Lack of cytochrome c in Arabidopsis decreases stability of Complex IV and modifies redox metabolism without affecting Complexes I and III

Cytochrome c levels affect the TOR pathway to regulate growth and metabolism under energy-deficient conditions

Mitochondrial function is essential for plant growth, but the mechanisms involved in adjusting growth and metabolism to changes in mitochondrial energy production are not fully understood. We studied plants with reduced expression of CYTC-1, one of two genes encoding the respiratory chain component cytochrome c (CYTc) in Arabidopsis, to understand how mitochondria communicate their status to coordinate metabolism and growth. Plants with CYTc deficiency show decreased mitochondrial membrane potential and lower ATP content, even when carbon sources are present. They also exhibit higher free amino acid content, induced autophagy, and increased resistance to nutritional stress caused by prolonged darkness, similar to plants with triggered starvation signals. CYTc deficiency affects target of rapamycin (TOR)-pathway activation, reducing S6 kinase (S6K) and RPS6A phosphorylation, as well as total S6K protein levels due to increased protein degradation via proteasome and autophagy. TOR overexpression restores growth and other parameters affected in cytc-1 mutants, even if mitochondrial membrane potential and ATP levels remain low. We propose that CYTc-deficient plants coordinate their metabolism and energy availability by reducing TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion, thus providing a mechanism by which changes in mitochondrial activity are transduced to the rest of the cell.

The biogenesis and regulation of the plant oxidative phosphorylation system

Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.

New insights into the combined toxicity of aflatoxin B1 and fumonisin B1 in HepG2 cells using Seahorse respirometry analysis and RNA transcriptome sequencing

Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) are widely (co-)detected in food and known for their hepatotoxicity in humans. Still, their combined toxicity needs to be investigated, especially the impact on mitochondria. In our previous work, we examined the effect of short-term exposure to different doses of AFB1, FB1, and their binary mixture (MIX) on the bioenergetic status of HepG2 cells, a well-recognized in vitro model system for studying liver cell function. In the current work, we further investigated the (combined) effect of AFB1 and FB1 on the mitochondrial and glycolytic activity of HepG2 cells using Seahorse respirometry analysis and RNA transcriptome sequencing. The results showed that the co-exposure, especially at high doses, is more toxic due to a more inhibition of all parameters of mitochondrial respiration. However, FB1 contributes more to the MIX effects than AFB1. RNA transcriptome sequencing showed that the p53 signaling pathway, a major orchestrator of mitochondrial apoptosis, was differentially expressed. Moreover, the co-exposure significantly downregulated the genes encoding for Complexes I, II, III, and IV, representing the onset of the suppressed mitochondrial respiration in HepG2 cells.

Mitochondrial H2S donor AP39 induces stomatal closure by modulating guard cell mitochondrial activity

Hydrogen sulfide (H2S) is a gaseous signaling molecule involved in numerous physiological processes in plants, including gas exchange with the environment through the regulation of stomatal pore width. Guard cells (GCs) are pairs of specialized epidermal cells that delimit stomatal pores and have a higher mitochondrial density and metabolic activity than their neighboring cells. However, there is no clear evidence on the role of mitochondrial activity in stomatal closure induction. In this work, we showed that the mitochondrial-targeted H2S donor AP39 induces stomatal closure in a dose-dependent manner. Experiments using inhibitors of the mitochondrial electron transport chain (mETC) or insertional mutants in cytochrome c (CYTc) indicated that the activity of mitochondrial CYTc and/or complex IV are required for AP39-dependent stomatal closure. By using fluorescent probes and genetically encoded biosensors we reported that AP39 hyperpolarized the mitochondrial inner potential (Δψm) and increased cytosolic ATP, cytosolic hydrogen peroxide levels, and oxidation of the glutathione pool in GCs. These findings showed that mitochondrial-targeted H2S donors induce stomatal closure, modulate guard cell mETC activity, the cytosolic energetic and oxidative status, pointing to an interplay between mitochondrial H2S, mitochondrial activity, and stomatal closure.

The Functions of Chloroplastic Ascorbate in Vascular Plants and Algae

Ascorbate (Asc) is a multifunctional metabolite essential for various cellular processes in plants and animals. The best-known property of Asc is to scavenge reactive oxygen species (ROS), in a highly regulated manner. Besides being an effective antioxidant, Asc also acts as a chaperone for 2-oxoglutarate-dependent dioxygenases that are involved in the hormone metabolism of plants and the synthesis of various secondary metabolites. Asc also essential for the epigenetic regulation of gene expression, signaling and iron transport. Thus, Asc affects plant growth, development, and stress resistance via various mechanisms. In this review, the intricate relationship between Asc and photosynthesis in plants and algae is summarized in the following major points: (i) regulation of Asc biosynthesis by light, (ii) interaction between photosynthetic and mitochondrial electron transport in relation to Asc biosynthesis, (iii) Asc acting as an alternative electron donor of photosystem II, (iv) Asc inactivating the oxygen-evolving complex, (v) the role of Asc in non-photochemical quenching, and (vi) the role of Asc in ROS management in the chloroplast. The review also discusses differences in the regulation of Asc biosynthesis and the effects of Asc on photosynthesis in algae and vascular plants.

Ascorbate synthesis as an alternative electron source for mitochondrial respiration: Possible implications for the plant performance

The molecule vitamin C, in the chemical form of ascorbic acid (AsA), is known to be essential for the metabolism of humans and animals. Humans do not produce AsA, so they depend on plants as a source of vitamin C for their food. The AsA synthesis pathway occurs partially in the cytosol, but the last oxidation step is physically linked to the respiratory chain of plant mitochondria. This oxidation step is catalyzed by l-galactono-1,4-lactone dehydrogenase (l-GalLDH). This enzyme is not considered a limiting step for AsA production; however, it presents a distinguishing characteristic: the l-GalLDH can introduce electrons directly into the respiratory chain through cytochrome c (Cytc) and therefore can be considered an extramitochondrial electron source that bypasses the phosphorylating Complex III. The use of Cytc as electron acceptor has been debated in terms of its need for AsA synthesis, but little has been said in relation to its impact on the functioning of the respiratory chain. This work seeks to offer a new view about the possible changes that result of the link between AsA synthesis and the mitochondrial respiration. We hypothesized that some physiological alterations related to low AsA may be not only explained by the deficiency of this molecule but also by the changes in the respiratory function. We discussed some findings showing that respiratory mutants contained changes in AsA synthesis. Besides, recent works that also indicate that the excessive electron transport via l-GalLDH enzyme may affect other respiratory pathways. We proposed that Cytc reduction by l-GalLDH may be part of an alternative respiratory pathway that is active during AsA synthesis. Also, it is proposed that possible links of this pathway with other pathways of alternative electron transport in plant mitochondria may exist. The review suggests potential implications of this relationship, particularly for situations of stress. We hypothesized that this pathway of alternative electron input would serve as a strategy for adaptation of plant respiration to changing conditions.

Cytochrome c and the transcription factor ABI4 establish a molecular link between mitochondria and ABA-dependent seed germination

During germination, seed reserves are mobilised to sustain the metabolic and energetic demands of plant growth. Mitochondrial respiration is presumably required to drive germination in several species, but only recently its role in this process has begun to be elucidated. Using Arabidopsis thaliana lines with changes in the levels of the respiratory chain component cytochrome c (CYTc), we investigated the role of this protein in germination and its relationship with hormonal pathways. Cytochrome c deficiency causes delayed seed germination, which correlates with decreased cyanide-sensitive respiration and ATP production at the onset of germination. In addition, CYTc affects the sensitivity of germination to abscisic acid (ABA), which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA and regulates its expression. The results show that CYTc is a main player during seed germination through its role in respiratory metabolism and energy production. In addition, the direct regulation of CYTC-2 by ABI4 and its effect on ABA-responsive germination establishes a link between mitochondrial and hormonal functions during this process.

Mitochondrial dysfunction associated with ascorbate synthesis in plants

Mitochondria are the major organelles of energy production; however, active mitochondria can decline their energetic role and show a dysfunctional status. Mitochondrial dysfunction was induced by high non-physiological level of L-galactone-1,4-lactone (L-GalL), the precursor of ascorbate (AsA), in plant mitochondria. The dysfunction induced by L-GalL was associated with the fault in the mitochondrial electron partition and reactive oxygen species (ROS) over-production. Using mitochondria from RNAi-plant lines harbouring silenced L-galactone-1,4-lactone dehydrogenase (L-GalLDH) activity, it was demonstrated that such dysfunction is dependent on this enzyme activity. The capacity of alternative respiration was strongly decreased by L-GalL, probably mediated by redox-inactivation of the alternative oxidase (AOX) enzyme. Although, alternative respiration was shown to be the key factor that helps support AsA synthesis in dysfunctional mitochondria. Experiments with respiratory inhibitors showed that ROS formation and mitochondrial dysfunction were more associated with the decline in the activities of COX (cytochrome oxidase) and particularly AOX than with the lower activities of respiratory complexes I and III. The application of high L-GalL concentrations induced proteomic changes that indicated alterations in proteins related to oxidative stress and energetic status. However, supra-optimal L-GalL concentration was not deleterious for plants. Instead, the L-GalLDH activity could be positive. Indeed, it was found that wild type plants performed better growth than L-GalLDH-RNAi plants in response to high non-physiological L-GalL concentrations.

Overexpression of GhKTI12 Enhances Seed Yield and Biomass Production in Nicotiana Tabacum

Crop molecular breeding primarily focuses on increasing the trait of plant yield. An elongator-associated protein, KTI12, is closely associated with plant biomass and yield. KTI12 is involved in developmental processes of most organs, including the leaf, root, flower, and seed, through regulating cell division and differentiation. Previous work has shown that in upland cotton (Gossypium hirsutum), GhKTI12 regulates plant height, flowering, and tolerance to salt and drought stress. However, little is known about the molecular regulation mechanism of GhKTI12 in plant developmental processes. In this study, we identified the main GhKTI12 (Gh_D02G144400) gene and transformed it into tobacco (Nicotonia tabacum cv NC89). From seven transgenic lines, we obtained three (OE5, OE6 and OE8) with high expression of GhKTI12; compared with wild type plants, these three lines exhibited larger plant size, later flowering, and higher seed yield. Microscopic observation revealed that the number of leaf epidermal cells and stem parenchyma cells was increased by ~55%. Biochemical analysis showed that chlorophyll content and starch accumulation were significantly increased in younger leaves at the top canopy of transgenic plants, which may contribute to improved photosynthetic rate and, in turn, increased seed yield. To understand the molecular mechanism of GhKTI12 in transgenic plants development, two lines (OE6 and OE8) with higher expression levels of GhKTI12 were used as representative plants to conduct RNA-seq analysis. Through transcriptome analysis of the plant's shoot apical meristematic tissue of these two lines, we identified 518 upregulated genes and 406 downregulated genes common to both overexpression lines. A large number of cellular component genes associated with cell division and differentiation, such as RD21, TET8, KTN80, AOX1, AOX2, CP1, and KIC, were found to be upregulated, and genes showing the most downregulation included MADS-box genes related to flowering time, such as MADS6, AP1, AP3, AGL8, AGL6, SEP1, and SEP2. Downregulation of these genes caused delayed flowering time and longer vegetative stage during development. Combined with the upregulation of the yield-related gene RD21, the GhKTI12 transgenic plants could produce a higher seed yield. We here show that the overexpression of GhKTI12 could positively improve key agronomic traits in tobacco by regulating cell proliferation, photosynthesis, and organ development, and suggest that homologs of GhKTI12 may also be important in the genetic improvement of other crop plants.

The role of the electron-transfer flavoprotein: ubiquinone oxidoreductase following carbohydrate starvation in Arabidopsis cell cultures

KEY MESSAGE

The functional absence of the electron-transfer flavoprotein: ubiquinone oxidoreductase (ETFQO) directly impacts electrons donation to the mitochondrial electron transport chain under carbohydrate-limiting conditions without major impacts on the respiration of cell cultures. Alternative substrates (e.g., amino acids) can directly feed electrons into the mitochondrial electron transport chain (mETC) via the electron transfer flavoprotein/electron-transfer flavoprotein: ubiquinone oxidoreductase (ETF/ETFQO) complex, which supports plant respiration during stress situations. By using a cell culture system, here we investigated the responses of Arabidopsis thaliana mutants deficient in the expression of ETFQO (etfqo-1) following carbon limitation and supplied with amino acids. Our results demonstrate that isovaleryl-CoA dehydrogenase (IVDH) activity was induced during carbon limitation only in wild-type and that these changes occurred concomit with enhanced protein content. By contrast, neither the activity nor the total amount of IVDH was altered in etfqo-1 mutants. We also demonstrate that the activities of mitochondrial complexes in etfqo-1 mutants, display a similar pattern as in wild-type cells. Our findings suggest that the defect of ETFQO protein culminates with an impaired functioning of the IVDH, since no induction of IVDH activity was observed. However, the functional absence of the ETFQO seems not to cause major impacts on plant respiration under carbon limiting conditions, most likely due to other alternative electron entry pathways.

The pentatricopeptide repeat protein GEND1 is required for root development and high temperature tolerance in Arabidopsis thaliana

Pentatricopeptide repeat (PPR) proteins are a large family in land plants that play a role in organellular RNA processing, editing, and splicing. Here, we identify an Arabidopsis thaliana mutant, gend1-1, which exhibits a short root phenotype with reduced meristem size and cell numbers. Positional cloning of GEND1 revealed that it encodes a PPR protein, and functional analysis showed that GEND1 can bind and edit mitochondrial ccmFn-1 mRNA, causing gend1 mutants to have decreased levels of cytochrome C. GEND1 was up-regulated by high temperature conditions, to which gend1 mutants were hypersensitive. Analysis of a set of PPR mutants under high temperature showed that mutants with defects in cytochrome C had comparable temperature sensitivity to gend1. Collectively, these results suggest that cytochrome C plays an important role in root development and high temperature response in Arabidopsis.

Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.)

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom^®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

Cytochrome c Deficiency Differentially Affects the In Vivo Mitochondrial Electron Partitioning and Primary Metabolism Depending on the Photoperiod

Plant respiration provides metabolic flexibility under changing environmental conditions by modulating the activity of the nonphosphorylating alternative pathways from the mitochondrial electron transport chain, which bypass the main energy-producing components of the cytochrome oxidase pathway (COP). While adjustments in leaf primary metabolism induced by changes in day length are well studied, possible differences in the in vivo contribution of the COP and the alternative oxidase pathway (AOP) between different photoperiods remain unknown. In our study, in vivo electron partitioning between AOP and COP and expression analysis of respiratory components, photosynthesis, and the levels of primary metabolites were studied in leaves of wild-type (WT) plants and cytochrome c (CYTc) mutants, with reduced levels of COP components, under short- and long-day photoperiods. Our results clearly show that differences in AOP and COP in vivo activities between WT and cytc mutants depend on the photoperiod likely due to energy and stress signaling constraints. Parallel responses observed between in vivo respiratory activities, TCA cycle intermediates, amino acids, and stress signaling metabolites indicate the coordination of different pathways of primary metabolism to support growth adaptation under different photoperiods.

The Oxidative Phosphorylation system of the mitochondria in plants

Mitochondrial Oxidative Phosphorylation (OXPHOS) provides ATP for driving cellular functions. In plants, OXPHOS takes place in the context of photosynthesis. Indeed, metabolism of mitochondria and chloroplasts is tightly linked. OXPHOS has several extra functions in plants. This review takes a view on the OXPHOS system of plants, the electron transfer chain (ETC), the ATP synthase complex and the numerous supplementary enzymes involved. Electron transport pathways are especially branched in plants. Furthermore, the "classical" OXPHOS complexes include extra subunits, some of which introduce side activities into these complexes. Consequently, and to a remarkable degree, OXPHOS is a multi-functional system in plants that needs to be efficiently regulated with respect to all its physiological tasks in the mitochondria, the chloroplasts, and beyond. Regulatory mechanisms based on posttranslational protein modifications and formation of supramolecular protein assemblies are summarized and discussed.

Inhibition of the mitochondrial respiratory components (Complex I and Complex III) as stimuli to induce oxidative damage in Oryza sativa L. under thiocyanate exposure

Repression of the electron transport in mitochondria can result in an increase of reactive oxygen species (ROS) in plant cells. This study was to clarify inhibition of the mitochondrial respiratory components (Complex I and Complex III) as stimuli to induce oxidative damage in Oryza sativa L. under exogenous SCN^- exposure with special emphasis on lipid peroxidation, protein modification, and DNA damage at the biochemical and molecular levels. Our results showed that enzymatic activity and gene expression of cytochrome c reductase (Complex III) in roots and shoots of rice seedlings were significantly repressed by SCN^- exposure, where significant inhibition of NADH dehydrogenase (Complex I) was only detected in shoots, suggesting that Complex III was the main target attacked by SCN^- ligand in rice roots, and both components were arrested in shoots. ROS analysis in tissues indicated that SCN^- exposure caused significant accumulation of H₂O₂ and O₂^-•, increased malondialdehyde (MDA) and carbonyl content in rice materials in a dose-dependent manner. Similarly, a remarkable elevation of electrolyte leakage was observed in rice tissue samples. The comet assay indicated a positive correlation between DNA damage and external SCN^- exposure. In conclusion, oxidative burst generated from the inhibitions of the electron transport in mitochondria in rice seedlings under SCN^- exposure can cause lipid peroxidation, protein modification and DNA damage, eventually decreasing fresh weight of rice seedlings.

Arabidopsis mtHSC70-1 plays important roles in the establishment of COX-dependent respiration and redox homeostasis

The 70 kDa heat shock proteins function as molecular chaperones and are involved in diverse cellular processes. However, the functions of the plant mitochondrial HSP70s (mtHSC70s) remain unclear. Severe growth defects were observed in the Arabidopsis thaliana mtHSC70-1 knockout lines, mthsc70-1a and mthsc70-1b. Conversely, the introduction of the mtHSC70-1 gene into the mthsc70-1a background fully reversed the phenotypes, indicating that mtHSC70-1 is essential for plant growth. The loss of mtHSC70-1 functions resulted in abnormal mitochondria and alterations to respiration because of an inhibition of the cytochrome c oxidase (COX) pathway and the activation of the alternative respiratory pathway. Defects in COX assembly were observed in the mtHSC70-1 knockout lines, leading to decreased COX activity. The mtHSC70-1 knockout plants have increased levels of reactive oxygen species (ROS). The introduction of the Mn-superoxide dismutase 1 (MSD1) or the catalase 1 (CAT1) gene into the mthsc70-1a plants decreased ROS levels, reduced the expression of alternative oxidase, and partially rescued growth. Taken together, our data suggest that mtHSC70-1 plays important roles in the establishment of COX-dependent respiration.

Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006

Background

Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture.

Results

PGPR of the genera Bacillus and Pseudomonas in banana cv. Williams were evaluated. These plants were produced through in vitro culture and inoculated individually with two rhizobacteria, Bacillus amyloliquefaciens strain Bs006 and Pseudomonas fluorescens strain Ps006. Control plants without microbial inoculum were also evaluated. These plants were kept in a controlled climate growth room with conditions required to favor plant-microorganism interactions. These interactions were evaluated at 1-, 48- and 96-h using transcriptome sequencing after inoculation to establish differentially expressed genes (DEGs) in plants elicited by the interaction with the two rhizobacteria. Additionally, droplet digital PCR was performed at 1, 48, 96 h, and also at 15 and 30 days to validate the expression patterns of selected DEGs. The banana cv. Williams transcriptome reported differential expression in a large number of genes of which 22 were experimentally validated. Genes validated experimentally correspond to growth promotion and regulation of specific functions (flowering, photosynthesis, glucose catabolism and root growth) as well as plant defense genes. This study focused on the analysis of 18 genes involved in growth promotion, defense and response to biotic or abiotic stress.

Conclusions

Differences in banana gene expression profiles in response to the rhizobacteria evaluated here (Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006) are influenced by separate bacterial colonization processes and levels that stimulate distinct groups of genes at various points in time.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5763-5) contains supplementary material, which is available to authorized users.

Cytochrome c: Surfing Off of the Mitochondrial Membrane on the Tops of Complexes III and IV

The proper arrangement of protein components within the respiratory electron transport chain is nowadays a matter of intense debate, since altering it leads to cell aging and other related pathologies. Here, we discuss three current views—the so-called solid, fluid and plasticity models—which describe the organization of the main membrane-embedded mitochondrial protein complexes and the key elements that regulate and/or facilitate supercomplex assembly. The soluble electron carrier cytochrome c has recently emerged as an essential factor in the assembly and function of respiratory supercomplexes. In fact, a ‘restricted diffusion pathway’ mechanism for electron transfer between complexes III and IV has been proposed based on the secondary, distal binding sites for cytochrome c at its two membrane partners recently discovered. This channeling pathway facilitates the surfing of cytochrome c on both respiratory complexes, thereby tuning the efficiency of oxidative phosphorylation and diminishing the production of reactive oxygen species. The well-documented post-translational modifications of cytochrome c could further contribute to the rapid adjustment of electron flow in response to changing cellular conditions.

Composition of Mitochondrial Complex I during the Critical Node of Seed Aging in Oryza sativa

Previous studies have documented mitochondrial dysfunction during the critical node (CN) of rice (Oryza sativa) seed aging, including a decrease in the capacity of NADH dependent O₂ consumption. This raises the hypothesis that changes in the activity of NADH:ubiquinone oxidoreductase (complex I) may play a role in seed aging. The composition and activity of complex I was investigated at the CN of aged rice seeds. Using BN-PAGE and SWATH-MS 52 complex I subunits were identified, nineteen for the first time to be experimentally detected in rice. The subunits of the matrix arm (N and Q modules) were reduced in abundance at the CN, in accordance with a reduction in the capacity to oxidise NADH, reducing substrate oxidation and increase ROS accumulation. In contrast, subunits in the P module increased in abundance that contains many mitochondrial encoded subunits. It is proposed that the changes in complex I abundance subunits may indicate a premature re-activation of mitochondrial biogenesis, as evidenced by the increase in mitochondrial encoded subunits. This premature activation of mitochondrial biogenesis may under-pin the decreased viability of aged seeds, as mitochondrial biogenesis is a crucial event in germination to drive growth before autotrophic growth of the seedling is established.

Role of cytochrome c in modulating chromium-induced oxidative stress in Oryza sativa

Cytochrome c (CYTc) is one of the redox-active molecules responsible for electron transport in plant mitochondria. It is important in the interaction of metal ions with mitochondrial proteome, it is also essential for insights into electron transport during oxidative stress. This study focused on the clarification of interactions of CYTc with metal accumulation and associated modulation of CYTc with reactive oxygen species (ROS) generation in rice seedlings exposed to chromium either hexavalent Cr(VI) or trivalent Cr(III). The result indicates that exposures to both Cr species resulted in significant accumulation of Cr in rice tissues. ROS-dependent growth inhibition of rice seedlings was also evident from both Cr treatments. Changes of CYTc content in roots and shoots maintained almost the same pattern after both Cr exposures. However, dynamically transcriptional levels of rice CYTc genes conducted by real-time quantitative RT-PCR were inconsistent in rice tissues. The results presented here demonstrate that oxidative stresses induced by ROS accumulation do not equally and/or detrimentally influence the perturbations of CYTc content and expression patterns of CYTc genes in rice tissues after Cr exposure, suggesting that the decrease of CYTc levels in roots did not originate ROS accumulation, it may be due to metal-binding properties, while enhancement of CYTc content in shoots was probably a signal of severe growth inhibition owing to ROS accumulation.

Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs produce by cell endogenously. They are 18-26 nucleotides in length and play important roles at the post-transcriptional stage of gene regulation. Evolutionarily, miRNAs are conserved and their conservation plays an important role in the prediction of new miRNAs in different plants. Wheat (Triticum aestivum L.) is an important diet and consumed as second major crop in the world. This significant cereal crop was focused here through comparative genomics-based approach to identify new conserved miRNAs and their targeted genes. This resulted into a total of 212 new conserved precursor miRNAs (pre-miRNAs) belonging to 185 miRNA families. These newly profiled wheat's miRNAs are also annotated for stem-loop secondary structures, length distribution, organ of expression, sense/antisense orientation and characterization from their expressed sequence tags (ESTs). Moreover, fifteen miRNAs along with housekeeping gene were randomly selected and subjected to RT-PCR expressional validation. A total of 32927 targets are also predicted and annotated for these newly profiled wheat miRNAs. These targets are found to involve in 50 gene ontology (GO) enrichment terms and significant processes. Some of the significant targets are RNA-dependent DNA replication (GO:0006278), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), DNA-directed RNA polymerase activity (GO:0003899), magnesium ion transmembrane transporter activity (GO:0015095), antiporter activity (GO:0015297), solute:hydrogen antiporter activity (GO:0015299), protein kinase activity (GO:0004672), ATP binding (GO:0005524), regulation of Rab GTPase activity (GO:0032313) Rab GTPase activator activity (GO:0005097), regulation of signal transduction (GO:0009966) and phosphoprotein phosphatase inhibitor activity (GO:0004864). These findings will be helpful to manage this economically important grain plant for desirable traits through miRNAs regulation.

Interplay between cytochrome c and gibberellins during Arabidopsis vegetative development

We studied the effect of reducing the levels of the mitochondrial electron carrier cytochrome c (CYTc) in Arabidopsis thaliana. Plants with CYTc deficiency have delayed growth and development, and reach flowering several days later than the wild-type but with the same number of leaves. CYTc-deficient plants accumulate starch and glucose during the day, and contain lower levels of active gibberellins (GA) and higher levels of DELLA proteins, involved in GA signaling. GA treatment abolishes the developmental delay and reduces glucose accumulation in CYTc-deficient plants, which also show a lower raise in ATP levels in response to glucose. Treatment of wild-type plants with inhibitors of mitochondrial energy production limits plant growth and increases the levels of DELLA proteins, thus mimicking the effects of CYTc deficiency. In addition, an increase in the amount of CYTc decreases DELLA protein levels and expedites growth, and this depends on active GA synthesis. We conclude that CYTc levels impinge on the activity of the GA pathway, most likely through changes in mitochondrial energy production. In this way, hormone-dependent growth would be coupled to the activity of components of the mitochondrial respiratory chain.

The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants

Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O₂ to H₂O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a₃), and metallic centers (Cu_A and Cu_B). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.

CMS-G from Beta vulgaris ssp. maritima is maintained in natural populations despite containing an atypical cytochrome c oxidase

While mitochondrial mutants of the respiratory machinery are rare and often lethal, cytoplasmic male sterility (CMS), a mitochondrially inherited trait that results in pollen abortion, is frequently encountered in wild populations. It generates a breeding system called gynodioecy. In Beta vulgaris ssp. maritima, a gynodioecious species, we found CMS-G to be widespread across the distribution range of the species. Despite the sequencing of the mitochondrial genome of CMS-G, the mitochondrial sterilizing factor causing CMS-G is still unknown. By characterizing biochemically CMS-G, we found that the expression of several mitochondrial proteins is altered in CMS-G plants. In particular, Cox1, a core subunit of the cytochrome c oxidase (complex IV), is larger but can still assemble into complex IV. However, the CMS-G-specific complex IV was only detected as a stabilized dimer. We did not observe any alteration of the affinity of complex IV for cytochrome c; however, in CMS-G, complex IV capacity is reduced. Our results show that CMS-G is maintained in many natural populations despite being associated with an atypical complex IV. We suggest that the modified complex IV could incur the associated cost predicted by theoretical models to maintain gynodioecy in wild populations.

A Functional Approach towards Understanding the Role of the Mitochondrial Respiratory Chain in an Endomycorrhizal Symbiosis

Arbuscular mycorrhizal fungi (AMF) are crucial components of fertile soils, able to provide several ecosystem services for crop production. Current economic, social and legislative contexts should drive the so-called "second green revolution" by better exploiting these beneficial microorganisms. Many challenges still need to be overcome to better understand the mycorrhizal symbiosis, among which (i) the biotrophic nature of AMF, constraining their production, while (ii) phosphate acts as a limiting factor for the optimal mycorrhizal inoculum application and effectiveness. Organism fitness and adaptation to the changing environment can be driven by the modulation of mitochondrial respiratory chain, strongly connected to the phosphorus processing. Nevertheless, the role of the respiratory function in mycorrhiza remains largely unexplored. We hypothesized that the two mitochondrial respiratory chain components, alternative oxidase (AOX) and cytochrome oxidase (COX), are involved in specific mycorrhizal behavior. For this, a complex approach was developed. At the pre-symbiotic phase (axenic conditions), we studied phenotypic responses of Rhizoglomus irregulare spores with two AOX and COX inhibitors [respectively, salicylhydroxamic acid (SHAM) and potassium cyanide (KCN)] and two growth regulators (abscisic acid - ABA and gibberellic acid - Ga3). At the symbiotic phase, we analyzed phenotypic and transcriptomic (genes involved in respiration, transport, and fermentation) responses in Solanum tuberosum/Rhizoglomus irregulare biosystem (glasshouse conditions): we monitored the effects driven by ABA, and explored the modulations induced by SHAM and KCN under five phosphorus concentrations. KCN and SHAM inhibited in vitro spore germination while ABA and Ga3 induced differential spore germination and hyphal patterns. ABA promoted mycorrhizal colonization, strong arbuscule intensity and positive mycorrhizal growth dependency (MGD). In ABA treated plants, R. irregulare induced down-regulation of StAOX gene isoforms and up-regulation of genes involved in plant COX pathway. In all phosphorus (P) concentrations, blocking AOX or COX induced opposite mycorrhizal patterns in planta: KCN induced higher Arum-type arbuscule density, positive MGD but lower root colonization compared to SHAM, which favored Paris-type formation and negative MGD. Following our results and current state-of-the-art knowledge, we discuss metabolic functions linked to respiration that may occur within mycorrhizal behavior. We highlight potential connections between AOX pathways and fermentation, and we propose new research and mycorrhizal application perspectives.

Cardiolipin Supports Respiratory Enzymes in Plants in Different Ways

In eukaryotes the presence of the dimeric phospholipid cardiolipin (CL) is limited to the mitochondrial membranes. It resides predominantly in the inner membrane where it interacts with components of the mitochondrial electron transfer chain. CL deficiency has previously been shown to affect abundances of the plant NADH-dehydrogenase complex and its association with dimeric cyctochrome c reductase. Using an Arabidopsis thaliana knock-out mutant for the final enzyme of CL biosynthesis we here extend current knowledge on the dependence of plant respiration on CL. By correlating respiratory enzyme abundances with enzymatic capacities in mitochondria isolated from wild type, CL deficient and CL complemented heterotrophic cell culture lines a new picture of the participation of CL in plant respiration is emerging. Data indicate a loss of a general reduction of respiratory capacity in CL deficient mitochondria which cannot solely be attributed to decreased abundances or capacities of mitochondrial electron transfer protein complexes and supercomplexes. Instead, it most likely is the result of a loss of the mobile electron carrier cytochrome c. Furthermore, enzymes of the tricarboxylic acid cycle are found to have lower maximum activities in the mutant, including the succinate dehydrogenase complex. Interestingly, abundance of the latter is not altered, indicative of a direct impact of CL deficiency on the enzymatic capacity of this electron transfer chain protein complex.

Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29

Glucosinolates (Gls) constitute a major group of natural metabolites represented by three major classes (aliphatic, indolic and aromatic) of more than 120 chemical structures. In our previous work, soluble proteins and metabolites in Arabidopsis mutants deficient of aliphatic (myb28/29) and indolic Gls (cyp79B2B3) were analyzed. Here we focus on investigating the changes at the level of membrane proteins in these mutants. Our LC/MS-MS analyses of tandem mass tag (TMT) labeled peptides derived from the cyp79B2/B3 and myb28/29 relative to wild type resulted in the identification of 4,673 proteins, from which 2,171 are membrane proteins. Fold changes and statistical analysis showed 64 increased and 74 decreased in cyp79B2/B3, while 28 increased and 17 decreased in myb28/29. As to the shared protein changes between the mutants, one protein was increased and eight were decreased. Bioinformatics analysis of the changed proteins led to the discovery of three cytochromes in glucosinolate molecular network (GMN): cytochrome P450 86A7 (At1g63710), cytochrome P450 71B26 (At3g26290), and probable cytochrome c (At1g22840). CYP86A7 and CYP71B26 may play a role in hydroxyl-indolic Gls production. In addition, flavone 3'-O-methyltransferase 1 represents an interesting finding as it is likely to participate in the methylation process of the hydroxyl-indolic Gls to form methoxy-indolic Gls. The analysis also revealed additional new nodes in the GMN related to stress and defense activity, transport, photosynthesis, and translation processes. Gene expression and protein levels were found to be correlated in the cyp79B2/B3, but not in the myb28/29.

Mitochondrial gamma carbonic anhydrases are required for complex I assembly and plant reproductive development

Complex I of the mitochondrial electron transport chain (mETC) in plants contains an extra domain that is made up from proteins homologous to prokaryotic gamma-carbonic anhydrases (γCA). This domain has been suggested to participate in complex I assembly or to support transport of mitochondrial CO2 to the chloroplast. Here, we generated mutants lacking CA1 and CA2 - two out of three CA proteins in Arabidopsis thaliana. Double mutants were characterized at the developmental and physiological levels. Furthermore, the composition and activity of the mETC were determined, and mutated CA versions were used for complementation assays. Embryo development of double mutants was strongly delayed and seed development stopped before maturation. Mutant plants could only be rescued on sucrose media, showed severe stress symptoms and never produced viable seeds. By contrast, callus cultures were only slightly affected in growth. Complex I was undetectable in the double mutants, but complex II and complex IV were upregulated concomitant with increased oxygen consumption in mitochondrial respiration. Ectopic expression of inactive CA variants was sufficient to complement the mutant phenotype. Data indicate that CA proteins are structurally required for complex I assembly and that reproductive development is dependent on the presence of complex I.

Cytochrome c, a hub linking energy, redox, stress and signaling pathways in mitochondria and other cell compartments

Cytochrome c (CYTc) is a soluble redox-active heme protein that transfers electrons from complex III to complex IV in the cyanide-sensitive mitochondrial respiratory pathway. CYTc biogenesis is a complex process that requires multiple steps until the mature active protein is obtained. CYTc levels and activity are finely regulated, revealing the importance of this protein not only as electron carrier but also in many other processes. In this article, we describe the role of CYTc in mitochondrial respiration, from its canonical role as electron carrier for ATP production to its involvement in protein import and the stabilization of respiratory complexes and supercomplexes. In plants, CYTc is connected to the synthesis of the antioxidant ascorbate and the detoxification of toxic compounds. Finally, CYTc is also a multi-functional signaling molecule that influences the balance between life and death, acting in energy provision for cellular functions or triggering programmed cell death. The confluence of several metabolic routes into a single protein that links redox reactions with energy producing pathways seems logical from the point of view of cellular economy, control and organization.

Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

In the present study, molecular mapping of high-resolution plant height QTLs was performed by integrating 3625 desi genome-derived GBS (genotyping-by-sequencing)-SNPs on an ultra-high resolution intra-specific chickpea genetic linkage map (dwarf/semi-dwarf desi cv. ICC12299 x tall kabuli cv. ICC8261). The identified six major genomic regions harboring six robust QTLs (11.5-21.3 PVE), associated with plant height, were mapped within <0.5 cM average marker intervals on six chromosomes. Five SNPs-containing genes tightly linked to the five plant height QTLs, were validated based upon their high potential for target trait association (12.9-20.8 PVE) in 65 desi and kabuli chickpea accessions. The vegetative tissue-specific expression, including higher differential up-regulation (>5-fold) of five genes especially in shoot, young leaf, shoot apical meristem of tall mapping parental accession (ICC8261) as compared to that of dwarf/semi-dwarf parent (ICC12299) was apparent. Overall, combining high-resolution QTL mapping with genetic association analysis and differential expression profiling, delineated natural allelic variants in five candidate genes (encoding cytochrome-c-biosynthesis protein, malic oxidoreductase, NADH dehydrogenase iron-sulfur protein, expressed protein and bZIP transcription factor) regulating plant height in chickpea. These molecular tags have potential to dissect complex plant height trait and accelerate marker-assisted genetic enhancement for developing cultivars with desirable plant height ideotypes in chickpea.

The roles of the zinc finger transcription factors XlnR, ClrA and ClrB in the breakdown of lignocellulose by Aspergillus niger

Genes encoding the key transcription factors (TF) XlnR, ClrA and ClrB were deleted from Aspergillus niger and the resulting strains were assessed for growth on glucose and wheat straw, transcription of genes encoding glycosyl hydrolases and saccharification activity. Growth of all mutant strains, based in straw on measurement of pH and assay of glucosamine, was impaired in relation to the wild-type (WT) strain although deletion of clrA had less effect than deletion of xlnR or clrB. Release of sugars from wheat straw was also lowered when culture filtrates from TF deletion strains were compared with WT culture filtrates. Transcript levels of cbhA, eglC and xynA were measured in all strains in glucose and wheat straw media in batch culture with and without pH control. Transcript levels from cbhA and eglC were lowered in all mutant strains compared to WT although the impact of deleting clrA was not pronounced with expression of eglC and had no effect on xynA. The impact on transcription was not related to changes in pH. In addition to impaired growth on wheat straw, the ΔxlnR strain was sensitive to oxidative stress and displayed cell wall defects in the glucose condition suggesting additional roles for XlnR. The characterisation of TFs, such as ClrB, provides new areas of improvement for industrial processes for production of second generation biofuels.

The cytochrome c oxidase biogenesis factor AtCOX17 modulates stress responses in Arabidopsis

COX17 is a soluble protein from the mitochondrial intermembrane space that participates in the transfer of copper for cytochrome c oxidase (COX) assembly in eukaryotic organisms. In this work, we studied the function of both Arabidopsis thaliana AtCOX17 genes using plants with altered expression levels of these genes. Silencing of AtCOX17-1 in a cox17-2 knockout background generates plants with smaller rosettes and decreased expression of genes involved in the response of plants to different stress conditions, including several genes that are induced by mitochondrial dysfunctions. Silencing of either of the AtCOX17 genes does not affect plant development or COX activity but causes a decrease in the response of genes to salt stress. In addition, these plants contain higher reactive oxygen and lipid peroxidation levels after irrigation with high NaCl concentrations and are less sensitive to abscisic acid. In agreement with a role of AtCOX17 in stress and abscisic acid responses, both AtCOX17 genes are induced by several stress conditions, abscisic acid and mutation of the transcription factor ABI4. The results indicate that AtCOX17 is required for optimal expression of a group of stress-responsive genes, probably as a component of signalling pathways that link stress conditions to gene expression responses.

The CA domain of the respiratory complex I is required for normal embryogenesis in Arabidopsis thaliana

The NADH-ubiquinone oxidoreductase [complex I (CI), EC 1.6.5.3] of the mitochondrial respiratory chain is the principal entry point of electrons, and vital in maintaining metabolism and the redox balance. In a variety of eukaryotic organisms, except animal and fungi (Opisthokonta), it contains an extra domain composed of putative gamma carbonic anhydrases subunits, named the CA domain, which was proposed to be essential for complex I assembly. There are two kinds of carbonic anhydrase subunits: CAs (of which there are three) and carbonic anhydrase-like proteins (CALs) (of which there are two). In plants, the CA domain has been linked to photorespiration. In this work, we report that Arabidopsis mutant plants affected in two specific CA subunits show a lethal phenotype. Double homozygous knockouts ca1ca2 embryos show a significant developmental delay compared to the non-homozygous embryos, which show a wild-type (WT) phenotype in the same silique. Mutant embryos show impaired mitochondrial membrane potential and mitochondrial reactive oxygen species (ROS) accumulation. The characteristic embryo greening does not take place and fewer but larger oil bodies are present. Although seeds look dark brown and wrinkled, they are able to germinate 12 d later than WT seeds. However, they die immediately, most likely due to oxidative stress.Since the CA domain is required for complex I biogenesis, it is predicted that in ca1ca2 mutants no complex I could be formed, triggering the lethal phenotype. The in vivo composition of a functional CA domain is proposed.

The Arabidopsis COX11 Homolog is Essential for Cytochrome c Oxidase Activity

Members of the ubiquitous COX11 (cytochrome c oxidase 11) protein family are involved in copper delivery to the COX complex. In this work, we characterize the Arabidopsis thaliana COX11 homolog (encoded by locus At1g02410). Western blot analyses and confocal microscopy identified Arabidopsis COX11 as an integral mitochondrial protein. Despite sharing high sequence and structural similarities, the Arabidopsis COX11 is not able to functionally replace the Saccharomyces cerevisiae COX11 homolog. Nevertheless, further analysis confirmed the hypothesis that Arabidopsis COX11 is essential for COX activity. Disturbance of COX11 expression through knockdown (KD) or overexpression (OE) affected COX activity. In KD lines, the activity was reduced by ~50%, resulting in root growth inhibition, smaller rosettes and leaf curling. In OE lines, the reduction was less pronounced (~80% of the wild type), still resulting in root growth inhibition. Additionally, pollen germination was impaired in COX11 KD and OE plants. This effect on pollen germination can only partially be attributed to COX deficiency and may indicate a possible auxiliary role of COX11 in ROS metabolism. In agreement with its role in energy production, the COX11 promoter is highly active in cells and tissues with high-energy demand for example shoot and root meristems, or vascular tissues of source and sink organs. In COX11 KD lines, the expression of the plasma-membrane copper transporter COPT2 and of several copper chaperones was altered, indicative of a retrograde signaling pathway pertinent to copper homeostasis. Based on our data, we postulate that COX11 is a mitochondrial chaperone, which plays an important role for plant growth and pollen germination as an essential COX complex assembly factor.

AtCOX10, a protein involved in haem o synthesis during cytochrome c oxidase biogenesis, is essential for plant embryogenesis and modulates the progression of senescence

Cytochrome c oxidase (CcO) biogenesis requires several accessory proteins implicated, among other processes, in copper and haem a insertion. In yeast, the farnesyltransferase Cox10p that catalyses the conversion of haem b to haem o is the limiting factor in haem a biosynthesis and is essential for haem a insertion in CcO. In this work, we characterized AtCOX10, a putative Cox10p homologue from Arabidopsis thaliana. AtCOX10 was localized in mitochondria and was able to restore growth of a yeast Δcox10 null mutant on non-fermentable carbon sources, suggesting that it also participates in haem o synthesis. Plants with T-DNA insertions in the coding region of both copies of AtCOX10 could not be recovered, and heterozygous mutant plants showed seeds with embryos arrested at early developmental stages that lacked CcO activity. Heterozygous mutant plants exhibited lower levels of CcO activity and cyanide-sensitive respiration but normal levels of total respiration at the expense of an increase in alternative respiration. AtCOX10 seems to be implicated in the onset and progression of senescence, since heterozygous mutant plants showed a faster decrease in chlorophyll content and photosynthetic performance than wild-type plants after natural and dark-induced senescence. Furthermore, complementation of mutants by expressing AtCOX10 under its own promoter allowed us to obtain plants with T-DNA insertions in both AtCOX10 copies, which showed phenotypic characteristics comparable to those of wild type. Our results highlight the relevance of haem o synthesis in plants and suggest that this process is a limiting factor that influences CcO activity levels, mitochondrial respiration, and plant senescence.

Empty pericarp7 encodes a mitochondrial E-subgroup pentatricopeptide repeat protein that is required for ccmFN editing, mitochondrial function and seed development in maize

RNA editing, converting cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, plays a critical role in organelle gene expression in land plants. Recently pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing. In this study, we characterized an empty pericarp7 mutant (emp7) in Zea mays (maize), which confers an embryo-lethal phenotype. In emp7 mutants, mitochondrial functions are seriously perturbed, resulting in a strikingly reduced respiration rate. Emp7 encodes an E-subgroup PPR protein that is localized exclusively in the mitochondrion. Null mutation of Emp7 abolishes the C → U editing of ccmF(N) transcript solely at position 1553. CcmF(N) is coding for a subunit of heme lyase complex in the cytochrome c maturation pathway. The resulting Phe → Ser substitution in CcmF(N) leads to the loss of CcmF(N) protein and a strikingly reduced c-type cytochrome. Consequently, the mitochondrial cytochrome-linked respiratory chain is impaired as a result of the disassembly of complex III in the emp7 mutant. These results indicate that the PPR-E subgroup protein EMP7 is required for C → U editing of ccmF(N) -1553 at a position essential for cytochrome c maturation and mitochondrial oxidative phosphorylation, and hence is essential to embryo and endosperm development in maize.

Complexity of Compensatory Effects in Nrf1 Knockdown: Linking Undeveloped Anxiety-Like Behavior to Prevented Mitochondrial Dysfunction and Oxidative Stress

Anxiety-related disorders are complex illnesses that underlying molecular mechanisms need to be understood. Mitochondria stand as an important link between energy metabolism, oxidative stress, and anxiety. The nuclear factor, erythroid-derived 2,-like 1(Nrf1) is a member of the cap "n" collar subfamily of basic region leucine zipper transcription factors and plays the major role in regulating the adaptive response to oxidants and electrophiles within the cell. Here, we injected small interfering RNA (siRNA) targeting Nrf1 in dorsal third ventricle of adult male albino Wistar rats and subsequently examined the effect of this silencing on anxiety-related behavior. We also evaluated apoptotic markers and mitochondrial biogenesis factors, along with electron transport chain activity in three brain regions: hippocampus, amygdala, and prefrontal cortex. Our data revealed that in the group that received Nrf1-siRNA, anxiety-related behavior did not show any significant changes compared to the control group. Caspase-3 did not increase in Nrf1-siRNA-injected rats even though Bax/Bcl2 ratio markedly elevated in Nrf1-knockdown rats in all three mentioned regions compared to control rats. Also, Nrf1 silencing of complex I and II-III did not alter, generally. In addition, Nrf1-knockdown affected mitochondrial biogenesis markers. The level of peroxisome proliferator-activated receptor gamma coactivator-1α and cytochrome-c increased, which indicates a possible role for mitochondrial biogenesis in anxiety.

Involvement of Iron-Containing Proteins in Genome Integrity in Arabidopsis Thaliana

The Arabidopsis genome encodes numerous iron-containing proteins such as iron-sulfur (Fe-S) cluster proteins and hemoproteins. These proteins generally utilize iron as a cofactor, and they perform critical roles in photosynthesis, genome stability, electron transfer, and oxidation-reduction reactions. Plants have evolved sophisticated mechanisms to maintain iron homeostasis for the assembly of functional iron-containing proteins, thereby ensuring genome stability, cell development, and plant growth. Over the past few years, our understanding of iron-containing proteins and their functions involved in genome stability has expanded enormously. In this review, I provide the current perspectives on iron homeostasis in Arabidopsis, followed by a summary of iron-containing protein functions involved in genome stability maintenance and a discussion of their possible molecular mechanisms.

Decreasing electron flux through the cytochrome and/or alternative respiratory pathways triggers common and distinct cellular responses dependent on growth conditions

Diverse signaling pathways are activated by perturbation of mitochondrial function under different growth conditions.Mitochondria have emerged as an important organelle for sensing and coping with stress in addition to being the sites of important metabolic pathways. Here, responses to moderate light and drought stress were examined in different Arabidopsis (Arabidopsis thaliana) mutant plants lacking a functional alternative oxidase (alternative oxidase1a [aox1a]), those with reduced cytochrome electron transport chain capacity (T3/T7 bacteriophage-type RNA polymerase, mitochondrial, and plastidial [rpoTmp]), and double mutants impaired in both pathways (aox1a:rpoTmp). Under conditions considered optimal for growth, transcriptomes of aox1a and rpoTmp were distinct. Under adverse growth conditions, however, transcriptome changes in aox1a and rpoTmp displayed a highly significant overlap and were indicative of a common mitochondrial stress response and down-regulation of photosynthesis. This suggests that the role of mitochondria to support photosynthesis is provided through either the alternative pathway or the cytochrome pathway, and when either pathway is inhibited, such as under environmental stress, a common, dramatic, and succinct mitochondrial signal is activated to alter energy metabolism in both organelles. aox1a:rpoTmp double mutants grown under optimal conditions showed dramatic reductions in biomass production compared with aox1a and rpoTmp and a transcriptome that was distinct from aox1a or rpoTmp. Transcript data indicating activation of mitochondrial biogenesis in aox1a:rpoTmp were supported by a proteomic analysis of over 200 proteins. Under optimal conditions, aox1a:rpoTmp plants seemed to switch on many of the typical mitochondrial stress regulators. Under adverse conditions, aox1a:rpoTmp turned off these responses and displayed a biotic stress response. Taken together, these results highlight the diverse signaling pathways activated by the perturbation of mitochondrial function under different growth conditions.

Cytoplasmic male sterility and mitochondrial metabolism in plants

Cytoplasmic male sterility (CMS) is a common feature encountered in plant species. It is the result of a genomic conflict between the mitochondrial and the nuclear genomes. CMS is caused by mitochondrial encoded factors which can be counteracted by nuclear encoded factors restoring male fertility. Despite extensive work, the molecular mechanism of male sterility still remains unknown. Several studies have suggested the involvement of respiration on the disruption of pollen production through an energy deficiency. By comparing recent works on CMS and respiratory mutants, we suggest that the "ATP hypothesis" might not be as obvious as previously suggested.

Divergent functions of the Arabidopsis mitochondrial SCO proteins: HCC1 is essential for COX activity while HCC2 is involved in the UV-B stress response

The two related putative cytochrome c oxidase (COX) assembly factors HCC1 and HCC2 from Arabidopsis thaliana are Homologs of the yeast Copper Chaperones Sco1p and Sco2p. The hcc1 null mutation was previously shown to be embryo lethal while the disruption of the HCC2 gene function had no obvious effect on plant development, but increased the expression of stress-responsive genes. Both HCC1 and HCC2 contain a thioredoxin domain, but only HCC1 carries a Cu-binding motif also found in Sco1p and Sco2p. In order to investigate the physiological implications suggested by this difference, various hcc1 and hcc2 mutants were generated and analyzed. The lethality of the hcc1 knockout mutation was rescued by complementation with the HCC1 gene under the control of the embryo-specific promoter ABSCISIC ACID INSENSITIVE 3. However, the complemented seedlings did not grow into mature plants, underscoring the general importance of HCC1 for plant growth. The HCC2 homolog was shown to localize to mitochondria like HCC1, yet the function of HCC2 is evidently different, because two hcc2 knockout lines developed normally and exhibited only mild growth suppression compared with the wild type (WT). However, hcc2 knockouts were more sensitive to UV-B treatment than the WT. Complementation of the hcc2 knockout with HCC2 rescued the UV-B-sensitive phenotype. In agreement with this, exposure of wild-type plants to UV-B led to an increase of HCC2 transcripts. In order to corroborate a function of HCC1 and HCC2 in COX biogenesis, COX activity of hcc1 and hcc2 mutants was compared. While the loss of HCC2 function had no significant effect on COX activity, the disruption of one HCC1 gene copy was enough to suppress respiration by more than half compared with the WT. Therefore, we conclude that HCC1 is essential for COX function, most likely by delivering Cu to the catalytic center. HCC2, on the other hand, seems to be involved directly or indirectly in UV-B-stress responses.

Surrogate mutants for studying mitochondrially encoded functions

Although chloroplast transformation is possible in some plant species, it is extremely difficult to create or select mutations in plant mitochondrial genomes, explaining why few genetic studies of mitochondrially encoded functions exist. In recent years it has become clear that many nuclear genes encode factors with key functions in organelle gene expression, and that often their action is restricted to a single organelle gene or transcript. Mutations in one of these nuclear genes thus leads to a specific primary defect in expression of a single organelle gene, and the nuclear mutation can be used as a surrogate for a phenotypically equivalent mutation in the organelle genome. These surrogate mutations often result in defective assembly of respiratory complexes, and lead to severe phenotypes including reduced growth and fertility, or even embryo-lethality. A wide collection of such mutants is now available, and this review summarises the progress in basic knowledge of mitochondrial biogenesis they have contributed to and points out areas where this resource has not been exploited yet.

GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana

Owing to duplication events in its progenitor, more than 90% of the genes in the Arabidopsis thaliana genome are members of multigene families. A set of 2108 gene families, each consisting of precisely two unlinked paralogous genes, was identified in the nuclear genome of A. thaliana on the basis of sequence similarity. A systematic method for the creation of double knock-out lines for such gene pairs, designated as DUPLO lines, was established and 200 lines are now publicly available. Their initial phenotypic characterisation led to the identification of seven lines with defects that emerge only in the adult stage. A further six lines display seedling lethality and 23 lines were lethal before germination. Another 14 lines are known to show phenotypes under non-standard conditions or at the molecular level. Knock-out of gene pairs with very similar coding sequences or expression profiles is more likely to produce a mutant phenotype than inactivation of gene pairs with dissimilar profiles or sequences. High coding sequence similarity and highly similar expression profiles are only weakly correlated, implying that promoter and coding regions of these gene pairs display different degrees of diversification.

Alternative oxidase: a mitochondrial respiratory pathway to maintain metabolic and signaling homeostasis during abiotic and biotic stress in plants

Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain. While respiratory carbon oxidation pathways, electron transport, and ATP turnover are tightly coupled processes, AOX provides a means to relax this coupling, thus providing a degree of metabolic homeostasis to carbon and energy metabolism. Beside their role in primary metabolism, plant mitochondria also act as "signaling organelles", able to influence processes such as nuclear gene expression. AOX activity can control the level of potential mitochondrial signaling molecules such as superoxide, nitric oxide and important redox couples. In this way, AOX also provides a degree of signaling homeostasis to the organelle. Evidence suggests that AOX function in metabolic and signaling homeostasis is particularly important during stress. These include abiotic stresses such as low temperature, drought, and nutrient deficiency, as well as biotic stresses such as bacterial infection. This review provides an introduction to the genetic and biochemical control of AOX respiration, as well as providing generalized examples of how AOX activity can provide metabolic and signaling homeostasis. This review also examines abiotic and biotic stresses in which AOX respiration has been critically evaluated, and considers the overall role of AOX in growth and stress tolerance.