Blocking the QB-binding site of photosystem II by tenuazonic acid, a non-host-specific toxin of Alternaria alternata, activates singlet oxygen-mediated and EXECUTER-dependent signalling in Arabidopsis

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.

What can reactive oxygen species (ROS) tell us about the action mechanism of herbicides and other phytotoxins?

Reactive oxygen species (ROS) are formed in plant cells continuously. When ROS production exceeds the antioxidant capacity of the cells, oxidative stress develops which causes damage of cell components and may even lead to the induction of programmed cell death (PCD). The levels of ROS production increase upon abiotic stress, but also during pathogen attack in response to elicitors, and upon application of toxic compounds such as synthetic herbicides or natural phytotoxins. The commercial value of many synthetic herbicides is based on weed death as result of oxidative stress, and for a number of them, the site and the mechanism of ROS production have been characterized. This review summarizes the current knowledge on ROS production in plants subjected to different groups of synthetic herbicides and natural phytotoxins. We suggest that the use of ROS-specific fluorescent probes and of ROS-specific marker genes can provide important information on the mechanism of action of these toxins. Furthermore, we propose that, apart from oxidative damage, elicitation of ROS-induced PCD is emerging as one of the important processes underlying the action of herbicides and phytotoxins.

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.

Mode-of-action of the natural herbicide radulanin A as an inhibitor of photosystem II

BACKGROUND

Radulanin A is a natural 2,5-dihydrobenzoxepin synthesized by several liverworts of the Radula genus. Breakthroughs in the total synthesis of radulanin A paved the way for the discovery of its phytotoxic activity. Nevertheless, its mode-of-action (MoA) has remained unknown so far and thus was investigated, in Arabidopsis thaliana.

RESULTS

Radulanin A phytotoxicity was associated with cell death and partially depended on light exposure. Photosynthesis measurements based on chlorophyll-a fluorescence evidenced that radulanin A and a Radula chromene inhibited photosynthetic electron transport with IC50 of 95 and 100 μm, respectively. We established a strong correlation between inhibition of photosynthesis and phytotoxicity for a range of radulanin A analogs. Based on these data, we also determined that radulanin A phytotoxicity was abolished when the hydroxyl group was modified, and was modulated by the presence of the heterocycle and its aliphatic chain. Thermoluminescence studies highlighted that radulanin A targeted the QB site of the Photosystem II (PSII) with a similar MoA as 3-(3,4-dichloropheny)-1,1-dimethylurea (DCMU).

CONCLUSION

We establish that radulanin A targets PSII, expanding QB sites inhibitors to bibenzyl compounds. The identification of an easy-to-synthesize analog of radulanin A with similar MoA and efficiency might be useful for future herbicide development. © 2023 Society of Chemical Industry.

Metabolite Analysis of Alternaria Mycotoxins by LC-MS/MS and Multiple Tools

Alternaria fungi are widely distributed plant pathogens that invade crop products, causing significant economic damage. In addition, toxic secondary metabolites produced by the fungi can also endanger consumers. Many of these secondary metabolites are chemically characterized as mycotoxins. In this study, Q Exactive Orbitrap mass spectrometry was used for the non-targeted analysis of the metabolome of seven Alternaria isolates cultured on Potato Carrot Agar (PCA), Potato Dextrose Agar (PDA) and Potato Sucrose Agar (PSA) medium. Due to the difficulty of detecting modified toxins, an analytical strategy with multiple visual analysis tools was also used to determine the presence of sulfate conjugated toxins, as well as to visualize the molecular network of Alternaria toxins. The results show that PSA medium exhibits more advantageous properties for the culture of Alternaria, with more toxigenic species and quantities and more obvious metabolic pathways. Based on high-resolution tandem mass spectrometry (MS/MS) data, the mycotoxins and their metabolites were mainly clustered into four groups: alternariol (AOH)/alternariol monomethyl ether (AME)/altenusin (ALU)/altenuene (ALT)/dehydroaltenusin (DHA)/Desmethyldehydroaltenusin (DMDA) families, Altertoxin-I (ATX-I) family, tentoxin (TEN) family and tenuazonic acid (TeA) family. Moreover, the PSA medium is more suitable for the accumulation of AOH, AME, ALU, ALT, DHA and DMDA, while the PDA medium is more suitable for the accumulation of ATX-I, TEN and TeA. This research may provide theoretical support for the metabolomics study of Alternaria.

Fungal NRPS-PKS Hybrid Enzymes Biosynthesize New γ-Lactam Compounds, Taslactams A-D, Analogous to Actinomycete Proteasome Inhibitors

Proteasome inhibitors with γ-lactam structure, such as lactacystin and salinosporamide A, have been isolated from actinomycetes and have attracted attention as lead compounds for anticancer drugs. Previously, we identified a unique enzyme TAS1, which is the first reported fungal NRPS-PKS hybrid enzyme, from the filamentous fungus Pyricularia oryzae for the biosynthesis of a mycotoxin tenuazonic acid, a tetramic acid compound without γ-lactam structure. Homologues of TAS1 have been identified in several fungal genomes and classified into four groups (A-D). Here, we show that the group D TAS1 homologues from two filamentous fungi can biosynthesize γ-lactam compounds, taslactams A-D, with high similarity to actinomycete proteasome inhibitors. One of the γ-lactam compounds, taslactam C, showed potent proteasome inhibitory activity. In contrast to actinomycete γ-lactam compounds which require multiple enzymes for biosynthesis, the TAS1 homologue alone was sufficient for the biosynthesis of the fungal γ-lactam compounds.

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.

Ethyl Phloretate and Ethyl p-Coumarate: Two Phytotoxins from Valsa mali and Their Pathogenic Activities

Valsa mali, the causal agent of apple Valsa canker, produces several phytotoxic metabolites to promote infection. Bioassay and ¹H nuclear magnetic resonance (NMR)-guided isolation from the culture filtrate of V. mali strain 03-8 led to the identification of seven compounds including three unreported ones, ethyl phloretate (1), ethyl p-coumarate (2), and 1-p-hydroxybenzoyl glycerol (3). Compounds 1 and 2 produced significant phytotoxicity, with average lesion areas of 6.22 and 3.74 mm², along with 2.96 and 3.47 mm² at 1 mg/ml on mature and tissue-cultured apple leaves, respectively, whereas compound 3 did not cause any symptoms on host plants. The necrotic lesion area of compounds 1 and 2 on tobacco leaves was 52.65 and 48.28 mm², respectively, compared with the negative control (0.46 mm²) at 1 mg/ml. At the same concentration, compounds 1 and 2 showed no significant influence on the germination rate of lettuce seeds while significantly decreasing the root length of lettuce seedlings to 6.74 and 4.67 mm, respectively, compared with that treated with sterile distilled water (22.01 mm). The discovery indicated that compounds 1 and 2 could be considered as non-host-specific toxins. Furthermore, compounds 1 and 2 could cause cell shrinkage, organelle damage, plasmolysis, and eventually ruptured protoplasmic membranes with cell death for their phytotoxicity in the host plants under optical microscopy and transmission electron microscopy. The results shed light on the mechanism for toxins 1 and 2 in V. mali-infected plants at the macroscopic and cellular levels.

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.

Biosynthesis and biological function of secondary metabolites of the rice blast fungus Pyricularia oryzae

Filamentous fungi have many secondary metabolism genes and produce a wide variety of secondary metabolites with complex and unique structures. However, the role of most secondary metabolites remains unclear. Moreover, most fungal secondary metabolism genes are silent or poorly expressed under laboratory conditions and are difficult to utilize. Pyricularia oryzae, the causal pathogen of rice blast disease, is a well-characterized plant pathogenic fungus. P. oryzae also has a large number of secondary metabolism genes and appears to be a suitable organism for analyzing secondary metabolites. However, in case of this fungus, biosynthetic genes for only four groups of secondary metabolites have been well characterized. Among two of the four groups of secondary metabolites, biosynthetic genes were identified by activating secondary metabolism. These secondary metabolites include melanin, a polyketide compound required for rice infection; tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique nonribosomal peptide synthetase-polyketide synthase hybrid enzyme; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi, including plant pathogens and endophytes, and pyriculols, phytotoxic polyketide compounds. This review mainly focuses on the biosynthesis and biological functions of the four groups of P. oryzae secondary metabolites.

Tenuazonic acid production is dispensable for virulence, but its biosynthetic gene expression pattern is associated with the infection of Pyricularia oryzae

Tenuazonic acid (TeA) is a toxin produced by the rice blast fungus Pyricularia oryzae. Although knockout of the TeA biosynthetic gene TAS1 did not affect the virulence of P. oryzae, constitutive TAS1 expression suppressed its infection. TAS1 expression was induced alongside transition of P. oryzae infection behavior. The results suggested that controlling TeA biosynthesis is important for P. oryzae infection.

Screening of tenuazonic acid production-inducing compounds and identification of NPD938 as a regulator of fungal secondary metabolism

The control of secondary metabolism in fungi is essential for the regulation of various cellular functions. In this study, we searched the RIKEN Natural Products Depository (NPDepo) chemical library for inducers of tenuazonic acid (TeA) production in the rice blast fungus Pyricularia oryzae and identified NPD938. NPD938 transcriptionally induced TeA production. We explored the mode of action of NPD938 and observed that this compound enhanced TeA production via LAE1, a global regulator of fungal secondary metabolism. NPD938 could also induce production of terpendoles and pyridoxatins in Tolypocladium album RK99-F33. Terpendole production was induced transcriptionally. We identified the pyridoxatin biosynthetic gene cluster among transcriptionally induced secondary metabolite biosynthetic gene clusters. Therefore, NPD938 is useful for the control of fungal secondary metabolism.

Tenuazonic Acid-Triggered Cell Death Is the Essential Prerequisite for Alternaria alternata (Fr.) Keissler to Infect Successfully Host Ageratina adenophora

The necrotrophic fungus Alternaria alternata contains different pathotypes that produce different mycotoxins. The pathotype Ageratina adenophora secretes the non-host-selective toxin tenuazonic acid (TeA), which can cause necrosis in many plants. Although TeA is thought to be a central virulence factor of the A. adenophora pathotype, the precise role of TeA in different stages of host infection by pathogens remains unclear. Here, an A. alternata wild-type and the toxin-deficient mutant ΔHP001 with a 75% reduction in TeA production were used. It was observed that wild-type pathogens could induce the reactive oxygen species (ROS) bursts in host leaves and killed photosynthetic cells before invading hyphae. The ROS interceptor catalase remarkably inhibited hyphal penetration and invasive hyphal growth and expansion in infected leaves and suppressed necrotic leaf lesion. This suggests that the production of ROS is critical for pathogen invasion and proliferation and disease symptom formation during infection. It was found that the mutant pathogens did not cause the formation of ROS and cell death in host leaves, showing an almost complete loss of disease susceptibility. In addition, the lack of TeA resulted in a significant reduction in the ability of the pathogen to penetrate invasive hyphal growth and spread. The addition of exogenous TeA, AAL-toxin, and bentazone to the mutant ΔHP001 pathogens during inoculation resulted in a significant restoration of pathogenicity by increasing the level of cell death, frequency of hyphal penetration, and extent of invasive hyphal spread. Our results suggest that cell death triggered by TeA is the essential requirement for successful colonization and disease development in host leaves during infection with A. adenophora pathogens.

Phytotoxic Secondary Metabolites from Fungi

Fungal phytotoxic secondary metabolites are poisonous substances to plants produced by fungi through naturally occurring biochemical reactions. These metabolites exhibit a high level of diversity in their properties, such as structures, phytotoxic activities, and modes of toxicity. They are mainly isolated from phytopathogenic fungal species in the genera of Alternaria, Botrytis, Colletotrichum, Fusarium, Helminthosporium, and Phoma. Phytotoxins are either host specific or non-host specific phytotoxins. Up to now, at least 545 fungal phytotoxic secondary metabolites, including 207 polyketides, 46 phenols and phenolic acids, 135 terpenoids, 146 nitrogen-containing metabolites, and 11 others, have been reported. Among them, aromatic polyketides and sesquiterpenoids are the main phytotoxic compounds. This review summarizes their chemical structures, sources, and phytotoxic activities. We also discuss their phytotoxic mechanisms and structure-activity relationships to lay the foundation for the future development and application of these promising metabolites as herbicides.

Secondary Metabolites of the Rice Blast Fungus Pyricularia oryzae: Biosynthesis and Biological Function

Plant pathogenic fungi produce a wide variety of secondary metabolites with unique and complex structures. However, most fungal secondary metabolism genes are poorly expressed under laboratory conditions. Moreover, the relationship between pathogenicity and secondary metabolites remains unclear. To activate silent gene clusters in fungi, successful approaches such as epigenetic control, promoter exchange, and heterologous expression have been reported. Pyricularia oryzae, a well-characterized plant pathogenic fungus, is the causal pathogen of rice blast disease. P. oryzae is also rich in secondary metabolism genes. However, biosynthetic genes for only four groups of secondary metabolites have been well characterized in this fungus. Biosynthetic genes for two of the four groups of secondary metabolites have been identified by activating secondary metabolism. This review focuses on the biosynthesis and roles of the four groups of secondary metabolites produced by P. oryzae. These secondary metabolites include melanin, a polyketide compound required for rice infection; pyriculols, phytotoxic polyketide compounds; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi including endophytes and plant pathogens; and tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique NRPS-PKS enzyme.

Complexity of Brassica oleracea-Alternaria brassicicola Susceptible Interaction Reveals Downregulation of Photosynthesis at Ultrastructural, Transcriptional, and Physiological Levels

Black spot disease, caused by Alternaria brassicicola in Brassica species, is one of the most devastating diseases all over the world, especially since there is no known fully resistant Brassica cultivar. In this study, the visualization of black spot disease development on Brassica oleracea var. capitata f. alba (white cabbage) leaves and subsequent ultrastructural, molecular and physiological investigations were conducted. Inter- and intracellular hyphae growth within leaf tissues led to the loss of host cell integrity and various levels of organelle disintegration. Severe symptoms of chloroplast damage included the degeneration of chloroplast envelope and grana, and the loss of electron denseness by stroma at the advanced stage of infection. Transcriptional profiling of infected leaves revealed that photosynthesis was the most negatively regulated biological process. However, in infected leaves, chlorophyll and carotenoid content did not decrease until 48 hpi, and several chlorophyll a fluorescence parameters, such as photosystem II quantum yield (Fv/Fm), non-photochemical quenching (NPQ), or plant vitality parameter (Rdf) decreased significantly at 24 and 48 hpi compared to control leaves. Our results indicate that the initial stages of interaction between B. oleracea and A. brassicicola are not uniform within an inoculation site and show a complexity of host responses and fungal attempts to overcome host cell defense mechanisms. The downregulation of photosynthesis at the early stage of this susceptible interaction suggests that it may be a part of a host defense strategy, or, alternatively, that chloroplasts are targets for the unknown virulence factor(s) of A. brassicicola. However, the observed decrease of photosynthetic efficiency at the later stages of infection is a result of the fungus-induced necrotic lesion expansion.

Overview of Alternaria alternata Membrane Proteins

Alternaria species are mainly saprophytic fungi, but some pathotypes of Alternaria alternata infect economically important plants including cereal crops, vegetables and fruits. Specially, A. alternata generates toxins which contaminate food and feed. To date, management of A. alternata relies primarily on fungicides. However, the control efficacy in most cases is below expectation due to ubiquity of A. alternata and resistance to fungicides. To mitigate resistance and develop long-lasting fungicides, uncovering multiple rather than single target is a prerequisite. Membrane proteins are potential targets of fungicides owing to wide participation in myriad biochemical events especially material transport, signal transduction and pathogenicity. However, so far, little is known about the distribution and molecular structure of A. alternata membrane proteins (AAMPs). Herein we summarize AAMPs by data mining and subsequent structure prediction. We also outline the state-of-the-art research advances of AAMPs especially those closely related to pathogenicity. Overall, this review aims to portray a picture of AAMPs and provide valuable insights for future development of highly efficient fungicides towards A. alternata or beyond.

Three phytotoxins produced by Neopestalotiopsis clavispora, the causal agent of ring spot on Kadsura coccinea

Phytotoxins are widely found in plant pathogens. In recent years, many diseases caused by Neopestalotiopsis clavispora have been reported. To better understand the pathogenicity of N. clavispora, a solid fermentation strategy was employed to isolate and identify virulence factors afritoxinone B, afritoxinone A and oxysporone. The phytotoxic activities of these toxins were evaluated. Oxysporone exhibited high levels of phytotoxic activity after 72 h and the lesion area ranged from 21.5-84.3 mm2 after 9 days of treatment. The phytotoxic activities of the other two compounds were lower than that for oxysporone. The phytotoxic activity towards non-host organisms was also assessed for the three analyzed compounds; phytotoxic activity was observed in each case. Based on these results, we conclude that oxysporone is the main virulence factor in N. clavispora. We also suggest that each of the three compounds were non-host-specific toxins (NHST). To our knowledge, this is the first study to analyze phytotoxins produced by N. clavispora.

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.

Antioxidant and signaling functions of the plastoquinone pool in higher plants

The review covers data representing the plastoquinone pool as the component integrated in plant antioxidant defense and plant signaling. The main goal of the review is to discuss the evidence describing the plastoquinone-involved biochemical reactions, which are incorporated in maintaining the sustainability of higher plants to stress conditions. In this context, the analysis of the reactions of various redox forms of plastoquinone with oxygen species is presented. The review describes how these reactions can constitute both the antioxidant and signaling functions of the pool. Special attention is paid to the reaction of superoxide anion radicals with plastohydroquinone molecules, producing hydrogen peroxide as signal molecules. Attention is also given to the processes affecting the redox state of the plastoquinone pool because the redox state of the pool is of special importance for antioxidant defense and signaling.

Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii

Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Despite the close association of the TOR signaling with the coordination between protein turn-over and growth, proteome and phosphoproteome acclimation to a rapamycin treatment have not yet been thoroughly investigated in Chlamydomonas reinhardtii. In this study, we have used in vivo label-free phospho-proteomic analysis to profile both protein and phosphorylation changes at 0, 24, and 48 h in Chlamydomonas cells treated with rapamycin. Using multivariate statistics we highlight the impact of TOR inhibition on both the proteome and the phosphoproteome. Two-way ANOVA distinguished differential levels of proteins and phosphoproteins in response either to culture duration and rapamycin treatment or combined effects. Finally, protein-protein interaction networks and functional enrichment analysis underlined the relation between plastid and mitochondrial metabolism. Prominent changes of proteins involved in sulfur, cysteine, and methionine as well as nucleotide metabolism on the one hand, and changes in the TCA cycle on the other highlight the interplay of chloroplast and mitochondria metabolism. Furthermore, TOR inhibition revealed changes in the endomembrane trafficking system. Phosphoproteomics data, on the other hand, highlighted specific differentially regulated phosphorylation sites for calcium-regulated protein kinases as well as ATG7, S6K, and PP2C. To conclude we provide a first combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition, which will support further investigations.

Chloroplast signaling and quality control

Although chloroplasts contain their own genetic system and are semi-autonomous cell organelles, plastid biogenesis and homeostasis are heavily dependent on the nucleo-cytosolic compartment. These two cellular compartments are closely co-ordinated through a complex signaling network comprising both anterograde and retrograde signaling chains. Developmental changes or any perturbation in the chloroplast system induced by a particular stress resulting from changes in environmental conditions such as excess light, elevated temperature, nutrient limitation, pathogen infection, give rise to specific signals. They migrate out of the chloroplast and are perceived by the nucleus where they elicit changes in expression of particular genes that allow for the maintenance of plastid homeostasis toward environmental cues. These genes mainly include those of photosynthesis-associated proteins, chaperones, proteases, nucleases and immune/defense proteins. Besides this transcriptional response, a chloroplast quality control system exists that is involved in the repair and turnover of damaged plastid proteins. This system degrades aggregated or damaged proteins and it can even remove entire chloroplasts when they have suffered heavy damage. This response comprises several processes such as plastid autophagy and ubiquitin–proteasome mediated proteolysis that occurs on the plastid envelope through the action of the ubiquitin–proteasome system.

Recent advances in tenuazonic acid as a potential herbicide

Tenuazonic acid (TeA), belonging to tetramic acids that are the largest family of natural products, is a mycotoxin produced by members of the genus Alternaria and other phytopathogenic fungi. TeA has many desirable bioactivities. In the past two decades, several studies have addressed its phytotoxic activity. Because it can cause brown leaf spot and kill seedlings of mono- and dicotyledonous plants, TeA is regarded as a potential herbicidal agent. TeA blocks electron transport beyond Q_A by interacting with D1 protein and is a PSII inhibitor. The chloroplast-derived oxidative burst is responsible for TeA-induced cell death and plant necrosis. Based on the model of molecular interaction between TeA and D1 protein, a series of its derivatives with stable herbicidal activity have been designed, evaluated and patented. Recently, some chemical synthetic approaches of TeA and its derivatives have been successfully developed. This paper will mainly focus on new developments regarding TeA's herbicidal activity, mode of action, biosynthesis and chemical synthesis, and characterization of new derivatives.

TeA is a key virulence factor for Alternaria alternata (Fr.) Keissler infection of its host

A toxin-deficient mutant strain, HP001 mutant of Alternaria alternata, whose mycelium is unable to infect its host, produces little tenuazonic acid (TeA) toxin. How TeA plays a role in initiating host infection by A. alternata remains unclear. In this research we use Imaging-PAM based on chlorophyll fluorescence parameters and transmission electron microscopy to explore the role of TeA toxin during the infection process of A. alternata. Photosystem II damage began even before wild type mycelium infected the leaves of its host, croftonweed (Ageratina adenophora). Compared with the wild type, HP001 mutant produces morphologically different colonies, hyphae with thinner cell walls, has higher reactive oxygen species (ROS) content and lower peroxidase activity, and fails to form appressoria on the host surface. Adding TeA toxin allows the mutant to partially recover these characters and more closely resemble the wild type. Additionally, we found that the mutant is able to elicit disease symptoms when its mycelium is placed on leaves whose epidermis has been manually removed, which indicates that TeA may be determinant in the fungus recognition of its plant host. Lack of TeA toxin appears responsible for the loss of pathogenicity of the HP001 mutant. As a key virulence factor, TeA toxin not only damages the host plant but also is involved in maintaining ROS content, host recognition, inducing appressoria to infect the host and for allowing completion of the infection process.

FtsH2-Dependent Proteolysis of EXECUTER1 Is Essential in Mediating Singlet Oxygen-Triggered Retrograde Signaling in Arabidopsis thaliana

Photosystem II reaction center (PSII RC) and light-harvesting complex inevitably generate highly reactive singlet oxygen (¹O₂) that can impose photo-oxidative damage, especially when the rate of generation exceeds the rate of detoxification. Besides being toxic, ¹O₂ has also been ascribed to trigger retrograde signaling, which leads to nuclear gene expression changes. Two distinctive molecular components appear to regulate ¹O₂ signaling: a volatile signaling molecule β-cyclocitral (β-CC) generated upon oxidation of β-carotene by ¹O₂ in PSII RC assembled in grana core, and a thylakoid membrane-bound FtsH2 metalloprotease that promotes ¹O₂-triggered signaling through the proteolysis of EXECUTER1 (EX1) proteins associated with PSII in grana margin. The role of FtsH2 protease in ¹O₂ signaling was established recently in the conditional fluorescent (flu) mutant of Arabidopsis thaliana that generates ¹O₂ upon dark-to-light shift. The flu mutant lacking functional FtsH2 significantly impairs ¹O₂-triggered and EX1-mediated cell death. In the present study, the role of FtsH2 in the induction of ¹O₂ signaling was further clarified by analyzing the FtsH2-dependent nuclear gene expression changes in the flu mutant. Genome-wide transcriptome analysis showed that the inactivation of FtsH2 repressed the majority (85%) of the EX1-dependent ¹O₂-responsive genes (SORGs), providing direct connection between FtsH2-mediated EX1 degradation and ¹O₂-triggered gene expression changes. Furthermore, the overlap between β-CC-induced genes and EX1-FtsH2-dependent genes was very limited, further supporting the coexistence of two distinctive ¹O₂ signaling pathways.

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress

Although RNA-Seq has revolutionized transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. Here, we describe the development and application of a rapid and convenient method, ChloroSeq, to delineate qualitative and quantitative features of chloroplast RNA metabolism from strand-specific RNA-Seq datasets, including processing, editing, splicing, and relative transcript abundance. The use of a single experiment to analyze systematically chloroplast transcript maturation and abundance is of particular interest due to frequent pleiotropic effects observed in mutants that affect chloroplast gene expression and/or photosynthesis. To illustrate its utility, ChloroSeq was applied to published RNA-Seq datasets derived from Arabidopsis thaliana grown under control and abiotic stress conditions, where the organellar transcriptome had not been examined. The most appreciable effects were found for heat stress, which induces a global reduction in splicing and editing efficiency, and leads to increased abundance of chloroplast transcripts, including genic, intergenic, and antisense transcripts. Moreover, by concomitantly analyzing nuclear transcripts that encode chloroplast gene expression regulators from the same libraries, we demonstrate the possibility of achieving a holistic understanding of the nucleus-organelle system. ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq

Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results. We tested our method on publicly available data from several experiments performed on the rat pineal gland and Toxoplasma gondii, successfully detecting known and previously validated AIR genes in 19 out of 19 gene-level hypothesis tests. Due to its ability to query novel splice sites, JunctionSeq is still able to detect these differences even when all alternative isoforms for these genes were not included in the transcript annotation. JunctionSeq thus provides a powerful method for detecting alternative isoform regulation even with low-quality annotations. An implementation of JunctionSeq is available as an R/Bioconductor package.

Learning the Languages of the Chloroplast: Retrograde Signaling and Beyond

The chloroplast can act as an environmental sensor, communicating with the cell during biogenesis and operation to change the expression of thousands of proteins. This process, termed retrograde signaling, regulates expression in response to developmental cues and stresses that affect photosynthesis and yield. Recent advances have identified many signals and pathways-including carotenoid derivatives, isoprenes, phosphoadenosines, tetrapyrroles, and heme, together with reactive oxygen species and proteins-that build a communication network to regulate gene expression, RNA turnover, and splicing. However, retrograde signaling pathways have been viewed largely as a means of bilateral communication between organelles and nuclei, ignoring their potential to interact with hormone signaling and the cell as a whole to regulate plant form and function. Here, we discuss new findings on the processes by which organelle communication is initiated, transmitted, and perceived, not only to regulate chloroplastic processes but also to intersect with cellular signaling and alter physiological responses.

A User's View of the Parameters Derived from the Induction Curves of Maximal Chlorophyll a Fluorescence: Perspectives for Analyzing Stress

Analysis of the fast kinetics of the induction curve of maximal fluorescence represents a relatively recent development for chlorophyll a fluorescence measurements. The parameters of the so-called JIP-test are exploited by an increasingly large community of users to assess plant stress and its consequences. We provide here evidence that these parameters are capable to distinguish between stresses of different natures or intensities, and between stressed plants of different genetic background or at different developmental stages at the time of stress. It is, however, important to keep in mind that the JIP-test is inherently limited in scope, that it is based on assumptions which are not fully validated and that precautions must be taken to ensure that measurements are meaningful. Recent advances suggest that some improvements could be implemented to increase the reliability of measurements and the pertinence of the parameters calculated. We moreover advocate for using the JIP-test in combination with other techniques to build comprehensive pictures of plant responses to stress.