Mitochondria/nuclear signaling of alternative oxidase gene expression occurs through distinct pathways involving organic acids and reactive oxygen species

Biomolecular interaction of purified recombinant Arabidopsis thaliana's alternative oxidase 1A with TCA cycle metabolites: Biophysical and molecular docking studies

In higher plants, the mitochondrial alternative oxidase (AOX) pathway plays an essential role in maintaining the TCA cycle/cellular carbon and energy balance under various physiological and stress conditions. Though the activation of AOX pathway upon exogenous addition of α-ketoacids/TCA cycle metabolites [pyruvate, α-ketoglutarate (α-KG), oxaloacetic acid (OAA), succinate and malic acid] to isolated mitochondria is known, the molecular mechanism of interaction of these metabolites with AOX protein is limited. The present study is designed to understand the biomolecular interaction of pure recombinant Arabidopsis thaliana AOX1A with TCA cycle metabolites under in vitro conditions using various biophysical and molecular docking studies. The binding of α-KG, fumaric acid and OAA to rAtAOX1A caused conformational change in the microenvironment of tryptophan residues as evidenced by red shift in the synchronous fluorescence spectra (∆λ = 60 nm). Besides, a decrease in conventional fluorescence emission spectra, tyrosine specific synchronous fluorescence spectra (∆λ = 15 nm) and α-helical content of CD spectra revealed the conformation changes in rAtAOX1A structure associated with binding of various TCA cycle metabolites. Further, surface plasmon resonance (SPR) and microscale thermophoresis (MST) studies revealed the binding affinity, while docking studies identified binding pocket residues, respectively, for these metabolites on rAtAOX1A.

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

Besides their central function in respiration, plant mitochondria play a crucial role in maintaining cellular homeostasis during stress by providing "retrograde" feedback to the nucleus. Despite the growing understanding of this signaling network, the nature of the signals that initiate mitochondrial retrograde regulation (MRR) in plants remains unknown. Here, we investigated the dynamics and causative relationship of a wide range of mitochondria-related parameters for MRR, using a combination of Arabidopsis fluorescent protein biosensor lines, in vitro assays, and genetic and pharmacological approaches. We show that previously linked physiological parameters, including changes in cytosolic ATP, NADH/NAD+ ratio, cytosolic reactive oxygen species (ROS), pH, free Ca2+, and mitochondrial membrane potential, may often be correlated with-but are not the primary drivers of-MRR induction in plants. However, we demonstrate that the induced production of mitochondrial ROS is the likely primary trigger for MRR induction in Arabidopsis. Furthermore, we demonstrate that mitochondrial ROS-mediated signaling uses the ER-localized ANAC017-pathway to induce MRR response. Finally, our data suggest that mitochondrially generated ROS can induce MRR without substantially leaking into other cellular compartments such as the cytosol or ER lumen, as previously proposed. Overall, our results offer compelling evidence that mitochondrial ROS elevation is the likely trigger of MRR.

Germination of Pisum sativum L. Seeds Is Associated with the Alternative Respiratory Pathway

The alternative oxidase (AOX) is a ubiquinol oxidase with a crucial role in the mitochondrial alternative respiratory pathway, which is associated with various processes in plants. In this study, the activity of AOX in pea seed germination was determined in two pea cultivars, 'Maravilha d'América' (MA) and 'Torta de Quebrar' (TQ), during a germination trial using cytochrome oxidase (COX) and AOX inhibitors [rotenone (RT) and salicylic hydroxamic acid (SHAM), respectively]. Calorespirometry was used to assess respiratory changes during germination. In both cultivars, SHAM had a greater inhibitory effect on germination than RT, demonstrating the involvement of AOX in germination. Although calorespirometry did not provide direct information on the involvement of the alternative pathway in seed germination, this methodology was valuable for distinguishing cultivars. To gain deeper insights into the role of AOX in seed germination, the AOX gene family was characterized, and the gene expression pattern was evaluated. Three PsAOX members were identified-PsAOX1, PsAOX2a and PsAOX2b-and their expression revealed a marked genotype effect. This study emphasizes the importance of AOX in seed germination, contributing to the understanding of the role of the alternative respiratory pathway in plants.

Fine Tuning of ROS, Redox and Energy Regulatory Systems Associated with the Functions of Chloroplasts and Mitochondria in Plants under Heat Stress

Heat stress severely affects plant growth and crop production. It is therefore urgent to uncover the mechanisms underlying heat stress responses of plants and establish the strategies to enhance heat tolerance of crops. The chloroplasts and mitochondria are known to be highly sensitive to heat stress. Heat stress negatively impacts on the electron transport chains, leading to increased production of reactive oxygen species (ROS) that can cause damages on the chloroplasts and mitochondria. Disruptions of photosynthetic and respiratory metabolisms under heat stress also trigger increase in ROS and alterations in redox status in the chloroplasts and mitochondria. However, ROS and altered redox status in these organelles also activate important mechanisms that maintain functions of these organelles under heat stress, which include HSP-dependent pathways, ROS scavenging systems and retrograde signaling. To discuss heat responses associated with energy regulating organelles, we should not neglect the energy regulatory hub involving TARGET OF RAPAMYCIN (TOR) and SNF-RELATED PROTEIN KINASE 1 (SnRK1). Although roles of TOR and SnRK1 in the regulation of heat responses are still unknown, contributions of these proteins to the regulation of the functions of energy producing organelles implicate the possible involvement of this energy regulatory hub in heat acclimation of plants.

Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review

The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.

A strategy for promoting carbon flux into fatty acid and astaxanthin biosynthesis by inhibiting the alternative oxidase respiratory pathway in Haematococcus pluvialis

In the present study, the mechanisms for facilitating fatty acid and astaxanthin biosynthesis-related processes by inhibiting the alternative oxidase (AOX) respiratory pathway in Haematococcus pluvialis was investigated. The restriction of the AOX pathway induced the accumulation of reactive oxygen species, NAD(P)H and its substrates (acetyl-CoA, pyruvate and glyceraldehy-3-phosphate), which are required for fatty acid and astaxanthin production, thereby promoting the carbon flux into fatty acid and astaxanthin biosynthesis. During a 9-day incubation period, the fatty acid and astaxanthin contents increased by 20.6% and 20.7%, respectively, when the AOX pathway was inhibited approximately 37.7%. The AOX pathway may be inhibited by nutrient (nitrogen and phosphorus) removal, inhibitor addition and air/CO₂ aeration adjustments in the large-scale cultivation of H. pluvialis. Therefore, the current study provides a useful enhancement strategy for fatty acid and astaxanthin coproduction and elucidates the roles of the AOX pathway in regulating fatty acid and astaxanthin biosynthesis.

ACONITASE 3 is part of theANAC017 transcription factor-dependent mitochondrial dysfunction response

Mitochondria are tightly embedded within metabolic and regulatory networks that optimize plant performance in response to environmental challenges. The best-known mitochondrial retrograde signaling pathway involves stress-induced activation of the transcription factor NAC DOMAIN CONTAINING PROTEIN 17 (ANAC017), which initiates protective responses to stress-induced mitochondrial dysfunction in Arabidopsis (Arabidopsis thaliana). Posttranslational control of the elicited responses, however, remains poorly understood. Previous studies linked protein phosphatase 2A subunit PP2A-B'γ, a key negative regulator of stress responses, with reversible phosphorylation of ACONITASE 3 (ACO3). Here we report on ACO3 and its phosphorylation at Ser91 as key components of stress regulation that are induced by mitochondrial dysfunction. Targeted mass spectrometry-based proteomics revealed that the abundance and phosphorylation of ACO3 increased under stress, which required signaling through ANAC017. Phosphomimetic mutation at ACO3-Ser91 and accumulation of ACO3S91D-YFP promoted the expression of genes related to mitochondrial dysfunction. Furthermore, ACO3 contributed to plant tolerance against ultraviolet B (UV-B) or antimycin A-induced mitochondrial dysfunction. These findings demonstrate that ACO3 is both a target and mediator of mitochondrial dysfunction signaling, and critical for achieving stress tolerance in Arabidopsis leaves.

DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera

The sacred lotus (Nelumbo nucifera) can maintain a stable floral chamber temperature between 30 and 35 °C when blooming despite fluctuations in ambient temperatures between about 8 and 45 °C, but the regulatory mechanism of floral thermogenesis remains unclear. Here, we obtained comprehensive protein profiles from receptacle tissue at five developmental stages using data-independent acquisition (DIA)-based quantitative proteomics technology to reveal the molecular basis of floral thermogenesis of N. nucifera. A total of 6913 proteins were identified and quantified, of which 3513 differentially abundant proteins (DAPs) were screened. Among them, 640 highly abundant proteins during the thermogenic stages were mainly involved in carbon metabolism processes such as the tricarboxylic acid (TCA) cycle. Citrate synthase was identified as the most connected protein in the protein-protein interaction (PPI) network. Next, the content of alternative oxidase (AOX) and plant uncoupling protein (pUCP) in different tissues indicated that AOX was specifically abundant in the receptacles. Subsequently, a protein module highly related to the thermogenic phenotype was identified by the weighted gene co-expression network analysis (WGCNA). In summary, the regulation mechanism of floral thermogenesis in N. nucifera involves complex regulatory networks, including TCA cycle metabolism, starch and sucrose metabolism, fatty acid degradation, and ubiquinone synthesis, etc.

The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of ALTERNATIVE OXIDASE1a under high intensity light

We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and AOX1a transgenic Arabidopsis thaliana following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The AOX1a overexpressing line (XX-2) showed the highest amount of AOX1a transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6-8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed 'overcompensation effects' prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with AOX1a, light- and stress-related cis-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of AOX1a expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.

Degradation of mitochondrial alternative oxidase in the appendices of Arum maculatum

Cyanide-resistant alternative oxidase (AOX) is a nuclear-encoded quinol oxidase located in the inner mitochondrial membrane. Although the quality control of AOX proteins is expected to have a role in elevated respiration in mitochondria, it remains unclear whether thermogenic plants possess molecular mechanisms for the mitochondrial degradation of AOX. To better understand the mechanism of AOX turnover in mitochondria, we performed a series of in organello AOX degradation assays using mitochondria from various stages of the appendices of Arum maculatum. Our analyses clearly indicated that AOX proteins at certain stages in the appendices are degraded at 30°C, which is close to the maximum appendix temperature observed during thermogenesis. Interestingly, such temperature-dependent protease activities were specifically inhibited by E-64, a cysteine protease inhibitor. Moreover, purification and subsequent nano LC–MS/MS analyses of E-64-sensitive and DCG-04-labeled active mitochondrial protease revealed an ∼30 kDa protein with an identical partial peptide sequence to the cysteine protease 1-like protein from Phoenix dactylifera. Our data collectively suggest that AOX is a potential target for temperature-dependent E-64-sensitive cysteine protease in the appendices of A. maculatum. A possible retrograde signalling cascade mediated by specific degradation of AOX proteins and its physiological significance are discussed.

Linking mitochondrial and chloroplast retrograde signalling in plants

Retrograde signalling refers to the regulation of nuclear gene expression in response to functional changes in organelles. In plants, the two energy-converting organelles, mitochondria and chloroplasts, are tightly coordinated to balance their activities. Although our understanding of components involved in retrograde signalling has greatly increased in the last decade, studies on the regulation of the two organelle signalling pathways have been largely independent. Thus, the mechanism of how mitochondrial and chloroplastic retrograde signals are integrated is largely unknown. Here, we summarize recent findings on the function of mitochondrial signalling components and their links to chloroplast retrograde responses. From this, a picture emerges showing that the major regulators are integrators of both organellar retrograde signalling pathways. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Citrate valve integrates mitochondria into photosynthetic metabolism

While in heterotrophic cells and in darkness mitochondria serve as main producers of energy, during photosynthesis this function is transferred to chloroplasts and the main role of mitochondria in bioenergetics turns to be the balance of the level of phosphorylation of adenylates and of reduction of pyridine nucleotides to avoid over-energization of the cell and optimize major metabolic fluxes. This is achieved via the establishment and regulation of local equilibria of the tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase and fumarase in one branch and aconitase and isocitrate dehydrogenase in another branch. In the conditions of elevation of redox level, the TCA cycle is transformed into a non-cyclic open structure (hemicycle) leading to the export of the tricarboxylic acid (citrate) to the cytosol and to the accumulation of the dicarboxylic acids (malate and fumarate). While the buildup of NADPH in chloroplasts provides operation of the malate valve leading to establishment of NADH/NAD⁺ ratios in different cell compartments, the production of NADH by mitochondria drives citrate export by establishing conditions for the operation of the citrate valve. The latter regulates the intercompartmental NADPH/NADP⁺ ratio and contributes to the biosynthesis of amino acids and other metabolic products during photosynthesis.

Nitric oxide acts as an antioxidant and inhibits programmed cell death induced by aluminum in the root tips of peanut (Arachis hypogaea L.)

Aluminum (Al) causes programmed cell death (PCD) in plants. Our previous studies have confirmed that nitric oxide (NO) inhibits Al-induced PCD in the root tips of peanut. However, the mechanism by which NO inhibits Al-induced PCD is unclear. Here the effects of NO on mitochondrial reactive oxygen species (ROS), malondialdehyde (MDA), activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX), expression of alternative oxidase (AhAOX) and cytochrome oxidase (AhCOX) were investigated in peanut (Arachis hypogaea L.) root tips treated with Al. The results showed that Al stress induced rapid accumulation of H₂O₂ and MDA and increased the ratio of SOD/APX. The up-regulation of AhAOX and AhCOX expressions was not enough to inhibit PCD occurrence. Sodium nitroprusside (SNP, a NO donor) decreased the ratio of SOD/APX and eliminated excess H₂O₂ and MDA, thereby inhibiting Al-induced PCD in the root tips of peanut. The expression of AhAOX and AhCOX was significantly enhanced in Al-induced PCD treated with SNP. But cPTIO (a NO specific scavenger) supply had the opposite effect. Taken together, these results suggested that lipid peroxidation induced by higher levels of H₂O₂ was an important cause of Al-induced PCD. NO-mediated inhibition of Al-induced PCD was related to a significant elimination of H₂O₂ accumulation by decreasing the ratio of SOD/APX and up-regulating the expression of AhAOX and AhCOX.

The comparative analysis of phenotypic and whole transcriptome gene expression data of ascites susceptible versus ascites resistant chickens

Ascites syndrome (AS) is a metabolic disorder that mainly occurs at later ages of meat-type chickens. Despite many research, there is no consensus about the origin of this syndrome. Our main purpose were to investigate the syndrome using both phenotypic and RNA-Seq data to elucidate the most causative factors predisposing the birds to AS. Phenotypic data analysis showed that AS indicator traits (AITs) were moderate to high heritable. Inexistence of consistent direct genetic correlation between AITs and growth related traits, indicated that neither faster growth rate nor heavier body weight is the most causative factor affecting the susceptibility of broilers to AS. However, respiratory capacity was revealed to be the most probable factor predisposing the birds to AS, as both lung weight and lung percentage were negatively correlated with AITs. Transcriptomic data analysis revealed 125 differentially expressed genes (DEGs) between the ascitic and healthy groups. Up-regulated genes in ascitic group enriched mainly in gas transport biological process, while down-regulated genes involved in defense response to bacteria, biological adhesion, cell adhesion, killing of cells of another organism and cell division. Genetic association of the DEGs with human cardiovascular diseases suggested excessive heart problems of the ascitic chicks. Heart is, probably, the first tissue suffering from the incompetence of small respiratory system of the AS-susceptible chickens. In other word, tissue hypoxia, that causes free radicals to concentrate in heart cells, may be the commencement of events that finally result to heart failure, suffocation and death of chicks due to the AS.

Mitochondrial alternative cyanide-resistant oxidase is involved in an increase of heat stress tolerance in spring wheat

The aim of this study was to determine the influence of different heat treatments on the alternative cyanide-resistant oxidase (AOX) capacity and establish a relation between the heat stress tolerance of spring wheat (Triticum aestivum L.), content of water-soluble carbohydrates in leaves and the alternative respiratory pathway (AP) capacity. We identified a positive relation between these studied parameters. Heat exposure at 39 °C for 24 h increased the heat stress tolerance of seedlings, content of water-soluble carbohydrates and AOX capacity, and the AOX capacity was also high after the subsequent influence of heat shock (50 °C for 3 h). The increased AOX capacity correlated with an increased level of water-soluble carbohydrates in leaves. The content of the AOX protein increased after heat exposure at 39 °C (for 3 h and 24 h) and after the subsequent influence of heat shock (50 °C for 1 and 3 h) at 39 °C for 24 h. We also detected that the content of AOX protein isoforms depends on the duration and intensity of heat treatment. It was concluded that AOX plays an important role in the acclimation of plants to high temperatures.

Modifications in Organic Acid Profiles During Fruit Development and Ripening: Correlation or Causation?

The pivotal role of phytohormones during fruit development and ripening is considered established knowledge in plant biology. Perhaps less well-known is the growing body of evidence suggesting that organic acids play a key function in plant development and, in particular, in fruit development, maturation and ripening. Here, we critically review the connection between organic acids and the development of both climacteric and non-climacteric fruits. By analyzing the metabolic content of different fruits during their ontogenetic trajectory, we noticed that the content of organic acids in the early stages of fruit development is directly related to the supply of substrates for respiratory processes. Although different organic acid species can be found during fruit development in general, it appears that citrate and malate play major roles in this process, as they accumulate on a broad range of climacteric and non-climacteric fruits. We further highlight the functional significance of changes in organic acid profile in fruits due to either the manipulation of fruit-specific genes or the use of fruit-specific promoters. Despite the complexity behind the fluctuation in organic acid content during fruit development and ripening, we extend our understanding on the importance of organic acids on fruit metabolism and the need to further boost future research. We suggest that engineering organic acid metabolism could improve both qualitative and quantitative traits of crop fruits.

Genome-wide identification and characterization of ALTERNATIVE OXIDASE genes and their response under abiotic stresses in Camellia sinensis (L.) O. Kuntze

Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L.) O. Kuntze cv. Longjing43). Our results showed that tea plant possesses four AOX genes, i.e., CsAOX1a, CsAOX1d, CsAOX2a and CsAOX2b. Gene structure and protein sequence analyses revealed that all CsAOXs share a four-exon/three-intron structure with highly conserved regions and amino acid residues, which are necessary for AOX secondary structures, catalytic activities and post-translational regulations. All CsAOX were shown to localize in mitochondria using the green fluorescent protein (GFP)-targeting assay. Both CsAOX1a and CsAOX1d were induced by cold, salt and drought stresses, and with different expression patterns in young and mature leaves. Reactive oxygen species (ROS) accumulated strongly after 72 and 96 h cold treatments in both young and mature leaves, while the polyphenol and total catechin decreased significantly only in mature leaves. In comparison to AtAOX1a in Arabidopsis thaliana, CsAOX1a lost almost all of the stress-responsive cis-acting regulatory elements in its promoter region (1500 bp upstream), but possesses a flavonoid biosynthesis-related MBSII cis-acting regulatory element. These results suggest a link between CsAOX1a function and the metabolism of some secondary metabolites in tea plant. Our studies provide a basis for the further elucidation of the biological function and regulation of the AOX pathway in tea plants.

Role of Mitochondria in Regulating Lutein and Chlorophyll Biosynthesis in Chlorella pyrenoidosa under Heterotrophic Conditions

The green alga Chlorella pyrenoidosa can accumulate lutein and chlorophyll under heterotrophic conditions. We propose that the mitochondrial respiratory electron transport chain (mRET) may be involved in this process. To verify this hypothesis, algal cells were treated with different mRET inhibitors. The biosynthesis of lutein and chlorophyll was found to be significantly stimulated by salicylhydroxamic acid (SHAM), whereas their contents substantially decreased after treatment with antimycin A and sodium azide (NaN₃). Proteomic studies revealed profound protein alterations related to the redox and energy states, and a network was proposed: The up-regulation of peroxiredoxin reduces oxidized glutathione (GSSG) to reduced glutathione (GSH); phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the conversion of oxaloacetic acid to phosphoenolpyruvate, and after entering the methylerythritol phosphate (MEP) pathway, 4-hydroxy-3-methylbut-2-en-1yl diphosphate synthase reduces 2-C-methyl-d-erythritol-2,4-cyclodiphosphate (ME-Cpp) to 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP), which is closely related to the synthesis of lutein; and coproporphyrinogen III oxidase and ChlI play important roles in the chlorophyll biosynthetic pathway. These results supported that for the heterotrophic C. pyrenoidosa, the signaling, oriented from mRET, may regulate the nuclear genes encoding the enzymes involved in photosynthetic pigment biosynthesis.

Stress responsive mitochondrial proteins in Arabidopsis thaliana

In the last decade plant mitochondria have emerged as a target, sensor and initiator of signalling cascades to a variety of stress and adverse growth conditions. A combination of various 'omic profiling approaches combined with forward and reverse genetic studies have defined how mitochondria respond to stress and the signalling pathways and regulators of these responses. Reactive oxygen species (ROS)-dependent and -independent pathways, specific metabolites, complex I dysfunction, and the mitochondrial unfolded protein response (UPR) pathway have been proposed to date. These pathways are regulated by kinases (sucrose non-fermenting response like kinase; cyclin dependent protein kinase E 1) and transcription factors from the abscisic acid-related, WRKY and NAC families. A number of independent studies have revealed that these mitochondrial signalling pathways interact with a variety of phytohormone signalling pathways. While this represents significant progress in the last decade there are more pathways to be uncovered. Post-transcriptional/translational regulation is also a likely determinant of the mitochondrial stress response. Unbiased analyses of the expression of genes encoding mitochondrial proteins in a variety of stress conditions reveal a modular network exerting a high degree of anterograde control. As abiotic and biotic stresses have significant impact on the yield of important crops such as rice, wheat and barley we will give an outlook of how knowledge gained in Arabidopsis may help to increase crop production and how emerging technologies may contribute.

Differential impact of amino acids on OXPHOS system activity following carbohydrate starvation in Arabidopsis cell suspensions

Plant respiration mostly depends on the activity of glycolysis and the oxidation of organic acids in the tricarboxylic acid cycle to synthesize ATP. However, during stress situations plant cells also use amino acids as alternative substrates to donate electrons through the electron-transfer flavoprotein (ETF)/ETF:ubiquinone oxidoreductase (ETF/ETFQO) complex to the mitochondrial electron transport chain (mETC). Given this, we investigated changes of the oxidative phosphorylation (OXPHOS) system in Arabidopsis thaliana cell culture under carbohydrate starvation supplied with a range of amino acids. Induction of isovaleryl-CoA dehydrogenase (IVDH) activity was observed under carbohydrate starvation which was associated with increased amounts of IVDH protein detected by immunoblotting. Furthermore, activities of the protein complexes of the mETC were reduced under carbohydrate starvation. We also observed that OXPHOS system activity behavior is differently affected by different amino acids and that proteins associated with amino acids catabolism are upregulated in cells following carbohydrate starvation. Collectively, our results support the contention that ETF/ETFQO is an essential pathway to donate electrons to the mETC and that amino acids are alternative substrates to maintain respiration under carbohydrate starvation.

Nitric oxide upregulates expression of alternative oxidase 1 in Chlamydomonas reinhardtii

The mitochondrial respiratory chain in plants, many fungi and some protists consists of the ATP-coupling cyanide-sensitive cytochrome pathway and the cyanide-resistant alternative respiratory pathway. The alternative pathway is mediated by alternative oxidase (AOX). In unicellular algae, AOXs are monomeric fungi-type proteins. Studies performed in the model plant Chlamydomonas reinhardtii showed that a range of stress factors lead to induction of its AOX1. However, signaling molecules that trigger upregulation of AOX1 have not yet been identified. Here, we were able to discriminate between two alternative oxidases of the alga. In this work, we demonstrated that exposure of C. reinhardtii to nitric oxide (NO) resulted in the up-regulation of AOX1 expression and an increased AOX1 protein. Furthermore, NO-treated C. reinhardtii cells displayed the enhanced AOX1 capacity. We also clearly demonstrated that AOX1 can function in C. reinhardtii when the cytochrome oxidase became inhibited by NO. Although the pathway(s) that leads to increased AOX1 levels and activity upon NO treatment is yet unknown, it is now clear that NO serves as the signal to trigger this regulatory process in C. reinhardtii.

Hydrogen cyanamide breaks grapevine bud dormancy in the summer through transient activation of gene expression and accumulation of reactive oxygen and nitrogen species

BACKGROUND

Hydrogen cyanamide (HC) and pruning (P) have frequently been used to break dormancy in grapevine floral buds. However, the exact underlying mechanism remains elusive. This study aimed to address the early mode of action of these treatments on accumulation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) and expression of related genes in the dormancy breaking buds of grapevine in the summer.

RESULTS

The budbreak rates induced by pruning (P), hydrogen cyanamide (HC), pruning plus hydrogen cyanamide (PHC) and water (control) after 8 days were 33, 53, 95, and 0 %, respectively. Clearly, HC was more effective in stimulating grapevine budbreak and P further enhanced its potency. In situ staining of longitudinal bud sections after 12 h of treatments detected high levels of ROS and nitric oxide (NO) accumulated in the buds treated with PHC, compared with HC or P alone. The amounts of ROS and NO accumulated were highly correlated with the rates of budbreak among these treatments, highlighting the importance of a rapid, transient accumulation of sublethal levels of ROS and RNS in dormancy breaking. Microarray analysis revealed specific alterations in gene expression in dormancy breaking buds induced by P, HC and PHC after 24 h of treatment. Relative to control, PHC altered the expression of the largest number of genes, while P affected the expression of the least number of genes. PHC also exerted a greater intensity in transcriptional activation of these genes. Gene ontology (GO) analysis suggests that alteration in expression of ROS related genes is the major factor responsible for budbreak. qRT-PCR analysis revealed the transient expression dynamics of 12 specific genes related to ROS generation and scavenge during the 48 h treatment with PHC.

CONCLUSION

Our results suggest that rapid accumulation of ROS and NO at early stage is important for dormancy release in grapevine in the summer, and the identification of the commonly expressed specific genes among the treatments allowed the construction of the signal transduction pathway related to ROS/RNS metabolism during dormancy release. The rapid accumulation of a sublethal level of ROS/RNS subsequently induces cell wall loosening and expansion for bud sprouting.

Analyzing Arabidopsis thaliana root proteome provides insights into the molecular bases of enantioselective imazethapyr toxicity

Imazethapyr (IM) is a widely used chiral herbicide that inhibits the synthesis of branched-chain amino acids (BCAAs). IM is thought to exert its toxic effects on amino acid synthesis mainly through inhibition of acetolactate synthase activity, but little is known about the potential effects of IM on other key biochemical pathways. Here, we exposed the model plant Arabidospsis thaliana to trace S- and R-IM enantiomer concentrations and examined IM toxicity effects on the root proteome using iTRAQ. Conventional analyses of root carbohydrates, organic acids, and enzyme activities were also performed. We discovered several previously unknown key biochemical pathways targeted by IM in Arabidospsis. 1,322 and 987 proteins were differentially expressed in response to R- and S-IM treatments, respectively. Bioinformatics and physiological analyses suggested that IM reduced the BCAA tissue content not only by strongly suppressing BCAA synthesis but also by increasing BCAA catabolism. IM also affected sugar and starch metabolism, changed the composition of root cell walls, increased citrate production and exudation, and affected the microbial community structure of the rhizosphere. The present study shed new light on the multiple toxicity mechanisms of a selective herbicide on a model plant.

Whole-plant respiration and its temperature sensitivity during progressive carbon starvation

Plant respiration plays a critical role in the C balance of plants. Respiration is highly temperature sensitive and small temperature-induced increases in whole-plant respiration could change the C balance of plants that operate close to their light-compensation points from positive to negative. Nonstructural carbohydrates are thought to play an important role in controlling respiration and its temperature sensitivity, but this role has not been studied at the whole-plant level. We measured respiration of whole Ardisia crenata Sims. seedlings and tested the hypothesis that darkness-induced C starvation would decrease the temperature sensitivity of whole-plant respiration. Compared with control plants, sugar and starch concentrations in darkened plants declined over time in all organs. Similarly, whole-plant respiration decreased. However, the temperature sensitivity of whole-plant respiration, expressed as the proportional increase in respiration per 10°C warming (Q10), increased with progressive C starvation. We hypothesise that growth respiration was suppressed in darkened plants and that whole-plant respiration represented maintenance respiration almost exclusively, which is more temperature sensitive. Alternatively, changes in the respiratory substrate during C starvation or increased involvement of alternative oxidase pathway respiration may explain the increase in Q10. Carbohydrates are important for respiration but it appears that even in C-starved A. crenata plants, carbohydrate availability does not limit respiration during short-term warming.

Modulation of alternative oxidase to enhance tolerance against cold stress of chickpea by chemical treatments

The alternative oxidase (AOX) is the enzyme responsible for the alternative respiratory pathway. This experiment was conducted to examine the influence on cold tolerance ability of chickpea (Cicer aurentium cv. Müfitbey) seedlings of AOX activator (pyruvate), AOX inhibitor (salicylhydroxamic acid (SHAM)) and an inhibitor of the cytochrome pathway of respiration (antimycin A) treatments. 5mM pyruvate, 2μM antimycin A and 4mM SHAM solutions were exogenously applied to thirteen-day-old chickpea leaves and then the seedlings were transferred to a different plant growth chamber arranged to 10/5°C (day/night) for 48h. Cold stress markedly increased the activities of antioxidant enzymes compared to controls. Pyruvate and antimycin A significantly increased the cold-induced increase in antioxidant activity but SHAM decreased it. Cold-induced increases in superoxide anion, hydrogen peroxide, and lipid peroxidation levels were significantly reduced by pyruvate and antimycin A, but increased by SHAM treatment. Pyruvate and antimycin A application increased both the activity and protein expression of AOX in comparison to cold stress alone. However, SHAM significantly decreased activity of AOX but did not affect its expression. Total cellular respiration values (TCRV) supported the changes in activity and expression of AOX. While TCRV were increased by cold and pyruvate, they were significantly reduced by SHAM and especially antimycin A. These results indicate that pyruvate and antimycin A applications were effective in reducing oxidative stress by activating the alternative respiratory pathway as well as antioxidant activity. Furthermore, direct activation of AOX, rather than inhibition of the cytochrome pathway, was the most effective way to mitigate cold stress.

Metabolic control of redox and redox control of metabolism in plants

SIGNIFICANCE

Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression.

RECENT ADVANCES

The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels.

CRITICAL ISSUES

It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels.

FUTURE DIRECTIONS

Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.

Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress

Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins (NGEMPs). The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regulate these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde (nuclear to mitochondrial) and retrograde (mitochondrial to nuclear) signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.

Inhibition of the electron transport strongly affects transcription and transcript levels in Arabidopsis mitochondria

Mitochondrial transcription rate and RNA steady-state levels were examined in shoots of Arabidopsis seedlings. The shoots were treated with inhibitors of complex III and IV of the cytochrome pathway (CP) and with an inhibitor of the alternative oxidase (AOX) of the mitochondrial electron transport chain. The inhibition of AOX and CP complexes III and IV affected transcription and transcript levels in different ways. CP and AOX inhibitors had opposite effects. Our data support the idea that the redox state of the electron transport chain is involved in the regulation of mitochondrial gene expression at transcriptional and post-transcriptional levels.

Mitochondrial genome of Babesia orientalis, apicomplexan parasite of water buffalo (Bubalus babalis, Linnaeus, 1758) endemic in China

BACKGROUND

Apicomplexan parasites of the genus Babesia, Theileria and Plasmodium are very closely related organisms. Interestingly, their mitochondrial (mt) genomes are highly divergent. Among Babesia, Babesia orientalis is a new species recently identified and specifically epidemic to the southern part of China, causing severe disease to water buffalo. However, no information on the mt genome of B. orientalis was available.

METHODS

Four pairs of primers were designed based on the full genome sequence of B. orientalis (unpublished data) and by aligning reported mt genomes of B. bovis, B. bigemina, and T. parva. The entire mt genome was amplified by four sets of PCR. The obtained mt genome was annotated by aligning with published apicomplexan mt genomes and Artemis software v11. Phylogenetic analysis was performed by using cox1 and cob amino acid sequences.

RESULTS

The complete mt genome of B. orientalis (Wuhan strain) was sequenced and characterized. The entire mt genome is 5996 bp in length with a linear form, containing three protein-coding genes including cytochrome c oxidase I (cox1), cytochrome b (cob) and cytochrome c oxidase III (cox3) and six rRNA large subunit gene fragments. The gene arrangement in B. orientalis mt genome is similar to those of B. bovis, B. gibsoni and Theileria parva, but different from those of T. orientalis, T. equi and Plasmodium falciparum. Comparative analysis indicated that cox1 and cob genes were more conserved than cox3. Phylogenetic analysis based on amino acid sequences of cox1, cob and cox1 + cob, respectively, revealed that B. orientalis fell into Babesia clade with the closest relationship to B. bovis.

CONCLUSIONS

The availability of the entire mt genome sequences of B. orientalis provides valuable information for future phylogenetic, population genetics and molecular epidemiological studies of apicomplexan parasites.

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

Upon disturbance of their function by stress, mitochondria can signal to the nucleus to steer the expression of responsive genes. This mitochondria-to-nucleus communication is often referred to as mitochondrial retrograde regulation (MRR). Although reactive oxygen species and calcium are likely candidate signaling molecules for MRR, the protein signaling components in plants remain largely unknown. Through meta-analysis of transcriptome data, we detected a set of genes that are common and robust targets of MRR and used them as a bait to identify its transcriptional regulators. In the upstream regions of these mitochondrial dysfunction stimulon (MDS) genes, we found a cis-regulatory element, the mitochondrial dysfunction motif (MDM), which is necessary and sufficient for gene expression under various mitochondrial perturbation conditions. Yeast one-hybrid analysis and electrophoretic mobility shift assays revealed that the transmembrane domain-containing no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon transcription factors (ANAC013, ANAC016, ANAC017, ANAC053, and ANAC078) bound to the MDM cis-regulatory element. We demonstrate that ANAC013 mediates MRR-induced expression of the MDS genes by direct interaction with the MDM cis-regulatory element and triggers increased oxidative stress tolerance. In conclusion, we characterized ANAC013 as a regulator of MRR upon stress in Arabidopsis thaliana.

Mitochondrial energy and redox signaling in plants

SIGNIFICANCE

For a plant to grow and develop, energy and appropriate building blocks are a fundamental requirement. Mitochondrial respiration is a vital source for both. The delicate redox processes that make up respiration are affected by the plant's changing environment. Therefore, mitochondrial regulation is critically important to maintain cellular homeostasis. This involves sensing signals from changes in mitochondrial physiology, transducing this information, and mounting tailored responses, by either adjusting mitochondrial and cellular functions directly or reprogramming gene expression.

RECENT ADVANCES

Retrograde (RTG) signaling, by which mitochondrial signals control nuclear gene expression, has been a field of very active research in recent years. Nevertheless, no mitochondrial RTG-signaling pathway is yet understood in plants. This review summarizes recent advances toward elucidating redox processes and other bioenergetic factors as a part of RTG signaling of plant mitochondria.

CRITICAL ISSUES

Novel insights into mitochondrial physiology and redox-regulation provide a framework of upstream signaling. On the other end, downstream responses to modified mitochondrial function have become available, including transcriptomic data and mitochondrial phenotypes, revealing processes in the plant that are under mitochondrial control.

FUTURE DIRECTIONS

Drawing parallels to chloroplast signaling and mitochondrial signaling in animal systems allows to bridge gaps in the current understanding and to deduce promising directions for future research. It is proposed that targeted usage of new technical approaches, such as quantitative in vivo imaging, will provide novel leverage to the dissection of plant mitochondrial signaling.

Transcriptomic analysis of the role of carboxylic acids in metabolite signaling in Arabidopsis leaves

The transcriptional response to metabolites is an important mechanism by which plants integrate information about cellular energy and nutrient status. Although some carboxylic acids have been implicated in the regulation of gene expression for select transcripts, it is unclear whether all carboxylic acids have the same effect, how many transcripts are affected, and how carboxylic acid signaling is integrated with other metabolite signals. In this study, we demonstrate that perturbations in cellular concentrations of citrate, and to a lesser extent malate, have a major impact on nucleus-encoded transcript abundance. Functional categories of transcripts that were targeted by both organic acids included photosynthesis, cell wall, biotic stress, and protein synthesis. Specific functional categories that were only regulated by citrate included tricarboxylic acid cycle, nitrogen metabolism, sulfur metabolism, and DNA synthesis. Further quantitative real-time polymerase chain reaction analysis of specific citrate-responsive transcripts demonstrated that the transcript response to citrate is time and concentration dependent and distinct from other organic acids and sugars. Feeding of isocitrate as well as the nonmetabolizable citrate analog tricarballylate revealed that the abundance of selected marker transcripts is responsive to citrate and not downstream metabolites. Interestingly, the transcriptome response to citrate feeding was most similar to those observed after biotic stress treatments and the gibberellin biosynthesis inhibitor paclobutrazol. Feeding of citrate to mutants with defects in plant hormone signaling pathways did not completely abolish the transcript response but hinted at a link with jasmonic acid and gibberellin signaling pathways. Our results suggest that changes in carboxylic acid abundances can be perceived and signaled in Arabidopsis (Arabidopsis thaliana) by as yet unknown signaling pathways.

Unravelling mitochondrial retrograde regulation in the abiotic stress induction of rice ALTERNATIVE OXIDASE 1 genes

Mitochondrial retrograde regulation (MRR) is the transduction of mitochondrial signals to mediate nuclear gene expression. It is not clear whether MRR is a common regulation mechanism in plant abiotic stress response. In this study, we analysed the early abiotic stress response of the rice OsAOX1 genes, and the induction of OsAOX1a and OsAOX1b (OsAOX1a/b) was selected as a working model for the stress-induced MRR studies. We found that the induction mediated by the superoxide ion (O2·(-) )-generating chemical methyl viologen was stronger than that of hydrogen peroxide (H2 O2 ). The addition of reactive oxygen species (ROS) scavengers demonstrated that the stress induction was reduced by eliminating O2·(-) . Furthermore, the stress induction did not rely on chloroplast- or cytosol-derived O2·(-) . Next, we generated transgenic plants overexpressing the superoxide dismutase (SOD) gene at different subcellular locations. The results suggest that only the mitochondrial SOD, OsMSD, attenuated the stress induction of OsAOX1a/b specifically. Therefore, our findings demonstrate that abiotic stress initiates the MRR on OsAOX1a/b and that mitochondrial O2·(-) is involved in the process.

Comparison of intact Arabidopsis thaliana leaf transcript profiles during treatment with inhibitors of mitochondrial electron transport and TCA cycle

Plant mitochondria signal to the nucleus leading to altered transcription of nuclear genes by a process called mitochondrial retrograde regulation (MRR). MRR is implicated in metabolic homeostasis and responses to stress conditions. Mitochondrial reactive oxygen species (mtROS) are a MRR signaling component, but whether all MRR requires ROS is not established. Inhibition of the cytochrome respiratory pathway by antimycin A (AA) or the TCA cycle by monofluoroacetate (MFA), each of which initiates MRR, can increase ROS production in some plant cells. We found that for AA and MFA applied to leaves of soil-grown Arabidopsis thaliana plants, ROS production increased with AA, but not with MFA, allowing comparison of transcript profiles under different ROS conditions during MRR. Variation in transcript accumulation over time for eight nuclear encoded mitochondrial protein genes suggested operation of both common and distinct signaling pathways between the two treatments. Consequences of mitochondrial perturbations for the whole transcriptome were examined by microarray analyses. Expression of 1316 and 606 genes was altered by AA and MFA, respectively. A subset of genes was similarly affected by both treatments, including genes encoding photosynthesis-related proteins. MFA treatment resulted in more down-regulation. Functional gene category (MapMan) and cluster analyses showed that genes with expression levels affected by perturbation from AA or MFA inhibition were most similarly affected by biotic stresses such as pathogens. Overall, the data provide further evidence for the presence of mtROS-independent MRR signaling, and support the proposed involvement of MRR and mitochondrial function in plant responses to biotic stress.

Involvement of alternative oxidase (AOX) in adventitious rooting of Olea europaea L. microshoots is linked to adaptive phenylpropanoid and lignin metabolism

Alternative oxidase (AOX) has been proposed as a functional marker candidate in a number of events involving cell differentiation, including rooting efficiency in semi-hardwood shoot cuttings of olive (Olea europaea L.). To ascertain the general importance of AOX in olive rooting, the auxin-induced rooting process was studied in an in vitro system for microshoot propagation. Inhibition of AOX by salicylhydroxamic acid (SHAM) significantly reduced rooting efficiency. However, the inhibitor failed to exhibit any effect on the preceding calli stage. This makes the system appropriate for distinguishing dedifferentiation and de novo differentiation during root induction. Metabolite analyses of microshoots showed that total phenolics, total flavonoids and lignin contents were significantly reduced upon SHAM treatment. It was concluded that the influence of alternative respiration on root formation was associated to adaptive phenylpropanoid and lignin metabolism. Transcript profiles of two olive AOX genes (OeAOX1a and OeAOX2) were examined during the process of auxin-induced root induction. Both genes displayed stable transcript accumulation in semi-quantitative RT-PCR analysis during all experimental stages. In contrary, when the reverse primer for OeAOX2 was designed from the 3'-UTR instead of the ORF, differential transcript accumulation was observed suggesting posttranscriptional regulation of OeAOX2 during metabolic acclimation. This result confirms former observations in olive semi-hardwood shoot cuttings on differential OeAOX2 expression during root induction. It further points to the importance of future studies on the functional role of sequence and length polymorphisms in the 3'-UTR of this gene.

KEY MESSAGE

The manuscript reports the general importance of AOX in olive adventitious rooting and the association of alternative respiration to adaptive phenylpropanoid and lignin metabolism.

Reduced expression of BjRCE1 gene modulated by nuclear-cytoplasmic incompatibility alters auxin response in cytoplasmic male-sterile Brassica juncea

The signal from organelle to nucleus, namely retrograde regulation of nuclear gene expression, was largely unknown. Due to the nuclear-cytoplasmic incompatibility in cytoplasmic male-sterile (CMS) plants, we employed CMS Brassica juncea to investigate the retrograde regulation of nuclear gene expression in this study. We studied how reduced BjRCE1 gene expression caused by the nuclear-cytoplasmic incompatibility altered the auxin response in CMS of B. juncea. We isolated the BjRCE1 gene that was located in the nucleus from B. juncea. Over-expression of BjRCE1 enhanced auxin response in transgenic Arabidopsis. The expression of BjRCE1 was significantly reduced in CMS compared with its maintainer fertile (MF) line of B. juncea. There were fewer lateral roots in CMS than MF under normal and treatment of indole-3-acetic acid (IAA) conditions. Expression patterns of several auxin-related genes together with their phenotypes indicated a reduced auxin response in CMS compared to MF. The phenotypes of auxin response and auxin-related gene expression pattern could be mimicked by inhibiting mitochondrial function in MF. Taken together, we proposed reduced expression of BjRCE1 gene modulated by nuclear-cytoplasmic incompatibility alters auxin response in CMS B. juncea. This may be an important mechanism of retrograde regulation of nuclear gene expression in plants.

CHARACTERIZATION OF THE ALTERNATIVE OXIDASE GENE IN PORPHYRA YEZOENSIS (RHODOPHYTA) AND CYANIDE-RESISTANT RESPIRATION ANALYSIS(1)

The full-length cDNA of the alternative oxidase (AOX) gene from Porphyra yezoensis Ueda (PyAOX) [currently assigned as Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi (http://www.algaebase.org)] an ancient member of the Rhodphyta, was cloned by electronic cloning, rapid amplification of cDNA ends (RACE), and reverse transcription PCR. The nucleotide sequence of PyAOX consists of 1,650 bp, including a 5' untranslated region (UTR) of 170 bp, a 3' UTR of 148 bp, and an open reading frame (ORF) of 1,332 bp that can be translated into a 443-amino-acid residue with a molecular mass of 47.33 kDa and a putative isoelectric point (pI) of 9.71. The putative amino acids had 50%-61% identity with AOX genes in Eukaryota and higher plants and had AOX-like characteristics. The expression of PyAOX mRNA in different stages of the life cycle, conchospores, filamentous thalli (conchocelis stage), and leafy thalli, was detected by real-time quantitative PCR (qPCR). The highest level of expression, which was observed in filamentous thalli, was three times higher than that observed in leafy thalli. The next highest level, which was observed in the conchospores, was twice as high as that observed in leafy thalli. We showed that an alternative respiration pathway existed in P. yezoensis with a noninvasive microsensing system. The contribution of the alternative pathway to total respiration in filamentous thalli was greater than that in leafy thalli. This result was consistent with the level of AOX gene expression observed in different stages of the life cycle.

Inhibition of aconitase by nitric oxide leads to induction of the alternative oxidase and to a shift of metabolism towards biosynthesis of amino acids

Nitric oxide (NO) is a free radical molecule involved in signalling and in hypoxic metabolism. This work used the nitrate reductase double mutant of Arabidopsis thaliana (nia) and studied metabolic profiles, aconitase activity, and alternative oxidase (AOX) capacity and expression under normoxia and hypoxia (1% oxygen) in wild-type and nia plants. The roots of nia plants accumulated very little NO as compared to wild-type plants which exhibited ∼20-fold increase in NO emission under low oxygen conditions. These data suggest that nitrate reductase is involved in NO production either directly or by supplying nitrite to other sites of NO production (e.g. mitochondria). Various studies revealed that NO can induce AOX in mitochondria, but the mechanism has not been established yet. This study demonstrates that the NO produced in roots of wild-type plants inhibits aconitase which in turn leads to a marked increase in citrate levels. The accumulating citrate enhances AOX capacity, expression, and protein abundance. In contrast to wild-type plants, the nia double mutant failed to show AOX induction. The overall induction of AOX in wild-type roots correlated with accumulation of glycine, serine, leucine, lysine, and other amino acids. The findings show that NO inhibits aconitase under hypoxia which results in accumulation of citrate, the latter in turn inducing AOX and causing a shift of metabolism towards amino acid biosynthesis.

The impact of impaired mitochondrial function on retrograde signalling: a meta-analysis of transcriptomic responses

Mitochondria occupy a central position in cellular metabolism. Their protein complement must therefore be dynamically adjusted to the metabolic demands of the cell. As >95% of mitochondrial proteins are encoded by nuclear DNA, regulation of the mitochondrial proteome requires signals that sense the status of the organelle and communicate it back to the nucleus. This is referred to as retrograde signalling. Mitochondria are tightly integrated into the network of cellular processes, and the output of mitochondrial retrograde signalling therefore not only feeds back to the mitochondrion, but also regulates functions across the cell. A number of transcriptomic studies have assessed the role of retrograde signalling in plants. However, single studies of a specific mitochondrial dysfunction may also measure secondary effects in addition to the specific transcriptomic output of mitochondrial signals. To gain an improved understanding of the output and role of mitochondrial retrograde signalling, a meta-analysis of 11 transcriptomic data sets from different models of plant mitochondrial dysfunction was performed. Comparing microarray data from stable mutants and short-term chemical treatments revealed unique features and commonalities in the responses that are under mitochondrial retrograde control. In particular, a common regulation of transcripts of the following functional categories was observed: plant-pathogen interactions, protein biosynthesis, and light reactions of photosynthesis. The possibility of a novel mode of interorganellar signalling, in which the mitochondrion influences processes in the plastid and other parts of the cell, is discussed.

Discovering the role of mitochondria in the iron deficiency-induced metabolic responses of plants

In plants, iron (Fe) deficiency-induced chlorosis is a major problem, affecting both yield and quality of crops. Plants have evolved multifaceted strategies, such as reductase activity, proton extrusion, and specialised storage proteins, to mobilise Fe from the environment and distribute it within the plant. Because of its fundamental role in plant productivity, several issues concerning Fe homeostasis in plants are currently intensively studied. The activation of Fe uptake reactions requires an overall adaptation of the primary metabolism because these activities need the constant supply of energetic substrates (i.e., NADPH and ATP). Several studies concerning the metabolism of Fe-deficient plants have been conducted, but research focused on mitochondrial implications in adaptive responses to nutritional stress has only begun in recent years. Mitochondria are the energetic centre of the root cell, and they are strongly affected by Fe deficiency. Nevertheless, they display a high level of functional flexibility, which allows them to maintain the viability of the cell. Mitochondria represent a crucial target of studies on plant homeostasis, and it might be of interest to concentrate future research on understanding how mitochondria orchestrate the reprogramming of root cell metabolism under Fe deficiency. In this review, I summarise what it is known about the effect of Fe deficiency on mitochondrial metabolism and morphology. Moreover, I present a detailed view of the possible roles of mitochondria in the development of plant responses to Fe deficiency, integrating old findings with new and discussing new hypotheses for future investigations.

Metal-induced oxidative stress and plant mitochondria

A general status of oxidative stress in plants caused by exposure to elevated metal concentrations in the environment coincides with a constraint on mitochondrial electron transport, which enhances ROS accumulation at the mitochondrial level. As mitochondria are suggested to be involved in redox signaling under environmental stress conditions, mitochondrial ROS can initiate a signaling cascade mediating the overall stress response, i.e., damage versus adaptation. This review highlights our current understanding of metal-induced responses in plants, with focus on the production and detoxification of mitochondrial ROS. In addition, the potential involvement of retrograde signaling in these processes will be discussed.

Ophiostoma mitovirus 3a, ascorbic acid, glutathione, and photoperiod affect the development of stromata and apothecia by Sclerotinia homoeocarpa

Hypovirulence in Sclerotinia homoeocarpa is associated with infection by Ophiostoma mitovirus 3a (OMV3a). OMV3a is also present in asymptomatic isolates, with growth and virulence comparable to that of virus-free isolates. Hypovirulent isolates have impaired mitochondrial function resulting in increased activity of the alternative oxidase pathway, which is implicated in the reduction of reactive oxygen species in other fungi. In this study, hypovirulent, asymptomatic, and virus-free isolates were grown on potato dextrose agar amended with ascorbic acid or glutathione and were incubated under various photoperiods to determine the importance of reactive oxygen species, light, and OMV3a infection for differentiation of stromata and apothecia by S. homoeocarpa. Hypovirulent isolates did not form stromata or apothecia. Glutathione and darkness reduced stromata size and apothecia production by virulent and asymptomatic isolates. Apothecia formed under several different photoperiods, and ascorbic acid increased apothecia production. Ascospores were not detected in these apothecia. The results suggest that hypovirulence, light, and the superoxide radical are important factors in the formation of stromata and apothecia by S. homoeocarpa isolates. This is the first report of sterile apothecia production by North American isolates of S. homoeocarpa and provides a starting point for attempts to produce fertile apothecia.

Integrative response of plant mitochondrial electron transport chain to nitrogen source

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.

Importance of AOX pathway in optimizing photosynthesis under high light stress: role of pyruvate and malate in activating AOX

The present study shows the importance of alternative oxidase (AOX) pathway in optimizing photosynthesis under high light (HL). The responses of photosynthesis and respiration were monitored as O(2) evolution and O(2) uptake in mesophyll protoplasts of pea pre-incubated under different light intensities. Under HL (3000 micromol m(-2) s(-1)), mesophyll protoplasts showed remarkable decrease in the rates of NaHCO(3)-dependent O(2) evolution (indicator of photosynthetic carbon assimilation), while decrease in the rates of respiratory O(2) uptake were marginal. While the capacity of AOX pathway increased significantly by two fold under HL, the capacity of cytochrome oxidase (COX) pathway decreased by >50% compared with capacities under darkness and normal light (NL). Further, the total cellular levels of pyruvate and malate, which are assimilatory products of active photosynthesis and stimulators of AOX activity, were increased remarkably parallel to the increase in AOX protein under HL. Upon restriction of AOX pathway using salicylhydroxamic acid (SHAM), the observed decrease in NaHCO(3)-dependent O(2) evolution or p-benzoquinone (BQ)-dependent O(2) evolution [indicator of photosystem II (PSII) activity] and the increase in total cellular levels of pyruvate and malate were further aggravated/promoted under HL. The significance of raised malate and pyruvate levels in activation of AOX protein/AOX pathway, which in turn play an important role in dissipating excess chloroplastic reducing equivalents and sustenance of photosynthetic carbon assimilation to balance the effects of HL stress on photosynthesis, was depicted as a model.

Aox gene structure, transcript variation and expression in plants

Alternative oxidase (Aox) has been proposed as a functional marker for breeding stress tolerant plant varieties. This requires presence of polymorphic Aox allele sequences in plants that affect plant phenotype in a recognizable way. In this review, we examine the hypothesis that organization of genomic Aox sequences and gene expression patterns are highly variable in relation to the possibility that such a variation may allow development of Aox functional markers in plants. Aox is encoded by a small multigene family, typically with four to five members in higher plants. The predominant structure of genomic Aox sequences is that of four exons interrupted by three introns at well conserved positions. Evolutionary intron loss and gain has resulted in the variation of intron numbers in some Aox members that may harbor two to four introns and three to five exons in their sequence. Accumulating evidence suggests that Aox gene structure is polymorphic enough to allow development of Aox markers in many plant species. However, the functional significance of Aox structural variation has not been examined exhaustively. Aox expression patterns display variability and typically Aox genes fall into two discrete subfamilies, Aox1 and Aox2, the former being present in all plants and the latter restricted in eudicot species. Typically, although not exclusively, the Aox1-type genes are induced by many different kinds of stress, whereas Aox2-type genes are expressed in a constitutive or developmentally regulated way. Specific Aox alleles are among the first and most intensively stress-induced genes in several experimental systems involving oxidative stress. Differential response of Aox genes to stress may provide a flexible plan of plant defense where an energy-dissipating system in mitochondria is involved. Evidence to link structural variation and differential allele expression patterns is scarce. Much research is still required to understand the significance of polymorphisms within AOX gene sequences for gene regulation and its potential for breeding on important agronomic traits. Association studies and mapping approaches will be helpful to advance future perspectives for application more efficiently.

Physiologic responses and gene diversity indicate olive alternative oxidase as a potential source for markers involved in efficient adventitious root induction

Olive (Olea europaea L.) trees are mainly propagated by adventitious rooting of semi-hardwood cuttings. However, efficient commercial propagation of valuable olive tree cultivars or landraces by semi-hardwood cuttings can often be restricted by a low rooting capacity. We hypothesize that root induction is a plant cell reaction linked to oxidative stress and that activity of stress-induced alternative oxidase (AOX) is importantly involved in adventitious rooting. To identify AOX as a source for potential functional marker sequences that may assist tree breeding, genetic variability has to be demonstrated that can affect gene regulation. The paper presents an applied, multidisciplinary research approach demonstrating first indications of an important relationship between AOX activity and differential adventitious rooting in semi-hardwood cuttings. Root induction in the easy-to-root Portuguese cultivar 'Cobrançosa' could be significantly reduced by treatment with salicyl-hydroxamic acid, an inhibitor of AOX activity. On the contrary, treatment with H2O2 or pyruvate, both known to induce AOX activity, increased the degree of rooting. Recently, identification of several O. europaea (Oe) AOX gene sequences has been reported from our group. Here we present for the first time partial sequences of OeAOX2. To search for polymorphisms inside of OeAOX genes, partial OeAOX2 sequences from the cultivars 'Galega vulgar', 'Cobrançosa' and 'Picual' were cloned from genomic DNA and cDNA, including exon, intron and 3'-untranslated regions (3'-UTRs) sequences. The data revealed polymorphic sites in several regions of OeAOX2. The 3'-UTR was the most important source for polymorphisms showing 5.7% of variability. Variability in the exon region accounted 3.4 and 2% in the intron. Further, analysis performed at the cDNA from microshoots of 'Galega vulgar' revealed transcript length variation for the 3'-UTR of OeAOX2 ranging between 76 and 301 bp. The identified polymorphisms and 3'-UTR length variation can be explored in future studies for effects on gene regulation and a potential linkage to olive rooting phenotypes in view of marker-assisted plant selection.