Mitochondria-derived reactive oxygen species are the likely primary trigger of mitochondrial retrograde signaling in Arabidopsis

The SnRK1-JMJ15-CRF6 module integrates energy and mitochondrial signaling to balance growth and the oxidative stress response in Arabidopsis

Mitochondria support plant growth and adaptation via energy production and signaling pathways. However, how mitochondria control the transition between growth and stress response is largely unknown in plants. Using molecular approaches, we identified the histone H3K4me3 demethylase JMJ15 and the transcription factor CRF6 as targets of SnRK1 in Arabidopsis. By analyzing antimycin A (AA)-triggered mitochondrial stress, we explored how SnRK1, JMJ15, and CRF6 form a regulatory module that gauges mitochondrial status to balance growth and the oxidative stress response. SnRK1a1, a catalytic α-subunit of SnRK1, phosphorylates and destabilizes JMJ15 to inhibit its H3K4me3 demethylase activity. While SnRK1a1 does not phosphorylate CRF6, it promotes its degradation via the proteasome pathway. CRF6 interacts with JMJ15 and prevents its SnRK1a1 phosphorylation-dependent degradation, forming an antagonistic feedback loop. SnRK1a1, JMJ15, and CRF6 are required for transcriptional reprogramming in response to AA stress. The transcriptome profiles of jmj15 and crf6 mutants were highly correlated with those of plants overexpressing SnRK1a1 under both normal and AA stress conditions. Genetic analysis revealed that CRF6 acts downstream of SnRK1 and JMJ15. Our findings identify the SnRK1-JMJ15-CRF6 module that integrates energy and mitochondrial signaling for the growth-defense trade-off, highlighting an epigenetic mechanism underlying mitonuclear communication.

Loss of flavonoids homeostasis leads to pistillody in sua-CMS of Nicotiana tabacum

The homeotic transformation of stamens into pistil-like structures (pistillody) causes cytoplasmic male sterility (CMS). This phenomenon is widely present in plants, and might be induced by intracellular communication (mitochondrial retrograde signaling), but its systemic regulating mechanism is still unclear. In this study, morphological observation showed that the stamens transformed into pistil-like structures, leading to flat and dehiscent pistils, and fruit set decrease in sua-CMS (MS K326, somatic fusion between Nicotiana. tabacum L. K326 and Nicotiana suaveolens). Transcriptome data analysis presented that the expression levels of B-class MADS genes, including pMADS1, GLO1, GLO2, pMADS2.1, pMADS2.2, significantly reduced in the pistil-like structure of sua-CMS. DEGs were enriched in flavonoid and phenylpropanoid biosynthesis pathways. Transcriptome and metabolomics analysis revealed that the expression levels of CHI/CHS (key enzymes regulating flavonoid synthesis), and the contents of flavonoids reduced significantly in the pistil-like structures of sua-CMS. Chemical fluorescence staining assay showed that reactive oxygen species (ROS) levels were higher in the pistil-like structure of sua-CMS. Application of external flavonoids (hesperetin) reduced the frequency of pistillody and ROS levels. These results suggested that the metabolism of flavonoids played important roles in regulating pistillody through ROS in sua-CMS. Our study provides new insights into the regulatory mechanism of pistillody in plants.

Jasmonic acid plays an important role in mediating retrograde signaling under mitochondrial translational stress to balance plant growth and defense

Proper mitochondrial function is crucial to plant growth and development. Inhibition of mitochondrial translation leads to mitochondrial proteotoxic stress, which triggers a protective transcriptional response that regulates nuclear gene expression, commonly referred to as the mitochondrial unfolded protein response (UPRmt). Although the UPRmt has been extensively studied in yeast and mammals, very little is known about the UPRmt in plants. Here, we show that mitochondrial translational stress inhibits plant growth and development by inducing jasmonic acid (JA) biosynthesis and signaling. The inhibitory effect of mitochondrial translational stress on plant growth was alleviated in the JA-signaling-defective mutants coi1-2, myc2, and myc234. Genetic analysis indicated that Arabidopsis mitochondrial ribosomal protein L1 (MRPL1), a key factor in the UPRmt, regulates plant growth in a CORONATINE-INSENSITIVE 1 (COI1)-dependent manner. Moreover, under mitochondrial translational stress, MYC2 shows direct binding to G boxes in the ETHYLENE RESPONSE FACTOR 109 (ERF109) promoter. The induction of ERF109 expression enhances hydrogen peroxide production, which acts as a feedback loop to inhibit root growth. In addition, mutation of MRPL1 increases JA accumulation, reduces plant growth, and enhances biotic stress resistance. Overall, our findings reveal that JA plays an important role in mediating retrograde signaling under mitochondrial translational stress to balance plant growth and defense.

ANAC044 orchestrates mitochondrial stress signaling to trigger iron-induced stem cell death in root meristems

While iron (Fe) is essential for life and plays important roles for almost all growth related processes, it can trigger cell death in both animals and plants. However, the underlying mechanisms for Fe-induced cell death in plants remain largely unknown. S-nitrosoglutathione reductase (GSNOR) has previously been reported to regulate nitric oxide homeostasis to prevent Fe-induced cell death within root meristems. Here, we found that in the absence of GSNOR, exposure to high Fe treatment results in DNA damage-dependent cell death specifically in vascular stem cells in root meristems within 48 h. Through a series of time-course transcriptomic analyses, we unveil that in the absence of GSNOR, mitochondrial dysfunction emerges as the most prominent response to high Fe treatment. Consistently, the application of mitochondrial respiratory inhibitors leads to stem cell death in root meristems, and pharmacological blockage of the voltage-dependent anion channel that is responsible for the release of mitochondrial-derived molecules into the cytosol or genetic changes that abolish the ANAC017- and ANAC013-mediated mitochondrial retrograde signaling effectively eliminate Fe-induced stem cell death in gsnor root meristems. We further identify the nuclear transcription factor ANAC044 as a mediator of this mitochondrial retrograde signaling. Disruption of ANAC044 completely abolishes the GSNOR-dependent, Fe-induced stem cell death in root meristems, while ectopic expression of ANAC044 causes severe root stem cell death. Collectively, our findings reveal a mechanism responsible for initiating Fe-induced stem cell death in the root meristem, which is the ANAC044-mediated GSNOR-regulated mitochondrial stress signaling pathway.

Role of aconitase in plant stress response and signaling

Mitochondria are the centres of carbon and energy metabolism in cells and are functionally integrated with other organelles. Under environmental stress, disturbances in organellar functions trigger stress signals that activate the necessary metabolic responses and maintain cell redox homeostasis. The tricarboxylic acid cycle enzyme aconitase has emerged as a key component in stress-induced organellar signalling and a regulator of metabolic and redox balance in photosynthetic organisms. Aconitase mediates mitochondrial and chloroplast retrograde signalling and contributes to the activation of the alternative oxidase (AOX) pathway in mitochondria. Aconitase-driven citrate metabolism plays a crucial role in providing reducing equivalents and metabolic precursors for cytosolic nitrogen metabolism and biosynthetic pathways relevant for stress acclimation. Besides its enzymatic activity, aconitase has a non-canonical function as it is a post-transcriptional regulator of specific gene transcripts. The varied functions of aconitase under stress are facilitated by the regulation of specific aconitase isoforms at multiple levels. This review discusses the emerging role of aconitase as a central regulator of stress responses and signalling in photosynthetic organisms.

Cytochrome c levels link mitochondrial function to plant growth and stress responses through changes in SnRK1 pathway activity

Energy is required for growth as well as for multiple cellular processes. During evolution, plants developed regulatory mechanisms to adapt energy consumption to metabolic reserves and cellular needs. Reduced growth is often observed under stress, leading to a growth-stress trade-off that governs plant performance under different conditions. In this work, we report that plants with reduced levels of the mitochondrial respiratory chain component cytochrome c (CYTc), required for electron transport coupled to oxidative phosphorylation and ATP production, show impaired growth and increased global expression of stress-responsive genes, similar to those observed after inhibiting the respiratory chain or the mitochondrial ATP synthase. CYTc-deficient plants also show activation of the SnRK1 pathway, which regulates growth, metabolism, and stress responses under carbon starvation conditions, even though their carbohydrate levels are not significantly different from wild-type. Notably, loss-of-function of the gene encoding the SnRK1α1 subunit restores the growth of CYTc-deficient plants, as well as autophagy, free amino acid and TOR pathway activity levels, which are affected in these plants. Moreover, increasing CYTc levels decreases SnRK1 pathway activation, reflected in reduced SnRK1α1 phosphorylation, with no changes in total SnRK1α1 protein levels. Under stress imposed by mannitol, the growth of CYTc-deficient plants is relatively less affected than that of wild-type plants, which is also related to the activation of the SnRK1 pathway. Our results indicate that SnRK1 function is affected by CYTc levels, thus providing a molecular link between mitochondrial function and plant growth under normal and stress conditions.

A mechanistic integration of hypoxia signaling with energy, redox, and hormonal cues

Oxygen deficiency (hypoxia) occurs naturally in many developing plant tissues but can become a major threat during acute flooding stress. Consequently, plants as aerobic organisms must rapidly acclimate to hypoxia and the associated energy crisis to ensure cellular and ultimately organismal survival. In plants, oxygen sensing is tightly linked with oxygen-controlled protein stability of group VII ETHYLENE-RESPONSE FACTORs (ERFVII), which, when stabilized under hypoxia, act as key transcriptional regulators of hypoxia-responsive genes (HRGs). Multiple signaling pathways feed into hypoxia signaling to fine-tune cellular decision-making under stress. First, ATP shortage upon hypoxia directly affects the energy status and adjusts anaerobic metabolism. Secondly, altered redox homeostasis leads to reactive oxygen and nitrogen species (ROS and RNS) accumulation, evoking signaling and oxidative stress acclimation. Finally, the phytohormone ethylene promotes hypoxia signaling to improve acute stress acclimation, while hypoxia signaling in turn can alter ethylene, auxin, abscisic acid, salicylic acid, and jasmonate signaling to guide development and stress responses. In this Update, we summarize the current knowledge on how energy, redox, and hormone signaling pathways are induced under hypoxia and subsequently integrated at the molecular level to ensure stress-tailored cellular responses. We show that some HRGs are responsive to changes in redox, energy, and ethylene independently of the oxygen status, and we propose an updated HRG list that is more representative for hypoxia marker gene expression. We discuss the synergistic effects of hypoxia, energy, redox, and hormone signaling and their phenotypic consequences in the context of both environmental and developmental hypoxia.

Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants

Plant cells regularly encounter hypoxia (low-oxygen conditions) as part of normal growth and development, or in response to environmental stresses such as flooding. In recent years, our understanding of the multi-layered control of hypoxia-responsive gene expression has greatly increased. In this Update, we take a broad look at the epigenetic, transcriptional, translational, and post-translational mechanisms that regulate responses to low-oxygen levels. We highlight how a network of post-translational modifications (including phosphorylation), secondary messengers, transcriptional cascades, and retrograde signals from the mitochondria and endoplasmic reticulum (ER) feed into the control of transcription factor activity and hypoxia-responsive gene transcription. We discuss epigenetic mechanisms regulating the response to reduced oxygen availability, through focussing on active and repressive chromatin modifications and DNA methylation. We also describe current knowledge of the co- and post-transcriptional mechanisms that tightly regulate mRNA translation to coordinate effective gene expression under hypoxia. Finally, we present a series of outstanding questions in the field and consider how new insights into the molecular workings of the hypoxia-triggered regulatory hierarchy could pave the way for developing flood-resilient crops.

Perception and processing of stress signals by plant mitochondria

In the course of their life, plants continuously experience a wide range of unfavourable environmental conditions in the form of biotic and abiotic stress factors. The perception of stress via various organelles and rapid, tailored cellular responses are essential for the establishment of plant stress resilience. Mitochondria as the biosynthetic sites of energy equivalents in the form of ATP-provided in order to enable a multitude of biological processes in the cell-are often directly impacted by external stress factors. At the same time, mitochondrial function may fluctuate to a tolerable extent without the need to activate downstream retrograde signalling cascades for stress adaptation. In this Focus Review, we summarise the current state of knowledge on the perception and processing of stress signals by mitochondria and show which layers of retrograde signalling, that is, those involving transcription factors, metabolites, but also enzymes with moonlighting functions, enable communication with the nucleus. Also, light is shed on signal integration between mitochondria and chloroplasts as part of retrograde signalling. With this Focus Review, we aim to show ways in which organelle-specific communication can be further researched and the collected data used in the long-term to strengthen plant resilience in the context of climate change.

Orf116b Induces Pollen Abortion in a Novel Cotton (Gossypium hirsutum L.) Cytoplasmic Male Sterile Line J4A

Cytoplasmic male sterile (CMS) systems have great potential in hybrid seed production in many plants. However, the incompatibility between the cytoplasmic and nuclear genes and the availability of fewer CMS lines limit the system's application in cotton heterosis. Therefore, the present study sequenced the mitochondrial (mt) genomes of a novel cotton (Gossypium hirsutum L.) CMS line J4A and its cytoplasmic nuclear homologous maintainer line J4B to investigate the mechanism underlying CMS and improve its application. A novel CMS gene, orf116b, was identified in the CMS line. Ectopic expression of orf116b in Escherichia coli suppressed growth, while its overexpression in Arabidopsis, rice, tobacco, and cotton led to complete or partial male sterility. Further analysis of anthers revealed mt disruption in J4A with higher levels of hydrogen peroxide (H2O2) and malondialdehyde (MDA), but lower levels of ATP and ribosomal protein (RP) than in J4B. Finally, a membrane-based yeast two-hybrid (MYTH) assay and bimolecular fluorescence complementation (BiFC) assays demonstrated that orf116b probably interacts with an anther-specific protein, LAT52. These observations collectively proved that orf116b is associated with early and stable pollen abortion in cotton, providing a foundation for further research on cotton fertility restoration and heterosis breeding.

Photorespiratory Metabolism and Its Regulatory Links to Plant Defence Against Pathogens

When plants face biotic stress, the induction of defence responses imposes a massive demand for carbon and energy resources, which could decrease the reserves allocated towards growth. These growth-defence trade-offs have important implications for plant fitness and productivity and influence the outcome of plant-pathogen interactions. Biotic stress strongly affects plant cells' primary metabolism, including photosynthesis and respiration, the main source of energy and carbon skeletons for plant growth, development, and defence. Although the nature of photosynthetic limitations imposed by pathogens is variable, infection often increases photorespiratory pressure, generating conditions that promote ribulose-1,5-bisphosphate oxygenation, leading to a metabolic shift from assimilation to photorespiration. Photorespiration, the significant metabolic flux following photosynthesis, protects the photosynthetic apparatus from photoinhibition. However, recent studies reveal that its role is far beyond photoprotection. The intermediates of the photorespiratory cycle regulate photosynthesis, and photorespiration interacts with the metabolic pathways of nitrogen and sulphur, shaping the primary metabolism for stress responses. This work aims to present recent insights into the integration of photorespiration within the network of primary metabolism under biotic stress. It also explores the potential implications of regulating photosynthetic-photorespiratory metabolism for plant defence against bacterial and fungal pathogens.

Mitochondrial ß-Cyanoalanine Synthase Participates in flg22-Induced Stomatal Immunity

Plants regulate gas exchange with the environment and modulate transpirational water flow through guard cells, which set the aperture of the stomatal pores. External and internal stimuli are detected by guard cells and integrated into a signalling network that modulate turgor pressure and, hence, pore size. Pathogen-associated molecular patterns are among the stimuli that induce stomatal closure, to prevent pathogen entry through the pores, and this response, also referred to as stomatal immunity, is one of the hallmarks of PAMP-triggered immunity. While reactive oxygen species (ROS)-mediated signalling plays a key role in stomatal immunity, also the gasotransmitter hydrogen sulphide (H2S) interacts with key components of the guard cell signalling network to induce stomatal closure. While the role of H2S, produced by the main cytosolic source L-cysteine desulfhydrase 1, has been already investigated, there are additional enzymatic sources that synthesize H2S in different subcellular compartments. Their function has remained enigmatic, however. In this work, we elucidate the involvement of the mitochondrial H2S source, β-cyanoalanine synthase CAS-C1, on stomatal immunity induced by the bacterial PAMP flagellin (flg22). We show that cas-c1 plants are impaired to induce flg22-triggered stomatal closure and apoplastic ROS production, while they are more susceptible to bacterial surface inoculation. Moreover, mitochondrial H2S donor AP39 induced stomatal closure in an RBOHD-dependent manner, while depletion of endogenous H2S, impaired RBOHD-mediated apoplastic ROS production. In addition, pharmacological disruption of mitochondrial electron transport chain activity, affected stomatal closure produced by flg22, indicating its participation in the stomatal immunity response. Our findings add evidence to the emerging realization that intracellular organelles play a decisive role in orchestrating stomatal signalling and immune responses and suggest that mitochondrial-derived H2S is an important player of the stomatal immunity signalling network.

Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth

The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control in both mitochondria and chloroplasts, although its function in plastids is still under discussion. Here, we show that the overexpression of RPOTmp in Arabidopsis, targeted either to mitochondria or chloroplasts, disturbs the dormant seed state, and it causes the following effects: earlier germination, decreased ABA sensitivity, faster seedling growth, and earlier flowering. The germination of RPOTmp overexpressors is less sensitive to NaCl, while rpotmp knockout is highly vulnerable to salt stress. We found that mitochondrial dysfunction in the rpotmp mutant induces an unknown retrograde response pathway that bypasses AOX and ANAC017. Here, we show that RPOTmp transcribes the accD, clpP, and rpoB genes in plastids and up to 22 genes in mitochondria.

Mitochondrial Reactive Oxygen Species in Infection and Immunity

Reactive oxygen species (ROS) contain at least one oxygen atom and one or more unpaired electrons and include singlet oxygen, superoxide anion radical, hydroxyl radical, hydroperoxyl radical, and free nitrogen radicals. Intracellular ROS can be formed as a consequence of several factors, including ultra-violet (UV) radiation, electron leakage during aerobic respiration, inflammatory responses mediated by macrophages, and other external stimuli or stress. The enhanced production of ROS is termed oxidative stress and this leads to cellular damage, such as protein carbonylation, lipid peroxidation, deoxyribonucleic acid (DNA) damage, and base modifications. This damage may manifest in various pathological states, including ageing, cancer, neurological diseases, and metabolic disorders like diabetes. On the other hand, the optimum levels of ROS have been implicated in the regulation of many important physiological processes. For example, the ROS generated in the mitochondria (mitochondrial ROS or mt-ROS), as a byproduct of the electron transport chain (ETC), participate in a plethora of physiological functions, which include ageing, cell growth, cell proliferation, and immune response and regulation. In this current review, we will focus on the mechanisms by which mt-ROS regulate different pathways of host immune responses in the context of infection by bacteria, protozoan parasites, viruses, and fungi. We will also discuss how these pathogens, in turn, modulate mt-ROS to evade host immunity. We will conclude by briefly giving an overview of the potential therapeutic approaches involving mt-ROS in infectious diseases.

The Arabidopsis Mitochondrial Nucleoid-Associated Protein WHIRLY2 Is Required for a Proper Response to Salt Stress

In the last years, plant organelles have emerged as central coordinators of responses to internal and external stimuli, which can induce stress. Mitochondria play a fundamental role as stress sensors being part of a complex communication network between the organelles and the nucleus. Among the different environmental stresses, salt stress poses a significant challenge and requires efficient signaling and protective mechanisms. By using the why2 T-DNA insertion mutant and a novel knock-out mutant prepared by CRISPR/Cas9-mediated genome editing, this study revealed that WHIRLY2 is crucial for protecting mitochondrial DNA (mtDNA) integrity during salt stress. Loss-of-function mutants show an enhanced sensitivity to salt stress. The disruption of WHIRLY2 causes the impairment of mtDNA repair that results in the accumulation of aberrant recombination products, coinciding with severe alterations in nucleoid integrity and overall mitochondria morphology besides a compromised redox-dependent response and misregulation of antioxidant enzymes. The results of this study revealed that WHIRLY2-mediated structural features in mitochondria (nucleoid compactness and cristae) are important for an effective response to salt stress.

Advances in membrane-tethered NAC transcription factors in plants

Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.

Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA

Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of chromosomal DNA mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondria can directly damage nuclear DNA is largely lacking. In this study, we investigated the effects of H2O2 released by mitochondria or produced at the nucleosomes using a titratable chemogenetic approach. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2. Nuclear H2O2 gives rise to DNA damage and mutations and a subsequent p53 dependent cell cycle arrest. Mitochondrial H2O2 release shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. We conclude that H2O2 released from mitochondria is unlikely to directly damage nuclear genomic DNA, limiting its contribution to oncogenic transformation and aging.

Plant biology: Unlocking mitochondrial stress signals

Environmental stress induces mitochondrial retrograde signals that prompt protective responses in plants. The elusive mitochondrial signal has now been uncovered in a new study, which identifies formation of reactive oxygen species inside mitochondria as the key trigger of stress signals.