants. Here, I highlight and discuss emerging evidence on how B vitamins are integrated into vital processes, from energy generation and nutrition to gene expression, and thereby contribute to the coordination of growth and developmental programs, particularly those that concern maintenance of a stable state, which is the foundational tenet of plant homeostasis.

Regulation of seed germination: ROS, epigenetic, and hormonal aspects

BACKGROUND

The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus.

AIM

of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.

A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase

Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.

Cross-talk and mutual shaping between the immune system and the microbiota during an oyster's life

The Pacific oyster Crassostrea gigas lives in microbe-rich marine coastal systems subjected to rapid environmental changes. It harbours a diversified and fluctuating microbiota that cohabits with immune cells expressing a diversified immune gene repertoire. In the early stages of oyster development, just after fertilization, the microbiota plays a key role in educating the immune system. Exposure to a rich microbial environment at the larval stage leads to an increase in immune competence throughout the life of the oyster, conferring a better protection against pathogenic infections at later juvenile/adult stages. This beneficial effect, which is intergenerational, is associated with epigenetic remodelling. At juvenile stages, the educated immune system participates in the control of the homeostasis. In particular, the microbiota is fine-tuned by oyster antimicrobial peptides acting through specific and synergistic effects. However, this balance is fragile, as illustrated by the Pacific Oyster Mortality Syndrome, a disease causing mass mortalities in oysters worldwide. In this disease, the weakening of oyster immune defences by OsHV-1 µVar virus induces a dysbiosis leading to fatal sepsis. This review illustrates the continuous interaction between the highly diversified oyster immune system and its dynamic microbiota throughout its life, and the importance of this cross-talk for oyster health. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Chromatin modifications and memory in regulation of stress-related polyphenols: finding new ways to control flavonoid biosynthesis

The influence of epigenetic factors on plant defense responses and the balance between growth and defense is becoming a central area in plant biology. It is believed that the biosynthesis of secondary metabolites can be regulated by epigenetic factors, but this is not associated with the formation of a "memory" to the previous biosynthetic status. This review shows that some epigenetic effects can result in epigenetic memory, which opens up new areas of research in secondary metabolites, in particular flavonoids. Plant-controlled chromatin modifications can lead to the generation of stress memory, a phenomenon through which information regarding past stress cues is retained, resulting in a modified response to recurring stress. How deeply are the mechanisms of chromatin modification and memory generation involved in the control of flavonoid biosynthesis? This article collects available information from the literature and interactome databases to address this issue. Visualization of the interaction of chromatin-modifying proteins with the flavonoid biosynthetic machinery is presented. Chromatin modifiers and "bookmarks" that may be involved in the regulation of flavonoid biosynthesis through memory have been identified. Through different mechanisms of chromatin modification, plants can harmonize flavonoid metabolism with: stress responses, developmental programs, light-dependent processes, flowering, and longevity programs. The available information points to the possibility of developing chromatin-modifying technologies to control flavonoid biosynthesis.

Two maize homologs of mammalian proton-coupled folate transporter, ZmMFS_1-62 and ZmMFS_1-73, are essential to salt and drought tolerance

Folates are essential to the maintenance of normal life activities in almost all organisms. Proton-coupled folate transporter (PCFT), belonging to the major facilitator superfamily, is one of the three major folate transporter types widely studied in mammals. However, information about plant PCFTs is limited. Here, a genome-wide identification of maize PCFTs was performed, and two PCFTs, ZmMFS_1-62 and ZmMFS_1-73, were functionally investigated. Both proteins contained the typical 12 transmembrane helixes with N- and C-termini located in the cytoplasm, and were localized in the plasma membrane. Molecular docking analysis indicated their binding activity with folates via hydrogen bonding. Interference with ZmMFS_1-62 and ZmMFS_1-73 in maize seedlings through virus-induced gene silencing disrupted folate homeostasis, mainly in the roots, and reduced tolerance to drought and salt stresses. Moreover, a molecular chaperone protein, ZmHSP20, was found to interact with ZmMFS_1-62 and ZmMFS_1-73, and interference with ZmHSP20 in maize seedlings also led to folate disruption and increased sensitivity to drought and salt stresses. Overall, this is the first report of functional identification of maize PCFTs, which play essential roles in salt and drought stress tolerance, thereby linking folate metabolism with abiotic stress responses in maize.

Decoding the molecular mechanism underlying salicylic acid (SA)-mediated plant immunity: an integrated overview from its biosynthesis to the mode of action

Salicylic acid (SA) is an important phytohormone, well-known for its regulatory role in shaping plant immune responses. In recent years, significant progress has been made in unravelling the molecular mechanisms underlying SA biosynthesis, perception, and downstream signalling cascades. Through the concerted efforts employing genetic, biochemical, and omics approaches, our understanding of SA-mediated defence responses has undergone remarkable expansion. In general, following SA biosynthesis through Avr effectors of the pathogens, newly synthesized SA undergoes various biochemical changes to achieve its active/inactive forms (e.g. methyl salicylate). The activated SA subsequently triggers signalling pathways associated with the perception of pathogen-derived signals, expression of defence genes, and induction of systemic acquired resistance (SAR) to tailor the intricate regulatory networks that coordinate plant immune responses. Nonetheless, the mechanistic understanding of SA-mediated plant immune regulation is currently limited because of its crosstalk with other signalling networks, which makes understanding this hormone signalling more challenging. This comprehensive review aims to provide an integrated overview of SA-mediated plant immunity, deriving current knowledge from diverse research outcomes. Through the integration of case studies, experimental evidence, and emerging trends, this review offers insights into the regulatory mechanisms governing SA-mediated immunity and signalling. Additionally, this review discusses the potential applications of SA-mediated defence strategies in crop improvement, disease management, and sustainable agricultural practices.

Application of Multi-Omics Technologies to the Study of Phytochromes in Plants

Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.

Histone Deacetylase Inhibitor, Sodium Butyrate-Induced Metabolic Modulation in Platycodon grandiflorus Roots Enhances Anti-Melanogenic Properties

While the status of histone acetylation is a critical regulator of chromatin's structure with a significant impact on plant physiology, our understanding of epigenetic regulation in the biosynthesis of active compounds in plants is limited. In this study, Platycodon grandiflorus was treated with sodium butyrate (NaB), a histone deacetylase inhibitor, to investigate the influence of histone acetylation on secondary metabolism. Its treatment with NaB increased the acetylation of histone H3 at lysine 9, 14, and 27 and enhanced the anti-melanogenic properties of P. grandiflorus roots. Through transcriptome and differentially expressed gene analyses, we found that NaB influenced the expression of genes that were involved in both primary and secondary metabolic pathways. In addition, NaB treatment caused the accumulation of polyphenolic compounds, including dihydroquercetin, gallic acid, and 2,4-dihydroxybenzoic acid. The NaB-induced transcriptional activation of genes in the phenylpropanoid biosynthetic pathway influenced the anti-melanogenic properties of P. grandiflorus roots. Overall, these findings suggest the potential of an epigenomic approach to enhance the medicinal qualities of medicinal plants.

Plant environmental memory: implications, mechanisms and opportunities for plant scientists and beyond

Plants are extremely plastic organisms. They continuously receive and integrate environmental information and adjust their growth and development to favour fitness and survival. When this integration of information affects subsequent life stages or the development of subsequent generations, it can be considered an environmental memory. Thus, plant memory is a relevant mechanism by which plants respond adaptively to different environments. If the cost of maintaining the response is offset by its benefits, it may influence evolutionary trajectories. As such, plant memory has a sophisticated underlying molecular mechanism with multiple components and layers. Nonetheless, when mathematical modelling is combined with knowledge of ecological, physiological, and developmental effects as well as molecular mechanisms as a tool for understanding plant memory, the combined potential becomes unfathomable for the management of plant communities in natural and agricultural ecosystems. In this review, we summarize recent advances in the understanding of plant memory, discuss the ecological requirements for its evolution, outline the multilayered molecular network and mechanisms required for accurate and fail-proof plant responses to variable environments, point out the direct involvement of the plant metabolism and discuss the tremendous potential of various types of models to further our understanding of the plant's environmental memory. Throughout, we emphasize the use of plant memory as a tool to unlock the secrets of the natural world.

Metabolic regulation of the plant epigenome

Chromatin modifications shape the epigenome and are essential for gene expression reprogramming during plant development and adaptation to the changing environment. Chromatin modification enzymes require primary metabolic intermediates such as S-adenosyl-methionine, acetyl-CoA, alpha-ketoglutarate, and NAD⁺ as substrates or cofactors. The availability of the metabolites depends on cellular nutrients, energy and reduction/oxidation (redox) states, and affects the activity of chromatin regulators and the epigenomic landscape. The changes in the plant epigenome and the activity of epigenetic regulators in turn control cellular metabolism through transcriptional and post-translational regulation of metabolic enzymes. The interplay between metabolism and the epigenome constitutes a basis for metabolic control of plant growth and response to environmental changes. This review summarizes recent advances regarding the metabolic control of plant chromatin regulators and epigenomes, which are involved in plant adaption to environmental stresses.

Harnessing enzyme cofactors and plant metabolism: an essential partnership

Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.

The carbon and nitrogen metabolisms of Ardisia quinquegona were altered in different degrees by canopy and understory nitrogen addition in a subtropical forest

Although effects of atmospheric nitrogen (N) deposition on forest plants have been widely investigated, N interception and absorption effects by forest canopy should not be neglected. Moreover, how N deposition change the molecular biological process of understory dominant plants, which was easily influenced by canopy interception so as to further change physiological performance, remains poorly understood. To assess the effects of N deposition on forest plants, we investigated the effects of understory (UAN) and canopy N addition (CAN) on the transcriptome and physiological properties of Ardisia quinquegona, a dominant subtropical understory plant species in an evergreen broad-leaved forest in China. We identified a total of 7394 differentially expressed genes (DEGs). Three of these genes were found to be co-upregulated in CAN as compared to control (CK) after 3 and 6 h of N addition treatment, while 133 and 3 genes were respectively found to be co-upregulated and co-downregulated in UAN as compared to CK. In addition, highly expressed genes including GP1 (a gene involved in cell wall biosynthesis) and STP9 (sugar transport protein 9) were detected in CAN, which led to elevated photosynthetic capacity and accumulation of protein and amino acid as well as decrease in glucose, sucrose, and starch contents. On the other hand, genes associated with transport, carbon and N metabolism, redox response, protein phosphorylation, cell integrity, and epigenetic regulation mechanism were affected by UAN, resulting in enhanced photosynthetic capacity and carbohydrates and accumulation of protein and amino acid. In conclusion, our results showed that the CAN compared to UAN treatment had less effects on gene regulation and carbon and N metabolism. Canopy interception of N should be considered through CAN treatment to simulate N deposition in nature.

LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells

Metabolism plays a fundamental role in regulating cellular functions and fate decisions. Liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomic approaches provide high-resolution insights into the metabolic state of a cell. However, the typical sample size is in the order of 10⁵-10⁷ cells and thus not compatible with rare cell populations, especially in the case of a prior flow cytometry-based purification step. Here, we present a comprehensively optimized protocol for targeted metabolomics on rare cell types, such as hematopoietic stem cells and mast cells. Only 5000 cells per sample are required to detect up to 80 metabolites above background. The use of regular-flow liquid chromatography allows for robust data acquisition, and the omission of drying or chemical derivatization avoids potential sources of error. Cell-type-specific differences are preserved while the addition of internal standards, generation of relevant background control samples, and targeted metabolite with quantifiers and qualifiers ensure high data quality. This protocol could help numerous studies to gain thorough insights into cellular metabolic profiles and simultaneously reduce the number of laboratory animals and the time-consuming and costly experiments associated with rare cell-type purification.

Genetic and epigenetic control of the plant metabolome

Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.

Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond

Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling, allowing nuclear gene expression to be adjusted appropriately. Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated "biogenic" and "operational" controls, respectively. A prominent example of the investigation of biogenic signaling is the screen for gun (genomes uncoupled) mutants. Although the first five gun mutants were identified 30 years ago, the functions of GUN proteins in retrograde signaling remain controversial, and that of GUN1 is hotly disputed. Here, we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants. Moreover, considering heme as a candidate in retrograde signaling, we revisit the spatial organization of heme biosynthesis and export from plastids. Although this review focuses on GUN pathways, we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants. Here, stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response, which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis. We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1. Finally, a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided, and we discuss future directions of dissection of organelle-nucleus communication.

Insights into the expression of DNA (de)methylation genes responsive to nitric oxide signaling in potato resistance to late blight disease

Our previous study concerning the pathogen-induced biphasic pattern of nitric oxide (NO) burst revealed that the decline phase and a low level of NO, due to S-nitrosoglutathione reductase (GSNOR) activity, might be decisive in the upregulation of stress-sensitive genes via histone H3/H4 methylation in potato leaves inoculated with avr P. infestans. The present study refers to the NO-related impact on genes regulating DNA (de)methylation, being in dialog with histone methylation. The excessive amounts of NO after the pathogen or GSNO treatment forced the transient upregulation of histone SUVH4 methylation and DNA hypermethylation. Then the diminished NO bioavailability reduced the SUVH4-mediated suppressive H3K9me2 mark on the R3a gene promoter and enhanced its transcription. However, we found that the R3a gene is likely to be controlled by the RdDM methylation pathway. The data revealed the time-dependent downregulation of the DCL3, AGO4, and miR482e genes, exerting upregulation of the targeted R3a gene correlated with ROS1 overexpression. Based on these results, we postulate that the biphasic waves of NO burst in response to the pathogen appear crucial in establishing potato resistance to late blight through the RdDM pathway controlling R gene expression.

Thermopriming-associated proteome and sugar content responses in Pinus radiata embryogenic tissue

Improving the capacity of plants to face adverse environmental conditions requires a deep understanding of the molecular mechanisms governing stress response and adaptation. Proteomics, combined with metabolic analyses, offers a wide resource of information to be used in plant breeding programs. Previous studies have shown that somatic embryogenesis in Pinus spp. is a suitable tool not only to investigate stress response processes but also to modulate the behaviour of somatic plants. Based on this, the objective of this study was to analyse the protein and soluble sugar profiles of Pinus radiata embryonal masses after the application of high temperatures to unravel the mechanisms involved in thermopriming and memory acquisition at early stages of the somatic embryogenesis process. Results confirmed that heat provokes deep readjustments in the life cycle of proteins, together with a significant reduction in the carbon-flux of central-metabolism pathways. Heat-priming also promotes the accumulation of proteins involved in oxidative stress defence, in the synthesis of specific amino acids such as isoleucine, influences cell division, the organization of the cytoskeleton and cell-walls, and modifies the levels of free soluble sugars like glucose or fructose. All this seems to be regulated by proteins linked with epigenetic, transcriptional and post-transcriptional mechanisms.

Epigenetic marks for mitigating abiotic stresses in plants

Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.

Activating stress memory: eustressors as potential tools for plant breeding

Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.

Local environment modulates whole-transcriptome expression in the seagrass Posidonia oceanica under warming and nutrients excess

The intensification of anomalous events of seawater warming and the co-occurrence with local anthropogenic stressors are threatening coastal marine habitats, including seagrasses, which form extensive underwater meadows. Eutrophication highly affects coastal environments, potentially summing up to the widespread effects of global climate changes. In the present study, we investigated for the first time in seagrasses, the transcriptional response of different plant organs (i.e., leaf and shoot apical meristem, SAM) of the Mediterranean seagrass Posidonia oceanica growing in environments with a different history of nutrient enrichment. To this end, a mesocosm experiment exposing plants to single (nutrient enrichment or temperature increase) and multiple stressors (nutrient enrichment plus temperature increase), was performed. Results revealed a differential transcriptome regulation of plants under single and multiple stressors, showing an organ-specific sensitivity depending on plants' origin. While leaf tissues were more responsive to nutrient stress, SAM revealed a higher sensitivity to temperature treatments, especially in plants already impacted in their native environment. The exposure to stress conditions induced the modulation of different biological processes. Plants living in an oligotrophic environment were more responsive to nutrients compared to plants from a eutrophic environment. Evidences that epigenetic mechanisms were involved in the regulation of transcriptional reprogramming were also observed in both plants' organs. These results represent a further step in the comprehension of seagrass response to abiotic stressors pointing out the importance of local pressures in a global warming scenario.

KNOX II transcription factor HOS59 functions in regulating rice grain size

Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA-mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.

Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds

Reactive oxygen species (ROS) release seed dormancy through an unknown mechanism. We used different seed dormancy-breaking treatments to decipher the dynamics and localization of ROS production during seed germination. We studied the involvement of ROS in the breaking of Arabidopsis seed dormancy by cold stratification, gibberellic acid (GA₃ ) and light. We characterized the effects of these treatments on abscisic acid and gibberellins biosynthesis and signalling pathways. ROS, mitochondrial redox status and peroxisomes were visualized and/or quantified during seed imbibition. Finally, we performed a cytogenetic characterization of the nuclei from the embryonic axes during seed germination. We show that mitochondria participate in the early ROS production during seed imbibition and that a possible involvement of peroxisomes in later stages should still be analysed. At the time of radicle protrusion, ROS accumulated within the nucleus, which correlated with nuclear expansion and chromatin decompaction. Taken together, our results provide evidence of the role of ROS trafficking between organelles and of the nuclear redox status in the regulation of seed germination by dormancy.

Nitric Oxide Implication in Potato Immunity to Phytophthora infestans via Modifications of Histone H3/H4 Methylation Patterns on Defense Genes

Nitric oxide (NO) is an essential redox-signaling molecule operating in many physiological and pathophysiological processes. However, evidence on putative NO engagement in plant immunity by affecting defense gene expressions, including histone modifications, is poorly recognized. Exploring the effect of biphasic NO generation regulated by S-nitrosoglutathione reductase (GNSOR) activity after avr Phytophthora infestans inoculation, we showed that the phase of NO decline at 6 h post-inoculation (hpi) was correlated with the rise of defense gene expressions enriched in the TrxG-mediated H3K4me3 active mark in their promoter regions. Here, we report that arginine methyltransferase PRMT5 catalyzing histone H4R3 symmetric dimethylation (H4R3sme2) is necessary to ensure potato resistance to avr P. infestans. Both the pathogen and S-nitrosoglutathione (GSNO) altered the methylation status of H4R3sme2 by transient reduction in the repressive mark in the promoter of defense genes, R3a and HSR203J (a resistance marker), thereby elevating their transcription. In turn, the PRMT5-selective inhibitor repressed R3a expression and attenuated the hypersensitive response to the pathogen. In conclusion, we postulate that lowering the NO level (at 6 hpi) might be decisive for facilitating the pathogen-induced upregulation of stress genes via histone lysine methylation and PRMT5 controlling potato immunity to late blight.

Biochemical and Physiological Plant Processes Affected by Seed Treatment with Non-Thermal Plasma

Among the innovative technologies being elaborated for sustainable agriculture, one of the most rapidly developing fields relies on the positive effects of non-thermal plasma (NTP) treatment on the agronomic performance of plants. A large number of recent publications have indicated that NTP effects are far more persistent and complex than it was supposed before. Knowledge of the molecular basis and the resulting outcomes of seed treatment with NTP is rapidly accumulating and requires to be analyzed and presented in a systematic way. This review focuses on the biochemical and physiological processes in seeds and plants affected by seed treatment with NTP and the resulting impact on plant metabolism, growth, adaptability and productivity. Wide-scale changes evolving at the epigenomic, transcriptomic, proteomic and metabolic levels are triggered by seed irradiation with NTP and contribute to changes in germination, early seedling growth, phytohormone amounts, metabolic and defense enzyme activity, secondary metabolism, photosynthesis, adaptability to biotic and abiotic stress, microbiome composition, and increased plant fitness, productivity and growth on a longer time scale. This review highlights the importance of these novel findings, as well as unresolved issues that remain to be investigated.

ODORANT1 targets multiple metabolic networks in petunia flowers

Scent bouquets produced by the flowers of Petunia spp. (petunia) are composed of a complex mixture of floral volatile benzenoid and phenylpropanoid compounds (FVBPs), which are specialized metabolites derived from phenylalanine (Phe) through an interconnected network of enzymes. The biosynthesis and emission of high levels of these volatiles requires coordinated transcriptional activation of both primary and specialized metabolic networks. The petunia R2R3-MYB transcription factor ODORANT 1 (ODO1) was identified as a master regulator of FVBP production and emission; however, our knowledge of the direct regulatory targets of ODO1 has remained limited. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq) in petunia flowers, we identify genome-wide ODO1-bound genes that are enriched not only in genes involved in the biosynthesis of the Phe precursor, as previously reported, but also genes associated with the specialized metabolic pathways involved in generating phenylpropanoid intermediates for FVBPs. ODO1-bound genes are also involved in methionine and S-adenosylmethionine metabolism, which could modulate methyl group supplies for certain FVBPs. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and RNA-seq analysis in an ODO1 RNAi knockdown line revealed that ODO1-bound targets are expressed at lower levels when ODO1 is suppressed. A cis-regulatory motif, CACCAACCCC, was identified as a potential binding site for ODO1 in the promoters of genes that are both bound and activated by ODO1, which was validated by in planta promoter reporter assays with wild-type and mutated promoters. Overall, our work presents a mechanistic model for ODO1 controlling an extensive gene regulatory network that contributes to FVBP production to give rise to floral scent.

Hydrogen peroxide-induced stress acclimation in plants

Among all reactive oxygen species (ROS), hydrogen peroxide (H2O2) takes a central role in regulating plant development and responses to the environment. The diverse role of H2O2 is achieved through its compartmentalized synthesis, temporal control exerted by the antioxidant machinery, and ability to oxidize specific residues of target proteins. Here, we examine the role of H2O2 in stress acclimation beyond the well-studied transcriptional reprogramming, modulation of plant hormonal networks and long-distance signalling waves by highlighting its global impact on the transcriptional regulation and translational machinery.

Investigation of the antioxidant activity of the peroxidase system of cell nuclei during germination of wheat embryos with different types of resistance to temperature stress

The yield of agricultural crops directly depends on their ability to adapt to a constantly changing environment, the unfavorable climatic conditions of which cause oxidative stress, accompanied by the generation of reactive oxygen species in plant cells, which can cause damage to heteropolymer cell structures, thereby leading to suppression of plant growth and a decrease in productivity grains. It has been shown that the profile of the antioxidant activity of the peroxidase system in histone and non-histone blocks of structures (nucleoplasm, chromatin) of cell nuclei during germination is more pronounced in the cold-resistant variety Mironovskaya 808 (winter) compared to Mironovskaya yarovaya (spring), which correlates with the intensity of growth processes and can be associated with participation in the realization of proliferation and differentiation programs. A direct relationship between the scavenging of ROS and plant resistance to temperature stress, which is often associated with the increased activity of antioxidant enzymes that impart stress resistance to both high and low temperature stress, apparently also exists at the level of the plant cell nucleus.

Investigation of the antioxidant activity of the peroxidase system of cell nuclei during germination of wheat embryos with different types of resistance to temperature stress

The yield of agricultural crops directly depends on their ability to adapt to a constantly changing environment, the unfavorable climatic conditions of which cause oxidative stress, accompanied by the generation of reactive oxygen species in plant cells, which can cause damage to heteropolymer cell structures, thereby leading to suppression of plant growth and a decrease in productivity grains. It has been shown that the profile of the antioxidant activity of the peroxidase system in histone and non-histone blocks of structures (nucleoplasm, chromatin) of cell nuclei during germination is more pronounced in the cold-resistant variety Mironovskaya 808 (winter) compared to Mironovskaya yarovaya (spring), which correlates with the intensity of growth processes and can be associated with participation in the realization of proliferation and differentiation programs. A direct relationship between the scavenging of ROS and plant resistance to temperature stress, which is often associated with the increased activity of antioxidant enzymes that impart stress resistance to both high and low temperature stress, apparently also exists at the level of the plant cell nucleus.

Paradoxes of Plant Epigenetics

Abstract

Plants have a unique ability to adapt ontogenesis to changing environmental conditions and the influence of stress factors. This ability is based on the existence of two specific features of epigenetic regulation in plants, which seem to be mutually exclusive at first glance. On the one hand, plants are capable of partial epigenetic reprogramming of the genome, which can lead to adaptation of physiology and metabolism to changed environmental conditions as well as to changes in ontogenesis programs. On the other hand, plants can show amazing stability of epigenetic modifications and the ability to transmit them to vegetative and sexual generations. The combination of these inextricably linked epigenetic features not only ensures survival in the conditions of a sessile lifestyle but also underlies a surprisingly wide morphological diversity of plants, which can lead to the appearance of morphs within one population and the existence of interpopulation morphological differences. The review discusses the molecular genetic mechanisms that cause a paradoxical combination of the stability and lability properties of epigenetic modifications and underlie the polyvariance of ontogenesis. We also consider the existing approaches for studying the role of epigenetic regulation in the manifestation of polyvariance of ontogenesis and discuss their limitations and prospects.

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals

In multicellular organisms, tissue generation, maintenance, and homeostasis depend on stem cells. Cellular metabolic status is an essential component of different differentiated states, from stem to fully differentiated cells. Threonine (Thr) metabolism has emerged as a critical factor required to maintain pluripotent/multipotent stem cells in both plants and animals. Thus, both kingdoms conserved or converged upon this fundamental feature of stem cell function. Here, we examine similarities and differences in Thr metabolism-dependent mechanisms supporting stem cell maintenance in these two kingdoms. We then consider common features of Thr metabolism in stem cell maintenance and predict and speculate that some knowledge about Thr metabolism and its role in stem cell function in one kingdom may apply to the other. Finally, we outline future research directions to explore these hypotheses.

Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression

Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. In addition to direct effects on transcriptional machinery, NO executes its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correspond to changes in global histone acetylation (H3, H3K9, and H3K9/K14) in Arabidopsis (Arabidopsis thaliana) wild-type leaves, and that this relationship depends on S-nitrosoglutathione reductase and histone deacetylase 6 (HDA6). The activity of HDA6 was sensitive to NO, demonstrating that NO participates in regulation of histone acetylation. Chromatin immunoprecipitation sequencing and RNA-seq analyses revealed that NO participates in the metabolic switch from growth and development to stress response. This coordinating function of NO might be particularly important in plant ability to adapt to a changing environment, and is therefore a promising foundation for mitigating the negative effects of climate change on plant productivity.

GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes

In the past, reactive nitrogen species (RNS) were supposed to be stress-induced by-products of disturbed metabolism that cause oxidative damage to biomolecules. However, emerging evidence demonstrates a substantial role of RNS as endogenous signals in eukaryotes. In plants, S-nitrosoglutathione (GSNO) is the dominant RNS and serves as the ^•NO donor for S-nitrosation of diverse effector proteins. Remarkably, the endogenous GSNO level is tightly controlled by S-nitrosoglutathione reductase (GSNOR) that irreversibly inactivates the glutathione-bound NO to ammonium. Exogenous feeding of diverse RNS, including GSNO, affected chromatin accessibility and transcription of stress-related genes, but the triggering function of RNS on these regulatory processes remained elusive. Here, we show that GSNO reductase-deficient plants (gsnor1-3) accumulate S-adenosylmethionine (SAM), the principal methyl donor for methylation of DNA and histones. This SAM accumulation triggered a substantial increase in the methylation index (MI = [SAM]/[S-adenosylhomocysteine]), indicating the transmethylation activity and histone methylation status in higher eukaryotes. Indeed, a mass spectrometry-based global histone profiling approach demonstrated a significant global increase in H3K9me2, which was independently verified by immunological detection using a selective antibody. Since H3K9me2-modified regions tightly correlate with methylated DNA regions, we also determined the DNA methylation status of gsnor1-3 plants by whole-genome bisulfite sequencing. DNA methylation in the CG, CHG, and CHH contexts in gsnor1-3 was significantly enhanced compared to the wild type. We propose that GSNOR1 activity affects chromatin accessibility by controlling the transmethylation activity (MI) required for maintaining DNA methylation and the level of the repressive chromatin mark H3K9me2.

Modulation of Organogenesis and Somatic Embryogenesis by Ethylene: An Overview

Ethylene is a plant hormone controlling physiological and developmental processes such as fruit maturation, hairy root formation, and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied, and progress in molecular biology techniques have contributed to unveiling the mechanisms behind its effects. The influence of ethylene on regeneration should not be overlooked. This compound affects regeneration differently, depending on the species, genotype, and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not additive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene in regeneration is markedly connected to biotic and abiotic stresses as well as to hormonal-crosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses, and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed. Further studies on the regulation of ERF gene expression induced by ethylene during regeneration can contribute to new insights on the exact role of ethylene in these processes. A possible role in epigenetic modifications should be considered, since some ethylene signaling components are directly related to histone acetylation.

The exposure of gadolinium at environmental relevant levels induced genotoxic effects in Arabidopsis thaliana (L.)

Rare Earth Elements (REEs) are increasingly being used in agriculture and are also used to produce high end technological devices, thereby increasing their anthropogenic presence in the environment. However, the ecotoxicological mechanism of REEs on organisms is not fully understood. In this study, the effects of gadolinium (Gd) addition on Arabidopsis thaliana (L.) were investigated at both physiological and molecular levels. Four treatments (0, 10, 50 and 200 μmol·L^-1 Gd) were used in the exposure tests. Biomass, root length and chlorophyll content in shoots/roots were measured to investigate the plant's physiological response to Gd stress. Random amplified polymorphic (RAPD)-Polymerase Chain Reaction (PCR) and methylation sensitive arbitrarily primed (MSAP)-PCR were used to investigate changes in genetic variation and DNA methylation of A. thaliana when exposed to Gd. At the physiological level, it was found that low concentration of Gd (10 μmol·L^-1) could significantly increase the plant biomass and root length, while the growth of A. thaliana was significantly inhibited when exposed to 200 μmol·L^-1 of Gd, yet the total soluble protein content in aerial plant parts increased significantly by 24.2% when compared to the control group. Among the 12 primers considered in the RAPD assessment, at the molecular level, only four primers revealed different patterns in their genomic DNA. Compared to the control group, the treatment with 50 μmol·L^-1 of Gd was associated with lower polymorphism, while the treatment with 200 μmol·L^-1 of Gd was associated with higher polymorphism. The polymorphism frequencies for the 50 μmol·L^-1 of Gd and the 200 μmol·L^-1 of Gd were 4.67% and 20.33%, respectively. The MSAP analysis revealed that the demethylation (D) type of Arabidopsis genomic DNA increased significantly under 10 and 50 μmol·L^-1 of Gd, while the methylation (M) type was also significantly increased under 200 μmol·L^-1 of Gd. Generally, the total methylation polymorphism (D+M) increased with an increase of Gd concentration. It was found that high concentrations of Gd appeared to cause DNA damage, but low concentrations of Gd (as low as 10 μmol·L^-1) were associated with DNA methylation change. Further, it was verified by Real time Reverse Transcription PCR (RT-PCR) on the bands detected by the MSAP analysis, that the genes relative to processes including cell cycle, oxidative stress and apoptosis, appeared to be regulated by methylation under Gd stress. These findings reveal new insight regarding ecotoxicity mechanisms of REEs on plants.

Plant chromatin, metabolism and development - an intricate crosstalk

Chromatin structure influences DNA accessibility and underlying gene expression. Disturbances of chromatin structure often result in pleiotropic developmental phenotypes. Interactions between chromatin modifications and development have been the main focus of epigenetic studies. Recent years brought major advance in uncovering and understanding connections between chromatin organisation in the nucleus and metabolic processes that take place in the cytoplasm or other cellular compartments. Products of primary metabolism and cell redox states influence chromatin-modifying complexes, and chromatin modifiers in turn affect expression of metabolic genes. Current evidence indicates that complex interaction loops between these biological system layers exist. Applying interdisciplinary and holistic approaches will decipher causality and molecular mechanisms of the dynamic crosstalk between chromatin structure, metabolism and plant growth and development.

The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells

Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.

Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response

Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.

Nitric oxide signaling in the plant nucleus: the function of nitric oxide in chromatin modulation and transcription

Nitric oxide (NO) is involved in a vast number of physiologically important processes in plants, such as organ development, stress resistance, and immunity. Transduction of NO bioactivity is generally achieved by post-translational modification of proteins, with S-nitrosation of cysteine residues as the predominant form. While traditionally the subcellular location of the factors involved was of lesser importance, recent studies identified the connection between NO and transcriptional activity and thereby raised the question about the route of NO into the nuclear sphere. Identification of NO-affected transcription factors and chromatin-modifying histone deacetylases implicated the important role of NO signaling in the plant nucleus as a regulator of epigenetic mechanisms and gene transcription. Here, we discuss the relationship between NO and its directly regulated protein targets in the nuclear environment, focusing on S-nitrosated chromatin modulators and transcription factors.

The regulation of ethylene biosynthesis: a complex multilevel control circuitry

The gaseous plant hormone ethylene is produced by a fairly simple two-step biosynthesis route. Despite this pathway's simplicity, recent molecular and genetic studies have revealed that the regulation of ethylene biosynthesis is far more complex and occurs at different layers. Ethylene production is intimately linked with the homeostasis of its general precursor S-adenosyl-l-methionine (SAM), which experiences transcriptional and posttranslational control of its synthesising enzymes (SAM synthetase), as well as the metabolic flux through the adjacent Yang cycle. Ethylene biosynthesis continues from SAM by two dedicated enzymes: 1-aminocyclopropane-1-carboxylic (ACC) synthase (ACS) and ACC oxidase (ACO). Although the transcriptional dynamics of ACS and ACO have been well documented, the first transcription factors that control ACS and ACO expression have only recently been discovered. Both ACS and ACO display a type-specific posttranslational regulation that controls protein stability and activity. The nonproteinogenic amino acid ACC also shows a tight level of control through conjugation and translocation. Different players in ACC conjugation and transport have been identified over the years, however their molecular regulation and biological significance is unclear, yet relevant, as ACC can also signal independently of ethylene. In this review, we bring together historical reports and the latest findings on the complex regulation of the ethylene biosynthesis pathway in plants.

Regulation of chlorogenic acid, flavonoid, and iridoid biosynthesis by histone H3K4 and H3K9 methylation in Lonicera japonica

Lonicera japonica is used in Chinese herbal medicines with a wide spectrum of pharmacological properties associated with chlorogenic acid, flavonoid and iridoid. The biosynthesis of these compounds could be affected by genetic inheritance and epigenetic modification. However, the mechanisms that regulate the expression of genes involved in the biosynthesis of these compounds are rarely known. The results of qRT-PCR showed that the biosynthesis gene expression of these compounds was related to histone H3K4 and H3K9 methylation levels. These active compounds content of L. japonica were measured by UPLC-MS/MS. H3K4me3 showed a positive correlation with chlorogenic acid and loganic acid content, and H3K9me positively correlated with luteolin content. The correlation between histone methylation levels and the levels of luteolin and loganic acid in L. japonica from different producing areas validate the regulatory role of histone methylation in biosynthesis of bioactive compounds. Our study demonstrated a potential regulatory network of H3K9/H3K4 methylation to gene expression and content of secondary metabolites, and provided a basis for understanding the mechanism underlying the variation of major bioactive compounds in L. japonica.

Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy

Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution.

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation

Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.

Nitric Oxide, an Essential Intermediate in the Plant-Herbivore Interaction

Reactive nitrogen species (RNS), mainly nitric oxide (NO), are highly reactive molecules with a prominent role in plant response to numerous stresses including herbivores, although the information is still very limited. This perspective article compiles the current progress in determining the NO function, as either a signal molecule, a metabolic intermediate, or a toxic oxidative product, as well as the contribution of molecules associated with NO metabolic pathway in the generation of plant defenses against phytophagous arthropods, in particular to insects and acari.