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

Light dependent protochlorophyllide oxidoreductase: a succinct look

Reducing protochlorophyllide (Pchlide) to chlorophyllide (Chlide) is a major regulatory step in the chlorophyll biosynthesis pathway. This reaction is catalyzed by light-dependent protochlorophyllide oxidoreductase (LPOR) in oxygenic phototrophs, particularly angiosperms. LPOR-NADPH and Pchlide form a ternary complex to be efficiently photo-transformed to synthesize Chlide and, subsequently, chlorophyll during the transition from skotomorphogenesis to photomorphogenesis. Besides lipids, carotenoids and poly-cis xanthophylls influence the formation of the photoactive LPOR complexes and the PLBs. The crystal structure of LPOR reveals evolutionarily conserved cysteine residues implicated in the Pchlide binding and catalysis around the active site. Different isoforms of LPOR viz PORA, PORB, and PORC expressed at different stages of chloroplast development play a photoprotective role by quickly transforming the photosensitive Pchlide to Chlide. Non-photo-transformed Pchlide acts as a photosensitizer to generate singlet oxygen that causes oxidative stress and cell death. Therefore, different isoforms of LPOR have evolved and differentially expressed during plant development to protect plants from photodamage and thus play a pivotal role during photomorphogenesis. This review brings out the salient features of LPOR structure, structure-function relationships, and ultra-fast photo transformation of Pchlide to Chlide by oligomeric and polymeric forms of LPOR.

Phytophthora infestans RXLR effector Pi23014 targets host RNA-binding protein NbRBP3a to suppress plant immunity

Phytophthora infestans is a destructive oomycete that causes the late blight of potato and tomato worldwide. It secretes numerous small proteins called effectors in order to manipulate host cell components and suppress plant immunity. Identifying the targets of these effectors is crucial for understanding P. infestans pathogenesis and host plant immunity. In this study, we show that the virulence RXLR effector Pi23014 of P. infestans targets the host nucleus and chloroplasts. By using a liquid chromatogrpahy-tandem mass spectrometry assay and co-immunoprecipitation assasys, we show that it interacts with NbRBP3a, a putative glycine-rich RNA-binding protein. We confirmed the co-localization of Pi23014 and NbRBP3a within the nucleus, by using bimolecular fluorescence complementation. Reverse transcription-quantitative PCR assays showed that the expression of NbRBP3a was induced in Nicotiana benthamiana during P. infestans infection and the expression of marker genes for multiple defence pathways were significantly down-regulated in NbRBP3-silenced plants compared with GFP-silenced plants. Agrobacterium tumefaciens-mediated transient overexpression of NbRBP3a significantly enhanced plant resistance to P. infestans. Mutations in the N-terminus RNA recognition motif (RRM) of NbRBP3a abolished its interaction with Pi23014 and eliminated its capability to enhance plant resistance to leaf colonization by P. infestans. We further showed that silencing NbRBP3 reduced photosystem II activity, reduced host photosynthetic efficiency, attenuated Pi23014-mediated suppression of cell death triggered by P. infestans pathogen-associated molecular pattern elicitor INF1, and suppressed plant immunity.

Components and processes involved in retrograde signaling from chloroplast to nucleus

Retrograde signaling conceptually means the transfer of signals from semi-autonomous cell organelles to the nucleus to modulate nuclear gene expression. A generalized explanation is that chloroplasts are highly sensitive to environmental stimuli and quickly generate signaling molecules (retrograde signals) and transport them to the nucleus through the cytosol to reprogram nuclear gene expression for cellular/metabolic adjustments to cope with environmental fluctuations. During the past decade, substantial advancements have been made in the area of retrograde signaling, including information on putative retrograde signals. Researchers have also proposed possible mechanisms for generating retrograde signals and their transmission. However, the exact mechanisms and processes responsible for transmitting retrograde signaling from the chloroplast to the nucleus remain elusive, demanding substantial attention. This review highlights strategies employed to detect retrograde signals, their possible modes of signaling to the nucleus, and their implications for cellular processes during stress conditions. The present review also summarizes the role of ROS-mediated retrograde signaling in plastid-nucleus communication and its functional significance in co-coordinating the physiological profile of plant cells.

Arabidopsis EXECUTER1 interacts with WRKY transcription factors to mediate plastid-to-nucleus singlet oxygen signaling

Chloroplasts produce singlet oxygen (1O2), which causes changes in nuclear gene expression through plastid-to-nucleus retrograde signaling to increase plant fitness. However, the identity of this 1O2-triggered pathway remains unclear. Here, we identify mutations in GENOMES UNCOUPLED4 (GUN4) and GUN5 as suppressors of phytochrome-interacting factor1 (pif1) pif3 in regulating the photo-oxidative response in Arabidopsis thaliana. GUN4 and GUN5 specifically interact with EXECUTER1 (EX1) and EX2 in plastids, and this interaction is alleviated by treatment with Rose Bengal (RB) or white light. Impaired expression of GUN4, GUN5, EX1, or EX2 leads to insensitivity to excess light and overexpression of EX1 triggers photo-oxidative responses. Strikingly, upon light irradiation or RB treatment, EX1 transiently accumulates in the nucleus and the nuclear fraction of EX1 shows a similar molecular weight as the plastid-located protein. Point mutagenesis analysis indicated that nuclear localization of EX1 is required for its function. EX1 acts as a transcriptional co-activator and interacts with the transcription factors WRKY18 and WRKY40 to promote the expression of 1O2-responsive genes. This study suggests that EX1 may act in plastid-to-nucleus signaling and establishes a 1O2-triggered retrograde signaling pathway that allows plants adapt to changing light environments during chloroplast development.

Plastid and cytoplasmic origins of 1O2-mediated transcriptomic responses

The reactive oxygen species singlet oxygen, ¹O₂, has an extremely short half-life, yet is intimately involved with stress signalling in the cell. We previously showed that the effects of ¹O₂ on the transcriptome are highly correlated with 80S ribosomal arrest due to oxidation of guanosine residues in mRNA. Here, we show that dysregulation of chlorophyll biosynthesis in the flu mutant or through feeding by δ-aminolevulinic acid can lead to accumulation of photoactive chlorophyll intermediates in the cytoplasm, which generates ¹O₂ upon exposure to light and causes the oxidation of RNA, eliciting ¹O₂-responsive genes. In contrast, transcriptomes derived from DCMU treatment, or the Ch1 mutant under moderate light conditions display commonalties with each other but do not induce ¹O₂ gene signatures. Comparing ¹O₂ related transcriptomes to an index transcriptome induced by cycloheximide inhibition enables distinction between ¹O₂ of cytosolic or of plastid origin. These comparisons provide biological insight to cases of mutants or environmental conditions that produce ¹O₂.

EXECUTER2 modulates the EXECUTER1 signalosome through its singlet oxygen-dependent oxidation

Oxidative post-translational modifications of specific chloroplast proteins contribute to the initiation of retrograde signaling. The Arabidopsis thaliana EXECUTER1 (EX1) protein, a chloroplast-localized singlet oxygen (¹O₂) sensor, undergoes tryptophan (Trp) 643 oxidation by ¹O₂, a chloroplast-derived and light-dependent reactive oxygen species. The indole side chain of Trp is vulnerable to ¹O₂, leading to the generation of oxidized Trp variants and priming EX1 for degradation by a membrane-bound FtsH protease. The perception of ¹O₂ via Trp643 oxidation and subsequent EX1 proteolysis facilitate chloroplast-to-nucleus retrograde signaling. In this study, we discovered that the EX1-like protein EX2 also undergoes ¹O₂-dependent Trp530 oxidation and FtsH-dependent turnover, which attenuates ¹O₂ signaling by decelerating EX1-Trp643 oxidation and subsequent EX1 degradation. Consistent with this finding, the loss of EX2 function reinforces EX1-dependent retrograde signaling by accelerating EX1-Trp643 oxidation and subsequent EX1 proteolysis, whereas overexpression of EX2 produces molecular phenotypes opposite to those observed in the loss-of- function mutants of EX2. Intriguingly, phylogenetic analysis suggests that EX2 may have emerged evolutionarily to attenuate the sensitivity of EX1 toward ¹O₂. Collectively, these results suggest that EX2 functions as a negative regulator of the EX1 signalosome through its own ¹O₂-dependent oxidation, providing a new mechanistic insight into the regulation of EX1-mediated ¹O₂ signaling.

Chloroplast ROS and stress signaling

Chloroplasts overproduce reactive oxygen species (ROS) under unfavorable environmental conditions, and these ROS are implicated in both signaling and oxidative damage. There is mounting evidence for their roles in translating environmental fluctuations into distinct physiological responses, but their targets, signaling cascades, and mutualism and antagonism with other stress signaling cascades and within ROS signaling remain poorly understood. Great efforts made in recent years have shed new light on chloroplast ROS-directed plant stress responses, from ROS perception to plant responses, in conditional mutants of Arabidopsis thaliana or under various stress conditions. Some articles have also reported the mechanisms underlying the complexity of ROS signaling pathways, with an emphasis on spatiotemporal regulation. ROS and oxidative modification of affected target proteins appear to induce retrograde signaling pathways to maintain chloroplast protein quality control and signaling at a whole-cell level using stress hormones. This review focuses on these seemingly interconnected chloroplast-to-nucleus retrograde signaling pathways initiated by ROS and ROS-modified target molecules. We also discuss future directions in chloroplast stress research to pave the way for discovering new signaling molecules and identifying intersectional signaling components that interact in multiple chloroplast signaling pathways.

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.

Photosynthetic signalling during high light stress and recovery: targets and dynamics

The photosynthetic apparatus is one of the major primary sensors of the plant's external environment. Changes in environmental conditions affect the balance between harvested light energy and the capacity to deal with excited electrons in the stroma, which alters the redox homeostasis of the photosynthetic electron transport chain. Disturbances to redox balance activate photosynthetic regulation mechanisms and trigger signalling cascades that can modify the transcription of nuclear genes. H₂O₂ and oxylipins have been identified as especially prominent regulators of gene expression in response to excess light stress. This paper explores the hypothesis that photosynthetic imbalance triggers specific signals that target discrete gene profiles and biological processes. Analysis of the major retrograde signalling pathways engaged during high light stress and recovery demonstrates both specificity and overlap in gene targets. This work reveals distinct, time-resolved profiles of gene expression that suggest a regulatory interaction between rapidly activated abiotic stress response and induction of secondary metabolism and detoxification processes during recovery. The findings of this study show that photosynthetic electron transport provides a finely tuned sensor for detecting and responding to the environment through chloroplast retrograde signalling. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Genome communication in plants mediated by organelle-n-ucleus-located proteins

An increasing number of eukaryotic proteins have been shown to have a dual localization in the DNA-containing organelles, mitochondria and plastids, and/or the nucleus. Regulation of dual targeting and relocation of proteins from organelles to the nucleus offer the most direct means for communication between organelles as well as organelles and nucleus. Most of the mitochondrial proteins of animals have functions in DNA repair and gene expression by modelling of nucleoid architecture and/or chromatin. In plants, such proteins can affect replication and early development. Most plastid proteins with a confirmed or predicted second location in the nucleus are associated with the prokaryotic core RNA polymerase and are required for chloroplast development and light responses. Few plastid–nucleus-located proteins are involved in pathogen defence and cell cycle control. For three proteins, it has been clearly shown that they are first targeted to the organelle and then relocated to the nucleus, i.e. the nucleoid-associated proteins HEMERA and Whirly1 and the stroma-located defence protein NRIP1. Relocation to the nucleus can be experimentally demonstrated by plastid transformation leading to the synthesis of proteins with a tag that enables their detection in the nucleus or by fusions with fluoroproteins in different experimental set-ups.

This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

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.

Beyond the darkness: recent lessons from etiolation and de-etiolation studies

The state of etiolation is generally defined by the presence of non-green plastids (etioplasts) in plant tissues that would normally contain chloroplasts. In the commonly used dark-grown seedling system, etiolation is coupled with a type of growth called skotomorphogenesis. Upon illumination, de-etiolation occurs, marked by the transition from etioplast to chloroplast, and, at the seedling level, a switch to photomorphogenic growth. Etiolation and de-etiolation systems are therefore important for understanding both the acquisition of photosynthetic capacity during chloroplast biogenesis and plant responses to light-the most relevant signal in the life and growth of the organism. In this review, we discuss recent discoveries (within the past 2-3 years) in the field of etiolation and de-etiolation, with a particular focus on post-transcriptional processes and ultrastructural changes. We further discuss ambiguities in definitions of the term 'etiolation', and benefits and biases of common etiolation/de-etiolation systems. Finally, we raise several open questions and future research possibilities.

Oxygen and ROS in Photosynthesis

Oxygen is a natural acceptor of electrons in the respiratory pathway of aerobic organisms and in many other biochemical reactions. Aerobic metabolism is always associated with the formation of reactive oxygen species (ROS). ROS may damage biomolecules but are also involved in regulatory functions of photosynthetic organisms. This review presents the main properties of ROS, the formation of ROS in the photosynthetic electron transport chain and in the stroma of chloroplasts, and ROS scavenging systems of thylakoid membrane and stroma. Effects of ROS on the photosynthetic apparatus and their roles in redox signaling are discussed.

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.