UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana

Functional divergence of Arabidopsis REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 and 2 in repression of flowering

Photoperiodic plants coordinate the timing of flowering with seasonal light cues, thereby optimizing their sexual reproductive success. The WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) functions as a potent repressor of UV RESISTANCE LOCUS 8 (UVR8) photoreceptor-mediated UV-B induction of flowering under noninductive, short-day conditions in Arabidopsis (Arabidopsis thaliana); however, in contrast, the closely related RUP1 seems to play no major role. Here, analysis of chimeric ProRUP1:RUP2 and ProRUP2:RUP1 expression lines suggested that the distinct functions of RUP1 and RUP2 in repressing flowering are due to differences in both their coding and regulatory DNA sequences. Artificial altered expression using tissue-specific promoters indicated that RUP2 functions in repressing flowering when expressed in mesophyll and phloem companion cells, whereas RUP1 functions only when expressed in phloem companion cells. Endogenous RUP1 expression in vascular tissue was quantified as lower than that of RUP2, likely underlying the functional difference between RUP1 and RUP2 in repressing flowering. Taken together, our findings highlight the importance of phloem vasculature expression of RUP2 in repressing flowering under short days and identify a basis for the functional divergence of Arabidopsis RUP1 and RUP2 in regulating flowering time.

Temporal regulation of vegetative phase change in plants

During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.

The roles of miR156 in abiotic and biotic stresses in plants

MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.

Uncovering the mechanisms of salicylic acid-mediated abiotic stress tolerance in horticultural crops

Salicylic acid (SA) has been recognized as a promising molecule for improving abiotic stress tolerance in plants due to its ability to enhance antioxidant defense system, and promote root architecture system. Recent research has focused on uncovering the mechanisms by which SA confers abiotic stress tolerance in horticultural crops. SA has been shown to act as a signaling molecule that triggers various physiological and morphological responses in plants. SA regulates the production of reactive oxygen species (ROS). Moreover, it can also act as signaling molecule that regulate the expression of stress-responsive genes. SA can directly interact with various hormones, proteins and enzymes involved in abiotic stress tolerance. SA regulates the antioxidant enzymes activities that scavenge toxic ROS, thereby reducing oxidative damage in plants. SA can also activate protein kinases that phosphorylate and activate transcription factors involved in stress responses. Understanding these mechanisms is essential for developing effective strategies to improve crop resilience in the face of changing environmental conditions. Current information provides valuable insights for farmers and plant researchers, offering new strategies to enhance crop resilience and productivity in the face of environmental challenges. By harnessing the power of SA and its signaling pathways, farmers can develop more effective stress management techniques and optimize crop performance. Plant researchers can also explore innovative approaches to breed or engineer crops with enhanced stress tolerance, thereby contributing to sustainable agriculture and food security.

Ultraviolet-B radiation in relation to agriculture in the context of climate change: a review

Over the past few decades, the amount of ultraviolet-B radiation (UV-B) reaching the earth's surface has been altered due to climate change and stratospheric ozone dynamics. This narrow but highly biologically active spectrum of light (280-320 nm) can affect plant growth and development. Depletion of ozone and climate change are interlinked in a very complicated manner, i.e., significantly contributing to each other. The interaction of climate change, ozone depletion, and changes in UV-B radiation negatively affects the growth, development, and yield of plants. Furthermore, this interaction will become more complex in the coming years. The ozone layer reduction is paving a path for UV-B radiation to impact the surface of the earth and interfere with the plant's normal life by negatively affecting the plant's morphology and physiology. The nature and degree of the future response of the agricultural ecosystem to the decreasing or increasing UV-B radiation in the background of climate change and ozone dynamics are still unclear. In this regard, this review aims to elucidate the effects of enhanced UV-B radiation reaching the earth's surface due to the depletion of the ozone layer on plants' physiology and the performance of major cereals.

Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.

Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms

As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.

Plant responses to UV-B radiation: signaling, acclimation and stress tolerance

Ultraviolet-B (UV-B) light is an intrinsic part of sunlight that reaches the earth's surface, and affects plant survival and adaptation. How plants respond to UV-B light is regulated by the wavelength, intensity and duration of UV-B radiation, and is also regulated by photosynthetically active radiation perceived by phytochrome and cryptochrome photoreceptors. Non-damaging UV-B light promotes plant photomorphogenesis and UV-B acclimation which enhances plant tolerance against UV-B stress. However, high-level UV-B radiation induces DNA damage, generates reactive oxygen species (ROS) and impairs photosynthesis. Plants have evolved efficient mechanisms to utilize informational UV-B signal, and protect themselves from UV-B stress. UV RESISTANCE LOCUS8 (UVR8) is a conserved plant-specific UV-B photoreceptor. It interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) to initiate UV-B-specific light signaling and regulate UV-B responsive gene expression. A set of transcription factors such as ELONGATED HYPOCOTYL5 (HY5) function downstream of the UVR8-COP1 module to promote seedling de-etiolation for photomorphogenic development and biosynthesis of sunscreen flavonoids for UV-B stress tolerance. In addition to UVR8 signaling pathways, plants subjected to damaging UV-B radiation initiate stress protection and repair mechanisms through UVR8-independent pathways. In this review, we summarize the emerging mechanisms underlying UV-B stress acclimation and protection in plants, primarily revealed in the model plant Arabidopsis thaliana.

MicroRNA miR394 regulates flowering time in Arabidopsis thaliana

miR394 regulates Arabidopsis flowering time in a LCR-independent manner. Arabidopsis plants harboring mutations in theMIR394 genes exhibit early flowering, lower expression of floral repressor FLC and higher expression of floral integrators FT and SOC1. Plant development occurs throughout its entire life cycle and involves a phase transition between vegetative and reproductive phases, leading to the flowering process, fruit formation and ultimately seed production. It has been shown that the microRNA394 (miR394) regulates the accumulation of the transcript coding for LEAF CURLING RESPONSIVENESS, a member of a family of F-Box proteins. The miR394 pathway regulates several processes including leaf morphology and development of the shoot apical meristem during embryogenesis, as well as having been assigned a role in the response to biotic and abiotic stress in Arabidopsis thaliana and other species. Here, we characterized plants harboring mutations in MIR394 precursor genes and demonstrate that mir394a mir394b double mutants display an early flowering phenotype which correlates with a lower expression of FLOWERING LOCUS C earlier in development and higher expression of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Consequently, mutant plants produce fewer branches and exhibit lower seed production. Our work reveals previously unknown developmental aspects regulated by the miR394 pathway, in an LCR-independent manner, contributing to the characterization of the multiple roles of this versatile plant regulatory miRNA.

Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV-B exposure

Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the nucleotide excision DNA repair system, but this function in plants has not been investigated. We studied the role of MED17 in Arabidopsis plants exposed to UV-B radiation. Our results demonstrate that med17 and OE MED17 plants have altered responses to UV-B, and that MED17 participates in various aspects of the DNA damage response (DDR). Comparison of the med17 transcriptome with that of wild-type (WT) plants showed that almost one-third of transcripts with altered expression in med17 plants were also changed by UV-B exposure in WT plants. Increased sensitivity to DNA damage after UV-B in med17 plants could result from the altered regulation of UV-B responsive transcripts but MED17 also physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we show that MED17 is necessary to regulate the DDR activated by ataxia telangiectasia and Rad3 related (ATR), and that programmed cell death 5 (PDCD5) overexpression reverts the deficiencies in DDR shown in med17 mutants. Our data demonstrate that MED17 is an important regulator of DDR after UV-B irradiation in Arabidopsis.

Low Fluence Ultraviolet-B Promotes Ultraviolet Resistance 8-Modulated Flowering in Arabidopsis

Ultraviolet-B (UV-B) irradiation (280-320 nm) is an integral part of sunlight and a pivotal environmental cue that triggers various plant responses, from photoprotection to photomorphogenesis and metabolic processes. UV-B is perceived by ULTRAVIOLET RESISTANCE 8 (UVR8), which orchestrates UV-B signal transduction and transcriptional control of UV-B-responsive genes. However, there is limited information on the molecular mechanism underlying the UV-B- and UVR8-dependent regulation of flowering time in plants. Here, we investigate the role of UV-B and UVR8 in photoperiodic flowering in Arabidopsis thaliana. Our findings suggest that UV-B controls photoperiodic flowering in an ecotype-specific manner and that UVR8 acts as a negative regulator of UV-B-induced flowering. Overall, our research shows that UV-B modulates flowering initiation through the action of UVR8 at the transcriptional level.

An Epigenetic Alphabet of Crop Adaptation to Climate Change

Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.

The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling

After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.

Transgenic Chrysanthemum indicum overexpressing cin-miR396a exhibits altered plant development and reduced salt and drought tolerance

The conserved microRNA396 (miR396) is involved in growth, development, and abiotic stress responses in a variety of plants by regulating target genes. Here, we obtained transgenic Chrysanthemum indicum (C. indicum) overexpressing the cin-miR396a gene. The transgenic plants (TGs) had longer internodes and fewer epidermal hairs in contrast with the wild-type (WT) control. cin-miR396a overexpression in C. indicum reduced salt tolerance and drought tolerance. After salt and drought stress compared with WT plants, the transgenic C. indicum exhibited a relative decrease in leaf water content, and the leaf free proline content, also exhibited a relative increase, in the leaf conductivity and leaf Malondialdehyde content, while the total chlorophyll content did not differ significantly from WT, and the Na⁺/K⁺ ratio in the roots of transgenic C. indicum increased after salt stress. We also identified two target genes of cin-miR396a, CiGRF1 and CiGRF5, whose expression was induced by salt and drought treatments and suppressed in transgenic C. indicum. Taken together, our results reveal a unique role for the regulatory module of miR396a-GRFs in C. indicum development and response to abiotic stresses. cin-miR396a plays a negative regulatory role in C. indicum in response to salt and drought stresses.

PRC2 activity, recruitment, and silencing: a comparative perspective

Polycomb repressive complex (PRC)-mediated gene silencing is vital for cell identity and development in both the plant and the animal kingdoms. It also modulates responses to stress. Two major protein complexes, PRC1 and PRC2, execute conserved nuclear functions in metazoans and plants through covalent modification of histones and by compacting chromatin. While a general requirement for Polycomb complexes in mitotically heritable gene repression in the context of chromatin is well established, recent studies have brought new insights into the regulation of Polycomb complex activity and recruitment. Here, we discuss these recent advances with emphasis on PRC2.

The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator

In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.

UV-B light and its application potential to reduce disease and pest incidence in crops

Ultraviolet-B radiation (280-315 nm), perceived by the plant photoreceptor UVR8, is a key environmental signal that influences plant growth and development and can reduce disease and pest incidence. The positive effect of UV-B on disease resistance and incidence in various plant species supports the implementation of supplemental UV-B radiation in sustainable crop production. However, despite many studies focusing on UV-B light, there is no consensus on the best mode of application. This review aims to analyze, evaluate, and organize the different application strategies of UV-B radiation in crop production with a focus on disease resistance. We summarize the physiological effects of UV-B light on plants and discuss how plants perceive and transduce UV-B light by the UVR8 photoreceptor as well as how this perception alters plant specialized metabolite production. Next, we bring together conclusions of various studies with respect to different UV-B application methods to improve plant resistance. In general, supplemental UV-B light has a positive effect on disease resistance in many plant-pathogen combinations, mainly through the induction of the production of specialized metabolites. However, many variables (UV-B light source, plant species, dose and intensity, timing during the day, duration, background light, etc.) make it difficult to compare and draw general conclusions. We compiled the information of recent studies on UV-B light applications, including e.g., details on the UV-B light source, experimental set-up, calculated UV-B light dose, intensity, and duration. This review provides practical insights and facilitates future research on UV-B radiation as a promising tool to reduce disease and pest incidence.

The Sw5a gene confers resistance to ToLCNDV and triggers an HR response after direct AC4 effector recognition

Several attempts have been made to identify antiviral genes against Tomato leaf curl New Delhi virus (ToLCNDV) and related viruses. This has led to the recognition of Ty genes (Ty1-Ty6), which have been successful in developing virus-resistant crops to some extent. Owing to the regular appearance of resistance-breaking strains of these viruses, it is important to identify genes related to resistance. In the present study, we identified a ToLCNDV resistance (R) gene, SlSw5a, in a ToLCNDV-resistant tomato cultivar, H-88-78-1, which lacks the known Ty genes. The expression of SlSw5a is controlled by the transcription factor SlMyb33, which in turn is regulated by microRNA159 (sly-miR159). Virus-induced gene silencing of either SlSw5a or SlMyb33 severely increases the disease symptoms and viral titer in leaves of resistant cultivar. Moreover, in SlMyb33-silenced plants, the relative messenger RNA level of SlSw5a was reduced, suggesting SlSw5a is downstream of the sly-miR159-SlMyb33 module. We also demonstrate that SlSw5a interacts physically with ToLCNDV-AC4 (viral suppressor of RNA silencing) to trigger a hypersensitive response (HR) and generate reactive oxygen species at infection sites to limit the spread of the virus. The "RTSK" motif in the AC4 C terminus is important for the interaction, and its mutation completely abolishes the interaction with Sw5a and HR elicitation. Overall, our research reports an R gene against ToLCNDV and establishes a connection between the upstream miR159-Myb33 module and its downstream target Sw5a to activate HR in the tomato, resulting in geminivirus resistance.

Safeguarding genome integrity under heat stress in plants

Heat stress adversely affects an array of molecular and cellular events in plant cells, such as denaturation of protein and lipid molecules and malformation of cellular membranes and cytoskeleton networks. Genome organization and DNA integrity are also disturbed under heat stress, and accordingly, plants have evolved sophisticated adaptive mechanisms that either protect their genomes from deleterious heat-induced damages or stimulate genome restoration responses. In particular, it is emerging that DNA damage responses are a critical defense process that underlies the acquirement of thermotolerance in plants, during which molecular players constituting the DNA repair machinery are rapidly activated. In recent years, thermotolerance genes that mediate the maintenance of genome integrity or trigger DNA repair responses have been functionally characterized in various plant species. Furthermore, accumulating evidence supports that genome integrity is safeguarded through multiple layers of thermoinduced protection routes in plant cells, including transcriptome adjustment, orchestration of RNA metabolism, protein homeostasis, and chromatin reorganization. In this review, we summarize topical progresses and research trends in understanding how plants cope with heat stress to secure genome intactness. We focus on molecular regulatory mechanisms by which plant genomes are secured against the DNA-damaging effects of heat stress and DNA damages are effectively repaired. We will also explore the practical interface between heat stress response and securing genome integrity in view of developing biotechnological ways of improving thermotolerance in crop species under global climate changes, a worldwide ecological concern in agriculture.

Short term UV-B radiation mediated modulation of physiological traits and withanolides production in Withania coagulans (L.) Dunal under in-vitro condition

Accumulation of secondary metabolites is a key process in the growth and development of plants under different biotic/abiotic constraints. Many studies highlighted the regulatory potential of UV-B treatment towards the secondary metabolism of plants. In the present study, we examined the impact of UV-B on the physiology and secondary metabolism of Withania coagulans, which is an important ayurvedic plant with high anti-diabetic potential. Results showed that in-vitro UV-B exposure negatively influenced chlorophyll content and photosynthetic machinery. However, Fv/Fm ratio was found non-significantly altered up to 3 h UV-B exposure. The maximum lipid peroxidation level was recorded with 46.8% higher malondialdehyde content in the plants supplemented with 5 h UV-B radiation, that was indicated the oxidative stress in W. coagulans. Conversely, UV-B treatment significantly increased the plant's stress protective compounds like carotenoids, anthocyanin, phenol and proline, in W. coagulans. Free radical scavenging activity was also significantly increased ~ 18% than the control with 3 h UV-B treatment. The maximum antioxidative enzymes activities were observed with the short-term (up to 3 h) UV-B treatment. Specifically, UV-B radiation exposure significantly increased the content of withaferin A and withanolide A in W. coagulans with maximum 1.38 and 3.42-folds, respectively. Additionally, withanolides biosynthesis related genes transcript levels were found over-expressed under the response of UV-B elicitation. The acquired results suggested that short-term UV-B supplementation triggers secondary metabolism along with combating oxidative stress via improving the antioxidative defense system in W. coagulans. Also, UV-B can be used as an efficient abiotic elicitor to increase pharmaceutical compounds (withanolides) production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01046-7.

Perception and Signaling of Ultraviolet-B Radiation in Plants

Ultraviolet-B (UV-B) radiation is an intrinsic fraction of sunlight that plants perceive through the UVR8 photoreceptor. UVR8 is a homodimer in its ground state that monomerizes upon UV-B photon absorption via distinct tryptophan residues. Monomeric UVR8 competitively binds to the substrate binding site of COP1, thus inhibiting its E3 ubiquitin ligase activity against target proteins, which include transcriptional regulators such as HY5. The UVR8-COP1 interaction also leads to the destabilization of PIF bHLH factor family members. Additionally, UVR8 directly interacts with and inhibits the DNA binding of a different set of transcription factors. Each of these UVR8 signaling mechanisms initiates nuclear gene expression changes leading to UV-B-induced photomorphogenesis and acclimation. The two WD40-repeat proteins RUP1 and RUP2 provide negative feedback regulation and inactivate UVR8 by facilitating redimerization. Here, we review the molecular mechanisms of the UVR8 pathway from UV-B perception and signal transduction to gene expression changes and physiological UV-B responses.

Chromatin dynamics during DNA damage and repair in plants: new roles for old players

The genome of plants is organized into chromatin. The chromatin structure regulates the rates of DNA metabolic processes such as replication, transcription, DNA recombination, and repair. Different aspects of plant growth and development are regulated by changes in chromatin status by the action of chromatin-remodeling activities. Recent data have also shown that many of these chromatin-associated proteins participate in different aspects of the DNA damage response, regulating DNA damage and repair, cell cycle progression, programmed cell death, and entry into the endocycle. In this review, we present different examples of proteins and chromatin-modifying enzymes with roles during DNA damage responses, demonstrating that rapid changes in chromatin structure are essential to maintain genome stability.

The complexity of PRC2 catalysts CLF and SWN in plants

Polycomb repressive complex 2 (PRC2) is an evolutionally conserved multisubunit complex essential for the development of eukaryotes. In Arabidopsis thaliana (Arabidopsis), CURLY LEAF (CLF) and SWINGER (SWN) are PRC2 catalytic subunits that repress gene expression through trimethylating histone H3 at lysine 27 (H3K27me3). CLF and SWN function to safeguard the appropriate expression of key developmental regulators throughout the plant life cycle. Recent researches have advanced our knowledge of the biological roles and the regulation of the activity of CLF and SWN. In this review, we summarize these recent findings and highlight the redundant and differential roles of CLF and SWN in plant development. Further, we discuss the molecular mechanisms underlying CLF and SWN recruitment to specific genomic loci, as well as their interplays with Trithorax-group (TrxG) proteins in plants.

Brassica rapa orphan genes largely affect soluble sugar metabolism

Orphan genes (OGs), which are genes unique to a specific taxon, play a vital role in primary metabolism. However, little is known about the functional significance of Brassica rapa OGs (BrOGs) that were identified in our previous study. To study their biological functions, we developed a BrOG overexpression (BrOGOE) mutant library of 43 genes in Arabidopsis thaliana and assessed the phenotypic variation of the plants. We found that 19 of the 43 BrOGOE mutants displayed a mutant phenotype and 42 showed a variable soluble sugar content. One mutant, BrOG1OE, with significantly elevated fructose, glucose, and total sugar contents but a reduced sucrose content, was selected for in-depth analysis. BrOG1OE showed reduced expression and activity of the Arabidopsis sucrose synthase gene (AtSUS); however, the activity of invertase was unchanged. In contrast, silencing of two copies of BrOG1 in B. rapa, BraA08002322 (BrOG1A) and BraSca000221 (BrOG1B), by the use of an efficient CRISPR/Cas9 system of Chinese cabbage (B. rapa ssp. campestris) resulted in decreased fructose, glucose, and total soluble sugar contents because of the upregulation of BrSUS1b, BrSUS3, and, specifically, the BrSUS5 gene in the edited BrOG1 transgenic line. In addition, we observed increased sucrose content and SUS activity in the BrOG1 mutants, with the activity of invertase remaining unchanged. Thus, BrOG1 probably affected soluble sugar metabolism in a SUS-dependent manner. This is the first report investigating the function of BrOGs with respect to soluble sugar metabolism and reinforced the idea that OGs are a valuable resource for nutrient metabolism.

Let it bloom: cross-talk between light and flowering signaling in Arabidopsis

The terrestrial environment is complex, with many parameters fluctuating on daily and seasonal basis. Plants, in particular, have developed complex sensory and signaling networks to extract and integrate information about their surroundings in order to maximize their fitness and mitigate some of the detrimental effects of their sessile lifestyles. Light and temperature each provide crucial insights on the surrounding environment and, in combination, allow plants to appropriately develop, grow and adapt. Cross-talk between light and temperature signaling cascades allows plants to time key developmental decisions to ensure they are 'in sync' with their environment. In this review, we discuss the major players that regulate light and temperature signaling, and the cross-talk between them, in reference to a crucial developmental decision faced by plants: to bloom or not to bloom?

Quantitative Proteomic Analyses Identify STO/BBX24 -Related Proteins Induced by UV-B

Plants use solar radiation for photosynthesis and are inevitably exposed to UV-B. To adapt to UV-B radiation, plants have evolved a sophisticated strategy, but the mechanism is not well understood. We have previously reported that STO (salt tolerance)/BBX24 is a negative regulator of UV-B-induced photomorphogenesis. However, there is limited knowledge of the regulatory network of STO in UV-B signaling. Here, we report the identification of proteins differentially expressed in the wild type (WT) and sto mutant after UV-B radiation by iTRAQ (isobaric tags for relative and absolute quantitation)-based proteomic analysis to explore differential proteins that depend on STO and UV-B signaling. A total of 8212 proteins were successfully identified, 221 of them were STO-dependent proteins in UV-B irradiated plants. The abundances of STO-dependent PSB and LHC (light-harvesting complex) proteins in sto mutants decreased under UV-B radiation, suggesting that STO is necessary to maintain the normal accumulation of photosynthetic system complex under UV-B radiation to facilitate photosynthesis photon capture. The abundance of phenylalanine lyase-1 (PAL1), chalcone synthetase (CHS), and flavonoid synthetase (FLS) increased significantly after UV-B irradiation, suggesting that the accumulation of flavonoids do not require STO, but UV-B is needed. Under UV-B radiation, STO stabilizes the structure of antenna protein complex by maintaining the accumulation of PSBs and LHCs, thereby enhancing the non-photochemical quenching (NPQ) ability, releasing extra energy, protecting photosynthesis, and ultimately promoting the elongation of hypocotyl. The accumulation of flavonoid synthesis key proteins is independent of STO under UV-B radiation. Overall, our results provide a comprehensive regulatory network of STO in UV-B signaling.

Histone tales: lysine methylation, a protagonist in Arabidopsis development

Histone methylation plays a fundamental role in the epigenetic regulation of gene expression driven by developmental and environmental cues in plants, including Arabidopsis. Histone methyltransferases and demethylases act as 'writers' and 'erasers' of methylation at lysine and/or arginine residues of core histones, respectively. A third group of proteins, the 'readers', recognize and interpret the methylation marks. Emerging evidence confirms the crucial roles of histone methylation in multiple biological processes throughout the plant life cycle. In this review, we summarize the regulatory mechanisms of lysine methylation, especially at histone H3 tails, and focus on the recent advances regarding the roles of lysine methylation in Arabidopsis development, from seed performance to reproductive development, and in callus formation.

CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants

CURLY LEAF (CLF) encodes the methyltransferase subunit of the Polycomb Repressor Complex 2 (PRC2), which regulates the expression of target genes through H3K27 trimethylation. We isolated a new CLF mutant allele (clf-78) using a genetic screen designed to identify microRNA (miRNA) deficient mutants. CLF mutant plants showed impaired miRNA activity caused by increased ubiquitination and enhanced degradation of ARGONAUTE 1 (AGO1) in specific tissues. Such CLF-mediated AGO1 regulation was evident when plants were exposed to UV radiation, which caused increased susceptibility of clf mutants to some UV-induced responses. Furthermore, we showed that CLF directly regulates FBW2, which in turn triggers AGO1 degradation in the clf mutants. Interestingly, AGO1 bound to a target appeared particularly prone to degradation in the mutant plants, a process that was exacerbated when the complex bound a non-cleavable target. Thus, prolonged AGO1-target interaction seems to favor AGO1 degradation, suggesting that non-cleavable miRNA targets may overcome translation inhibition by modulating AGO1 stability in plants.

Flowering-mediated root-fungus symbiosis loss is related to jasmonate-dependent root soluble sugar deprivation

The role of flowering in root-fungal symbiosis is not well understood. Because flowering and fungal symbionts are supported by carbohydrates, we hypothesized that flowering modulates root-beneficial fungal associations through alterations in carbohydrate metabolism and transport. We monitored fungal colonization and soluble sugars in the roots of Arabidopsis thaliana following inoculation with a mutualistic fungus Phomopsis liquidambari across different plant developmental stages. Jasmonate signalling of wild-type plants, sugar transport, and root invertase of wild-type and jasmonate-insensitive plants were exploited to assess whether and how jasmonate-dependent sugar dynamics are involved in flowering-mediated fungal colonization alterations. We found that flowering restricts root-fungal colonization and activates root jasmonate signalling upon fungal inoculation. Jasmonates reduce the constitutive and fungus-induced accumulation of root glucose and fructose at the flowering stage. Further experiments with sugar transport and metabolism mutant lines revealed that root glucose and fructose positively influence fungal colonization. Diurnal, jasmonate-dependent inhibitions of sugar transport and soluble invertase activity were identified as likely mechanisms for flowering-mediated root sugar depletion upon fungal inoculation. Collectively, our results reveal that flowering drives root-fungus cooperation loss, which is related to jasmonate-dependent root soluble sugar depletion. Limiting the spread of root-fungal colonization may direct more resources to flower development.

New Insights into the Molecular Mechanism Underlying Seed Size Control under Drought Stress

In higher plants, seed size is an important parameter and agricultural trait in many aspects of evolutionary fitness. The loss of water-deficiency-induced crop yield is the largest among all natural hazards. Under water-deficient stress, the most prevalent response to terminal stress is to accelerate the early arrest of floral development and, thereby, to accelerate fruit/seed production, which consequently reduces seed size. This phenomenon is well-known, but its molecular mechanism is not well-reviewed and characterized. However, increasing evidence have indicated that water-deficient stress is always coordinated with three genetic signals (i.e., seed size regulators, initial seed size, and fruit number) that decide the final seed size. Here, our review presents new insights into the mechanism underlying cross-talk water-deficient stress signaling with three genetic signals controlling final seed size. These new insights may aid in preliminary screening, identifying novel genetic factors and future design strategies, or breeding to increase crop yield.

A perspective on ecologically relevant plant-UV research and its practical application

Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.

The influence of spectral composition on spring and autumn phenology in trees

Several recent reviews highlight the molecular mechanisms that underpin phenological responses to temperature and photoperiod; however, these have mostly overlooked the influence of solar radiation and its spectral composition on these processes. For instance, solar radiation in the blue and ultraviolet (UV) regions of the spectrum, as well as the red/far-red (R:FR) ratio, can influence spring and autumn phenology. Solar radiation reaching the Earth changes diurnally and seasonally; however, rising global temperatures, latitudinal range shifts and light pollution are likely to produce novel combinations of phenological cues for tree species. Here, we review the literature on phenological responses to spectral composition. Our objective was to explore the natural variation in spectral composition using radiative transfer models and to reveal any species-specific or ecotype-specific responses relating to latitudinal origin. These responses are likely to be most pronounced at high latitudes where spectral composition varies most throughout the year. For instance, trees from high latitudes tend to be more sensitive to changes in R:FR than those from low latitudes. The effects of blue light and UV radiation on phenology have not been studied as much as those of R:FR, but the limited results available suggest both could be candidate cues affecting autumn leaf colouration and senescence. Failure of more-southern species and ecotypes to adapt and use spectral cues during northwards range shifts could result in mistimed phenology, potentially resulting in frost damage, reduced fitness and limited range expansion. Future areas for research should look to establish how consistently different functional types of tree respond to spectral cues and identify photoreceptor-mediated mechanisms that allow plants to combine information from multiple light cues to coordinate the timing of phenological events. It should then be feasible to consider the synchronous or sequential action of light cues within a hierarchy of environmental factors regulating phenology.

Exploring miRNAs for developing climate-resilient crops: A perspective review

Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.

Beyond Arabidopsis: Differential UV-B Response Mediated by UVR8 in Diverse Species

Ultraviolet-B radiation (UV-B, 280-315 nm) is an important environmental signal that regulates growth and development in plants. Two dose-dependent UV-B response pathways were described in plants: a specific one, mediated by UVR8 (the specific UV-B receptor) and an unspecific one, activated by the oxidative damage produced by radiation. The constitutively expressed receptor appears inactive as a dimer, with the two monomers dissociating upon UV-B irradiation. The monomer then interacts with COP1, an ubiquitin ligase, hindering its ability to poly-ubiquitinate transcriptional factor HY5, thus averting its degradation and activating the photomorphogenic response. HY5 induces the synthesis of proteins RUP1 and RUP2, which interact with UVR8, releasing COP1, and inducing the re-dimerization of UVR8. This mechanism has been thoroughly characterized in Arabidopsis, where studies have demonstrated that the UVR8 receptor is key in UV-B response. Although Arabidopsis importance as a model plant many mechanisms described in this specie differ in other plants. In this paper, we review the latest information regarding UV-B response mediated by UVR8 in different species, focusing on the differences reported compared to Arabidopsis. For instance, UVR8 is not only induced by UV-B but also by other agents that are expressed differentially in diverse tissues. Also, in some of the species analyzed, proteins with low homology to RUP1 and RUP2 were detected. We also discuss how UVR8 is involved in other developmental and stress processes unrelated to UV-B. We conclude that the receptor is highly versatile, showing differences among species.

Arabidopsis RUP2 represses UVR8-mediated flowering in noninductive photoperiods

Arongaus et al. show that genetic mutation of REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) renders the facultative long day plant Arabidopsis thaliana a day-neutral plant (specifically under light conditions that include UV-B radiation) and dependent on the UV RESISTANCE LOCUS 8 (UVR8) UV-B photoreceptor.

Plants have evolved complex photoreceptor-controlled mechanisms to sense and respond to seasonal changes in day length. This ability allows plants to optimally time the transition from vegetative growth to flowering. UV-B is an important part intrinsic to sunlight; however, whether and how it affects photoperiodic flowering has remained elusive. Here, we report that, in the presence of UV-B, genetic mutation of REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) renders the facultative long day plant Arabidopsis thaliana a day-neutral plant and that this phenotype is dependent on the UV RESISTANCE LOCUS 8 (UVR8) UV-B photoreceptor. We provide evidence that the floral repression activity of RUP2 involves direct interaction with CONSTANS, repression of this key activator of flowering, and suppression of FLOWERING LOCUS T transcription. RUP2 therefore functions as an essential repressor of UVR8-mediated induction of flowering under noninductive short day conditions and thus provides a crucial mechanism of photoperiodic flowering control.

Epigenetic Regulation of Juvenile-to-Adult Transition in Plants

Epigenetic regulation is referred to as changes in gene function that do not involve changes in the DNA sequence, it is usually accomplished by DNA methylation, histone modifications (repressive marks such as H3K9me, H3K27me, H2Aub, or active marks such as H3K4me, H3K36me, H3Ac), and chromatin remodeling (nucleosome composition, occupancy, and location). In plants, the shoot apex produces different lateral organs during development to give rise to distinguishable phases of a juvenile, an adult and a reproductive phase after embryogenesis. The juvenile-to-adult transition is a key developmental event in plant life cycle, and it is regulated by a decrease in the expression of a conserved microRNA-miR156/157, and a corresponding increase in the expression of its target genes encoding a set of plant specific SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) proteins. Recent work has revealed that the miR156/157-SPL pathway is the master regulator of juvenile-to-adult transition in plants, and genes in this pathway are subjected to epigenetic regulation, such as DNA methylation, histone modifications, and chromatin remodeling. In this review, we summarized the recent progress in understanding the epigenetic regulation of the miR156/157-SPL pathway during juvenile-to-adult transition and bring forward some perspectives of future research in this field.