Enzymatic, but not non-enzymatic, 1O2-mediated peroxidation of polyunsaturated fatty acids forms part of the EXECUTER1-dependent stress response program in the flu mutant of Arabidopsis thaliana

Plastidial metabolites and retrograde signaling: A case study of MEP pathway intermediate MEcPP that orchestrates plant growth and stress responses

Plants are frequently exposed to environmental stresses. In a plant cell, chloroplast acts as machinery that rapidly senses changing environmental conditions and coordinates with the nucleus and other subcellular organelles by exchanging plastidial metabolites, proteins/peptides, or lipid derivatives, some of which may act as retrograde signals. These specific plastidial metabolites include carotenoid derivatives, isoprenes, phosphoadenosines, tetrapyrroles, phytohormone (like salicylic acid), and reactive electrophile species (RES), which mediate retrograde communications to sustain stress conditions. The methylerythritol phosphate (MEP) pathway is an essential and evolutionarily conserved isoprenoid biosynthetic pathway operating in bacteria and plastids, synthesizing metabolites such as terpenoids, gibberellins, abscisic acid, phytol chain of chlorophyll, carotenoids, tocopherols, and glycosides. The MEP pathway is susceptible to oxidative stress, which results in the overaccumulation of its intermediates, such as methylerythritol cyclodiphosphate (MEcPP). Recent studies revealed that under stress conditions, leading to its accumulation, MEcPP mediates retrograde signaling that alters the nuclear gene expression, leading to growth inhibition and acclimation. This review covers aspects of its generation, signaling, mechanism of action, and interplay with other factors to acquire adaptive responses during stress conditions. The review highlights the importance of plastids as sensors of stress and plastidial metabolites as retrograde signals communicating with nucleus and other sub-cellular organelles to regulate plants' response to different stress conditions.

Low-temperature-induced singlet oxygen adaptation decreases susceptibility to the mycotoxin TeA in invasive plant Ageratina adenophora

The mycotoxin tenuazonic acid (TeA) inhibits photosynthesis and is expected to be developed as a bioherbicide to control Ageratina adenophora that is one of the most serious invasive alien plants in China. New leaves sprouting from A. adenophora at low temperatures (LT) in early spring are less sensitive to TeA compared to those growing in summer. However, the molecular mechanism of LT-caused decrease in the susceptibility of A. adenophora to TeA is unclear. In this study, three singlet oxygen-responsive genes (SORGs) and three jasmonic acid responsive genes (JARGs) were cloned to further probe the role of singlet oxygen (1O2) signaling during TeA-induced disease development in A. adenophora leaves exposed to LT. TeA triggered chloroplast-derived 1O2 production as a result of photosystem II (PSII) photoinhibition during leaf lesion formation in A. adenophora. Moreover, TeA indeed induced the expression of SORGs and JARGs as well as a high level of JA generation, activating the 1O2 signaling pathway in A. adenophora. LT (12°C) pretreatment can cause PSII photoinhibition and increase the SORG AaAAA-ATPase expression level in A. adenophora leaves, meaning that 1O2 signaling was activated by LT. Thus TeA led to less increase of the SORGs and JARGs expression and JA level in plants pretreated by LT compared with non-pretreated plants, although both of them had the same level of 1O2 production after TeA treatment. It was concluded that the low susceptibility to TeA of A. adenophora subjected to LT can be attributed to the occurrence of 1O2 acclimation.

Understanding the photosynthesis in relation to climate change in grapevines

Due to predicted global climate change, there have been significant alterations in agricultural production patterns, which had a negative impact on ecosystems as well as the commercial and export prospects for the production of grapevines. The natural biochemistry of grapevines, including their chlorophyll content, net photosynthetic rate, Fv/Fm ratio, photorespiration, reduced yield, and quality is also anticipated to be negatively impacted by the various effects of light, temperature, and carbon dioxide at elevated scales. Grapevine phenology, physiology, and quality are impacted by the inactivation of photosystems (I and II), the Rubisco enzyme system, pigments, chloroplast integrity, and light intensity by temperature and increasing CO2 levels. Grape phenological events are considerably altered by climatic conditions; in particular, berries mature earlier, increasing the sugar-to-acid ratio. In enology, the sugar-to-acid ratio is crucial since it determines the wine's final alcohol concentration and flavour. As light intensity and CO2 levels rise, the biosynthesis of anthocyanins and tannins declines. As the temperature rises, the production of antioxidants diminishes, affecting the quality of raisins. Table grapes are more sensitive to temperature because of physiological problems like pink berries and a higher sugar-to-acidity ratio. Therefore, the systemic impact of light intensity, temperature, and increasing CO2 levels on grapevine physiology, phenology, photosystems, photosynthesis enzyme system, and adaptive strategies for grape producers and researchers are highlighted in this article.

The interplay of singlet oxygen and ABI4 in plant growth regulation

Abscisic acid (ABA) and the AP2/ERF (APETALA 2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor ABA INSENSITIVE 4 (ABI4) control plant growth and development. We review how singlet oxygen, which is produced in chloroplasts of the fluorescent mutant of Arabidopsis thaliana (arabidopsis), and ABI4 may cooperate in transcriptional and translational reprogramming to cause plants to halt growth or demise. Key elements of singlet oxygen- and ABI4-dependent chloroplast-to-nucleus retrograde signaling involve the chloroplast EXECUTER (EX) 1 and EX2 proteins as well as nuclear WRKY transcription factors. Mutants designed to study singlet oxygen signaling, that lack either ABI4 or the EX1 and EX2 proteins, do not show most of the growth effects of singlet oxygen. We propose a model that positions ABI4 downstream of WRKY transcription factors and EX1 and EX2.

The Octadecanoids: Synthesis and Bioactivity of 18-Carbon Oxygenated Fatty Acids in Mammals, Bacteria, and Fungi

The octadecanoids are a broad class of lipids consisting of the oxygenated products of 18-carbon fatty acids. Originally referring to production of the phytohormone jasmonic acid, the octadecanoid pathway has been expanded to include products of all 18-carbon fatty acids. Octadecanoids are formed biosynthetically in mammals via cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) activity, as well as nonenzymatically by photo- and autoxidation mechanisms. While octadecanoids are well-known mediators in plants, their role in the regulation of mammalian biological processes has been generally neglected. However, there have been significant advancements in recognizing the importance of these compounds in mammals and their involvement in the mediation of inflammation, nociception, and cell proliferation, as well as in immuno- and tissue modulation, coagulation processes, hormone regulation, and skin barrier formation. More recently, the gut microbiome has been shown to be a significant source of octadecanoid biosynthesis, providing additional biosynthetic routes including hydratase activity (e.g., CLA-HY, FA-HY1, FA-HY2). In this review, we summarize the current field of octadecanoids, propose standardized nomenclature, provide details of octadecanoid preparation and measurement, summarize the phase-I metabolic pathway of octadecanoid formation in mammals, bacteria, and fungi, and describe their biological activity in relation to mammalian pathophysiology as well as their potential use as biomarkers of health and disease.

Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4

Background

In response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen (1O2), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates 1O2 and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating 1O2 signals for chloroplast turnover and cellular degradation. Thus, the fc2 and fc2 pub4 mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of 1O2 in promoting cellular degradation in fc2 mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of 1O2 production) is poorly understood.

Results

To gain mechanistic insights into 1O2 signaling pathways, we compared transcriptomes of adult wt, fc2, and fc2 pub4 plants. The accumulation of 1O2 in fc2 plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in 1O2-stressed fc2 plants. pub4 reversed most of this 1O2-induced gene expression and reduced the JA content in fc2 plants. The pub4 mutation also blocked JA-induced senescence pathways in the dark. However, fc2 pub4 plants maintained constitutively elevated levels of SA even in the absence of bulk 1O2 accumulation.

Conclusions

Together, this work demonstrates that in fc2 plants, 1O2 leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that 1O2-induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect of pub4 on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.

Photosynthetic ROS and retrograde signaling pathways

Sessile plants harness mitochondria and chloroplasts to sense and adapt to diverse environmental stimuli. These complex processes involve the generation of pivotal signaling molecules, including reactive oxygen species (ROS), phytohormones, volatiles, and diverse metabolites. Furthermore, the specific modulation of chloroplast proteins, through activation or deactivation, significantly enhances the plant's capacity to engage with its dynamic surroundings. While existing reviews have extensively covered the role of plastidial retrograde modules in developmental and light signaling, our focus lies in investigating how chloroplasts leverage photosynthetic ROS to navigate environmental fluctuations and counteract oxidative stress, thereby sustaining primary metabolism. Unraveling the nuanced interplay between photosynthetic ROS and plant stress responses holds promise for uncovering new insights that could reinforce stress resistance and optimize net photosynthesis rates. This exploration aspires to pave the way for innovative strategies to enhance plant resilience and agricultural productivity amidst changing environmental conditions.

Plant competition cues activate a singlet oxygen signaling pathway in Arabidopsis thaliana

Oxidative stress responses of Arabidopsis to reflected low red to far-red signals (R:FR ≈ 0.3) generated by neighboring weeds or an artificial source of FR light were compared with a weed-free control (R:FR ≈1.6). In the low R:FR treatments, induction of the shade avoidance responses (SAR) coincided with increased leaf production of singlet oxygen (1O2). This 1O2 increase was not due to protochlorophyllide accumulation and did not cause cell death. Chemical treatments, however, with 5-aminolevulinic acid (the precursor of tetrapyrrole biosynthesis) and glutathione (a quinone A reductant) enhanced cell death and growth inhibition. RNA sequencing revealed that transcriptome responses to the reflected low R:FR light treatments minimally resembled previously known Arabidopsis 1O2 generating systems that rapidly generate 1O2 following a dark to light transfer. The upregulation of only a few early 1O2 responsive genes (6 out of 1931) in the reflected low R:FR treatments suggested specificity of the 1O2 signaling. Moreover, increased expression of two enzyme genes, the SULFOTRANSFERASE ST2A (ST2a) and the early 1O2-responsive IAA-LEUCINE RESISTANCE (ILR)-LIKE6 (ILL6), which negatively regulate jasmonate level, suggested that repression of bioactive JAs may promote the shade avoidance (versus defense) and 1O2 acclimation (versus cell death) responses to neighboring weeds.

NAD+ deficiency primes defense metabolism via 1O2-escalated jasmonate biosynthesis in plants

Nicotinamide adenine dinucleotide (NAD+) is a redox cofactor and signal central to cell metabolisms. Disrupting NAD homeostasis in plant alters growth and stress resistance, yet the underlying mechanisms remain largely unknown. Here, by combining genetics with multi-omics, we discover that NAD+ deficiency in qs-2 caused by mutation in NAD+ biosynthesis gene-Quinolinate Synthase retards growth but induces biosynthesis of defense compounds, notably aliphatic glucosinolates that confer insect resistance. The elevated defense in qs-2 is resulted from activated jasmonate biosynthesis, critically hydroperoxidation of α-linolenic acid by the 13-lipoxygenase (namely LOX2), which is escalated via the burst of chloroplastic ROS-singlet oxygen (1O2). The NAD+ deficiency-mediated JA induction and defense priming sequence in plants is recapitulated upon insect infestation, suggesting such defense mechanism operates in plant stress response. Hence, NAD homeostasis is a pivotal metabolic checkpoint that may be manipulated to navigate plant growth and defense metabolism for stress acclimation.

Novel Types of Phyllobilins in a Fern - Molecular Reporters of the Evolution of Chlorophyll Breakdown in the Paleozoic Era

Breakdown of chlorophyll (Chl), as studied in angiosperms, follows the pheophorbide a oxygenase/phyllobilin (PaO/PB) pathway, furnishing linear tetrapyrroles, named phyllobilins (PBs). In an investigation with fern leaves we have discovered iso-phyllobilanones (iPBs) with an intriguingly rearranged and oxidized carbon skeleton. We report here a key second group of iPBs from the fern and on their structure analysis. Previously, these additional Chl-catabolites escaped their characterization, since they exist in aqueous media as mixtures of equilibrating isomers. However, their chemical dehydration furnished stable iPB-derivatives that allowed the delineation of the enigmatic structures and chemistry of the original natural catabolites. The structures of all fern-iPBs reflect the early core steps of a PaO/PB-type pathway and the PB-to-iPB carbon skeleton rearrangement. A striking further degradative chemical ring-cleavage was observed, proposed to consume singlet molecular oxygen (1O2). Hence, Chl-catabolites may play a novel active role in detoxifying cellular 1O2. The critical deviations from the PaO/PB pathway, found in the fern, reflect evolutionary developments of Chl-breakdown in the green plants in the Paleozoic era.

Singlet oxygen signalling and its potential roles in plant biotic interactions

Singlet oxygen (SO) is among the most potent reactive oxygen species, and readily oxidizes proteins, lipids and DNA. It can be generated at the plant surface by phototoxins in the epidermis, acting as a direct defense against pathogens and herbivores (including humans). SO can also accumulate within mitochondria, peroxisomes, cytosol and the nucleus through multiple enzymatic and nonenzymatic processes. However, the majority of research on intracellular SO generation in plants has focused on transfer of light energy to triplet oxygen by photopigments from the chloroplast. SO accumulates in response to diverse stresses that perturb chloroplast metabolism, and while its high reactivity limits diffusion distances, it participates in retrograde signalling through the EXECUTER1 sensor, generation of carotenoid metabolites and possibly other unknown pathways. SO thereby reprogrammes nuclear gene expression and modulates hormone signalling and programmed cell death. While SO signalling has long been known to regulate plant responses to high-light stress, recent literature also suggests a role in plant interactions with insects, bacteria and fungi. The goals of this review are to provide a brief overview of SO, summarize evidence for its involvement in biotic stress responses and discuss future directions for the study of SO in defense signalling.

Alternaria TeA toxin activates a chloroplast retrograde signaling pathway to facilitate JA-dependent pathogenicity

The chloroplast is a critical battleground in the arms race between plants and pathogens. Among microbe-secreted mycotoxins, tenuazonic acid (TeA), produced by the genus Alternaria and other phytopathogenic fungi, inhibits photosynthesis, leading to a burst of photosynthetic singlet oxygen (1O2) that is implicated in damage and chloroplast-to-nucleus retrograde signaling. Despite the significant crop damage caused by Alternaria pathogens, our understanding of the molecular mechanism by which TeA promotes pathogenicity and cognate plant defense responses remains fragmentary. We now reveal that A. alternata induces necrotrophic foliar lesions by harnessing EXECUTER1 (EX1)/EX2-mediated chloroplast-to-nucleus retrograde signaling activated by TeA toxin-derived photosynthetic 1O2 in Arabidopsis thaliana. Mutation of the 1O2-sensitive EX1-W643 residue or complete deletion of the EX1 singlet oxygen sensor domain compromises expression of 1O2-responsive nuclear genes and foliar lesions. We also found that TeA toxin rapidly induces nuclear genes implicated in jasmonic acid (JA) synthesis and signaling, and EX1-mediated retrograde signaling appears to be critical for establishing a signaling cascade from 1O2 to JA. The present study sheds new light on the foliar pathogenicity of A. alternata, during which EX1-dependent 1O2 signaling induces JA-dependent foliar cell death.

A genetic screen for dominant chloroplast reactive oxygen species signaling mutants reveals life stage-specific singlet oxygen signaling networks

Introduction

Plants employ intricate molecular mechanisms to respond to abiotic stresses, which often lead to the accumulation of reactive oxygen species (ROS) within organelles such as chloroplasts. Such ROS can produce stress signals that regulate cellular response mechanisms. One ROS, singlet oxygen (1O2), is predominantly produced in the chloroplast during photosynthesis and can trigger chloroplast degradation, programmed cell death (PCD), and retrograde (organelle-to-nucleus) signaling. However, little is known about the molecular mechanisms involved in these signaling pathways or how many different signaling 1O2 pathways may exist.

Methods

The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates chloroplast 1O2, making fc2 a valuable genetic system for studying chloroplast 1O2-initiated signaling. Here, we have used activation tagging in a new forward genetic screen to identify eight dominant fc2 activation-tagged (fas) mutations that suppress chloroplast 1O2-initiated PCD.

Results

While 1O2-triggered PCD is blocked in all fc2 fas mutants in the adult stage, such cellular degradation in the seedling stage is blocked in only two mutants. This differential blocking of PCD suggests that life-stage-specific 1O2-response pathways exist. In addition to PCD, fas mutations generally reduce 1O2-induced retrograde signals. Furthermore, fas mutants have enhanced tolerance to excess light, a natural mechanism to produce chloroplast 1O2. However, general abiotic stress tolerance was only observed in one fc2 fas mutant (fc2 fas2). Together, this suggests that plants can employ general stress tolerance mechanisms to overcome 1O2 production but that this screen was mostly specific to 1O2 signaling. We also observed that salicylic acid (SA) and jasmonate (JA) stress hormone response marker genes were induced in 1O2-stressed fc2 and generally reduced by fas mutations, suggesting that SA and JA signaling is correlated with active 1O2 signaling and PCD.

Discussion

Together, this work highlights the complexity of 1O2 signaling by demonstrating that multiple pathways may exist and introduces a suite of new 1O2 signaling mutants to investigate the mechanisms controlling chloroplast-initiated degradation, PCD, and retrograde signaling.

PSI Photoinhibition and Changing CO2 Levels Initiate Retrograde Signals to Modify Nuclear Gene Expression

Photosystem I (PSI) is a critical component of the photosynthetic machinery in plants. Under conditions of environmental stress, PSI becomes photoinhibited, leading to a redox imbalance in the chloroplast. PSI photoinhibition is caused by an increase in electron pressure within PSI, which damages the iron-sulfur clusters. In this study, we investigated the susceptibility of PSI to photoinhibition in plants at different concentrations of CO2, followed by global gene expression analyses of the differentially treated plants. PSI photoinhibition was induced using a specific illumination protocol that inhibited PSI with minimal effects on PSII. Unexpectedly, the varying CO2 levels combined with the PSI-PI treatment neither increased nor decreased the likelihood of PSI photodamage. All PSI photoinhibition treatments, independent of CO2 levels, upregulated genes generally involved in plant responses to excess iron and downregulated genes involved in iron deficiency. PSI photoinhibition also induced genes encoding photosynthetic proteins that act as electron acceptors from PSI. We propose that PSI photoinhibition causes a release of iron from damaged iron-sulfur clusters, which initiates a retrograde signal from the chloroplast to the nucleus to modify gene expression. In addition, the deprivation of CO2 from the air initiated a signal that induced flavonoid biosynthesis genes, probably via jasmonate production.

Endocytosis-mediated entry of a caterpillar effector into plants is countered by Jasmonate

Insects and pathogens release effectors into plant cells to weaken the host defense or immune response. While the imports of some bacterial and fungal effectors into plants have been previously characterized, the mechanisms of how caterpillar effectors enter plant cells remain a mystery. Using live cell imaging and real-time protein tracking, we show that HARP1, an effector from the oral secretions of cotton bollworm (Helicoverpa armigera), enters plant cells via protein-mediated endocytosis. The entry of HARP1 into a plant cell depends on its interaction with vesicle trafficking components including CTL1, PATL2, and TET8. The plant defense hormone jasmonate (JA) restricts HARP1 import by inhibiting endocytosis and HARP1 loading into endosomes. Combined with the previous report that HARP1 inhibits JA signaling output in host plants, it unveils that the effector and JA establish a defense and counter-defense loop reflecting the robust arms race between plants and insects.

Salicylate and jasmonate intertwine in ROS-triggered chloroplast-to-nucleus retrograde signaling

Plants, being sessile, are frequently exposed to environmental perturbations, affecting their sustenance and survival. In response, distinct inherent mechanisms emerged during plant evolution to deal with environmental stresses. Among various organelles, chloroplast plays an indispensable role in plant cells. Besides providing the site for photosynthesis and biosynthesis of many important primary and secondary metabolites, including hormones, chloroplasts also act as environmental sensors. Any environmental perturbation directly influences the photosynthetic electron transport chain, leading to excess accumulation of reactive oxygen species (ROS), causing oxidative damages to biomolecules in the vicinity. To prevent excess ROS accumulation and the consequent oxidative damages, the chloroplast activates retrograde signaling (RS) pathways to reprogramme nuclear gene expression, defining plant's response to stress. Based on levels and site of ROS accumulation, distinct biomolecules are oxidized, generating specific derivatives that act as genuine signaling molecules, triggering specific RS pathways to instigate distinctive responses, including growth inhibition, acclimation, and programmed cell death. Though various RS pathways independently modulate nuclear gene expression, they also implicate the defense hormone salicylic acid (SA) and oxylipins, including 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA), by promoting their biosynthesis and utilizing them for intra- and intercellular communications. Several studies reported the involvement of both hormones in individual RS pathways, but the precise dissection of their activation and participation in a given RS pathway remains an enigma. The present review describes the current understanding of how SA and JA intertwine in ROS-triggered RS pathways. We have also emphasized the future perspectives for elucidating stress specificity and spatiotemporal accumulation of respective hormones in a given RS pathway.

Electrochemical biosensor based on singlet oxygen generated by molecular photosensitizers

Here a sensing strategy with the integration of photosensitizer and electrochemical analysis was present. The photosensitizer, Zinc(II) tetraphenylporphyrin (ZnTCPP), was functionalized graphene oxide (GO) to form complex (ZnTCPP/GO) as the electrode material and generated singlet-oxygen (¹O₂) in the presence of air under light illumination. Due to the special electronic structure of ¹O₂, hydroquinone (HQ) could react with ¹O₂ to produce electrochemically-detectable products, benzoquinone (BQ). Meanwhile, the formed BQ could be reduced on the electrode, completing the redox cycling. The ZnTCPP/GO modified ITO electrode produces a stable and enhanced photocurrent signal under 420 nm irradiation in air-saturated buffer, compared with in N₂-saturated buffer. On the other hand, l-glutathione (GSH) as a signalling molecule plays important role in physiological process, which was employed as model to investigated the sensing performance. Coupling with HQ oxidized by ¹O₂, a GSH sensor was constructed on the basis the redox cycling of HQ. A sensitive reduction of photocurrent is observed with the addition of GSH, due to the GSH could be oxidized by the generated ¹O₂ to form GSSG. The biosensor displayed good performance in a broad concentration range of 0-150 μM, with a lower detection limit of 1.3 μM at an S/N ratio of 3, and could be used in practical application. This work affords a platform for constructing the biosensor with ¹O₂ instead of enzyme via on/off light switching.

Chlamydomonas as a model for reactive oxygen species signaling and thiol redox regulation in the green lineage

One-sentence summary: Advances in proteomic and transcriptomic studies have made Chlamydomonas a powerful research model in redox and reactive oxygen species regulation with unique and overlapping mechanisms with plants.

The threshold between life and death in Cistus albidus L. seedlings: mechanisms underlying drought tolerance and resilience

Drought can lead to important shifts in population dynamics if it occurs during seedling establishment. With the aim of elucidating the underlying mechanisms of drought tolerance and resilience, here we monitored the survival of seedlings of the Mediterranean shrub Cistus albidus L. throughout a year growing in the natural Park of the Montserrat Mountains (Spain) and, additionally, we studied the response to severe drought and subsequent recovery after rewatering of seedlings grown in growth chambers. To find possible mechanisms explaining how seedlings respond to drought, growth and survival together with physiological-related parameters such as chlorophyll contents, vitamin E and stress-related phytohormones were measured. We found that survival decreased by 30% at the end of summer and that the main proxy of seedling survival was total chlorophyll. This proxy was further confirmed in the growth chambers, where we found that seedlings that recovered from drought had higher levels of total chlorophyll compared with the seedlings that did not recover. Furthermore, modulation of vitamin E and jasmonates contents appeared to be crucial in the drought response of C. albidus seedlings. We propose a prediction model of survival that includes total chlorophyll height, leaf mass area and maximum photosystem II efficiency with chlorophyll contents being a good long-term predictor of C. albidus seedling survival under severe stress, which, in turn, could help to better foresee population fluctuations in the field.

Oxylipins From Different Pathways Trigger Mitochondrial Stress Signaling Through Respiratory Complex III

Plant oxylipins are signaling molecules produced from fatty acids by oxidative pathways, mainly initiated by 9- and 13-lipoxygenases (9-LOX and 13-LOX), alpha-dioxygenases or non-enzymatic oxidation. Oxylipins from the 9-LOX pathway induce oxidative stress and control root development and plant defense. These activities have been associated with mitochondrial processes, but precise cellular targets and pathways remain unknown. In order to study oxylipin signaling, we previously generated a collection of Arabidopsis thaliana mutants that were insensitive to the 9-LOX products 9(S)-hydroxy-10,12, 15-octadecatrienoic acid (9-HOT) and its ketone derivative 9-KOT (noxy mutants). Here, we describe noxy1, noxy3, noxy5, noxy23, and noxy54 mutants, all affected in nucleus-encoded mitochondrial proteins, and use them to study the role of mitochondria in oxylipin signaling. Functional and phenotypic analyses showed that noxy plants displayed mitochondrial aggregation, reduced respiration rates and resistance to the complex III inhibitor Antimycin A (AA), thus indicating a close similarity of the oxylipin signaling and mitochondrial stress. Application of 9-HOT and 9-KOT protected plants against subsequent mitochondrial stress, whereas they boosted root growth reduction when applied in combination with complex III inhibitors but did not with inhibitors of other respiratory complexes. A similar effect was caused by linear-chain oxylipins from 13-LOX or non-enzymatic pathways having α,β-unsaturated hydroxyl or keto groups in their structure. Studies to investigate 9-HOT and 9-KOT activity indicated that they do not reduce respiration rates, but their action is primarily associated with enhanced ROS responses. This was supported by the results showing that 9-HOT or 9-KOT combined with AA amplified the expression of oxylipin- and ROS-responding genes but not of the AA marker AOX1a, thus implying the activation of a specific mitochondria retrograde signaling pathway. Our results implicate mitochondrial complex III as a hub in the signaling activity of multiple oxylipin pathways and point at downstream ROS responses as components of oxylipin function.

Cellular oxidative stress in programmed cell death: focusing on chloroplastic 1O2 and mitochondrial cytochrome-c release

The programmed cell death (PCD) occurs when the targeted cells have fulfilled their task or under conditions as oxidative stress generated by ROS species. Thus, plants have to deal with the singlet oxygen ¹O₂ produced in chloroplasts. ¹O₂ is unlikely to act as a primary retrograde signal owing to its high reactivity and short half-life. In addition to its high toxicity, the ¹O₂ generated under an excess or low excitation energy might also act as a highly versatile signal triggering chloroplast-to-nucleus retrograde signaling (ChNRS) and nuclear reprogramming or cell death. Molecular and biochemical studies with the flu mutant, which accumulates protochlorophyllide in the dark, demonstrated that chloroplastic ¹O₂-driven EXECUTER-1 (EX1) and EX2 proteins are involved in the ¹O₂-dependent response. Both EX1 and EX2 are necessary for full suppression of ¹O₂-induced gene expression. That is, EXECUTER proteolysis via the ATP-dependent zinc protease (FtsH) is an integral part of ¹O₂-triggered retrograde signaling. The existence of at least two independent ChNRS involving EX1 and β-cyclocitral, and dihydroactinidiolide and OXI1, respectively, seem clear. Besides, this update also focuses on plant PCD and its relation with mitochondrial cytochrome-c (Cytc) release to cytosol. Changes in the dynamics and morphology of mitochondria were shown during the onset of cell death. The mitochondrial damage and translocation of Cytc may be one of the major causes of PCD triggering. Together, this current overview illustrates the complexity of the cellular response to oxidative stress development. A puzzle with the majority of its pieces still not placed.

Singlet Oxygen and Protochlorophyllide Detection in Arabidopsis thaliana

Since the recognition of the reactive oxygen species singlet oxygen (¹O₂) as a versatile signal that induces various stress responses, the mechanisms underlying ¹O₂-induced signaling transduction pathways have become the subject of much current research. This in turn highlights the need for reliable detection methods for ¹O₂. Here we describe a protocol for the detection of ¹O₂ using a commercially available fluorescent probe (Singlet Oxygen Sensor Green) and provide a simple method for direct visualization and quantification of the ¹O₂-evolving photosensitizer protochlorophyllide in the Arabidopsis fluorescent mutant.

Cell death resulted from loss of fumarylacetoacetate hydrolase in Arabidopsis is related to phytohormone jasmonate but not salicylic acid

Fumarylacetoacetate hydrolase (FAH) catalyzes the final step in Tyr degradation pathway essential to animals but not well understood in plants. Previously, we found that mutation of SSCD1 encoding Arabidopsis FAH causes cell death under short day, which uncovered an important role of Tyr degradation pathway in plants. Since phytohormones salicylic acid (SA) and jasmonate (JA) are involved in programmed cell death, in this study, we investigated whether sscd1 cell death is related to SA and JA, and found that (1) it is accompanied by up-regulation of JA- and SA-inducible genes as well as accumulation of JA but not SA; (2) it is repressed by breakdown of JA signaling but not SA signaling; (3) the up-regulation of reactive oxygen species marker genes in sscd1 is repressed by breakdown of JA signaling; (4) treatment of wild-type Arabidopsis with succinylacetone, an abnormal metabolite caused by loss of FAH, induces expression of JA-inducible genes whereas treatment with JA induces expression of some Tyr degradation genes with dependence of JA signaling. These results demonstrated that cell death resulted from loss of FAH in Arabidopsis is related to JA but not SA, and suggested that JA signaling positively regulates sscd1 cell death by up-regulating Tyr degradation.

Singlet Oxygen in Plants: Generation, Detection, and Signaling Roles

Singlet oxygen (1O2) refers to the lowest excited electronic state of molecular oxygen. It easily oxidizes biological molecules and, therefore, is cytotoxic. In plant cells, 1O2 is formed mostly in the light in thylakoid membranes by reaction centers of photosystem II. In high concentrations, 1O2 destroys membranes, proteins and DNA, inhibits protein synthesis in chloroplasts leading to photoinhibition of photosynthesis, and can result in cell death. However, 1O2 also acts as a signal relaying information from chloroplasts to the nucleus, regulating expression of nuclear genes. In spite of its extremely short lifetime, 1O2 can diffuse from the chloroplasts into the cytoplasm and the apoplast. As shown by recent studies, 1O2-activated signaling pathways depend not only on the levels but also on the sites of 1O2 production in chloroplasts, and can activate two types of responses, either acclimation to high light or programmed cell death. 1O2 can be produced in high amounts also in root cells during drought stress. This review summarizes recent advances in research on mechanisms and sites of 1O2 generation in plants, on 1O2-activated pathways of retrograde- and cellular signaling, and on the methods to study 1O2 production in plants.

The Arabidopsis SAFEGUARD1 suppresses singlet oxygen-induced stress responses by protecting grana margins

Singlet oxygen (¹O₂), the major reactive oxygen species (ROS) produced in chloroplasts, has been demonstrated recently to be a highly versatile signal that induces various stress responses. In the fluorescent (flu) mutant, its release causes seedling lethality and inhibits mature plant growth. However, these drastic phenotypes are suppressed when EXECUTER1 (EX1) is absent in the flu ex1 double mutant. We identified SAFEGUARD1 (SAFE1) in a screen of ethyl methanesulfonate (EMS) mutagenized flu ex1 plants for suppressor mutants with a flu-like phenotype. In flu ex1 safe1, all ¹O₂-induced responses, including transcriptional rewiring of nuclear gene expression, return to levels, such as, or even higher than, those in flu Without SAFE1, grana margins (GMs) of chloroplast thylakoids (Thys) are specifically damaged upon ¹O₂ generation and associate with plastoglobules (PGs). SAFE1 is localized in the chloroplast stroma, and release of ¹O₂ induces SAFE1 degradation via chloroplast-originated vesicles. Our paper demonstrates that flu-produced ¹O₂ triggers an EX1-independent signaling pathway and proves that SAFE1 suppresses this signaling pathway by protecting GMs.

Insights Into Oxidized Lipid Modification in Barley Roots as an Adaptation Mechanism to Salinity Stress

Lipidomics is an emerging technology, which aims at the global characterization and quantification of lipids within biological matrices including biofluids, cells, whole organs and tissues. The changes in individual lipid molecular species in stress treated plant species and different cultivars can indicate the functions of genes affecting lipid metabolism or lipid signaling. Mass spectrometry-based lipid profiling has been used to track the changes of lipid levels and related metabolites in response to salinity stress. We have developed a comprehensive lipidomics platform for the identification and direct qualification and/or quantification of individual lipid species, including oxidized lipids, which enables a more systematic investigation of peroxidation of individual lipid species in barley roots under salinity stress. This new lipidomics approach has improved with an advantage of analyzing the composition of acyl chains at the molecular level, which facilitates to profile precisely the 18:3-containing diacyl-glycerophosphates and allowed individual comparison of lipids across varieties. Our findings revealed a general decrease in most of the galactolipids in plastid membranes, and an increase of glycerophospholipids and acylated steryl glycosides, which indicate that plastidial and extraplastidial membranes in barley roots ubiquitously tend to form a hexagonal II (HII) phase under salinity stress. In addition, salt-tolerant and salt-sensitive cultivars showed contrasting changes in the levels of oxidized membrane lipids. These results support the hypothesis that salt-induced oxidative damage to membrane lipids can be used as an indication of salt stress tolerance in barley.

The xanthophyll cycle as an early pathogenic target to deregulate guard cells during Sclerotinia sclerotiorum infection

Stomata not only control the important balance between gaseous fluxes and water loss, but also act as a route of invading pathogen entry into the plant. Here, the stomatal opening was observed to be induced by a necrotrophic pathogen Sclerotinia sclerotiorum at the early stages of infection. In contrast to uninfected control, the stomatal pores were still opened in S. sclerotiorum-infected regions after dark adaption. Mutation of violaxanthin de-epoxidase, a key enzyme in the xanthophyll cycle, could partially restore the S. sclerotiorum-induced stomatal opening. Further studies showed that S. sclerotiorum invasion led to a decrease in electron transport rate, but a significant increase in non-photochemical quenching (NPQ). The decay kinetics of NPQ revealed that zeaxanthin epoxidase (ZEP, also known as ABA1) was continuous deactivation in S. sclerotiorum-infected region. HPLC-MS/MS analysis showed a slight increase of jasmonate acid (JA), but a great decrease of abscisic acid (ABA) content in S. sclerotiorum-inoculated tissue. Exogenous application of ABA but not JA could rescue the abnormal stomatal opening. Together, these results suggested that the S. sclerotiorum-induced decrease of ABA biosynthesis reduced stomatal closing via dysfunction of the xanthophyll cycle during early pathogenesis.

Chloroplast stress signals: regulation of cellular degradation and chloroplast turnover

For 40 years, it has been known that chloroplasts signal to the nucleus and the cell to coordinate gene expression, maximize photosynthesis, and avoid stress. However, the signaling mechanisms have been challenging to uncover due to the complexity of these signals and the stresses that induce them. New research has shown that many signals are induced by singlet oxygen, a natural by-product of inefficient photosynthesis. Chloroplast singlet oxygen not only regulates nuclear gene expression, but also cellular degradation and cell death. Stressed chloroplasts also induce post-translational mechanisms, including autophagy, that allows individual chloroplasts to regulate their own degradation and turnover. Such chloroplast quality control pathways may allow cells to maintain healthy populations of chloroplasts and to avoid cumulative photo-oxidative stress in stressful environments.

Acquiring control: The evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses

Reactive oxygen species (ROS) - the byproducts of aerobic metabolism - influence numerous aspects of the plant life cycle and environmental response mechanisms. In plants, ROS act like a double-edged sword; they play multiple beneficial roles at low concentrations, whereas at high concentrations ROS and related redox-active compounds cause cellular damage through oxidative stress. To examine the dual role of ROS as harmful oxidants and/or crucial cellular signals, this review elaborates that (i) how plants sense and respond to ROS in various subcellular organelles and (ii) the dynamics of subsequent ROS-induced signaling processes. The recent understanding of crosstalk between various cellular compartments in mediating their redox state spatially and temporally is discussed. Emphasis on the beneficial effects of ROS in maintaining cellular energy homeostasis, regulating diverse cellular functions, and activating acclimation responses in plants exposed to abiotic and biotic stresses are described. The comprehensive view of cellular ROS dynamics covering the breadth and versatility of ROS will contribute to understanding the complexity of apparently contradictory ROS roles in plant physiological responses in less than optimum environments.

Oxidative post-translational modification of EXECUTER1 is required for singlet oxygen sensing in plastids

Environmental information perceived by chloroplasts can be translated into retrograde signals that alter the expression of nuclear genes. Singlet oxygen (¹O₂) generated by photosystem II (PSII) can cause photo-oxidative damage of PSII but has also been implicated in retrograde signaling. We previously reported that a nuclear-encoded chloroplast FtsH2 metalloprotease coordinates ¹O₂-triggered retrograde signaling by promoting the degradation of the EXECUTER1 (EX1) protein, a putative ¹O₂ sensor. Here, we show that a ¹O₂-mediated oxidative post-translational modification of EX1 is essential for initiating ¹O₂-derived signaling. Specifically, the Trp643 residue in DUF3506 domain of EX1 is prone to oxidation by ¹O₂. Both the substitution of Trp643 with ¹O₂-insensitive amino acids and the deletion of the DUF3506 domain abolish the EX1-mediated ¹O₂ signaling. We thus provide mechanistic insight into how EX1 senses ¹O₂ via Trp643 located in the DUF3506 domain.

DNA damage and reactive oxygen species cause cell death in the rice local lesions 1 mutant under high light and high temperature

High light and high temperature (HLHT) stress may become more frequent and severe as the climate changes, affecting crop growth and resulting in reduced production. However, the mechanism of the response to HLHT stress in rice is not yet fully understood. In the present study, we screened a rice mutant library using HLHT conditions and isolated an HLHT-sensitive mutant, local lesions 1 (ls1), which showed decreased pigment contents, defective stomata and chloroplasts, and a local lesions phenotype under HLHT. We characterized and cloned LS1 by map-based cloning and genetic complementation. LS1 encodes the A subunit of the RNase H2 complex (RNASEH2A). Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) and comet assays indicated that mutation of LS1 led to severe DNA damage under HLHT stress. Furthermore, we found excessive reactive oxygen species (ROS) accumulation in the ls1 mutant under HLHT stress. Exogenous antioxidants eased the local lesions phenotype of the ls1 mutant under HLHT. DNA damage caused by HLHT stress induces ROS accumulation, which causes the injury and apoptosis of leaf cells in the ls1 mutant. These results enhance our understanding of the regulatory mechanism in the response to HLHT stress in higher plants.

Endosperm-specific transcriptome analysis by applying the INTACT system

KEY MESSAGE

We report the adaptation of the INTACT method for RNA-sequencing in the endosperm and demonstrate its feasibility for allele-specific expression analysis. Tissue-specific transcriptome analyses provide important insights into the developmental programs of defined cell types. The isolation of nuclei tagged in specific cell types (INTACT) is a versatile method that allows to isolate highly pure nuclei from defined tissue types that can be used for several downstream applications. Here, we describe the adaptation of INTACT from endosperm nuclei for high-throughput RNA-sequencing. By analyzing the ratio of parental reads and tissue-specific gene expression in the endosperm, we could assess the contamination level of our samples. Based on this analysis, we estimate that in most of the samples the contamination level is lower than in previously published datasets. We further show that the nuclear transcriptome and total transcriptome of the endosperm are well correlated. Together, our data show that INTACT of the endosperm is a reliable methodology for endosperm-specific transcriptome analysis that overcomes the limitation of time-consuming manual endosperm dissection that is connected with high levels of maternal tissue contamination. INTACT does not rely on expensive equipment and can be set up in every standard molecular biology laboratory, making it the method of choice for future molecular studies of the endosperm.

Dose-dependent effects of 1O2 in chloroplasts are determined by its timing and localization of production

In plants, highly reactive singlet oxygen (1O2) is known to inhibit photosynthesis and to damage the cell as a cytotoxin. However, more recent studies have also proposed 1O2 as a signal. In plants under stress, not only 1O2 but also other reactive oxygen species (ROS) are generated simultaneously, thus making it difficult to link a particular response to the release of 1O2 and establish a signaling role for this ROS. This obstacle has been overcome by the identification of conditional mutants of Arabidopsis thaliana that selectively generate 1O2 and trigger various 1O2-mediated responses. In chloroplasts of these mutants, chlorophyll or its biosynthetic intermediates may act as a photosensitizer and generate 1O2. These 1O2-mediated responses are not only dependent on the dosage of 1O2 but also are determined by the timing and suborganellar localization of its production. This spatial- and temporal-dependent variability of 1O2-mediated responses emphasizes the importance of 1O2 as a highly versatile and short-lived signal that acts throughout the life cycle of a plant.

Singlet Oxygen Metabolism: From Genesis to Signaling

Singlet oxygen (¹O₂) is an excited state of molecular oxygen with an electron spin shift in the molecular orbitals, which is extremely unstable and highly reactive. In plants, ¹O₂ is primarily generated as a byproduct of photosynthesis in the photosystem II reaction center (PSII RC) and the light-harvesting antenna complex (LHC) in the grana core (GC). This occurs upon the absorption of light energy when the excited chlorophyll molecules in the PSII transfer the excess energy to molecular oxygen, thereby generating ¹O₂. As a potent oxidant, ¹O₂ promotes oxidative damage. However, at sub-lethal levels, it initiates chloroplast-to-nucleus retrograde signaling to contribute to plant stress responses, including acclimation and cell death. The thylakoid membranes comprise two spatially separated ¹O₂ sensors: β-carotene localized in the PSII RC in the GC and the nuclear-encoded chloroplast protein EXECUTER1 (EX1) residing in the non-appressed grana margin (GM). Finding EX1 in the GM suggests the existence of an additional source of ¹O₂ in the GM and the presence of two distinct ¹O₂-signaling pathways. In this review, we mainly discuss the genesis and impact of ¹O₂ in plant physiology.

Reactive oxygen species, oxidative signaling and the regulation of photosynthesis

Reduction-oxidation (redox) reactions, in which electrons move from a donor to an acceptor, are the functional heart of photosynthesis. It is not surprising therefore that reactive oxygen species (ROS) are generated in abundance by photosynthesis, providing a plethora of redox signals as well as functioning as essential regulators of energy and metabolic fluxes. Chloroplasts are equipped with an elaborate and multifaceted protective network that allows photosynthesis to function with high productivity even in resource-limited natural environments. This includes numerous antioxidants with overlapping functions that provide enormous flexibility in redox control. ROS are an integral part of the repertoire of chloroplast signals that are transferred to the nucleus to convey essential information concerning redox pressure within the electron transport chain. Current evidence suggests that there is specificity in the gene-expression profiles triggered by the different ROS signals, so that singlet oxygen triggers programs related to over excitation of photosystem (PS) II while superoxide and hydrogen peroxide promote the expression of other suites of genes that may serve to alleviate electron pressure on the reducing side of PSI. Not all chloroplasts are equal in their signaling functions, with some sub-populations appearing to have better contacts/access to the nucleus than others to promote genetic and epigenetic responses. While the concept that light-induced increases in ROS result in damage to PSII and photoinhibition is embedded in the photosynthesis literature, there is little consensus concerning the extent to which such oxidative damage happens in nature. Slowly reversible decreases in photosynthetic capacity are not necessarily the result of light-induced damage to PSII reaction centers.

Singlet oxygen-triggered chloroplast-to-nucleus retrograde signalling pathways: An emerging perspective

Singlet oxygen (¹ O₂ ) is a prime cause of photo-damage of the photosynthetic apparatus. The chlorophyll molecules in the photosystem II reaction center and in the light-harvesting antenna complex are major sources of ¹ O₂ generation. It has been thought that the generation of ¹ O₂ mainly takes place in the appressed regions of the thylakoid membranes, namely, the grana core, where most of the active photosystem II complexes are localized. Apart from being a toxic molecule, new evidence suggests that ¹ O₂ significantly contributes to chloroplast-to-nucleus retrograde signalling that primes acclimation and cell death responses. Interestingly, recent studies reveal that chloroplasts operate two distinct ¹ O₂ -triggered retrograde signalling pathways in which β-carotene and a nuclear-encoded chloroplast protein EXECUTER1 play essential roles as signalling mediators. The coexistence of these mediators raises several questions: their crosstalk, source(s) of ¹ O₂ , downstream signalling components, and the perception and reaction mechanism of these mediators towards ¹ O₂ . In this review, we mainly discuss the molecular genetic basis of the mode of action of these two putative ¹ O₂ sensors and their corresponding retrograde signalling pathways. In addition, we also propose the possible existence of an alternative source of ¹ O₂ , which is spatially and functionally separated from the grana core.

ROS-dependent signalling pathways in plants and algae exposed to high light: Comparisons with other eukaryotes

Like all aerobic organisms, plants and algae co-opt reactive oxygen species (ROS) as signalling molecules to drive cellular responses to changes in their environment. In this respect, there is considerable commonality between all eukaryotes imposed by the constraints of ROS chemistry, similar metabolism in many subcellular compartments, the requirement for a high degree of signal specificity and the deployment of thiol peroxidases as transducers of oxidising equivalents to regulatory proteins. Nevertheless, plants and algae carry out specialised signalling arising from oxygenic photosynthesis in chloroplasts and photoautotropism, which often induce an imbalance between absorption of light energy and the capacity to use it productively. A key means of responding to this imbalance is through communication of chloroplasts with the nucleus to adjust cellular metabolism. Two ROS, singlet oxygen (¹O₂) and hydrogen peroxide (H₂O₂), initiate distinct signalling pathways when photosynthesis is perturbed. ¹O₂, because of its potent reactivity means that it initiates but does not transduce signalling. In contrast, the lower reactivity of H₂O₂ means that it can also be a mobile messenger in a spatially-defined signalling pathway. How plants translate a H₂O₂ message to bring about changes in gene expression is unknown and therefore, we draw on information from other eukaryotes to propose a working hypothesis. The role of these ROS generated in other subcellular compartments of plant cells in response to HL is critically considered alongside other eukaryotes. Finally, the responses of animal cells to oxidative stress upon high irradiance exposure is considered for new comparisons between plant and animal cells.

Mechanisms of glacial-to-future atmospheric CO2 effects on plant immunity

The impacts of rising atmospheric CO2 concentrations on plant disease have received increasing attention, but with little consensus emerging on the direct mechanisms by which CO2 shapes plant immunity. Furthermore, the impact of sub-ambient CO2 concentrations, which plants have experienced repeatedly over the past 800 000 yr, has been largely overlooked. A combination of gene expression analysis, phenotypic characterisation of mutants and mass spectrometry-based metabolic profiling was used to determine development-independent effects of sub-ambient CO2 (saCO2 ) and elevated CO2 (eCO2 ) on Arabidopsis immunity. Resistance to the necrotrophic Plectosphaerella cucumerina (Pc) was repressed at saCO2 and enhanced at eCO2 . This CO2 -dependent resistance was associated with priming of jasmonic acid (JA)-dependent gene expression and required intact JA biosynthesis and signalling. Resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) increased at both eCO2 and saCO2 . Although eCO2 primed salicylic acid (SA)-dependent gene expression, mutations affecting SA signalling only partially suppressed Hpa resistance at eCO2 , suggesting additional mechanisms are involved. Induced production of intracellular reactive oxygen species (ROS) at saCO2 corresponded to a loss of resistance in glycolate oxidase mutants and increased transcription of the peroxisomal catalase gene CAT2, unveiling a mechanism by which photorespiration-derived ROS determined Hpa resistance at saCO2 . By separating indirect developmental impacts from direct immunological effects, we uncover distinct mechanisms by which CO2 shapes plant immunity and discuss their evolutionary significance.

FtsH Protease in the Thylakoid Membrane: Physiological Functions and the Regulation of Protease Activity

Protein homeostasis in the thylakoid membranes is dependent on protein quality control mechanisms, which are necessary to remove photodamaged and misfolded proteins. An ATP-dependent zinc metalloprotease, FtsH, is the major thylakoid membrane protease. FtsH proteases in the thylakoid membranes of Arabidopsis thaliana form a hetero-hexameric complex consisting of four FtsH subunits, which are divided into two types: type A (FtsH1 and FtsH5) and type B (FtsH2 and FtsH8). An increasing number of studies have identified the critical roles of FtsH in the biogenesis of thylakoid membranes and quality control in the photosystem II repair cycle. Furthermore, the involvement of FtsH proteolysis in a singlet oxygen- and EXECUTER1-dependent retrograde signaling mechanism has been suggested recently. FtsH is also involved in the degradation and assembly of several protein complexes in the photosynthetic electron-transport pathways. In this minireview, we provide an update on the functions of FtsH in thylakoid biogenesis and describe our current understanding of the D1 degradation processes in the photosystem II repair cycle. We also discuss the regulation mechanisms of FtsH protease activity, which suggest the flexible oligomerization capability of FtsH in the chloroplasts of seed plants.

Singlet oxygen initiates a plastid signal controlling photosynthetic gene expression

Retrograde signals from the plastid regulate photosynthesis-associated nuclear genes and are essential to successful chloroplast biogenesis. One model is that a positive haem-related signal promotes photosynthetic gene expression in a pathway that is abolished by the herbicide norflurazon. Far-red light (FR) pretreatment and transfer to white light also results in plastid damage and loss of photosynthetic gene expression. Here, we investigated whether norflurazon and FR pretreatment affect the same retrograde signal. We used transcriptome analysis and real-time reverse transcription-polymerase chain reaction (RT-PCR) to analyse the effects of these treatments on nuclear gene expression in various Arabidopsis (Arabidopsis thaliana) retrograde signalling mutants. Results showed that the two treatments inhibited largely different nuclear gene sets, suggesting that they affected different retrograde signals. Moreover, FR pretreatment resulted in singlet oxygen (¹ O₂ ) production and a rapid inhibition of photosynthetic gene expression. This inhibition was partially blocked in the executer1executer2 mutant, which is impaired in ¹ O₂ signalling. Our data support a new model in which a ¹ O₂ retrograde signal, generated by chlorophyll precursors, inhibits expression of key photosynthetic and chlorophyll synthesis genes to prevent photo-oxidative damage during de-etiolation. Such a signal would provide a counterbalance to the positive haem-related signal to fine tune regulation of chloroplast biogenesis.

Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles

The early endosperm tissue of dicot species is very difficult to isolate by manual dissection. This protocol details how to apply the INTACT (isolation of nuclei tagged in specific cell types) system for isolating early endosperm nuclei of Arabidopsis at high purity and how to generate parental-specific epigenome profiles. As a Protocol Extension, this article describes an adaptation of an existing Nature Protocol that details the use of the INTACT method for purification of root nuclei. We address how to obtain the INTACT lines, generate the starting material and purify the nuclei. We describe a method that allows purity assessment, which has not been previously addressed. The purified nuclei can be used for ChIP and DNA bisulfite treatment followed by next-generation sequencing (seq) to study histone modifications and DNA methylation profiles, respectively. By using two different Arabidopsis accessions as parents that differ by a large number of single-nucleotide polymorphisms (SNPs), we were able to distinguish the parental origin of epigenetic modifications. Our protocol describes the only working method to our knowledge for generating parental-specific epigenome profiles of the early Arabidopsis endosperm. The complete protocol, from silique collection to finished libraries, can be completed in 2 d for bisulfite-seq (BS-seq) and 3 to 4 d for ChIP-seq experiments.This protocol is an extension to: Nat. Protoc. 6, 56-68 (2011); doi:10.1038/nprot.2010.175; published online 16 December 2010.

Singlet oxygen detection in biological systems: Uses and limitations

The study of singlet oxygen in biological systems is challenging in many ways. Singlet oxygen is a relatively unstable ephemeral molecule, and its properties make it highly reactive with many biomolecules, making it difficult to quantify accurately. Several methods have been developed to study this elusive molecule, but most studies thus far have focused on those conditions that produce relatively large amounts of singlet oxygen. However, the need for more sensitive methods is required as one begins to explore the levels of singlet oxygen required in signaling and regulatory processes. Here we discuss the various methods used in the study of singlet oxygen, and outline their uses and limitations.

Singlet oxygen- and EXECUTER1-mediated signaling is initiated in grana margins and depends on the protease FtsH2

Formation of singlet oxygen ((1)O2) has been implicated with damaging photosystem II (PSII) that needs to undergo continuous repair to maintain photosynthetic electron transport. In addition to its damaging effect, (1)O2 has also been shown to act as a signal that triggers stress acclimation and an enhanced stress resistance. A signaling role of (1)O2 was first documented in the fluorescent (flu) mutant of Arabidopsis It strictly depends on the chloroplast protein EXECUTER1 (EX1) and happens under nonphotoinhibitory light conditions. Under severe light stress, signaling is initiated independently of EX1 by (1)O2 that is thought to be generated at the acceptor side of active PSII within the core of grana stacks. The results of the present study suggest a second source of (1)O2 formation in grana margins close to the site of chlorophyll synthesis where EX1 is localized and the disassembly of damaged and reassembly of active PSII take place. The initiation of (1)O2 signaling in grana margins depends on EX1 and the ATP-dependent zinc metalloprotease FtsH. As FtsH cleaves also the D1 protein during the disassembly of damaged PSII, EX1- and (1)O2-mediated signaling seems to be not only spatially but also functionally associated with the repair of PSII.

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm

Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethylation to imprinted gene expression. Our data furthermore suggest an absence of de novo DNA methylation in the early endosperm, providing an explanation how DME-mediated hypomethylation of the maternal genome is maintained after fertilization. Lastly, we show that paternal-specific H3K27me3-marked regions are located at pericentromeric regions, suggesting that H3K27me3 and DNA methylation are not necessarily exclusive marks at pericentromeric regions in the endosperm.

A ruthenium(ii) based photosensitizer and transferrin complexes enhance photo-physical properties, cell uptake, and photodynamic therapy safety and efficacy

Metal-based photosensitizers are of interest as their absorption and chemical binding properties can be modified via the use of different ligands. Ru(2+) based photosensitizers are known to be effective photodynamic therapy (PDT) agents against bacteria, whereas use for oncological indications in vivo has not been demonstrated with the same level of evidence. We present data showing that premixing the Ru(2+)-complex TLD1433 with transferrin increases the molar extinction coefficient, including longer activation wavelengths, reduces photobleaching rates, and reduces the toxicity of the complex improving overall PDT efficacy. As the transferrin receptor is upregulated in most malignancies, premixing the Ru(2+) complex with transferrin converts the active pharmaceutical ingredient TLD1433 into a drug of potentially considerable clinical utility.

Redox regulation in shoot growth, SAM maintenance and flowering

Reactive oxygen species (ROS) and associated reduction/oxidation (redox) controls involving glutathione, glutaredoxins and thioredoxins play key roles in the regulation of plant growth and development. While many questions remain concerning redox functions in the shoot apical meristem (SAM), accumulating evidence suggests that redox master switches integrate major hormone signals and transcriptional networks in the SAM, and so regulate organ growth, polarity and floral development. Auxin-induced activation of plasma-membrane located NADPH-oxidases and mitochondrial respiratory bioenergetics are likely regulators of the ROS bursts that drive the cell cycle in proliferating regions, with other hormones such as jasmonic acid playing propagating or antagonistic roles in gene regulation. Moreover, the activation of oxygen production by photosynthesis and oxygen-dependent N-end rule controls are linked to the transition from cell proliferation to cell expansion and differentiation. While much remains to be understood, the nexus of available redox controls provides a key underpinning mechanism linking hormonal controls, energy metabolism and bioenergetics to plant growth and development.

Production of Reactive Oxygen Species by Photosystem II as a Response to Light and Temperature Stress

The effect of various abiotic stresses on photosynthetic apparatus is inevitably associated with formation of harmful reactive oxygen species (ROS). In this review, recent progress on ROS production by photosystem II (PSII) as a response to high light and high temperature is overviewed. Under high light, ROS production is unavoidably associated with energy transfer and electron transport in PSII. Singlet oxygen is produced by the energy transfer form triplet chlorophyll to molecular oxygen formed by the intersystem crossing from singlet chlorophyll in the PSII antennae complex or the recombination of the charge separated radical pair in the PSII reaction center. Apart to triplet chlorophyll, triplet carbonyl formed by lipid peroxidation transfers energy to molecular oxygen forming singlet oxygen. On the PSII electron acceptor side, electron leakage to molecular oxygen forms superoxide anion radical which dismutes to hydrogen peroxide which is reduced by the non-heme iron to hydroxyl radical. On the PSII electron donor side, incomplete water oxidation forms hydrogen peroxide which is reduced by manganese to hydroxyl radical. Under high temperature, dark production of singlet oxygen results from lipid peroxidation initiated by lipoxygenase, whereas incomplete water oxidation forms hydrogen peroxide which is reduced by manganese to hydroxyl radical. The understanding of molecular basis for ROS production by PSII provides new insight into how plants survive under adverse environmental conditions.

Production of Reactive Oxygen Species by Photosystem II as a Response to Light and Temperature Stress

The effect of various abiotic stresses on photosynthetic apparatus is inevitably associated with formation of harmful reactive oxygen species (ROS). In this review, recent progress on ROS production by photosystem II (PSII) as a response to high light and high temperature is overviewed. Under high light, ROS production is unavoidably associated with energy transfer and electron transport in PSII. Singlet oxygen is produced by the energy transfer form triplet chlorophyll to molecular oxygen formed by the intersystem crossing from singlet chlorophyll in the PSII antennae complex or the recombination of the charge separated radical pair in the PSII reaction center. Apart to triplet chlorophyll, triplet carbonyl formed by lipid peroxidation transfers energy to molecular oxygen forming singlet oxygen. On the PSII electron acceptor side, electron leakage to molecular oxygen forms superoxide anion radical which dismutes to hydrogen peroxide which is reduced by the non-heme iron to hydroxyl radical. On the PSII electron donor side, incomplete water oxidation forms hydrogen peroxide which is reduced by manganese to hydroxyl radical. Under high temperature, dark production of singlet oxygen results from lipid peroxidation initiated by lipoxygenase, whereas incomplete water oxidation forms hydrogen peroxide which is reduced by manganese to hydroxyl radical. The understanding of molecular basis for ROS production by PSII provides new insight into how plants survive under adverse environmental conditions.

Transcriptional Regulation of Tetrapyrrole Biosynthesis in Arabidopsis thaliana

Biosynthesis of chlorophyll (Chl) involves many enzymatic reactions that share several first steps for biosynthesis of other tetrapyrroles such as heme, siroheme, and phycobilins. Chl allows photosynthetic organisms to capture light energy for photosynthesis but with simultaneous threat of photooxidative damage to cells. To prevent photodamage by Chl and its highly photoreactive intermediates, photosynthetic organisms have developed multiple levels of regulatory mechanisms to coordinate tetrapyrrole biosynthesis (TPB) with the formation of photosynthetic and photoprotective systems and to fine-tune the metabolic flow with the varying needs of Chl and other tetrapyrroles under various developmental and environmental conditions. Among a wide range of regulatory mechanisms of TPB, this review summarizes transcriptional regulation of TPB genes during plant development, with focusing on several transcription factors characterized in Arabidopsis thaliana. Key TPB genes are tightly coexpressed with other photosynthesis-associated nuclear genes and are induced by light, oscillate in a diurnal and circadian manner, are coordinated with developmental and nutritional status, and are strongly downregulated in response to arrested chloroplast biogenesis. LONG HYPOCOTYL 5 and PHYTOCHROME-INTERACTING FACTORs, which are positive and negative transcription factors with a wide range of light signaling, respectively, target many TPB genes for light and circadian regulation. GOLDEN2-LIKE transcription factors directly regulate key TPB genes to fine-tune the formation of the photosynthetic apparatus with chloroplast functionality. Some transcription factors such as FAR-RED ELONGATED HYPOCOTYL3, REVEILLE1, and scarecrow-like transcription factors may directly regulate some specific TPB genes, whereas other factors such as GATA transcription factors are likely to regulate TPB genes in an indirect manner. Comprehensive transcriptional analyses of TPB genes and detailed characterization of key transcriptional regulators help us obtain a whole picture of transcriptional control of TPB in response to environmental and endogenous cues.