Accelerated cell death 2 suppresses mitochondrial oxidative bursts and modulates cell death in Arabidopsis

Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant

As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen (1O2), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1O2 (fluorescent in blue light (flu), chlorina 1 (ch1), and plastid ferrochelatase 2 (fc2)). We previously demonstrated that these mutants reveal at least two chloroplast 1O2 signaling pathways (represented by flu and fc2/ch1). Here, we test if the 1O2-accumulating lesion mimic mutant, accelerated cell death 2 (acd2), also utilizes these pathways. The pub4-6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4-6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1O2 signaling pathways are independent from spontaneous lesion formation. Thus, 1O2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.

γ-Aminobutyric Acid Alleviates Programmed Cell Death in Two Brassica Species Under Cadmium Stress

Previous studies have demonstrated that γ-Aminobutyric acid (GABA) effectively alleviates heavy metal stresses by maintaining the redox balance and reducing the accumulation of reactive oxygen species (ROS). However, little is known about the role of GABA on programmed cell death (PCD) under Cd treatments in plants. The present study investigated the effects of GABA on Cd-induced PCD in two Brassica species, oilseed rape (Brassica napus, Bn), and black mustard (Brassica juncea, Bj). We observed that GABA significantly alleviated Cd-induced PCD by enhancing antioxidant systems, inhibiting chromatin condensation in the nucleus, and reducing DNA fragmentation under Cd stress. Moreover, GABA may not only reduce caspase-3-like activity by repressing gene expression, but also regulate transcription of PCD-related genes. Bn showed lower Cd accumulation and lower tolerance, with more pronounced PCD, compared with Bj. Our results provide new insights into the mechanism that GABA enhances Cd tolerance in plants.

Singlet Oxygen and Superoxide Anion Radical Detection by EPR Spin Trapping in Thylakoid Preparations

Reactive oxygen species (ROS) are produced by energy transfer and electron transport in plant chloroplast thylakoids at non-toxic levels under normal growth conditions, but at threatening levels under adverse or fluctuating environmental conditions. Among chloroplast ROS, singlet oxygen and superoxide anion radical, respectively, produced by photosystem II (PSII) and PSI, are known to be the major ROS under several stress conditions. Both are very unlikely to diffuse out of chloroplasts, but they are instead capable of triggering ROS-mediated chloroplast operational retrograde signalling to activate defence gene expression in concert with hormones and other molecular compounds. Therefore, their detection, identification and localization in vivo or in biological preparations is a priority for a deeper understanding of their role in (concurrent) regulation of plant growth and defence responses. Here, we present two EPR spin traps, abbreviated as TEMPD-HCl and DEPMPO, to detect and identify ROS in complex systems, such as isolated thylakoids, together with some hints and cautions to perform reliable spin trapping experiments.

Singlet Oxygen Detection by Chemiluminescence Probes in Living Cells

Singlet oxygen is a reactive oxygen species that causes oxidative damage to plant cells, but intriguingly it can also act as a signalling molecule to reprogram gene expression required to induce plant physiological/cellular responses. Singlet oxygen photosensitization in plants mainly occurs in chloroplasts after the molecular collision of ground-state molecular oxygen with triplet-excited-state chlorophyll. Singlet oxygen direct detection through phosphorescence emission in chloroplasts is a herculean task due to its extremely low luminescence quantum yield. Because of this, indirect alternative methods have been developed for its detection in biological systems, for example, by measuring the changes in the EPR signal or fluorescence intensity of singlet oxygen reaction-based probes. The singlet oxygen chemiluminescence (SOCL) is a chemiluminescence probe with high sensitivity and selectivity towards singlet oxygen and promising use to detect it in living cells without the inconvenience of low stability of the EPR signal of spin probes in the presence of redox compounds, spurious light scattering coming from the light source required for the excitation of fluorescence probes or the light emission of endogenous fluorescent molecules like chlorophyll in chloroplasts. The protocol presented in this chapter describes the first steps to characterizing singlet oxygen production within the biological system under study; this is accomplished through monitoring molecular oxygen consumption by SOCL using a Clark-type oxygen electrode and measuring the chemiluminescence generated by SOCL 1,2-dioxetane using a spectrofluorometer. For singlet oxygen detection within living cells, a version of SOCL with increased membrane permeability (SOCL-CPP) is described.

(±)-3-Deoxyradicinin Induces Stomata Opening and Chloroplast Oxidative Stress in Tomato (Solanum lycopersicum L.)

Radicinin is a phytotoxic dihydropyranopyran-4,5-dione isolated from the culture filtrates of Cochliobolus australiensis, a phytopathogenic fungus of the invasive weed buffelgrass (Cenchrus ciliaris). Radicinin proved to have interesting potential as a natural herbicide. Being interested in elucidating the mechanism of action and considering radicinin is produced in small quantities by C. australiensis, we opted to use (±)-3-deoxyradicinin, a synthetic analogue of radicinin that is available in larger quantities and shows radicinin-like phytotoxic activities. To obtain information about subcellular targets and mechanism(s) of action of the toxin, the study was carried out by using tomato (Solanum lycopersicum L.), which, apart from its economic relevance, has become a model plant species for physiological and molecular studies. Results of biochemical assays showed that (±)-3-deoxyradicinin administration to leaves induced chlorosis, ion leakage, hydrogen peroxide production, and membrane lipid peroxidation. Remarkably, the compound determined the uncontrolled opening of stomata, which, in turn, resulted in plant wilting. Confocal microscopy analysis of protoplasts treated with (±)-3-deoxyradicinin ascertained that the toxin targeted chloroplasts, eliciting an overproduction of reactive singlet oxygen species. This oxidative stress status was related by qRT-PCR experiments to the activation of transcription of genes of a chloroplast-specific pathway of programmed cell death.

Multiple pathways mediate chloroplast singlet oxygen stress signaling

Chloroplast singlet oxygen initiates multiple pathways to control chloroplast degradation, cell death, and nuclear gene expression. Chloroplasts can respond to stress and changes in the environment by producing reactive oxygen species (ROS). Aside from being cytotoxic, ROS also have signaling capabilities. For example, the ROS singlet oxygen (¹O₂) can initiate nuclear gene expression, chloroplast degradation, and cell death. To unveil the signaling mechanisms involved, researchers have used several ¹O₂-producing Arabidopsis thaliana mutants as genetic model systems, including plastid ferrochelatase two (fc2), fluorescent in blue light (flu), chlorina 1 (ch1), and accelerated cell death 2 (acd2). Here, we compare these ¹O₂-producing mutants to elucidate if they utilize one or more signaling pathways to control cell death and nuclear gene expression. Using publicly available transcriptomic data, we demonstrate fc2, flu, and ch1 share a core response to ¹O₂ accumulation, but maintain unique responses, potentially tailored to respond to their specific stresses. Subsequently, we used a genetic approach to determine if these mutants share ¹O₂ signaling pathways by testing the ability of genetic suppressors of one ¹O₂ producing mutant to suppress signaling in a different ¹O₂ producing mutant. Our genetic analyses revealed at least two different chloroplast ¹O₂ signaling pathways control cellular degradation: one specific to the flu mutant and one shared by fc2, ch1, and acd2 mutants, but with life-stage-specific (seedling vs. adult) features. Overall, this work reveals chloroplast stress signaling involving ¹O₂ is complex and may allow cells to finely tune their physiology to environmental inputs.

Fine Mapping and Candidate Gene Analysis of BnC08.cds, a Recessive Gene Responsible for Sepal-Specific Chlorophyll-Deficiency in Brassica napus L

Chloroplast development is crucial for photosynthesis and plant growth and many factors are involved in its regulation. The regulatory mechanism differs in different green tissues, and previous studies have focused on chloroplasts in leaves. In this study, a mutant with sepal-specific chlorophyll-deficiency was observed in Brassica napus and named as df74. Genetic analysis indicated that the phenotype was controlled by a single recessive nuclear gene. The gene was located on chromosome C08 by bulked-segregant analysis with whole-genome sequencing, which was designated as BnC08.cds. To fine-map the BnC08.cds, a F₂ population was created from the cross of df74 and Zhongshuang11 (ZS11). Finally, the BnC08.cds was fine-mapped in the region between the single-nucleotide polymorphism (SNP) markers M5 and M6, corresponding to a 228.72 kb interval of the B. napus "ZS11" genome. Eighteen genes were predicted in the target region, and it was speculated that BnaC08G0442100ZS was the most likely candidate gene based on the results of transcriptome analyses and sequence variation analyses. These results provide a foundation to explore the regulation of chloroplast development in sepals.

Series-Spatial Transcriptome Profiling of Leafy Head Reveals the Key Transition Leaves for Head Formation in Chinese Cabbage

Chinese cabbage is an important leaf heading vegetable crop. At the heading stage, its leaves across inner to outer show significant morphological differentiation. However, the genetic control of this complex leaf morphological differentiation remains unclear. Here, we reported the transcriptome profiling of Chinese cabbage plant at the heading stage using 24 spatially dissected tissues representing different regions of the inner to outer leaves. Genome-wide transcriptome analysis clearly separated the inner leaf tissues from the outer leaf tissues. In particular, we identified the key transition leaf by the spatial expression analysis of key genes for leaf development and sugar metabolism. We observed that the key transition leaves were the first inwardly curved ones. Surprisingly, most of the heading candidate genes identified by domestication selection analysis obviously showed a corresponding expression transition, supporting that key transition leaves are related to leafy head formation. The key transition leaves were controlled by a complex signal network, including not only internal hormones and protein kinases but also external light and other stimuli. Our findings provide new insights and the rich resource to unravel the genetic control of heading traits.

Proline metabolism as regulatory hub

Proline is a multifunctional amino acid that is accumulated in high concentrations in plants under various stress conditions. Proline accumulation is intimately connected to many cellular processes, such as osmotic pressure, energy status, nutrient availability, changes in redox balance, and defenses against pathogens. Proline biosynthesis and catabolism is linked to photosynthesis and mitochondrial respiration, respectively. Proline can function as a signal, modulating gene expression and certain metabolic processes. We review important findings on proline metabolism and function of the last decade, giving a more informative picture about the function of this unusual amino acid in maintaining cellular homeostasis, modulating plant development, and promoting stress acclimation.

Rice Lesion Mimic Mutants (LMM): The Current Understanding of Genetic Mutations in the Failure of ROS Scavenging during Lesion Formation

Rice lesion mimic mutants (LMMs) form spontaneous lesions on the leaves during vegetative growth without pathogenic infections. The rice LMM group includes various mutants, including spotted leaf mutants, brown leaf mutants, white-stripe leaf mutants, and other lesion-phenotypic mutants. These LMM mutants exhibit a common phenotype of lesions on the leaves linked to chloroplast destruction caused by the eruption of reactive oxygen species (ROS) in the photosynthesis process. This process instigates the hypersensitive response (HR) and programmed cell death (PCD), resulting in lesion formation. The reasons for lesion formation have been studied extensively in terms of genetics and molecular biology to understand the pathogen and stress responses. In rice, the lesion phenotypes of most rice LMMs are inherited according to the Mendelian principles of inheritance, which remain in the subsequent generations. These rice LMM genetic traits have highly developed innate self-defense mechanisms. Thus, although rice LMM plants have undesirable agronomic traits, the genetic principles of LMM phenotypes can be used to obtain high grain yields by deciphering the efficiency of photosynthesis, disease resistance, and environmental stress responses. From these ailing rice LMM plants, rice geneticists have discovered novel proteins and physiological causes of ROS in photosynthesis and defense mechanisms. This review discusses recent studies on rice LMMs for the Mendelian inheritances, molecular genetic mapping, and the genetic definition of each mutant gene.

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 red chlorophyll catabolite (RCC) is an inefficient sensitizer of singlet oxygen - photochemical studies of the methyl ester of RCC

The red chlorophyll catabolite (RCC) is a proposed cryptic intermediate of chlorophyll (Chl) breakdown in higher plants. Its accumulation in higher plants is believed to be metabolically suppressed, as RCC is commonly suspected to efficiently sensitize for the formation of the cell poison singlet oxygen (¹O₂). We report here a study on luminescence of the methyl ester of RCC (Me-RCC) and of its capacity to generate ¹O₂ in ethanolic solution. A solution of Me-RCC fluoresces at room temperature with a maximum near 670 nm and features a fluorescence spectrum with pronounced vibrational spacing at 77 K. As shown here, sensitization of the generation of ¹O₂ by Me-RCC in an oxygen-saturated solution in hexadeutero-ethanol occurs with a maximal quantum yield of only about 0.015. This low quantum yield suggests that the specific catabolic suppression of the accumulation of RCC during Chl breakdown is not primarily a countermeasure against the formation of ¹O₂ by RCC in the plant, but has other crucial reasons mainly.

A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism

Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.

Deficiencies in the Mitochondrial Electron Transport Chain Affect Redox Poise and Resistance Toward Colletotrichum higginsianum

To investigate if and how the integrity of the mitochondrial electron transport chain (mETC) influences susceptibility of Arabidopsis toward Colletotrichum higginsianum, we have selected previously characterized mutants with defects at different stages of the mETC, namely, the complex I mutant ndufs4, the complex II mutant sdh2-1, the complex III mutant ucr8-1, and a mutant of the uncoupling protein ucp1-2. Relative to wild type, the selected complex I, II, and III mutants showed decreased total respiration, increased alternative respiration, as well as increased redox charge of the NADP(H) pool and decreased redox charge of the NAD(H) pool in the dark. In the light, mETC mutants accumulated free amino acids, albeit to varying degrees. Glycine and serine, which are involved in carbon recycling from photorespiration, and N-rich amino acids were predominantly increased in mETC mutants compared to the wild type. Taking together the physiological phenotypes of all examined mutants, our results suggest a connection between the limitation in the re-oxidation of reducing equivalents in the mitochondrial matrix and the induction of nitrate assimilation into free amino acids in the cytosol, which seems to be engaged as an additional sink for reducing power. The sdh2-1 mutant was less susceptible to C. higginsianum and did not show hampered salicylic acid (SA) accumulation as previously reported for SDH1 knock-down plants. The ROS burst remained unaffected in sdh2-1, emonstrating that subunit SDH2 is not involved in the control of ROS production and SA signaling by complex II. Moreover, the ndufs4 mutant showed only 20% of C. higginsianum colonization compared to wild type, with the ROS burst and the production of callose papillae being significantly increased compared to wild type. This indicates that a restriction of respiratory metabolism can positively affect pre-penetration resistance of Arabidopsis. Taking metabolite profiling data from all investigated mETC mutants, a strong positive correlation of resistance toward C. higginsianum with NADPH pool size, pyruvate contents, and other metabolites associated with redox poise and energy charge was evident, which fosters the hypothesis that limitations in the mETC can support resistance at post-penetration stages by improving the availability of metabolic power.

Signaling interactions between mitochondria and chloroplasts in Nicotiana tabacum leaf

Research has begun to elucidate the signal transduction pathway(s) that control cellular responses to changes in mitochondrial status. Important tools in such studies are chemical inhibitors used to initiate mitochondrial dysfunction. This study compares the effect of different inhibitors and treatment conditions on the transcript amount of nuclear genes specifically responsive to mitochondrial dysfunction in leaf of Nicotiana tabacum L. cv. Petit Havana. The Complex III inhibitors antimycin A (AA) and myxothiazol (MYXO), and the Complex V inhibitor oligomycin (OLIGO), each increased the transcript amount of the mitochondrial dysfunction genes. Transcript responses to OLIGO were greater during treatment in the dark than in the light, and the dark treatment resulted in cell death. In the dark, transcript responses to AA and MYXO were similar to one another, despite MYXO leading to cell death. In the light, transcript responses to AA and MYXO diverged, despite cell viability remaining high with either inhibitor. This divergent response may be due to differential signaling from the chloroplast because only AA also inhibited cyclic electron transport, resulting in a strong acceptor-side limitation in photosystem I. In the light, chemical inhibition of chloroplast electron transport reduced transcript responses to AA, while having no effect on the response to MYXO, and increasing the response to OLIGO. Hence, when studying mitochondrial dysfunction signaling, different inhibitor and treatment combinations differentially affect linked processes (e.g. chloroplast function and cell fate) that then contribute to measured responses. Therefore, inhibitor and treatment conditions should be chosen to align with specific study goals.

PROHIBITIN3 Forms Complexes with ISOCHORISMATE SYNTHASE1 to Regulate Stress-Induced Salicylic Acid Biosynthesis in Arabidopsis

Salicylic acid (SA) is a major defense signal in plants. In Arabidopsis (Arabidopsis thaliana), the chloroplast-localized isochorismate pathway is the main source of SA biosynthesis during abiotic stress or pathogen infections. In the first step of the pathway, the enzyme ISOCHORISMATE SYNTHASE1 (ICS1) converts chorismate to isochorismate. An unknown enzyme subsequently converts isochorismate to SA. Here, we show that ICS1 protein levels increase during UV-C stress. To identify proteins that may play roles in SA production by regulating ICS1, we analyzed proteins that coimmunoprecipitated with ICS1 via mass spectrometry. The ICS1 complexes contained a large number of peptides from the PROHIBITIN (PHB) protein family, with PHB3 the most abundant. PHB proteins have diverse biological functions that include acting as scaffolds for protein complex formation and stabilization. PHB3 was reported previously to localize to mitochondria. Using fractionation, protease protection, and live imaging, we show that PHB3 also localizes to chloroplasts, where ICS1 resides. Notably, loss of PHB3 function led to decreased ICS1 protein levels in response to UV-C stress. However, ICS1 transcript levels remain unchanged, indicating that ICS1 is regulated posttranscriptionally. The phb3 mutant displayed reduced levels of SA, the SA-regulated protein PR1, and hypersensitive cell death in response to UV-C and avirulent strains of Pseudomonas syringae and, correspondingly, supported increased growth of P. syringae The expression of a PHB3 transgene in the phb3 mutant complemented all of these phenotypes. We suggest a model in which the formation of PHB3-ICS1 complexes stabilizes ICS1 to promote SA production in response to stress.

Plant-microbe interactions: organelles and the cytoskeleton in action

Contents Summary 1012 I. Introduction 1012 II. The endomembrane system in plant-microbe interactions 1013 III. The cytoskeleton in plant-microbe interactions 1017 IV. Organelles in plant-microbe interactions 1019 V. Inter-organellar communication in plant-microbe interactions 1022 VI. Conclusions and prospects 1023 Acknowledgements 1024 References 1024 SUMMARY: Plants have evolved a multilayered immune system with well-orchestrated defense strategies against pathogen attack. Multiple immune signaling pathways, coordinated by several subcellular compartments and interactions between these compartments, play important roles in a successful immune response. Pathogens use various strategies to either directly attack the plant's immune system or to indirectly manipulate the physiological status of the plant to inhibit an immune response. Microscopy-based approaches have allowed the direct visualization of membrane trafficking events, cytoskeleton reorganization, subcellular dynamics and inter-organellar communication during the immune response. Here, we discuss the contributions of organelles and the cytoskeleton to the plant's defense response against microbial pathogens, as well as the mechanisms used by pathogens to target these compartments to overcome the plant's defense barrier.

Singlet oxygen triggers chloroplast rupture and cell death in the zeaxanthin epoxidase defective mutant aba1 of Arabidopsis thaliana under high light stress

The two Arabidopsis thaliana mutants, aba1 and max4, were previously identified as sharing a number of co-regulated genes with both the flu mutant and Arabidopsis cell suspension cultures exposed to high light (HL). On this basis, we investigated whether aba1 and max4 were generating high amounts of singlet oxygen (¹O₂) and activating ¹O₂-mediated cell death. Thylakoids of aba1 produced twice as much ¹O₂ as thylakoids of max4 and wild type (WT) plants when illuminated with strong red light. ¹O₂ was measured using the spin probe 2,2,6,6-tetramethyl-4-piperidone hydrochloride. 77-K chlorophyll fluorescence emission spectra of thylakoids revealed lower aggregation of the light harvesting complex II in aba1. This was rationalized as a loss of connectivity between photosystem II (PSII) units and as the main cause for the high yield of ¹O₂ generation in aba1. Up-regulation of the ¹O₂ responsive gene AAA-ATPase was only observed with statistical significant in aba1 under HL. Two early jasmonate (JA)-responsive genes, JAZ1 and JAZ5, encoding for two repressor proteins involved in the negative feedback regulation of JA signalling, were not up-regulated to the WT plant levels. Chloroplast aggregation followed by chloroplast rupture and eventual cell death was observed by confocal imaging of the fluorescence emission of leaf cells of transgenic aba1 plants expressing the chimeric fusion protein SSU-GFP. Cell death was not associated with direct ¹O₂ cytotoxicity in aba1, but rather with a delayed stress response. In contrast, max4 did not show evidence of ¹O₂-mediated cell death. In conclusion, aba1 may serve as an alternative model to other ¹O₂-overproducing mutants of Arabidopsis for investigating ¹O₂-mediated cell death.

Convergence of mitochondrial and chloroplastic ANAC017/PAP-dependent retrograde signalling pathways and suppression of programmed cell death

The energy-converting organelles mitochondria and chloroplasts are tightly embedded in cellular metabolism and stress response. To appropriately control organelle function, extensive regulatory mechanisms are at play that involve two-way exchange between the nucleus and mitochondria/chloroplasts. In recent years, our understanding of how mitochondria and chloroplasts provide 'retrograde' feedback to the nucleus, resulting in targeted transcriptional changes, has greatly increased. Nevertheless, mitochondrial and chloroplast retrograde signalling have largely been studied independently, and only few points of interaction have been found or proposed. Through reassessment of recent publications, this perspective proposes that two of the most well-studied retrograde signalling pathways in plants, those mediated by ANAC017 and those mediated by phosphoadenosine phosphate (PAP), are most likely convergent and can direct overlapping genes. Furthermore, at least part of this common retrograde response appears targeted towards suppression of programmed cell death (PCD) triggered by organellar defects. The identified target genes are discussed in light of their roles in PCD suppression and amplifying the signalling cascade via positive-feedback loops. Finally, a mechanism is proposed that may explain why the convergence of PAP/ANAC017-dependent signalling appears capable of suppressing some types of PCD lesions, but not others, based on the subcellular location of the initial PCD-inducing dysfunction.

The Roles of Mitochondrial Reactive Oxygen Species in Cellular Signaling and Stress Response in Plants

Mitochondria produce ATP via respiratory oxidation of organic acids and transfer of electrons to O2 via the mitochondrial electron transport chain. This process produces reactive oxygen species (ROS) at various rates that can impact respiratory and cellular function, affecting a variety of signaling processes in the cell. Roles in redox signaling, retrograde signaling, plant hormone action, programmed cell death, and defense against pathogens have been attributed to ROS generated in plant mitochondria (mtROS). The shortcomings of the black box-idea of mtROS are discussed in the context of mechanistic considerations and the measurement of mtROS The overall aim of this update is to better define our current understanding of mtROS and appraise their potential influence on cellular function in plants. Furthermore, directions for future research are provided, along with suggestions to increase reliability of mtROS measurements.

Intracellular Redox Compartmentation and ROS-Related Communication in Regulation and Signaling

Recent years have witnessed enormous progress in understanding redox signaling related to reactive oxygen species (ROS) in plants. The consensus view is that such signaling is intrinsic to many developmental processes and responses to the environment. ROS-related redox signaling is tightly wedded to compartmentation. Because membranes function as barriers, highly redox-active powerhouses such as chloroplasts, peroxisomes, and mitochondria may elicit specific signaling responses. However, transporter functions allow membranes also to act as bridges between compartments, and so regulated capacity to transmit redox changes across membranes influences the outcome of triggers produced at different locations. As well as ROS and other oxidizing species, antioxidants are key players that determine the extent of ROS accumulation at different sites and that may themselves act as signal transmitters. Like ROS, antioxidants can be transported across membranes. In addition, the intracellular distribution of antioxidative enzymes may be modulated to regulate or facilitate redox signaling appropriate to the conditions. Finally, there is substantial plasticity in organellar shape, with extensions such as stromules, peroxules, and matrixules playing potentially crucial roles in organelle-organelle communication. We provide an overview of the advances in subcellular compartmentation, identifying the gaps in our knowledge and discussing future developments in the area.

Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses

Bryophytes (liverworts, hornworts and mosses) comprise the three earliest diverging lineages of land plants (embryophytes). Marchantia polymorpha, a complex thalloid Marchantiopsida liverwort that has been developed into a model genetic system, occupies a key phylogenetic position. Therefore, M. polymorpha is useful in studies aiming to elucidate the evolution of gene regulation mechanisms in plants. In this study, we used computational, transcriptomic, small RNA and degradome analyses to characterize microRNA (miRNA)-mediated pathways of gene regulation in M. polymorpha. The data have been integrated into the open access ContigViews-miRNA platform for further reference. In addition to core components of the miRNA pathway, 129 unique miRNA sequences, 11 of which could be classified into seven miRNA families that are conserved in embryophytes (miR166a, miR390, miR529c, miR171-3p, miR408a, miR160 and miR319a), were identified. A combination of computational and degradome analyses allowed us to identify and experimentally validate 249 targets. In some cases, the target genes are orthologous to those of other embryophytes, but in other cases, the conserved miRNAs target either paralogs or members of different gene families. In addition, the newly discovered Mpo-miR11707.1 and Mpo-miR11707.2 are generated from a common precursor and target MpARGONAUTE1 (LW1759). Two other newly discovered miRNAs, Mpo-miR11687.1 and Mpo-miR11681.1, target the MADS-box transcription factors MpMADS1 and MpMADS2, respectively. Interestingly, one of the pentatricopeptide repeat (PPR) gene family members, MpPPR_66 (LW9825), the protein products of which are generally involved in various steps of RNA metabolism, has a long stem-loop transcript that can generate Mpo-miR11692.1 to autoregulate MpPPR_66 (LW9825) mRNA. This study provides a foundation for further investigations of the RNA-mediated silencing mechanism in M. polymorpha as well as of the evolution of this gene silencing pathway in embryophytes.

Licensed to Kill: Mitochondria, Chloroplasts, and Cell Death

Programmed cell death (PCD) is crucial in plant organogenesis and survival. In this review the involvement of mitochondria and chloroplasts in PCD execution is critically assessed. Recent findings support a central role for mitochondria in PCD, with newly identified components of the mitochondrial electron transport chain (mETC), FOF1 ATP synthase, cardiolipins, and ATPase AtOM66. While chloroplasts received less attention, their contribution to PCD is well supported, suggesting that they possibly contribute by producing reactive oxygen species (ROS) in the presence of light or even contribute through cytochrome f release. Finally we discuss two working models where mitochondria and chloroplasts could cooperatively execute PCD: mitochondria initiate the commitment steps and recruit chloroplasts for swift execution or, alternatively, mitochondria and chloroplasts could operate in parallel.

Arabidopsis AZI1 family proteins mediate signal mobilization for systemic defence priming

Priming is a major mechanism behind the immunological 'memory' observed during two key plant systemic defences: systemic acquired resistance (SAR) and induced systemic resistance (ISR). Lipid-derived azelaic acid (AZA) is a mobile priming signal. Here, we show that the lipid transfer protein (LTP)-like AZI1 and its closest paralog EARLI1 are necessary for SAR, ISR and the systemic movement and uptake of AZA in Arabidopsis. Imaging and fractionation studies indicate that AZI1 and EARLI1 localize to expected places for lipid exchange/movement to occur. These are the ER/plasmodesmata, chloroplast outer envelopes and membrane contact sites between them. Furthermore, these LTP-like proteins form complexes and act at the site of SAR establishment. The plastid targeting of AZI1 and AZI1 paralogs occurs through a mechanism that may enable/facilitate their roles in signal mobilization.

ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis

Robust immunity requires basal defense machinery to mediate timely responses and feedback cycles to amplify defenses against potentially spreading infections. AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1) is needed for the accumulation of the plant defense signal salicylic acid (SA) during the first hours after infection with the pathogen Pseudomonas syringae and is also upregulated by infection and SA. ALD1 is an aminotransferase with multiple substrates and products in vitro. Pipecolic acid (Pip) is an ALD1-dependent bioactive product induced by P. syringae. Here, we addressed roles of ALD1 in mediating defense amplification as well as the levels and responses of basal defense machinery. ALD1 needs immune components PAD4 and ICS1 (an SA synthesis enzyme) to confer disease resistance, possibly through a transcriptional amplification loop between them. Furthermore, ALD1 affects basal defense by controlling microbial-associated molecular pattern (MAMP) receptor levels and responsiveness. Vascular exudates from uninfected ALD1-overexpressing plants confer local immunity to the wild type and ald1 mutants yet are not enriched for Pip. We infer that, in addition to affecting Pip accumulation, ALD1 produces non-Pip metabolites that play roles in immunity. Thus, distinct metabolite signals controlled by the same enzyme affect basal and early defenses versus later defense responses, respectively.

The metabolomics of oxidative stress

Oxidative stress resulting from increased availability of reactive oxygen species (ROS) is a key component of many responses of plants to challenging environmental conditions. The consequences for plant metabolism are complex and manifold. We review data on small compounds involved in oxidative stress, including ROS themselves and antioxidants and redox buffers in the membrane and soluble phases, and we discuss the wider consequences for plant primary and secondary metabolism. While metabolomics has been exploited in many studies on stress, there have been relatively few non-targeted studies focused on how metabolite signatures respond specifically to oxidative stress. As part of the discussion, we present results and reanalyze published datasets on metabolite profiles in catalase-deficient plants, which can be considered to be model oxidative stress systems. We emphasize the roles of ROS-triggered changes in metabolites as potential oxidative signals, and discuss responses that might be useful as markers for oxidative stress. Particular attention is paid to lipid-derived compounds, the status of antioxidants and antioxidant breakdown products, altered metabolism of amino acids, and the roles of phytohormone pathways.

Programmed cell death in plants: A chloroplastic connection

Programmed cell death (PCD) is an integral cellular program by which targeted cells culminate to demise under certain developmental and pathological conditions. It is essential for controlling cell number, removing unwanted diseased or damaged cells and maintaining the cellular homeostasis. The details of PCD process has been very well elucidated and characterized in animals but similar understanding of the process in plants has not been achieved rather the field is still in its infancy that sees some sporadic reports every now and then. The plants have 2 energy generating sub-cellular organelles- mitochondria and chloroplasts unlike animals that just have mitochondria. The presence of chloroplast as an additional energy transducing and ROS generating compartment in a plant cell inclines to advocate the involvement of chloroplasts in PCD execution process. As chloroplasts are supposed to be progenies of unicellular photosynthetic organisms that evolved as a result of endosymbiosis, the possibility of retaining some of the components involved in bacterial PCD by chloroplasts cannot be ruled out. Despite several excellent reviews on PCD in plants, there is a void on an update of information at a place on the regulation of PCD by chloroplast. This review has been written to provide an update on the information supporting the involvement of chloroplast in PCD process and the possible future course of the field.

To die or not to die? Lessons from lesion mimic mutants

Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting in an activation of finely controlled signaling pathways that lead to cellular suicide. Although some aspects of PCD control appear evolutionary conserved between plants, animals and fungi, the extent of conservation remains controversial. Over the last decades, identification and characterization of several lesion mimic mutants (LMM) has been a powerful tool in the quest to unravel PCD pathways in plants. Thanks to progress in molecular genetics, mutations causing the phenotype of a large number of LMM and their related suppressors were mapped, and the identification of the mutated genes shed light on major pathways in the onset of plant PCD such as (i) the involvements of chloroplasts and light energy, (ii) the roles of sphingolipids and fatty acids, (iii) a signal perception at the plasma membrane that requires efficient membrane trafficking, (iv) secondary messengers such as ion fluxes and ROS and (v) the control of gene expression as the last integrator of the signaling pathways.

Loss of ceramide kinase in Arabidopsis impairs defenses and promotes ceramide accumulation and mitochondrial H2O2 bursts

Arabidopsis thaliana plants that lack ceramide kinase, encoded by ACCELERATED CELL DEATH5 (ACD5), display spontaneous programmed cell death late in development and accumulate substrates of ACD5. Here, we compared ceramide accumulation kinetics, defense responses, ultrastructural features, and sites of reactive oxygen species (ROS) production in wild-type and acd5 plants during development and/or Botrytis cinerea infection. Quantitative sphingolipid profiling indicated that ceramide accumulation in acd5 paralleled the appearance of spontaneous cell death, and it was accompanied by autophagy and mitochondrial ROS accumulation. Plants lacking ACD5 differed significantly from the wild type in their responses to B. cinerea, showing earlier and higher increases in ceramides, greater disease, smaller cell wall appositions (papillae), reduced callose deposition and apoplastic ROS, and increased mitochondrial ROS. Together, these data show that ceramide kinase greatly affects sphingolipid metabolism and the site of ROS accumulation during development and infection, which likely explains the developmental and infection-related cell death phenotypes. The acd5 plants also showed an early defect in restricting B. cinerea germination and growth, which occurred prior to the onset of cell death. This early defect in B. cinerea restriction in acd5 points to a role for ceramide phosphate and/or the balance of ceramides in mediating early antifungal responses that are independent of cell death.

Update on the biochemistry of chlorophyll breakdown

In land plants, chlorophyll is broken down to colorless linear tetrapyrroles in a highly conserved multi-step pathway. The pathway is termed the 'PAO pathway', because the opening of the chlorine macrocycle present in chlorophyll catalyzed by pheophorbide a oxygenase (PAO), the key enzyme of the pathway, provides the characteristic structural basis found in all further downstream chlorophyll breakdown products. To date, most of the biochemical steps of the PAO pathway have been elucidated and genes encoding many of the chlorophyll catabolic enzymes been identified. This review summarizes the current knowledge on the biochemistry of the PAO pathway and provides insight into recent progress made in the field that indicates that the pathway is more complex than thought in the past.

Production, detection, and signaling of singlet oxygen in photosynthetic organisms

SIGNIFICANCE

In photosynthetic organisms, excited chlorophylls (Chl) can stimulate the formation of singlet oxygen ((1)O(2)), a highly toxic molecule that acts in addition to its damaging nature as an important signaling molecule. Thus, due to this dual role of (1)O(2), its production and detoxification have to be strictly controlled.

RECENT ADVANCES

Regulation of pigment synthesis is essential to control (1)O(2) production, and several components of the Chl synthesis and pigment insertion machineries to assemble and disassemble protein/pigment complexes have recently been identified. Once produced, (1)O(2) activates a signaling cascade from the chloroplast to the nucleus that can involve multiple mechanisms and stimulate a specific gene expression response. Further, (1)O(2) signaling was shown to interact with signal cascades of other reactive oxygen species, oxidized carotenoids, and lipid hydroperoxide-derived reactive electrophile species.

CRITICAL ISSUES

Despite recent progresses, hardly anything is known about how and where the (1)O(2) signal is sensed and transmitted to the cytoplasm. One reason for that is the limitation of available detection methods challenging the reliable quantification and localization of (1)O(2) in plant cells. In addition, the process of Chl insertion into the reaction centers and antenna complexes is still unclear.

FUTURE DIRECTIONS

Unraveling the mechanisms controlling (1)O(2) production and signaling would help clarifying the specific role of (1)O(2) in cellular stress responses. It would further enable to investigate the interaction and sensitivity to other abiotic and biotic stress signals and thus allow to better understand why some stressors activate an acclimation, while others provoke a programmed cell death response.

Programmed cell death in plants: lessons from bacteria?

Programmed cell death (PCD) has well-established roles in the development and physiology of animals, plants, and fungi. Although aspects of PCD control appear evolutionarily conserved between these organisms, the extent of conservation remains controversial. Recently, a putative bacterial PCD protein homolog in plants was found to play a significant role in cell death control, indicating a conservation of function between these highly divergent organisms. Interestingly, these bacterial proteins are thought to be evolutionarily linked to the Bcl-2 family of proteins. In this opinion article, we propose a new unifying model to describe the relationship between bacterial and plant PCD systems and propose that the underlying control of PCD is conserved across at least three Kingdoms of life.

Alternative oxidase impacts the plant response to biotic stress by influencing the mitochondrial generation of reactive oxygen species

Previously, we showed that inoculation of tobacco with Pseudomonas syringae incompatible pv. maculicola results in a rapid and persistent burst of superoxide (O(2) (-) ) from mitochondria, no change in amount of mitochondrial alternative oxidase (AOX) and induction of the hypersensitive response (HR). However, inoculation with incompatible pv. phaseolicola resulted in increased AOX, no O(2) (-) burst and no HR. Here, we show that in transgenic plants unable to induce AOX in response to pv. phaseolicola, there is now a strong mitochondrial O(2) (-) burst, similar to that normally seen only with pv. maculicola. This interaction did not however result in a HR. This indicates that AOX amount is a key determinant of the mitochondrial O(2) (-) burst but also that the burst itself is not sufficient to induce the HR. Surprisingly, the O(2) (-) burst normally seen towards pv. maculicola is delayed in plants lacking AOX. This delay is associated with a delayed HR, suggesting that the burst does promote the HR. A O(2) (-) burst can also be induced by the complex III inhibitor antimycin A (AA), but is again delayed in plants lacking AOX. The similar mitochondrial response induced by pv. maculicola and AA suggests that electron transport is a target during HR-inducing biotic interactions.

The signaling role of a mitochondrial superoxide burst during stress

Plant mitochondria are proposed to act as signaling organelles in the orchestration of defense responses to biotic stress and acclimation responses to abiotic stress. However, the primary signal(s) being generated by mitochondria and then interpreted by the cell are largely unknown. Recently, we showed that mitochondria generate a sustained burst of superoxide (O 2(-)) during particular plant-pathogen interactions. This O 2(-) burst appears to be controlled by mitochondrial components that influence rates of O 2(-) generation and scavenging within the organelle. The O 2(-) burst appears to influence downstream processes such as the hypersensitive response, indicating that it could represent an important mitochondrial signal in support of plant stress responses. The findings generate many interesting questions regarding the upstream factors required to generate the O 2(-) burst, the mitochondrial events that occur in support of and in parallel with this burst and the downstream events that respond to this burst.

ROS-mediated lipid peroxidation and RES-activated signaling

Nonenzymatic lipid oxidation is usually viewed as deleterious. But if this is the case, then why does it occur so frequently in cells? Here we review the mechanisms of membrane peroxidation and examine the genesis of reactive electrophile species (RES). Recent evidence suggests that during stress, both lipid peroxidation and RES generation can benefit cells. New results from genetic approaches support a model in which entire membranes can act as supramolecular sinks for singlet oxygen, the predominant reactive oxygen species (ROS) in plastids. RES reprogram gene expression through a class II TGA transcription factor module as well as other, unknown signaling pathways. We propose a framework to explain how RES signaling promotes cell "REScue" by stimulating the expression of genes encoding detoxification functions, cell cycle regulators, and chaperones. The majority of the known biological activities of oxygenated lipids (oxylipins) in plants are mediated either by jasmonate perception or through RES signaling networks.