The alternative respiratory pathway mediates carboxylate synthesis in white lupin cluster roots under phosphorus deprivation

Genome-Wide Identification and Characterization of Alternative Oxidase (AOX) Genes in Foxtail Millet (Setaria italica): Insights into Their Abiotic Stress Response

Alternative oxidase (AOX) serves as a critical terminal oxidase within the plant respiratory pathway, playing a significant role in cellular responses to various stresses. Foxtail millet (Setaria italica), a crop extensively cultivated across Asia, is renowned for its remarkable tolerance to abiotic stresses and minimal requirement for fertilizer. In this study, we conducted a comprehensive genome-wide identification of AOX genes in foxtail millet genome, discovering a total of five SiAOX genes. Phylogenetic analysis categorized these SiAOX members into two subgroups. Prediction of cis-elements within the promoter regions, coupled with co-expression network analysis, intimated that SiAOX proteins are likely involved in the plant's adaptive response to abiotic stresses. Employing RNA sequencing (RNA-seq) and real-time quantitative PCR (RT-qPCR), we scrutinized the expression patterns of the SiAOX genes across a variety of tissues and under multiple abiotic stress conditions. Specifically, our analysis uncovered that SiAOX1, SiAOX2, SiAOX4, and SiAOX5 display distinct tissue-specific expression profiles. Furthermore, SiAOX2, SiAOX3, SiAOX4, and SiAOX5 exhibit responsive expression patterns under abiotic stress conditions, with significant differences in expression levels observed between the shoot and root tissues of foxtail millet seedlings. Haplotype analysis of SiAOX4 and SiAOX5 revealed that these genes are in linkage disequilibrium, with Hap_2 being the superior haplotype for both, potentially conferring enhanced cold stress tolerance in the cultivar group. These findings suggest that both SiAOX4 and SiAOX5 may be targeted for selection in future breeding programs aimed at improving foxtail millet's resilience to cold stress.

Comparative physiological and transcriptomic analysis of two salt-tolerant soybean germplasms response to low phosphorus stress: role of phosphorus uptake and antioxidant capacity

BACKGROUND

Phosphorus (P) and salt stress are common abiotic stressors that limit crop growth and development, but the response mechanism of soybean to low phosphorus (LP) and salt (S) combined stress remains unclear.

RESULTS

In this study, two soybean germplasms with similar salt tolerance but contrasting P-efficiency, A74 (salt-tolerant and P-efficient) and A6 (salt-tolerant and P-inefficient), were selected as materials. By combining physiochemical and transcriptional analysis, we aimed to elucidate the mechanism by which soybean maintains high P-efficiency under salt stress. In total, 14,075 differentially expressed genes were identified through pairwise comparison. PageMan analysis subsequently revealed several significantly enriched categories in the LP vs. control (CK) or low phosphorus + salt (LPS) vs. S comparative combination when compared to A6, in the case of A74. These categories included genes involved in mitochondrial electron transport, secondary metabolism, stress, misc, transcription factors and transport. Additionally, weighted correlation network analysis identified two modules that were highly correlated with acid phosphatase and antioxidant enzyme activity. Citrate synthase gene (CS), acyl-coenzyme A oxidase4 gene (ACX), cytokinin dehydrogenase 7 gene (CKXs), and two-component response regulator ARR2 gene (ARR2) were identified as the most central hub genes in these two modules.

CONCLUSION

In summary, we have pinpointed the gene categories responsible for the LP response variations between the two salt-tolerant germplasms, which are mainly related to antioxidant, and P uptake process. Further, the discovery of the hub genes layed the foundation for further exploration of the molecular mechanism of salt-tolerant and P-efficient in soybean.

ATP yield of plant respiration: potential, actual and unknown

BACKGROUND AND AIMS

The ATP yield of plant respiration (ATP/hexose unit respired) quantitatively links active heterotrophic processes with substrate consumption. Despite its importance, plant respiratory ATP yield is uncertain. The aim here was to integrate current knowledge of cellular mechanisms with inferences required to fill knowledge gaps to generate a contemporary estimate of respiratory ATP yield and identify important unknowns.

METHOD

A numerical balance sheet model combining respiratory carbon metabolism and electron transport pathways with uses of the resulting transmembrane electrochemical proton gradient was created and parameterized for healthy, non-photosynthesizing plant cells catabolizing sucrose or starch to produce cytosolic ATP.

KEY RESULTS

Mechanistically, the number of c subunits in the mitochondrial ATP synthase Fo sector c-ring, which is unquantified in plants, affects ATP yield. A value of 10 was (justifiably) used in the model, in which case respiration of sucrose potentially yields about 27.5 ATP/hexose (0.5 ATP/hexose more from starch). Actual ATP yield often will be smaller than its potential due to bypasses of energy-conserving reactions in the respiratory chain, even in unstressed plants. Notably, all else being optimal, if 25 % of respiratory O2 uptake is via the alternative oxidase - a typically observed fraction - ATP yield falls 15 % below its potential.

CONCLUSIONS

Plant respiratory ATP yield is smaller than often assumed (certainly less than older textbook values of 36-38 ATP/hexose) leading to underestimation of active-process substrate requirements. This hinders understanding of ecological/evolutionary trade-offs between competing active processes and assessments of crop growth gains possible through bioengineering of processes that consume ATP. Determining the plant mitochondrial ATP synthase c-ring size, the degree of any minimally required (useful) bypasses of energy-conserving reactions in the respiratory chain, and the magnitude of any 'leaks' in the inner mitochondrial membrane are key research needs.

Metabolic footprints in phosphate-starved plants

Plants' requirement of Phosphorus (P) as an essential macronutrient is obligatory for their normal growth and metabolism. Besides restricting plants' primary growth, P depletion affects both primary and secondary metabolism and leads to altered levels of sugars, metabolites, amino acids, and other secondary compounds. Such metabolic shifts help plants optimize their metabolism and growth under P limited conditions. Under P deprivation, both sugar levels and their mobilization change that influences the expression of Pi starvation-inducible genes. Increased sugar repartitioning from shoot to root help root growth and organic acids secretion that in turn promotes phosphate (Pi) uptake from the soil. Other metabolic changes such as lipid remodeling or P reallocation from older to younger leaves release the P from its bound forms in the cell. In this review, we summarize the metabolic footprinting of Pi-starved plants with respect to the benefits offered by such metabolic changes to intracellular Pi homeostasis.

Adaptive strategies of plants to conserve internal phosphorus under P deficient condition to improve P utilization efficiency

Phosphorus (P) is one of the limiting factors for plant growth and productivity due to its slow diffusion and immobilization in the soil which necessitates application of phosphatic fertilizers to meet the crop demand and obtain maximum yields. However, plants have evolved mechanisms to adapt to low P stress conditions either by increasing acquisition (alteration of belowground processes) or by internal inorganic P (Pi) utilization (cellular Pi homeostasis) or both. In this review, we have discussed the adaptive strategies that conserve the use of P and maintain cellular Pi homeostasis in the cytoplasm. These strategies involve modification in membrane lipid composition, flavanol/anthocyanin level, scavenging and reutilization of Pi adsorbed in cell wall pectin, remobilization of Pi during senescence by enzymes like RNases and purple acid phosphatases, alternative mitochondrial electron transport, and glycolytic pathways. The remobilization of Pi from senescing tissues and its internal redistribution to various cellular organelles is mediated by various Pi transporters. Although much efforts have been made to enhance P acquisition efficiency, an understanding of the physiological mechanisms conserving internal Pi and their manipulation would be useful for plants that can utilize P more efficiently to produce optimum growth per unit P uptake.

Metabolite shift in Medicago truncatula occurs in phosphorus deprivation

Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in -P leaves, with a moderate reduction in -P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.

Linking root exudation to belowground economic traits for resource acquisition

The concept of a root economics space (RES) is increasingly adopted to explore root trait variation and belowground resource-acquisition strategies. Much progress has been made on interactions of root morphology and mycorrhizal symbioses. However, root exudation, with a significant carbon (C) cost (c. 5-21% of total photosynthetically fixed C) to enhance resource acquisition, remains a missing link in this RES. Here, we argue that incorporating root exudation into the structure of RES is key to a holistic understanding of soil nutrient acquisition. We highlight the different functional roles of root exudates in soil phosphorus (P) and nitrogen (N) acquisition. Thereafter, we synthesize emerging evidence that illustrates how root exudation interacts with root morphology and mycorrhizal symbioses at the level of species and individual plant and argue contrasting patterns in species evolved in P-impoverished vs N-limited environments. Finally, we propose a new conceptual framework, integrating three groups of root functional traits to better capture the complexity of belowground resource-acquisition strategies. Such a deeper understanding of the integrated and dynamic interactions of root morphology, root exudation, and mycorrhizal symbioses will provide valuable insights into the mechanisms underlying species coexistence and how to explore belowground interactions for sustainable managed systems.

Recent insights into the metabolic adaptations of phosphorus-deprived plants

Inorganic phosphate (Pi) is an essential macronutrient required for many fundamental processes in plants, including photosynthesis and respiration, as well as nucleic acid, protein, and membrane phospholipid synthesis. The huge use of Pi-containing fertilizers in agriculture demonstrates that the soluble Pi levels of most soils are suboptimal for crop growth. This review explores recent advances concerning the understanding of adaptive metabolic processes that plants have evolved to alleviate the negative impact of nutritional Pi deficiency. Plant Pi starvation responses arise from complex signaling pathways that integrate altered gene expression with post-transcriptional and post-translational mechanisms. The resultant remodeling of the transcriptome, proteome, and metabolome enhances the efficiency of root Pi acquisition from the soil, as well as the use of assimilated Pi throughout the plant. We emphasize how the up-regulation of high-affinity Pi transporters and intra- and extracellular Pi scavenging and recycling enzymes, organic acid anion efflux, membrane remodeling, and the remarkable flexibility of plant metabolism and bioenergetics contribute to the survival of Pi-deficient plants. This research field is enabling the development of a broad range of innovative and promising strategies for engineering phosphorus-efficient crops. Such cultivars are urgently needed to reduce inputs of unsustainable and non-renewable Pi fertilizers for maximum agronomic benefit and long-term global food security and ecosystem preservation.

Effects of root morphology, respiration and carboxylate exudation on carbon economy in two non-mycorrhizal lupines under phosphorus deficiency

Under phosphorus (P) deficiency, Lupinus albus develops cluster roots that allow efficient P acquisition, while L. angustifolius without cluster roots also grows well. Both species are non-mycorrhizal. We quantitatively examined the carbon budgets to investigate the different strategies of these species. Biomass allocation, respiratory rates, protein amounts and carboxylate exudation rates were examined in hydroponically-grown plants treated with low (1 μM; P1) or high (100 μM; P100) P. At P1, L. albus formed cluster roots, and L. angustifolius increased biomass allocation to the roots. The respiratory rates of the roots were faster in L. albus than in L. angustifolius. The protein amounts of the non-phosphorylating alternative oxidase and uncoupling protein were greater in the cluster roots of L. albus at P1 than in the roots at P100, but similar between the P treatments in L. angustifolius roots. At P1, L. albus exuded carboxylates at a faster rate than L. angustifolius. The carbon budgets at P1 were surprisingly similar between the two species, which is attributed to the contrasting root growth and development strategies. L. albus developed cluster roots with rapid respiratory and carboxylate exudation rates, while L. angustifolius developed a larger root system with slow respiratory and exudation rates.

A 1.84-Mb region on rice chromosome 2 carrying SPL4, SPL5 and MLO8 genes is associated with higher yield under phosphorus-deficient acidic soil

Phosphorus (P) deficiency is one of the major limiting factors for rice productivity with only one locus (PSTOL1) available for field based application. A biparental mapping population (F₆) derived from two P deficiency tolerant genotypes (Sahbhagi Dhan (SD) (PSTOL1⁺) and Chakhao Poreiton (CP) (PSTOL1^-)), in which, transcriptome data generated from our lab had previously shown existence of diverse mechanisms was used to identify novel regions for better yield under lowland acidic soils. Phenotyping at F₄, F₅ and F₆ generations revealed significant correlation between traits like tiller number at 30 days (TN 30), tiller number at 60 days (TN 60), filled grains (FG), percent spikelet fertility (SF%), panicle number (PN) and grain yield per panicle (GYPP) and also association with better yield/performance under low P acidic soil conditions. Through selected genotyping on a set of forty superior and inferior lines using SSR, candidate gene-based and SNP polymorphic markers, 5 genomic regions associated with various yield-related traits were identified. Marker trait association studies revealed 13 markers significantly associated with yield attributing traits and PUE under lowland acidic field conditions. Chi-square and regression analyses of markers run on the entire population identified seven and six markers for SF% and GYPP, respectively, and two for biological yield with positive allele derived from SD which constitute a novel 1.847-Mb region on chromosome 2 flanked by two markers RM12550 and PR9-2. Expression analysis of 7 candidate genes lying within this region across SD, CP and two low P susceptible rice genotypes has revealed that expression of four genes including SPL4, SPL5, ACA9 and MLO8 is significantly upregulated only in SD under low P conditions. In CP, there is low expression of MLO8 under low P conditions, whereas SPL4, SPL5 and Os02g08120 are downregulated. In the case of the two susceptible genotypes, there is no expression of Os02g08120 either in optimum or limiting conditions. Sequence data across a panel of 3024 rice genotypes also suggests that there is polymorphism for these differentially expressed genes. The genes and underlying markers identified on chromosome 2 will be key to imparting tolerance to low P in diverse genetic backgrounds and for marker-assisted selection for higher yield under lowland acidic conditions.

Photoprotection by mitochondrial alternative pathway is enhanced at heat but disabled at chilling

The mitochondrial alternative pathway (AP) represents an important photoprotective mechanism for the chloroplast, but the temperature sensitivity of its photoprotective role is unknown. In this study, using the aox1a Arabidopsis mutant, the photoprotective role of the AP was verified under various temperatures, and the mechanism underlying the temperature sensitivity of the AP's photoprotective role was clarified. It was observed that the photoprotective role of the AP increased with rising temperature but was absent at low temperature. The photoprotective role of the AP was severely reduced under non-photorespiratory conditions. Disturbance of the AP inhibited the conversion of glycine to serine in mitochondria, which may restrain upstream photorespiratory metabolism and aggravate photoinhibition. With rising temperatures, photorespiration accelerated and the restraint of photorespiration caused by disturbance of the AP also increased, determining the temperature sensitivity of the AP's photoprotective role. We also verified that not only the AP but also the cytochrome pathway in mitochondria contributes to photoprotection by maintaining photorespiration.

In Vivo Metabolic Regulation of Alternative Oxidase under Nutrient Deficiency-Interaction with Arbuscular Mycorrhizal Fungi and Rhizobium Bacteria

The interaction of the alternative oxidase (AOX) pathway with nutrient metabolism is important for understanding how respiration modulates ATP synthesis and carbon economy in plants under nutrient deficiency. Although AOX activity reduces the energy yield of respiration, this enzymatic activity is upregulated under stress conditions to maintain the functioning of primary metabolism. The in vivo metabolic regulation of AOX activity by phosphorus (P) and nitrogen (N) and during plant symbioses with Arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria is still not fully understood. We highlight several findings and open questions concerning the in vivo regulation of AOX activity and its impact on plant metabolism during P deficiency and symbiosis with AMF. We also highlight the need for the identification of which metabolic regulatory factors of AOX activity are related to N availability and nitrogen-fixing legume-rhizobia symbiosis in order to improve our understanding of N assimilation and biological nitrogen fixation.

Visualising spatio-temporal distributions of assimilated carbon translocation and release in root systems of leguminous plants

The release of rhizodeposits differs depending on the root position and is closely related to the assimilated carbon (C) supply. Therefore, quantifying the C partitioning over a short period may provide crucial information for clarifying root-soil carbon metabolism. A non-invasive method for visualising the translocation of recently assimilated C into the root system inside the rhizobox was established using 11CO2 labelling and the positron-emitting tracer imaging system. The spatial distribution of recent 11C-photoassimilates translocated and released in the root system and soil were visualised for white lupin (Lupinus albus) and soybean (Glycine max). The inputs of the recently assimilated C in the entire root that were released into the soil were approximately 0.3%-2.9% for white lupin within 90 min and 0.9%-2.3% for soybean within 65 min, with no significant differences between the two plant species; however, the recently assimilated C of lupin was released at high concentrations in specific areas (hotspots), whereas that of soybean was released uniformly in the soil. Our method enabled the quantification of the spatial C allocations in roots and soil, which may help to elucidate the relationship between C metabolism and nutrient cycling at specific locations of the root-soil system in response to environmental conditions over relatively short periods.

Photosynthesis, respiration and growth: A carbon and energy balancing act for alternative oxidase

This review summarizes knowledge of alternative oxidase, a mitochondrial electron transport chain component that lowers the ATP yield of plant respiration. Analysis of mutant and transgenic plants has established that alternative oxidase activity supports leaf photosynthesis. The interaction of alternative oxidase respiration with chloroplast metabolism is important under conditions that challenge energy and/or carbon balance in the photosynthetic cell. Under such conditions, alternative oxidase provides an extra-chloroplastic means to optimize the status of chloroplast energy pools (ATP, NADPH) and to manage cellular carbohydrate pools in response to changing rates of carbon fixation and carbon demand for growth and maintenance. Transcriptional and post-translational mechanisms ensure that alternative oxidase can respond effectively when carbon and energy balance are being challenged. This function appears particularly significant under abiotic stress conditions such as water deficit, high salinity, or temperature extremes. Under such conditions, alternative oxidase respiration positively affects growth and stress tolerance, despite it lowering the energy yield and carbon use efficiency of respiration. In part, this beneficial effect relates to the ability of alternative oxidase respiration to prevent excessive reactive oxygen species generation in both mitochondria and chloroplasts. Recent evidence suggests that alternative oxidase respiration is an interesting target for crop improvement.

Does the alternative respiratory pathway offer protection against the adverse effects resulting from climate change?

Elevated greenhouse gases (GHGs) induce adverse conditions directly and indirectly, causing decreases in plant productivity. To deal with climate change effects, plants have developed various mechanisms including the fine-tuning of metabolism. Plant respiratory metabolism is highly flexible due to the presence of various alternative pathways. The mitochondrial alternative oxidase (AOX) respiratory pathway is responsive to these changes, and several lines of evidence suggest it plays a role in reducing excesses of reactive oxygen species (ROS) and reactive nitrogen species (RNS) while providing metabolic flexibility under stress. Here we discuss the importance of the AOX pathway in dealing with elevated carbon dioxide (CO2), nitrogen oxides (NOx), ozone (O3), and the main abiotic stresses induced by climate change.

Improved in vivo measurement of alternative oxidase respiration in field-collected pine roots

Cellular respiration via the alternative oxidase pathway (AOP) leads to a considerable loss in efficiency. Compared to the cytochrome pathway (COP), AOP produces 0-50% as much ATP per carbon (C) respired. Relative partitioning between the pathways can be measured in vivo based on their differing isotopic discriminations against ¹⁸ O in O₂ . Starting from published methods, we have refined and tested a new protocol to improve measurement precision and efficiency. The refinements detect an effect of tissue water content (P < 0.0001), which we have removed, and yield precise discrimination endpoints in the presence of pathway-specific respiratory inhibitors [CN^- and salicylhydroxamic acid (SHAM)], which improves estimates of AOP/COP partitioning. Fresh roots of Pinus sylvestris were sealed in vials with a CO₂ trap. The air was replaced to ensure identical starting conditions. Headspace air was repeatedly sampled and isotopically analyzed using isotope-ratio mass spectrometry. The method allows high-precision measurement of the discrimination against ¹⁸ O in O₂ because of repeated measurements of the same incubation vial. COP and AOP respiration discriminated against ¹⁸ O by 15.1 ± 0.3‰ and 23.8 ± 0.4‰, respectively. AOP contributed to root respiration by 23 ± 0.2% of the total in an unfertilized stand. In a second, nitrogen-fertilized, stand AOP contribution was only 14 ± 0.2% of the total. These results suggest the improved method can be used to assess the relative importance of COP and AOP activities in ecosystems, potentially yielding information on the role of each pathway for the carbon use efficiency of organisms.

Metabolic and physiological analyses reveal that Populus cathayana males adopt an energy-saving strategy to cope with phosphorus deficiency

Dioecious trees have evolved sex-specific adaptation strategies to cope with inorganic phosphorus (Pi) limitation. Yet, little is known about the effects of Pi limitation on plant metabolism, particularly in dioecious woody plants. To identify potential gender-specific metabolites appearing in response to Pi limitation in poplars, we studied the metabolic and ionomic responses in the roots and leaves of Populus cathayana Rehd males and females exposed to a 60-day period of Pi deficiency. Besides significant decreases in phosphorus contents in both Pi-deficient roots and leaves, the calcium level decreased significantly and the sulfur content increased significantly in Pi-deficient male roots, while the zinc and ferrum contents increased significantly in Pi-deficient female roots. Inorganic P deficiency caused a smaller change in the abscisic acid content, but a significant increase in the jasmonic acid content was detected in both leaves and roots. Salicylic acid significantly decreased under Pi deficiency in male leaves and female roots. Changes were found in phospholipids and phosphorylated metabolites (e.g., fructose-6-phosphate, glycerol-3-phosphate, glucose-6-phosphate, phosphoric acid and inositol-1-phosphate) in roots and leaves. Both P. cathayana males and females relied on inorganic pyrophosphate-dependent but not on Pi-dependent glycolysis under Pi-deficient conditions. Sex-specific metabolites in leaves were primarily in the category of primary metabolites (e.g., amino acids), while in roots primarily in the category of secondary metabolites (e.g., organic acids) and sugars. The metabolome analysis revealed that sexually different pathways occurred mainly in amino acid metabolism, and the tissue-related differences were in the shikimate pathway and glycolysis. We observed changes in carbon flow, reduced root biomass and increased amino acid contents in P. cathayana males but not in females, which indicated that males have adopted an energy-saving strategy to adapt to Pi deficiency. Thus, this study provides new insights into sex-specific metabolic responses to Pi deficiency.

Physiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots

In agricultural soil, the bioavailability of iron (Fe) and phosphorus (P) is often below the plant's requirement causing nutritional deficiency in crops. Under P-limiting conditions, white lupin (Lupinus albus L.) activates mechanisms that promote P solubility in the soil through morphological, physiological and molecular adaptations. Similar changes occur also in Fe-deficient white lupin roots; however, no information is available on the molecular bases of the response. In the present work, responses to Fe and P deficiency and their reciprocal interactions were studied. Transcriptomic analyses indicated that white lupin roots upregulated Fe-responsive genes ascribable to Strategy-I response, this behaviour was mainly evident in cluster roots. The upregulation of some components of Fe-acquisition mechanism occurred also in P-deficient cluster roots. Concerning P acquisition, some P-responsive genes (as phosphate transporters and transcription factors) were upregulated by P deficiency as well by Fe deficiency. These data indicate a strong cross-connection between the responses activated under Fe or P deficiency in white lupin. The activation of Fe- and P-acquisition mechanisms might play a crucial role to enhance the plant's capability to mobilize both nutrients in the rhizosphere, especially P from its associated metal cations.

Core principles which explain variation in respiration across biological scales

Contents Summary 670 I. Introduction 671 II. Principle 1 - Plant respiration performs three distinct functions 673 III. Principle 2 - Metabolic pathway flexibility underlies plant respiratory performance 676 IV. Principle 3 - Supply and demand interact over time to set plant respiration rate 677 V. Principle 4 - Plant respiratory acclimation involves adjustments in enzyme capacities 679 VI. Principle 5 - Respiration is a complex trait that helps to define, and is impacted by, plant lifestyle strategies 680 VII. Future directions 680 Acknowledgements 682 References 682 SUMMARY: Respiration is a core biological process that has important implications for the biochemistry, physiology, and ecology of plants. The study of plant respiration is thus conducted from several different perspectives by a range of scientific disciplines with dissimilar objectives, such as metabolic engineering, crop breeding, and climate-change modelling. One aspect in common among the different objectives is a need to understand and quantify the variation in respiration across scales of biological organization. The central tenet of this review is that different perspectives on respiration can complement each other when connected. To better accommodate interdisciplinary thinking, we identify distinct mechanisms which encompass the variation in respiratory rates and functions across biological scales. The relevance of these mechanisms towards variation in plant respiration are explained in the context of five core principles: (1) respiration performs three distinct functions; (2) metabolic pathway flexibility underlies respiratory performance; (3) supply and demand interact over time to set respiration rates; (4) acclimation involves adjustments in enzyme capacities; and (5) respiration is a complex trait that helps to define, and is impacted by, plant lifestyle strategies. We argue that each perspective on respiration rests on these principles to varying degrees and that broader appreciation of how respiratory variation occurs can unite research across scales.

Unraveling the Initial Plant Hormone Signaling, Metabolic Mechanisms and Plant Defense Triggering the Endomycorrhizal Symbiosis Behavior

Arbuscular mycorrhizal (AM) fungi establish probably one of the oldest mutualistic relationships with the roots of most plants on earth. The wide distribution of these fungi in almost all soil ecotypes and the broad range of host plant species demonstrate their strong plasticity to cope with various environmental conditions. AM fungi elaborate fine-tuned molecular interactions with plants that determine their spread within root cortical tissues. Interactions with endomycorrhizal fungi can bring various benefits to plants, such as improved nutritional status, higher photosynthesis, protection against biotic and abiotic stresses based on regulation of many physiological processes which participate in promoting plant performances. In turn, host plants provide a specific habitat as physical support and a favorable metabolic frame, allowing uptake and assimilation of compounds required for the life cycle completion of these obligate biotrophic fungi. The search for formal and direct evidences of fungal energetic needs raised strong motivated projects since decades, but the impossibility to produce AM fungi under axenic conditions remains a deep enigma and still feeds numerous debates. Here, we review and discuss the initial favorable and non-favorable metabolic plant context that may fate the mycorrhizal behavior, with a focus on hormone interplays and their links with mitochondrial respiration, carbon partitioning and plant defense system, structured according to the action of phosphorus as a main limiting factor for mycorrhizal symbiosis. Then, we provide with models and discuss their significances to propose metabolic targets that could allow to develop innovations for the production and application of AM fungal inocula.

Measurements of Electron Partitioning Between Cytochrome and Alternative Oxidase Pathways in Plant Tissues

Plant respiration is characterized by the existence of the alternative oxidase pathway (AOP) that competes with cytochrome oxidase pathway (COP) for the electrons of the ubiquinone pool of the mitochondrial electron transport chain, thus reducing ATP synthesis. The oxygen (O₂) isotope fractionation technique is the only available to determine the electron partitioning between the two pathways and their in vivo activities in plant tissues. In this chapter, the basis of the O₂ isotope fractionation technique and its derived calculations are carefully explained together with a detailed description of the dual-inlet isotope ratio mass spectrometry (DI-IRMS) system and the protocol developed at the University of Balearic Islands. The key advantages of the DI-IRMS over other systems are highlighted as well as the potential problems of this technique. Among these problems, those associated with leakage, diffusion, and inhibitor treatments are noted and solutions to prevent, detect, and repair these problems are detailed.

Phosphorus concentration coordinates a respiratory bypass, synthesis and exudation of citrate, and the expression of high-affinity phosphorus transporters in Solanum lycopersicum

Plants exhibit respiratory bypasses (e.g., the alternative oxidase [AOX]) and increase the synthesis of carboxylates in their organs (leaves and roots) in response to phosphorus (P) deficiency, which increases P uptake capacity. They also show differential expression of high-affinity inorganic phosphorus (Pi) transporters, thus avoiding P toxicity at a high P availability. The association between AOX and carboxylate synthesis was tested in Solanum lycopersicum plants grown at different soil P availability, by using plants grown under P-sufficient and P-limiting conditions and by applying a short-term (24 hr) P-sufficient pulse to plants grown under P limitation. Tests were also performed with plants colonized with arbuscular mycorrhizal fungi, which increased plant P concentration under reduced P availability. The in vivo activities of AOX and cytochrome oxidase were measured together with the concentration of carboxylates and the P concentration in plant organs. Gene transcription of Pi transporters (LePT1 and LePT2) was also studied. A coordinated response between plant P concentration with these traits was observed, indicating that a sufficient P availability in soil led to a suppression of both AOX activity and synthesis of citrate and a downregulation of the transcription of genes encoding high-affinity Pi transporters, presumably to avoid P toxicity.

An In Vivo Perspective of the Role(s) of the Alternative Oxidase Pathway

Despite intense research on the in vitro characterization of regulatory factors modulating the alternative oxidase (AOX) pathway, the regulation of its activity in vivo is still not fully understood. Advances concerning in vivo regulation of AOX based on the oxygen-isotope fractionation technique are reviewed, and regulatory factors that merit future research are highlighted. In addition, we review and discuss the main biological functions assigned to the plant AOX, and suggest future experiments involving in vivo activity measurements to test different hypothesized physiological roles.

Arbuscular Mycorrhizal Symbiosis with Arundo donax Decreases Root Respiration and Increases Both Photosynthesis and Plant Biomass Accumulation

The effect of arbuscular mycorrhiza (AM) symbiosis on plant growth is associated with the balance between costs and benefits. A feedback regulation loop has been described in which the higher carbohydrate cost to plants for AM symbiosis is compensated by increases in their photosynthetic rates. Nevertheless, plant carbon balance depends both on photosynthetic carbon uptake and respiratory carbon consumption. The hypothesis behind this research was that the role of respiration in plant growth under AM symbiosis may be as important as that of photosynthesis. This hypothesis was tested in Arundo donax L. plantlets inoculated with Rhizophagus irregularis and Funneliformis mosseae. We tested the effects of AM inoculation on both photosynthetic capacity and in vivo leaf and root respiration. Additionally, analyses of the primary metabolism and ion content were performed in both leaves and roots. AM inoculation increased photosynthesis through increased CO₂ diffusion and electron transport in the chloroplast. Moreover, respiration decreased only in AM roots via the cytochrome oxidase pathway (COP) as measured by the oxygen isotope technique. This decline in the COP can be related to the reduced respiratory metabolism and substrates (sugars and tricarboxylic acid cycle intermediates) observed in roots.

Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions

Mitochondrial thioredoxin-o (AtTrxo1) was characterized and its expression examined in different organs of Arabidopsis thaliana. AtTrxo1 transcript levels were particularly high in dry seeds and cotyledons where they reached a maximum 36 h after imbibition with water, coinciding with 50% germination. Expression was lower in seeds germinating in 100 mM NaCl. To gain insight into the transcriptional regulation of the AtTrxo1 gene, a phylogenomic analysis was coupled with the screening of an arrayed library of Arabidopsis transcription factors in yeast. The basic leucine zipper AtbZIP9 and the zinc finger protein AZF2 were identified as putative transcriptional regulators. Transcript regulation of AtbZIP9 and AtAFZ2 during germination was compatible with the proposed role in transcriptional regulation of AtTrxo1. Transient over-expression of AtbZIP9 and AtAZF2 in Nicotiana benthamiana leaves demonstrated an activation effect of AtbZIP9 and a repressor effect of AtAZF2 on AtTrxo1 promoter-driven reporter expression. Although moderate concentrations of salt delayed germination in Arabidopsis wild-type seeds, those of two different AtTrxo1 knock-out mutants germinated faster and accumulated higher H2O2 levels than the wild-type. All these data indicate that AtTrxo1 has a role in redox homeostasis during seed germination under salt conditions.

Salinity tolerance is related to cyanide-resistant alternative respiration in Medicago truncatula under sudden severe stress

Salt respiration is defined as the increase of respiration under early salt stress. However, the response of respiration varies depending on the degree of salt tolerance and salt stress. It has been hypothesized that the activity of the alternative pathway may increase preventing over-reduction of the ubiquinone pool in response to salinity, which in turn can increase respiration. Three genotypes of Medicago truncatula are reputed as differently responsive to salinity: TN1.11, A17 and TN6.18. We used the oxygen-isotope fractionation technique to study the in vivo respiratory activities of the cytochrome oxidase pathway (COP) and the alternative oxidase pathway (AOP) in leaves and roots of these genotypes treated with severe salt stress (300 mM) during 1 and 3 days. In parallel, AOX capacity, gas exchange measurements, relative water content and metabolomics were determined in control and treated plants. Our study shows for first time that salt respiration is induced by the triggered AOP in response to salinity. Moreover, this phenomenon coincides with increased levels of metabolites such as amino and organic acids, and is shown to be related with higher photosynthetic rate and water content in TN6.18.

Physiological role of alternative oxidase (from yeasts to plants)

Mitochondria of all so far studied organisms, with the exception of Archaea, mammals, some yeasts, and protists, contain, along with the classical phosphorylating cytochrome pathway, a so-called cyanide-insensitive alternative oxidase (AOX) localized on the matrix side of the mitochondrial inner membrane, and electron transport through which is not coupled with ATP synthesis and energy accumulation. Mechanisms underlying plentiful functions of AOX in organisms at various levels of organization ranging from yeasts to plants are considered. First and foremost, AOX provides a chance of cell survival after inhibiting the terminal components of the main respiratory chain or losing the ability to synthesize these components. The vitally important role of AOX is obvious in thermogenesis of thermogenic plant organs where it becomes the only terminal oxidase with a very high activity, and the energy of substrate oxidation by this respiratory pathway is converted into heat, thus promoting evaporation of volatile substances attracting pollinating insects. AOX plays a fundamentally significant role in alleviating or preventing oxidative stress, thus ensuring the defense against a wide range of stresses and adverse environmental conditions, such as changes in temperature and light intensities, osmotic stress, drought, and attack by incompatible strains of bacterial pathogens, phytopathogens, or their elicitors. Participation of AOX in pathogen survival during its existence inside the host, in antivirus defense, as well as in metabolic rearrangements in plants during embryogenesis and cell differentiation is described. Examples are given to demonstrate that AOX might be an important tool to overcome the adverse aftereffects of restricted activity of the main respiratory chain in cells and whole animals.

Metabolic Adaptations of White Lupin Roots and Shoots under Phosphorus Deficiency

White lupin (Lupinus albus L.) is highly adapted to phosphorus-diminished soils. P-deficient white lupin plants modify their root architecture and physiology to acquire sparingly available soil phosphorus. We employed gas chromatography-mass spectrometry (GC-MS) for metabolic profiling of P-deficient white lupins, to investigate biochemical pathways involved in the P-acquiring strategy. After 14 days of P-deficiency, plants showed reduced levels of fructose, glucose, and sucrose in shoots. Phosphorylated metabolites such as glucose-6-phosphate, fructose-6-phosphate, myo-inositol-phosphate and glycerol-3-phosphate were reduced in both shoots and roots. After 22 days of P-deficiency, no effect on shoot or root sugar metabolite levels was found, but the levels of phosphorylated metabolites were further reduced. Organic acids, amino acids and several shikimate pathway products showed enhanced levels in 22-day-old P-deficient roots and shoots. These results indicate that P-deficient white lupins adapt their carbohydrate partitioning between shoot and root in order to supply their growing root system as an early response to P-deficiency. Organic acids are released into the rhizosphere to mobilize phosphorus from soil particles. A longer period of P-deficiency leads to scavenging of Pi from P-containing metabolites and reduced protein anabolism, but enhanced formation of secondary metabolites. The latter can serve as stress protection molecules or actively acquire phosphorus from the soil.

Alternative oxidase: distribution, induction, properties, structure, regulation, and functions

The respiratory chain in the majority of organisms with aerobic type metabolism features the concomitant existence of the phosphorylating cytochrome pathway and the cyanide- and antimycin A-insensitive oxidative route comprising a so-called alternative oxidase (AOX) as a terminal oxidase. In this review, the history of AOX discovery is described. Considerable evidence is presented that AOX occurs widely in organisms at various levels of organization and is not confined to the plant kingdom. This enzyme has not been found only in Archaea, mammals, some yeasts and protists. Bioinformatics research revealed the sequences characteristic of AOX in representatives of various taxonomic groups. Based on multiple alignments of these sequences, a phylogenetic tree was constructed to infer their possible evolution. The ways of AOX activation, as well as regulatory interactions between AOX and the main respiratory chain are described. Data are summarized concerning the properties of AOX and the AOX-encoding genes whose expression is either constitutive or induced by various factors. Information is presented on the structure of AOX, its active center, and the ubiquinone-binding site. The principal functions of AOX are analyzed, including the cases of cell survival, optimization of respiratory metabolism, protection against excess of reactive oxygen species, and adaptation to variable nutrition sources and to biotic and abiotic stress factors. It is emphasized that different AOX functions complement each other in many instances and are not mutually exclusive. Examples are given to demonstrate that AOX is an important tool to overcome the adverse aftereffects of restricted activity of the main respiratory chain in cells and whole animals. This is the first comprehensive review on alternative oxidases of various organisms ranging from yeasts and protists to vascular plants.

Plant adaptations to severely phosphorus-impoverished soils

Mycorrhizas play a pivotal role in phosphorus (P) acquisition of plant roots, by enhancing the soil volume that can be explored. Non-mycorrhizal plant species typically occur either in relatively fertile soil or on soil with a very low P availability, where there is insufficient P in the soil solution for mycorrhizal hyphae to be effective. Soils with a very low P availability are either old and severely weathered or relatively young with high concentrations of oxides and hydroxides of aluminium and iron that sorb P. In such soils, cluster roots and other specialised roots that release P-mobilising carboxylates are more effective than mycorrhizas. Cluster roots are ephemeral structures that release carboxylates in an exudative burst. The carboxylates mobilise sparingly-available sources of soil P. The relative investment of biomass in cluster roots and the amount of carboxylates that are released during the exudative burst differ between species on severely weathered soils with a low total P concentration and species on young soils with high total P concentrations but low P availability. Taking a modelling approach, we explore how the optimal cluster-root strategy depends on soil characteristics, thus offering insights for plant breeders interested in developing crop plants with optimal cluster-root strategies.

Assessment of the role of silicon in the Cu-tolerance of the C4 grass Spartina densiflora

An experiment was designed to investigate the effect of silicon supply (0 and 500 μM) on Spartina densiflora plants grown at two copper (Cu) concentrations: 0 and 15 mM. Growth parameters together with total concentrations of calcium, Cu, potassium, magnesium, manganese, sodium and nitrogen were determined in roots and leaves. Photosynthetic traits were followed by measurement of leaf gas exchange, efficiency of PSII biochemistry, total content of photosynthetic pigments and concentration and carbamylation of Rubisco sites concentration ([Rubisco]). Respiration and oxygen isotope fractionation were measured in roots to study the in vivo activities of cytochrome oxidase (COX) and alternative oxidase (AOX) pathways, as well as AOX capacity. The results confirm that Si supply improves growth of S. densiflora under Cu stress. Improved growth was associated with higher net photosynthetic rate. Beneficial effect of Si on S. densiflora photosynthetic apparatus was associated with a reduction of the Cu impact on active Rubisco sites, as well as on the photochemical apparatus and chlorophyll concentration. Moreover, ameliorative effects of Si were associated with the avoidance of Cu translocation from roots to leaves. Finally in vivo activities of COX and AOX pathways were strongly inhibited in Cu-treated plants, and this reduction was not mitigated by Si-treatment. Therefore, Si appears to play an important role in Cu-tolerance of S. densiflora, not by avoiding its uptake by roots, but via some mechanism to avoid Cu translocation from roots to leaves, resulting in a general reduction of Cu-induced deleterious effects on the leaf photosynthetic apparatus.

Comparison of the response to phosphorus deficiency in two lupin species, Lupinus albus and L. angustifolius, with contrasting root morphology

White lupin (Lupinus albus) produces cluster roots, an adaptation to low soil phosphorus (P). Cluster roots exude large levels of P-solubilizing compounds such as citrate and malate. In contrast, narrow leaf lupin (L. angustifolius) is closely related to L. albus, but does not produce cluster roots. To examine the different strategies for P acquisition, we compared the growth, biomass allocation, respiratory properties and construction cost between L. albus and L. angustifolius under P-deficient conditions. Both Lupinus species were grown in hydroponic culture with 1 or 100 μM P. Under the P-deficient regime, L. albus produced cluster roots with little change in biomass allocation, while L. angustifolius significantly increased biomass allocation to roots. The rate of cyanide-resistant SHAM (salicylhydroxamic acid)-sensitive respiration was high in cluster roots and very low in roots of L. angustifolius. These results suggest a low alternative oxidase (AOX) activity in L. angustifolius roots, and thus, ATP would be produced efficiently in L. angustifolius roots. The construction cost was highest in cluster roots and lowest in L. angustifolius roots. This study shows that under P deficiency, L. albus produces high-cost cluster roots to increase the P availability, while L. angustifolius produces large quantities of low-cost roots to enhance P uptake.

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin

Background

Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dense lateral roots formed by several plant species for the effective mining of nutrient rich soil patches through a combination of increased surface area and exudation of carboxylates. White lupin is becoming a model-species allowing for the discovery of gene networks involved in CR development. A greater understanding of the underlying molecular mechanisms driving these developmental processes is important for the generation of smarter plants for a world with diminishing resources to improve food security.

Results

RNA-seq analyses for three developmental stages of the CR formed under phosphorus-limited conditions and two of non-cluster roots have been performed for white lupin. In total 133,045,174 high-quality paired-end reads were used for a de novo assembly of the root transcriptome and merged with LAGI01 (Lupinus albus gene index) to generate an improved LAGI02 with 65,097 functionally annotated contigs. This was followed by comparative gene expression analysis. We show marked differences in the transcriptional response across the various cluster root stages to adjust to phosphate limitation by increasing uptake capacity and adjusting metabolic pathways. Several transcription factors such as PLT, SCR, PHB, PHV or AUX/IAA with a known role in the control of meristem activity and developmental processes show an increased expression in the tip of the CR. Genes involved in hormonal responses (PIN, LAX, YUC) and cell cycle control (CYCA/B, CDK) are also differentially expressed. In addition, we identify primary transcripts of miRNAs with established function in the root meristem.

Conclusions

Our gene expression analysis shows an intricate network of transcription factors and plant hormones controlling CR initiation and formation. In addition, functional differences between the different CR developmental stages in the acclimation to phosphorus starvation have been identified.