Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis

Epigenetic control of gene expression by cellular metabolisms in plants

Covalent modifications on DNA and histones can regulate eukaryotic gene expression and are often referred to as epigenetic modifications. These chemical reactions require various metabolites as donors or co-substrates, such as acetyl coenzyme A, S-adenosyl-l-methionine, and α-ketoglutarate. Metabolic processes that take place in the cytoplasm, nucleus, or other cellular compartments may impact epigenetic modifications in the nucleus. Here, we review recent advances on metabolic control of chromatin modifications and thus gene expression in plants, with a focus on the functions of nuclear compartmentalization of metabolic processes and enzymes in DNA and histone modifications. Furthermore, we discuss the functions of cellular metabolisms in fine-tuning gene expression to facilitate the responses or adaptation to environmental changes in plants.

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.

Genome-Wide Identification and Characterization of Tomato Fatty Acid β-Oxidase Family Genes KAT and MFP

Fatty acids and their derivatives play a variety of roles in living organisms. Fatty acids not only store energy but also comprise membrane lipids and act as signaling molecules. There are three main proteins involved in the fatty acid β-oxidation pathway in plant peroxisomes, including acyl-CoA oxidase (ACX), multifunctional protein (MFP), and 3-ketolipoyl-CoA thiolase (KAT). However, genome-scale analysis of KAT and MFP has not been systemically investigated in tomatoes. Here, we conducted a bioinformatics analysis of KAT and MFP genes in tomatoes. Their physicochemical properties, protein secondary structure, subcellular localization, gene structure, phylogeny, and collinearity were also analyzed. In addition, a conserved motif analysis, an evolutionary pressure selection analysis, a cis-acting element analysis, tissue expression profiling, and a qRT-PCR analysis were conducted within tomato KAT and MFP family members. There are five KAT and four MFP family members in tomatoes, which are randomly distributed on four chromosomes. By analyzing the conserved motifs of tomato KAT and MFP family members, we found that both KAT and MFP members are highly conserved. In addition, the results of the evolutionary pressure selection analysis indicate that the KAT and MFP family members have evolved mainly from purifying selection, which makes them more structurally stable. The results of the cis-acting element analysis show that SlKAT and SlMFP with respect may respond to light, hormones, and adversity stresses. The tissue expression analysis showed that KAT and MFP family members have important roles in regulating the development of floral organs as well as fruit ripening. The qRT-PCR analysis revealed that the expressions of SlKAT and SlMFP genes can be regulated by ABA, MeJA, darkness, NaCl, PEG, UV, cold, heat, and H2O2 treatments. These results provide a basis for the involvement of the SlKAT and SlMFP genes in tomato floral organ development and abiotic stress response, which lay a foundation for future functional study of SlKAT and SlMFP in tomatoes.

The Genome of the Korean Island-Originated Perilla citriodora 'Jeju17' Sheds Light on Its Environmental Adaptation and Fatty Acid and Lipid Production Pathways

Perilla is a key component of Korean food. It contains several plant-specialized metabolites that provide medical benefits. In response to an increased interest in healthy supplement food from the public, people are focusing on the properties of Perilla. Nevertheless, unlike rice and soybeans, there are few studies based on molecular genetics on Perilla, so it is difficult to systematically study the molecular breed. The wild Perilla, Perilla citriodora 'Jeju17', was identified a decade ago on the Korean island of Jeju. Using short-reads, long-reads, and Hi-C, a chromosome-scale genome spanning 676 Mbp, with high contiguity, was assembled. Aligning the 'Jeju17' genome to the 'PC002' Chinese species revealed significant collinearity with respect to the total length. A total of 31,769 coding sequences were predicted, among which 3331 were 'Jeju17'-specific. Gene enrichment of the species-specific gene repertoire highlighted environment adaptation, fatty acid metabolism, and plant-specialized metabolite biosynthesis. Using a homology-based approach, genes involved in fatty acid and lipid triacylglycerol biosynthesis were identified. A total of 22 fatty acid desaturases were found and comprehensively characterized. Expression of the FAD genes in 'Jeju17' was examined at the seed level, and hormone signaling factors were identified. The results showed that the expression of FAD genes in 'Jeju17' at the seed level was high 25 days after flowering, and their responses of hormones and stress were mainly associated with hormone signal transduction and abiotic stress via cis-elements patterns. This study presents a chromosome-level genome assembly of P. citriodora 'Jeju17', the first wild Perilla to be sequenced from the Korean island of Jeju. The analyses provided can be useful in designing ALA-enhanced Perilla genotypes in the future.

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.

p53 promotes peroxisomal fatty acid β-oxidation to repress purine biosynthesis and mediate tumor suppression

The metabolic pathways through which p53 functions as a potent tumor suppressor are incompletely understood. Here we report that, by associating with the Vitamin D receptor (VDR), p53 induces numerous genes encoding enzymes for peroxisomal fatty acid β-oxidation (FAO). This leads to increased cytosolic acetyl-CoA levels and acetylation of the enzyme 5-Aminoimidazole-4-Carboxamide Ribonucleotide Formyltransferase/IMP Cyclohydrolase (ATIC), which catalyzes the last two steps in the purine biosynthetic pathway. This acetylation step, mediated by lysine acetyltransferase 2B (KAT2B), occurs at ATIC Lys 266, dramatically inhibits ATIC activity, and inversely correlates with colorectal cancer (CRC) tumor growth in vitro and in vivo, and acetylation of ATIC is downregulated in human CRC samples. p53-deficient CRCs with high levels of ATIC is more susceptible to ATIC inhibition. Collectively, these findings link p53 to peroxisomal FAO, purine biosynthesis, and CRC pathogenesis in a manner that is regulated by the levels of ATIC acetylation.

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.

Ischemic Postconditioning Protects against Aged Myocardial Ischemia/Reperfusion Injury by Transcriptional and Epigenetic Regulation of miR-181a-2-3p

Ischemic postconditioning (IPostC) has been proposed as a strategy to mitigate the risk of ischemia/reperfusion (I/R) injury, and autophagy is involved in I/R-induced aged myocardial injury, while the underlying mechanism of IPostC-regulated autophagy is unknown. Here, we implemented miRNA sequencing analysis in aged cardiomyocytes to identify a novel miR-181a-2-3p after HPostC, which inhibits autophagy by targeting AMBRA1 in aged myocardium to protect I/R-induced aged myocardial injury. Mechanistically, we identified that IPostC can induce DNA hypomethylation and H3K14 hyperacetylation of miR-181a-2-3p promoter due to the decreased binding of DNMT3b and HDAC2 at its promoter, which contributes to enhancing the expression of miR-181a-2-3p. More importantly, cooperation of DNMT3b and HDAC2 inhibits the binding of c-Myc at the miR-181a-2-3p promoter in aged cardiomyocytes. In summary, IPostC attenuates I/R-induced aged myocardial injury through upregulating miR-181a-2-3p expression, which is an attribute to transcriptional and epigenetic regulation of its promoter. Our data indicate that miR-181a-2-3p may be a potential therapeutic target against I/R injury in aged myocardium.

Advances in Understanding the Genetic Basis of Fatty Acids Biosynthesis in Perilla: An Update

Perilla, also termed as purple mint, Chinese basil, or Perilla mint, is a flavoring herb widely used in East Asia. Both crude oil and essential oil are employed for consumption as well as industrial purposes. Fatty acids (FAs) biosynthesis and oil body assemblies in Perilla have been extensively investigated over the last three decades. Recent advances have been made in order to reveal the enzymes involved in the fatty acid biosynthesis in Perilla. Among those fatty acids, alpha-linolenic acid retained the attention of scientists mainly due to its medicinal and nutraceutical properties. Lipids synthesis in Perilla exhibited similarities with Arabidopsis thaliana lipids’ pathway. The homologous coding genes for polyunsaturated fatty acid desaturases, transcription factors, and major acyl-related enzymes have been found in Perilla via de novo transcriptome profiling, genome-wide association study, and in silico whole-genome screening. The identified genes covered de novo fatty acid synthesis, acyl-CoA dependent Kennedy pathway, acyl-CoA independent pathway, Triacylglycerols (TAGs) assembly, and acyl editing of phosphatidylcholine. In addition to the enzymes, transcription factors including WRINKLED, FUSCA3, LEAFY COTYLEDON1, and ABSCISIC ACID INSENSITIVE3 have been suggested. Meanwhile, the epigenome aspect impacting the transcriptional regulation of FAs is still unclear and might require more attention from the scientific community. This review mainly outlines the identification of the key gene master players involved in Perilla FAs biosynthesis and TAGs assembly that have been identified in recent years. With the recent advances in genomics resources regarding this orphan crop, we provided an updated overview of the recent contributions into the comprehension of the genetic background of fatty acid biosynthesis. The provided resources can be useful for further usage in oil-bioengineering and the design of alpha-linolenic acid-boosted Perilla genotypes in the future.

Methylation related genes affect sex differentiation in dioecious and gynodioecious papaya

Morphological, genic and epigenetic differences often exist in separate sexes of dioecious and trioecious plants. However, the connections and relationships among them in different breeding systems are still unclear. Papaya has three sex types, which is genetically determined and epigenetically regulated, and was chosen as a model to study sex differentiation. Bisulfite sequencing of genomic DNA extracted from early-stage flowers revealed sex-specific genomic methylation landscapes and seasonally methylome reprogramming processes in dioecious and gynodioecious papaya grown in spring and summer. Extensive methylation of sex-determining region (SDR) was the distinguishing epigenetic characteristics of nascent XY sex chromosomes in papaya. Seasonal methylome reprogramming of early-stage flowers in both dioecy and gynodioecy systems were detected, resulting from transcriptional expression pattern alterations of methylation-modification-related and chromatin-remodeling-related genes, particularly from those genes involved in active demethylation. Genes involved in phytohormone signal transduction pathway in male flowers have played an important role in the formation of male-specific characteristics. These findings enhanced the understanding of the genetic and epigenetic contributions to sex differentiation and the complexity of sex chromosome evolution in trioecious plants.

The C4 cycle and beyond: diverse metabolic adaptations accompany dual-cell photosynthetic functions in Setaria

C4 photosynthesis is typically characterized by the spatial compartmentalization of the photosynthetic reactions into mesophyll (M) and bundle sheath (BS) cells. Initial carbon fixation within M cells gives rise to C4 acids, which are transported to the BS cells. There, C4 acids are decarboxylated so that the resulting CO2 is incorporated into the Calvin cycle. This work is focused on the study of Setaria viridis, a C4 model plant, closely related to several major feed and bioenergy grasses. First, we performed the heterologous expression and biochemical characterization of Setaria isoforms for chloroplastic NADP-malic enzyme (NADP-ME) and mitochondrial NAD-malic enzyme (NAD-ME). The kinetic parameters obtained agree with a major role for NADP-ME in the decarboxylation of the C4 acid malate in the chloroplasts of BS cells. In addition, mitochondria-located NAD-ME showed regulatory properties that could be important in the context of the operation of the C4 carbon shuttle. Secondly, we compared the proteomes of M and BS compartments and found 825 differentially accumulated proteins that could support different metabolic scenarios. Most interestingly, we found evidence of metabolic strategies to insulate the C4 core avoiding the leakage of intermediates by either up-regulation or down-regulation of chloroplastic, mitochondrial, and peroxisomal proteins. Overall, the results presented in this work provide novel data concerning the complexity of C4 metabolism, uncovering future lines of research that will undoubtedly contribute to the expansion of knowledge on this topic.

AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana

Pericentromeric DNA, consisting of high-copy-number tandem repeats and transposable elements, is normally silenced through DNA methylation and histone modifications to maintain chromosomal integrity and stability. Although histone deacetylase 6 (HDA6) has been known to participate in pericentromeric silencing, the mechanism is still yet unclear. Here, using whole genome bisulfite sequencing (WGBS) and chromatin immunoprecipitation-sequencing (ChIP-Seq), we mapped the genome-wide patterns of differential DNA methylation and histone H3 lysine 18 acetylation (H3K18ac) in wild-type and hda6 mutant strains. Results show pericentromeric CHG hypomethylation in hda6 mutants was mediated by DNA demethylases, not by DNA methyltransferases as previously thought. DNA demethylases can recognize H3K18ac mark and then be recruited to the chromatin. Using biochemical assays, we found that HDA6 could function as an ‘eraser’ enzyme for H3K18ac mark to prevent DNA demethylation. Oxford Nanopore Technology Direct RNA Sequencing (ONT DRS) also revealed that hda6 mutants with H3K18ac accumulation and CHG hypomethylation were shown to have transcriptionally active pericentromeric DNA.

Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis

DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Our results are also consistent with CMT3-induced ectopic methylation of promoters or bodies of genes undergoing transcriptional activation reducing their expression. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.

Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.

Histone deacetylases control lysine acetylation of ribosomal proteins in rice

Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.

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.

Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein level. Here, we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 hr light:12 hr dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5,000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin-dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.

Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

BACKGROUND

DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. However, no information is available regarding the identification of cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes in the orchid Dendrobium officinale.

RESULTS

In this study, we performed a genome-wide analysis of DoC5-MTase and DodMTase gene families in D. officinale. Integrated analysis of conserved motifs, gene structures and phylogenetic analysis showed that eight DoC5-MTases were divided into four subfamilies (DoCMT, DoDNMT, DoDRM, DoMET) while three DodMTases were divided into two subfamilies (DoDML3, DoROS1). Multiple cis-acting elements, especially stress-responsive and hormone-responsive ones, were found in the promoter region of DoC5-MTase and DodMTase genes. Furthermore, we investigated the expression profiles of DoC5-MTase and DodMTase in 10 different tissues, as well as their transcript abundance under abiotic stresses (cold and drought) and at the seedling stage, in protocorm-like bodies, shoots, and plantlets. Interestingly, most DoC5-MTases were downregulated whereas DodMTases were upregulated by cold stress. At the seedling stage, DoC5-MTase expression decreased as growth proceeded, but DodMTase expression increased.

CONCLUSIONS

These results provide a basis for elucidating the role of DoC5-MTase and DodMTase in secondary metabolite production and responses to abiotic stresses in D. officinale.

Functional Characterization of GhACX3 Gene Reveals Its Significant Role in Enhancing Drought and Salt Stress Tolerance in Cotton

The acyl-coenzyme A oxidase 3 (ACX3) gene involved in the β-oxidation pathway plays a critical role in plant growth and development as well as stress response. Earlier on, studies focused primarily on the role of β-oxidation limited to fatty acid breakdown. However, ACX3 peroxisomal β-oxidation pathways result in a downstream cascade of events that act as a transduction of biochemical and physiological responses to stress. A role that is yet to be studied extensively. In this study, we identified 20, 18, 22, 23, 20, 11, and 9 proteins in Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, G. darwinii, G. arboretum, and G. raimondii genomes, respectively. The tetraploid cotton genome had protein ranging between 18 and 22, while diploids had between 9 and 11. After analyzing the gene family evolution or selection pressure, we found that this gene family undergoes purely segmental duplication both in diploids and tetraploids. W-Box (WRKY-binding site), ABRE, CAAT-Box, TATA-box, MYB, MBS, LTR, TGACG, and CGTCA-motif are abiotic stress cis-regulatory elements identified in this gene family. All these are the binding sites for abiotic stress transcription factors, indicating that this gene is essential. Genes found in G. hirsutum showed a clear response to drought and salinity stress, with higher expression under drought and salt stress, particularly in the leaf and root, according to expression analysis. We selected Gh_DO1GO186, one of the highly expressed genes, for functional characterization. We functionally characterized the GhACX3 gene through overexpression and virus-induced gene silencing (VIGS). Overexpression of this gene enhanced tolerance under stress, which was exhibited by the germination assay. The overexpressed seed growth rate was faster relative to control under drought and salt stress conditions. The survival rate was also higher in overexpressed plants relative to control plants under stress. In contrast, the silencing of the GhACX3 gene in cotton plants resulted in plants showing the stress susceptibility phenotype and reduced root length compared to control. Biochemical analysis also demonstrated that GhACX3-silenced plants experienced oxidative stress while the overexpressed plants did not. This study has revealed the importance of the ACX3 family during stress tolerance and can breed stress-resilient cultivar.

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.

Who Rules the Cell? An Epi-Tale of Histone, DNA, RNA, and the Metabolic Deep State

Epigenetics refers to the mode of inheritance independent of mutational changes in the DNA. Early evidence has revealed methylation, acetylation, and phosphorylation of histones, as well as methylation of DNA as part of the underlying mechanisms. The recent awareness that many human diseases have in fact an epigenetic basis, due to unbalanced diets, has led to a resurgence of interest in how epigenetics might be connected with, or even controlled by, metabolism. The Next-Generation genomic technologies have now unleashed torrents of results exposing a wondrous array of metabolites that are covalently attached to selective sites on histones, DNA and RNA. Metabolites are often cofactors or targets of chromatin-modifying enzymes. Many metabolites themselves can be acetylated or methylated. This indicates that the acetylome and methylome can actually be deep and pervasive networks to ensure the nuclear activities are coordinated with the metabolic status of the cell. The discovery of novel histone marks also raises the question on the types of pathways by which their corresponding metabolites are replenished, how they are corralled to the specific histone residues and how they are recognized. Further, atypical cytosines and uracil have also been found in eukaryotic genomes. Although these new and extensive connections between metabolism and epigenetics have been established mostly in animal models, parallels must exist in plants, inasmuch as many of the basic components of chromatin and its modifying enzymes are conserved. Plants are chemical factories constantly responding to stress. Plants, therefore, should lend themselves readily for identifying new endogenous metabolites that are also modulators of nuclear activities in adapting to stress.

Interactions between metabolism and chromatin in plant models

BACKGROUND

One of the fascinating aspects of epigenetic regulation is that it provides means to rapidly adapt to environmental change. This is particularly relevant in the plant kingdom, where most species are sessile and exposed to increasing habitat fluctuations due to global warming. Although the inheritance of epigenetically controlled traits acquired through environmental impact is a matter of debate, it is well documented that environmental cues lead to epigenetic changes, including chromatin modifications, that affect cell differentiation or are associated with plant acclimation and defense priming. Still, in most cases, the mechanisms involved are poorly understood. An emerging topic that promises to reveal new insights is the interaction between epigenetics and metabolism.

SCOPE OF REVIEW

This study reviews the links between metabolism and chromatin modification, in particular histone acetylation, histone methylation, and DNA methylation, in plants and compares them to examples from the mammalian field, where the relationship to human diseases has already generated a larger body of literature. This study particularly focuses on the role of reactive oxygen species (ROS) and nitric oxide (NO) in modulating metabolic pathways and gene activities that are involved in these chromatin modifications. As ROS and NO are hallmarks of stress responses, we predict that they are also pivotal in mediating chromatin dynamics during environmental responses.

MAJOR CONCLUSIONS

Due to conservation of chromatin-modifying mechanisms, mammals and plants share a common dependence on metabolic intermediates that serve as cofactors for chromatin modifications. In addition, plant-specific non-CG methylation pathways are particularly sensitive to changes in folate-mediated one-carbon metabolism. Finally, reactive oxygen and nitrogen species may fine-tune epigenetic processes and include similar signaling mechanisms involved in environmental stress responses in plants as well as animals.

Peroxisomes: versatile organelles with diverse roles in plants

Peroxisomes are small, ubiquitous organelles that are delimited by a single membrane and lack genetic material. However, these simple-structured organelles are highly versatile in morphology, abundance and protein content in response to various developmental and environmental cues. In plants, peroxisomes are essential for growth and development and perform diverse metabolic functions, many of which are carried out coordinately by peroxisomes and other organelles physically interacting with peroxisomes. Recent studies have added greatly to our knowledge of peroxisomes, addressing areas such as the diverse proteome, regulation of division and protein import, pexophagy, matrix protein degradation, solute transport, signaling, redox homeostasis and various metabolic and physiological functions. This review summarizes our current understanding of plant peroxisomes, focusing on recent discoveries. Current problems and future efforts required to better understand these organelles are also discussed. An improved understanding of peroxisomes will be important not only to the understanding of eukaryotic cell biology and metabolism, but also to agricultural efforts aimed at improving crop performance and defense.

Plant Unsaturated Fatty Acids: Multiple Roles in Stress Response

Land plants are exposed to not only biotic stresses such as pathogen infection and herbivore wounding, but abiotic stresses such as cold, heat, drought, and salt. Elaborate strategies have been developed to avoid or abide the adverse effects, with unsaturated fatty acids (UFAs) emerging as general defenders. In higher plants, the most common UFAs are three 18-carbon species, namely, oleic (18:1), linoleic (18:2), and α-linolenic (18:3) acids. These simple compounds act as ingredients and modulators of cellular membranes in glycerolipids, reserve of carbon and energy in triacylglycerol, stocks of extracellular barrier constituents (e.g., cutin and suberin), precursors of various bioactive molecules (e.g., jasmonates and nitroalkenes), and regulators of stress signaling. Nevertheless, they are also potential inducers of oxidative stress. In this review, we will present an overview of these roles and then shed light on genetic engineering of FA synthetic genes for improving plant/crop stress tolerance.

The mechanism and function of active DNA demethylation in plants

DNA methylation is a conserved and important epigenetic mark in both mammals and plants. DNA methylation can be dynamically established, maintained, and removed through different pathways. In plants, active DNA demethylation is initiated by the RELEASE OF SILENCING 1 (ROS1) family of bifunctional DNA glycosylases/lyases. Accumulating evidence suggests that DNA demethylation is important in many processes in plants. In this review, we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway. We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses. Finally, we highlight those aspects of DNA demethylation that require additional research.

Histone Acetylation Dynamics Integrates Metabolic Activity to Regulate Plant Response to Stress

Histone lysine acetylation is an essential chromatin modification for epigenetic regulation of gene expression during plant response to stress. On the other hand, enzymes involved in histone acetylation homeostasis require primary metabolites as substrates or cofactors whose levels are greatly influenced by stress and growth conditions in plants. In addition, histone lysine acylation that requires similar enzymes for deposition and removal as histone acetylation has been recently characterized in plant. Results on understanding the intrinsic relationship between histone acetylation/acylation, metabolism and stress response in plants are accumulating. In this review, we summarize recent advance in the field and propose a model of interplay between metabolism and epigenetic regulation of genes expression in plant adaptation to stress.