Response to Anoxia in Rice and Wheat Seedlings: Changes in the pH of Intracellular Compartments, Glucose-6-Phosphate Level, and Metabolic Rate

The real reason why ATP hydrolysis is spontaneous at pH > 7: It's (mostly) the proton concentration!

Common wisdom holds that ATP hydrolysis is spontaneous because of the weakness of its phosphoanhydride bonds, electrostatic repulsion within the polyanionic ATP4- molecule, and resonance stabilization of the inorganic phosphate and ADP products. By examining the pH-dependence of the hydrolysis Gibbs free energy, we show that in fact, above pH 7, ATP hydrolysis is spontaneous due mainly to the low concentration of the H+ that is released as product. Hence, ATP is essentially just an electrophilic target whose attack by H2 O causes the acidity of the water nucleophile to increase dramatically; the spontaneity of the resulting acid ionization supplies much of the released Gibbs free energy. We also find that fermentation lowers pH not due to its organic acid products (e.g., lactic, acetic, formic, or succinic acids), but again, due to the H+ product of ATP hydrolysis.

The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry

The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pK _a and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H⁺. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.

Pyrophosphate as an alternative energy currency in plants

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

Potassium Efflux and Cytosol Acidification as Primary Anoxia-Induced Events in Wheat and Rice Seedlings

Both ion fluxes and changes of cytosolic pH take an active part in the signal transduction of different environmental stimuli. Here we studied the anoxia-induced alteration of cytosolic K⁺ concentration, [K⁺]_cyt, and cytosolic pH, pH_cyt, in rice and wheat, plants with different tolerances to hypoxia. The [K⁺]_cyt and pH_cyt were measured by fluorescence microscopy in single leaf mesophyll protoplasts loaded with the fluorescent potassium-binding dye PBFI-AM and the pH-sensitive probe BCECF-AM, respectively. Anoxic treatment caused an efflux of K⁺ from protoplasts of both plants after a lag-period of 300-450 s. The [K⁺]_cyt decrease was blocked by tetraethylammonium (1 mM, 30 min pre-treatment) suggesting the involvement of plasma membrane voltage-gated K⁺ channels. The protoplasts of rice (a hypoxia-tolerant plant) reacted upon anoxia with a higher amplitude of the [K⁺]_cyt drop. There was a simultaneous anoxia-dependent cytosolic acidification of protoplasts of both plants. The decrease of pH_cyt was slower in wheat (a hypoxia-sensitive plant) while in rice protoplasts it was rapid and partially reversible. Ion fluxes between the roots of intact seedlings and nutrient solutions were monitored by ion-selective electrodes and revealed significant anoxia-induced acidification and potassium leakage that were inhibited by tetraethylammonium. The K⁺ efflux from rice was more distinct and reversible upon reoxygenation when compared with wheat seedlings.

Tolerant mechanisms to O2 deficiency under submergence conditions in plants

Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.

Germination: an alternative source to promote phytonutrients in edible seeds

Consumption of less phytonutrient foods has shown to cause different chronic diseases, despite over 50,000 edible plant breed available in various countries around the globe. These edible plants consist of seeds that can be consumed which possessed high health benefits. Moreover, nutritive values such as phytochemicals of edible seeds increased after germination. Therefore, germination has been reported to enhance various bioactive compounds such as γ-amino butyric acid, polyphenols, and vitamins which lead to greater bioactivity such as anti-diabetic, anti-bacteria, and anti-cancer effects when these seeds are consumed. Consequently, germination can be regarded as a cheap and effective way to enhance the nutritional value of edible seeds.

An Arabidopsis protoplast isolation method reduces cytosolic acidification and activation of the chloroplast stress sensor SENSITIVE TO FREEZING 2

Chloroplasts adapt to freezing and other abiotic stresses in part by modifying their membranes. One key-remodeling enzyme is SENSITIVE TO FREEZING2 (SFR2). SFR2 is unusual because it does not respond to initial cold stress or cold acclimation, instead it responds during freezing conditions in Arabidopsis. This response has been shown to be sensitive to cytosolic acidification. The unique lipid products of SFR2 have also been detected in response to non-freezing stresses, but what causes SFR2 to respond in these stresses is unknown. Here, we investigate protoplast isolation as a representative of wounding stress. We show that SFR2 oligogalactolipid products accumulate during protoplast isolation. Notably, we show that protoplast cytosol is acidified during isolation. Modification of the buffers reduces oligogalactolipid accumulation, while prolonged incubation in the isolated state increases it. We conclude that SFR2 activation during protoplast isolation correlates with cytosolic acidification, implying that all SFR2 activation may be dependent on cytosolic acidification. We also conclude that protoplasts can be more gently isolated, reducing their stress.

Energy-crises in well-aerated and anoxic tissue: does tolerance require the same specific proteins and energy-efficient transport?

Many of the profound changes in metabolism that are caused by O2 deficiency also occur in well-aerated tissues when oxidative phosphorylation is partially or wholly inhibited. For these well-aerated tissues, reduction in energy formation occurs during exposure to inhibitors of oxidative phosphorylation, cold/chilling and wounding, so we prefer the term 'energy crisis' metabolism over 'anaerobic' metabolism. In this review, we note that the overwhelming body of data on energy crises has been obtained by exposure to hypoxia-anoxia, which we will indicate when discussing the particular experiments. We suggest that even transient survival of an energy crisis requires a network of changes common to a large number of conditions, ranging from changes in development to various adverse conditions such as high salinity, drought and nutrient deficiency, all of which reduce growth. During an energy crisis this general network needs to be complemented by energy specific proteins, including the so called 'anaerobic proteins' and the group of ERFVII transcription factors, which induces the synthesis of these proteins. Crucially, the difference between anoxia-intolerant and -tolerant tissues in the event of a severe energy crisis would mainly depend on changes in some 'key' energy crisis proteins: we suggest these proteins would include phytoglobin, the V-H+PPiase and pyruvate decarboxylase. A second characteristic of a high tolerance to an energy crisis is engagement of energy efficient transport. This feature includes a sharp reduction in rates of solute transport and use of energy-efficient modifications of transport systems by primary H+ transport and secondary H+-solute transport systems. Here we also discuss the best choice of species to study an energy crisis. Further, we consider confounding of the acclimative response by responses to injury, be it due to the use of tissues intolerant to an energy crisis, or to faulty techniques.

Temperature-dependent metabolic adaptation of Triticum aestivum seedlings to anoxia

Wheat (Triticum aestivum) is considered anoxia intolerant but it shows variance in anoxia responses between genotypes and environmental treatments. We firstly examined 4 day old seedlings of five wheat genotypes in response to anoxia at 15 °C and 28 °C by assessing growth rate, tissue damage and changes in metabolite abundances. Significant genotypic variations in anoxia tolerance were observed, especially at 28 °C. Wheat seedlings grown at 15 °C appeared to be more anoxia tolerant and showed less genotypic variation than those at 28 °C. To minimize seedling size variations and define the temperature effects, we grew two contrasting genotypes at 15 °C for 3.5 d and adapted to 4 different temperatures for 0.5 d before exposing them to anoxia at each adapted temperature. Genotypic variation in abundance of anoxia induced metabolites occurred at 24 °C and 28 °C but not at 15 °C and 20 °C. Tissue- and temperature-dependent metabolic adaptations to anoxia were revealed. In roots, the ability to maintain sugar/sugar-phosphate and TCA cycle metabolite levels and the accumulation of amino acids when temperature was below 24 °C correlated with anoxia tolerance. Temperatures between 20 °C–24 °C are critical for metabolic adaptation and suggest that further assessment of waterlogging/flooding tolerance of wheat seedlings should consider the temperature-dependence of tolerance in evaluations.

Catalytic and functional aspects of different isozymes of glycolate oxidase in rice

BACKGROUND

Glycolate oxidase (GLO) is a key enzyme for photorespiration in plants. There are four GLO genes encoding and forming different isozymes in rice, but their functional differences are not well understood. In this study, enzymatic and physiological characteristics of the GLO isozymes were comparatively analyzed.

RESULTS

When expressed heterologously in yeast, GLO1, GLO4 and GLO1 + 4 showed the highest activities and lowest K _m for glycolate as substrate, whereas GLO3 displayed high activities and affinities for both glycolate and L-lactate, and GLO5 was catalytically inactive with all substrates tested. To further reveal the physiological role of each GLO isozyme in plants, various GLO genetically modified rice lines were generated and functionally analyzed. GLO activity was significantly increased both in GLO1 and GLO4 overexpression lines. Nevertheless, when either GLO1 or GLO4 was knocked out, the activity was suppressed much more significantly in GLO1 knockout lines than in GLO4 knockout lines, and both knockout mutants exhibited obvious dwarfism phenotypes. Among GLO3 and GLO5 overexpression lines and RNAi lines, only GLO3 overexpression lines showed significantly increased L-lactate-oxidizing activity but no other noticeable phenotype changes.

CONCLUSIONS

These results indicate that rice GLO isozymes have distinct enzymatic characteristics, and they may have different physiological functions in rice.

Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel

Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.

Energetics of acclimation to NaCl by submerged, anoxic rice seedlings

BACKGROUND AND AIMS

Our aim was to elucidate how plant tissues under a severe energy crisis cope with imposition of high NaCl, which greatly increases ion fluxes and hence energy demands. The energy requirements for ion regulation during combined salinity and anoxia were assessed to gain insights into ion transport processes in the anoxia-tolerant coleoptile of rice.

METHODS

We studied the combined effects of anoxia plus 50 or 100 mm NaCl on tissue ions and growth of submerged rice (Oryza sativa) seedlings. Excised coleoptiles allowed measurements in aerated or anoxic conditions of ion net fluxes and O2 consumption or ethanol formation and by inference energy production.

KEY RESULTS

Over 80 h of anoxia, coleoptiles of submerged intact seedlings grew at 100 mm NaCl, but excised coleoptiles, with 50 mm exogenous glucose, survived only at 50 mm NaCl, possibly due to lower energy production with glucose than for intact coleoptiles with sucrose as substrate. Rates of net uptake of Na+ and Cl- by coleoptiles in anoxia were about half those in aerated solution. Ethanol formation in anoxia and O2 uptake in aerobic solution were each increased by 13-15 % at 50 mm NaCl, i.e. ATP formation was stimulated. For acclimation to 50 mm NaCl, the anoxic tissues used only 25 % of the energy that was expended by aerobic tissues. Following return of coleoptiles to aerated non-saline solution, rates of net K+ uptake recovered to those in continuously aerated solution, demonstrating there was little injury during anoxia with 50 mm NaCl.

CONCLUSION

Rice seedlings survive anoxia, without the coleoptile incurring significant injury, even with the additional energy demands imposed by NaCl (100 mm when intact, 50 mm when excised). Energy savings were achieved in saline anoxia by less coleoptile growth, reduced ion fluxes as compared to aerobic coleoptiles and apparent energy-economic ion transport systems.

Mechanisms of waterlogging tolerance in wheat--a review of root and shoot physiology

We review the detrimental effects of waterlogging on physiology, growth and yield of wheat. We highlight traits contributing to waterlogging tolerance and genetic diversity in wheat. Death of seminal roots and restriction of adventitious root length due to O2 deficiency result in low root:shoot ratio. Genotypes differ in seminal root anoxia tolerance, but mechanisms remain to be established; ethanol production rates do not explain anoxia tolerance. Root tip survival is short-term, and thereafter, seminal root re-growth upon re-aeration is limited. Genotypes differ in adventitious root numbers and in aerenchyma formation within these roots, resulting in varying waterlogging tolerances. Root extension is restricted by capacity for internal O2 movement to the apex. Sub-optimal O2 restricts root N uptake and translocation to the shoots, with N deficiency causing reduced shoot growth and grain yield. Although photosynthesis declines, sugars typically accumulate in shoots of waterlogged plants. Mn or Fe toxicity might occur in shoots of wheat on strongly acidic soils, but probably not more widely. Future breeding for waterlogging tolerance should focus on root internal aeration and better N-use efficiency; exploiting the genetic diversity in wheat for these and other traits should enable improvement of waterlogging tolerance.

Jasmonic acid induced protein response to biophoton emissions and flooding stress in soybean

Biophoton emissions were elevated by the exogenous plant hormone application such as jasmonic (JA) and salicylic acid (SA). To reveal the molecular mechanisms underlying flooding stress responses in soybean treated with JA and SA, biophoton emissions from plants were quantified in combination with proteomic analyses. Furthermore, treatment with exogenous JA inhibited lateral root growth and markedly reduced root weight. Out of 649 proteins identified in the JA- and JA/SA-treated plants, 44 were unique to JA-treated plants, 403 were unique to JA/SA-treated plants, and 202 were shared between the groups. These proteins were involved in stress, signaling, degradation, glycolysis, fermentation, and hormone metabolism. The abundances of glutathione-S-transferase, alanine aminotransferase, and malate dehydrogenase were decreased; however, the activities of these enzymes were increased. In contrast, the abundance and activity of monodehydroascorbate reductase increased in the roots of plants treated with JA and SA under flooding stress. This suggests that the quantity of lateral roots, total root mass, and free radicals generated during oxidation and reduction reactions and reactive oxygen species scavenging largely contribute to biophoton emission. Furthermore, monodehydroascorbate reductase, which is involved in detoxification and controlling hydrogen peroxide levels, may protect plant cells against oxidative damage during flooding.

BIOLOGICAL SIGNIFICANCE

To understand the source of biophoton emission and molecular mechanism by the application of jasmonic and salicylic acid under flooding conditions in soybean plants, the label-free quantitative techniques were performed in roots. Root lengths and weights were significantly reduced by the effect of jasmonic and salicylic acid while it inhibited growth of the lateral roots in normal conditions using the jasmonic acid. Finally, identified proteins were functionally annotated by MAPMAN software application; that were assigned to different functional categories, such as stress, signaling, protein, glycolysis, metabolism, cell wall, and cell organization. Consequently, this study offers to learn the photon emission in plants and to know the molecular mechanism under flooding stress in soybean.

Proteins involved in biophoton emission and flooding-stress responses in soybean under light and dark conditions

To know the molecular systems basically flooding conditions in soybean, biophoton emission measurements and proteomic analyses were carried out for flooding-stressed roots under light and dark conditions. Photon emission was analyzed using a photon counter. Gel-free quantitative proteomics were performed to identify significant changes proteins using the nano LC-MS along with SIEVE software. Biophoton emissions were significantly increased in both light and dark conditions after flooding stress, but gradually decreased with continued flooding exposure compared to the control plants. Among the 120 significantly identified proteins in the roots of soybean plants, 73 and 19 proteins were decreased and increased in the light condition, respectively, and 4 and 24 proteins were increased and decreased, respectively, in the dark condition. The proteins were mainly functionally grouped into cell organization, protein degradation/synthesis, and glycolysis. The highly abundant lactate/malate dehydrogenase proteins were decreased in flooding-stressed roots exposed to light, whereas the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme was increased in both light and dark conditions. Notably, however, specific enzyme assays revealed that the activities of these enzymes and biophoton emission were sharply increased after 3 days of flooding stress. This finding suggests that the source of biophoton emission in roots might involve the chemical excitation of electron or proton through enzymatic or non-enzymatic oxidation and reduction reactions. Moreover, the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme may play important roles in responses in flooding stress of soybean under the light condition and as a contributing factor to biophoton emission.

Presence of unique glyoxalase III proteins in plants indicates the existence of shorter route for methylglyoxal detoxification

Glyoxalase pathway, comprising glyoxalase I (GLY I) and glyoxalase II (GLY II) enzymes, is the major pathway for detoxification of methylglyoxal (MG) into D-lactate involving reduced glutathione (GSH). However, in bacteria, glyoxalase III (GLY III) with DJ-1/PfpI domain(s) can do the same conversion in a single step without GSH. Our investigations for the presence of DJ-1/PfpI domain containing proteins in plants have indicated the existence of GLY III-like proteins in monocots, dicots, lycopods, gymnosperm and bryophytes. A deeper in silico analysis of rice genome identified twelve DJ-1 proteins encoded by six genes. Detailed analysis has been carried out including their chromosomal distribution, genomic architecture and localization. Transcript profiling under multiple stress conditions indicated strong induction of OsDJ-1 in response to exogenous MG. A member of OsDJ-1 family, OsDJ-1C, showed high constitutive expression at all developmental stages and tissues of rice. MG depletion study complemented by simultaneous formation of D-lactate proved OsDJ-1C to be a GLY III enzyme that converts MG directly into D-lactate in a GSH-independent manner. Site directed mutagenesis of Cys-119 to Alanine significantly reduces its GLY III activity indicating towards the existence of functional GLY III enzyme in rice—a shorter route for MG detoxification.

Efficient use of energy in anoxia-tolerant plants with focus on germinating rice seedlings

Anoxia tolerance in plants is distinguished by direction of the sparse supply of energy to processes crucial to cell maintenance and sometimes to growth, as in rice seedlings. In anoxic rice coleoptiles energy is used to synthesise proteins, take up K(+) , synthesise cell walls and lipids, and in cell maintenance. Maintenance of electrochemical H(+) gradients across the tonoplast and plasma membrane is crucial for solute compartmentation and thus survival. These gradients sustain some H(+) -solute cotransport and regulate cytoplasmic pH. Pyrophosphate (PPi ), the alternative energy donor to ATP, allows direction of energy to the vacuolar H(+) -PPi ase, sustaining H(+) gradients across the tonoplast. When energy production is critically low, operation of a biochemical pHstat allows H(+) -solute cotransport across plasma membranes to continue for at least for 18 h. In active (e.g. growing) cells, PPi produced during substantial polymer synthesis allows conversion of PPi to ATP by PPi -phosphofructokinase (PFK). In quiescent cells with little polymer synthesis and associated PPi formation, the PPi required by the vacuolar H(+) -PPi ase and UDPG pyrophosphorylase involved in sucrose mobilisation via sucrose synthase might be produced by conversion of ATP to PPi through reversible glycolytic enzymes, presumably pyruvate orthophosphate dikinase. These hypotheses need testing with species characterised by contrasting anoxia tolerance.

What happens to plant mitochondria under low oxygen? An omics review of the responses to low oxygen and reoxygenation

Floods can rapidly submerge plants, limiting oxygen to the extent that oxidative phosphorylation no longer generates adequate ATP supplies. Low-oxygen tolerant plants, such as rice, are able to adequately respond to low oxygen by successfully remodelling primary and mitochondrial metabolism to partially counteract the energy crisis that ensues. In this review, we discuss how plants respond to low-oxygen stress at the transcriptomic, proteomic, metabolomic and enzyme activity levels, particularly focusing on mitochondria and interacting pathways. The role of reactive oxygen species and nitrite as an alternative electron acceptor as well as their links to respiratory chain components is discussed. By making intra-kingdom as well as cross-kingdom comparisons, conserved mechanisms of anoxia tolerance are highlighted as well as tolerance mechanisms that are specific to anoxia-tolerant rice during germination and in coleoptiles. We discuss reoxygenation as an often overlooked, yet essential stage of this environmental stress and consider the possibility that changes occurring during low oxygen may also provide benefits upon re-aeration. Finally, we consider what it takes to be low-oxygen tolerant and argue that alternative mechanisms of ATP production, glucose signalling, starch/sucrose signalling as well as reverse metabolism of fermentation end products promote the survival of rice after this debilitating stress.

Rice alcohol dehydrogenase 1 promotes survival and has a major impact on carbohydrate metabolism in the embryo and endosperm when seeds are germinated in partially oxygenated water

BACKGROUND AND AIMS

Rice (Oryza sativa) has the rare ability to germinate and elongate a coleoptile under oxygen-deficient conditions, which include both hypoxia and anoxia. It has previously been shown that ALCOHOL DEHYDROGENASE 1 (ADH1) is required for cell division and cell elongation in the coleoptile of submerged rice seedlings by means of studies using a rice ADH1-deficient mutant, reduced adh activity (rad). The aim of this study was to understand how low ADH1 in rice affects carbohydrate metabolism in the embryo and endosperm, and lactate and alanine synthesis in the embryo during germination and subsequent coleoptile growth in submerged seedlings.

METHODS

Wild-type and rad mutant rice seeds were germinated and grown under complete submergence. At 1, 3, 5 and 7 d after imbibition, the embryo and endosperm were separated and several of their metabolites were measured and compared.

KEY RESULTS

In the rad embryo, the rate of ethanol fermentation was halved, while lactate and alanine concentrations were 2·4- and 5·7- fold higher in the mutant than in the wild type. Glucose and fructose concentrations in the embryos increased with time in the wild type, but not in the rad mutant. The rad mutant endosperm had lower amounts of the α-amylases RAMY1A and RAMY3D, resulting in less starch degradation and lower glucose concentrations.

CONCLUSIONS

These results suggest that ADH1 is essential for sugar metabolism via glycolysis to ethanol fermentation in both the embryo and endosperm. In the endosperm, energy is presumably needed for synthesis of the amylases and for sucrose synthesis in the endosperm, as well as for sugar transport to the embryo.

Tolerance of anaerobic conditions caused by flooding during germination and early growth in rice (Oryza sativa L.)

Rice is semi-aquatic, adapted to a wide range of hydrologies, from aerobic soils in uplands to anaerobic and flooded fields in waterlogged lowlands, to even deeply submerged soils in flood-prone areas. Considerable diversity is present in native rice landraces selected by farmers over centuries. Our understanding of the adaptive features of these landraces to native ecosystems has improved considerably over the recent past. In some cases, major genes associated with tolerance have been cloned, such as SUB1A that confers tolerance of complete submergence and SNORKEL genes that control plant elongation to escape deepwater. Modern rice varieties are sensitive to flooding during germination and early growth, a problem commonly encountered in rainfed areas, but few landraces capable of germination under these conditions have recently been identified, enabling research into tolerance mechanisms. Major QTLs were also identified, and are being targeted for molecular breeding and for cloning. Nevertheless, limited progress has been made in identifying regulatory processes for traits that are unique to tolerant genotypes, including faster germination and coleoptile elongation, formation of roots and leaves under hypoxia, ability to catabolize starch into simple sugars for subsequent use in glycolysis and fermentative pathways to generate energy. Here we discuss the state of knowledge on the role of the PDC-ALDH-ACS bypass and the ALDH enzyme as the likely candidates effective in tolerant rice genotypes. Potential involvement of factors such as cytoplasmic pH regulation, phytohormones, reactive oxygen species scavenging and other metabolites is also discussed. Further characterization of contrasting genotypes would help in elucidating the genetic and biochemical regulatory and signaling mechanisms associated with tolerance. This could facilitate breeding rice varieties suitable for direct seeding systems and guide efforts for improving waterlogging tolerance in other crops.

Proteomics of rice seed germination

Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles, and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS) technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.

pH regulation in anoxic rice coleoptiles at pH 3.5: biochemical pHstats and net H+ influx in the absence and presence of NOFormula

During anoxia, cytoplasmic pH regulation is crucial. Mechanisms of pH regulation were studied in the coleoptile of rice exposed to anoxia and pH 3.5, resulting in H(+) influx. Germinating rice seedlings survived a combination of anoxia and exposure to pH 3.5 for at least 4 d, although development was retarded and net K(+) efflux was continuous. Further experiments used excised coleoptile tips (7-10 mm) in anoxia at pH 6.5 or 3.5, either without or with 0.2 mM NO(3)(-), which distinguished two processes involved in pH regulation. Net H(+) influx (μmol g(-1) fresh weight h(-1)) for coleoptiles with NO(3)(-) was ∼1.55 over the first 24 h, being about twice that in the absence of NO(3)(-), but then decreased to 0.5-0.9 as net NO(3)(-) uptake declined from ∼1.3 to 0.5, indicating reduced uptake via H(+)-NO(3)(-) symports. NO(3)(-) reduction presumably functioned as a biochemical pHstat. A second biochemical pHstat consisted of malate and succinate, and their concentrations decreased substantially with time after exposure to pH 3.5. In anoxic coleoptiles, K(+) balancing the organic anions was effluxed to the medium as organic anions declined, and this efflux rate was independent of NO(3)(-) supply. Thus, biochemical pHstats and reduced net H(+) influx across the plasma membrane are important features contributing to pH regulation in anoxia-tolerant rice coleoptiles at pH 3.5.

Aspects of plant behaviour under anoxia and post-anoxia

All plants are able to survive anoxic periods, but the degree of tolerance shows large variation. The main injuries related to anoxia are eventually due to changes in energy metabolism. Low energy charge values indicate a cessation of many ATP consuming processes. Sugar starvation, lactic acid fermentation and proton release from leaky vacuoles are responsible for cell death. Long-term anoxia tolerance is dependent on storage products in the vicinity of sinks, on an adequate control of glycolysis, synthesis of essential proteins, and stability of membranes and organelles. However, no fundamental differences between the metabolic pathways of tolerant and non-tolerant tissues are known. It is rather a question of minor changes and the regulation of anaerobic metabolism.

Re-exposure of anoxic tissues to air may even be more detrimental than anoxia itself. These injuries are mainly due to enhanced radical generation. Lipid peroxidation processes lead to membrane damage, disintegration, and leakage of solutes. Under natural conditions plants are equipped with radical-detoxifying systems (SOD, peroxidases and antioxidants). Natural detoxifying systems can be reduced in non-adapted plants under anoxia and they become more sensitive to post-anoxic damage. In addition, the rapid conversion of ethanol to extremely toxic acetaldehyde seems to be a cause of tissue injury and death.

Differential molecular responses of rice and wheat coleoptiles to anoxia reveal novel metabolic adaptations in amino acid metabolism for tissue tolerance

Rice (Oryza sativa) and wheat (Triticum aestivum) are the most important starch crops in world agriculture. While both germinate with an anatomically similar coleoptile, this tissue defines the early anoxia tolerance of rice and the anoxia intolerance of wheat seedlings. We combined protein and metabolite profiling analysis to compare the differences in response to anoxia between the rice and wheat coleoptiles. Rice coleoptiles responded to anoxia dramatically, not only at the level of protein synthesis but also at the level of altered metabolite pools, while the wheat response to anoxia was slight in comparison. We found significant increases in the abundance of proteins in rice coleoptiles related to protein translation and antioxidant defense and an accumulation of a set of enzymes involved in serine, glycine, and alanine biosynthesis from glyceraldehyde-3-phosphate or pyruvate, which correlates with an observed accumulation of these amino acids in anoxic rice. We show a positive effect on wheat root anoxia tolerance by exogenous addition of these amino acids, indicating that their synthesis could be linked to rice anoxia tolerance. The potential role of amino acid biosynthesis contributing to anoxia tolerance in cells is discussed.

Involvement of plasma membrane H+-ATPase in anoxic elongation of stems in pondweed (Potamogeton distinctus) turions

• Pondweed (Potamogeton distinctus) turions can elongate in the absence of O(2). Alcoholic fermentation serves to produce energy for anoxic elongation via the breakdown of starch stored in cells. However, the mechanism of cell growth during anoxic elongation is not fully understood. • Changes in pH, H(+) equivalent and lactate content of the incubation medium were measured during anoxic elongation. The effects of fusicoccin (FC), indole-3-acetic acid (IAA), vanadate, erythrosine B and K(+) channel blockers on anoxic elongation were examined. Cytoplasmic pH and vacuolar pH were measured by (31)P nuclear magnetic resonance (NMR) spectroscopy. • Acidification of the incubation medium occurred during anoxic elongation. The contribution of CO(2) and lactic acid was not sufficient to explain the acidification. FC and IAA enhanced the elongation of stem segments. Vanadate and erythrosine B inhibited anoxic elongation. Acid growth of notched segments was observed. The activity of plasma membrane H(+)-ATPase extracted from pondweed turions was increased slightly in anoxic conditions, but that from pea epicotyls sensitive to anoxic conditions was decreased by incubation in anoxic conditions. Both the cytoplasmic pH and vacuolar pH of pondweed turion cells chased by (32)P NMR spectroscopy were stabilized during a short period < 3 h after anoxic conditions. • We propose that the enhancement of H(+) extrusion by anoxic conditions induces acidification in the apoplast and may contribute to the stabilization of pH in the cytoplasm.

Expression of vacuolar H+-pyrophosphatase (OVP3) is under control of an anoxia-inducible promoter in rice

Vacuolar H(+)-pyrophosphatase (V-PPase) expression increases in a number of abiotic stresses and is thought to play a role in adaptation to abiotic stresses. This paper reports on the regulation of six V-PPase genes in rice (Oryza sativa L.) coleoptiles under anoxia, using flood tolerant and intolerant cultivars to test our hypothesis. Quantitative PCR analysis showed that one vacuolar H(+)-pyrophosphatase (OVP3) was induced by anoxia, particularly in flood-tolerant rice. Regulation of OVP3 expression under anoxia was investigated by analysing putative OVP promoters. The putative OVP3 promoter contained more previously identified anoxia-inducible motifs than the putative promoters of the other five OVP genes. GUS activity in transgenic rice plants containing the OVP3 promoter region linked to the GUS reporter gene was induced only by anoxia. Salt and cold treatments had little effect on OVP3 promoter-driven GUS expression when compared to the anoxic treatment.

Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings

Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.

The metabolome of Chlamydomonas reinhardtii following induction of anaerobic H2 production by sulfur depletion

The metabolome of the model species Chlamydomonas reinhardtii has been analyzed during 120 h of sulfur depletion to induce anaerobic hydrogen (H(2)) production, using NMR spectroscopy, gas chromatography coupled to mass spectrometry, and TLC. The results indicate that these unicellular green algae consume freshly supplied acetate in the medium to accumulate energy reserves during the first 24 h of sulfur depletion. In addition to the previously reported accumulation of starch, large amounts of triacylglycerides were deposited in the cells. During the early 24- to 72-h time period fermentative energy metabolism lowered the pH, H(2) was produced, and amino acid levels generally increased. In the final phase from 72 to 120 h, metabolism slowed down leading to a stabilization of pH, even though some starch and most triacylglycerides remained. We conclude that H(2) production does not slow down due to depletion of energy reserves but rather due to loss of essential functions resulting from sulfur depletion or due to a build-up of the toxic fermentative products formate and ethanol.

Regulation of intracellular pH during anoxia in rice coleoptiles in acidic and near neutral conditions

Rice coleoptiles, renowned for anoxia tolerance, were hypoxically pretreated, excised, 'healed', and then exposed to a combination of anoxia and pH 3.5. The putative acid load was confirmed by net effluxes of K(+) to the medium, with concurrent net decreases of H(+) in the medium, presumably mainly due to H(+) influx. Yet the coleoptiles survived the combination of anoxia and pH 3.5 for at least 90 h, and even for at least 40 h when the energy crisis, inherent to anoxia, had been aggravated by supplying the coleoptiles with 2.5 mM rather than 50 mM glucose. Even in the case of coleoptiles with 2.5 mM glucose, an accumulation ratio of 6 for Cl(-) was attained at 4 h after the start of re-aeration, implying plasma membrane integrity was either maintained during anoxia, or rapidly restored after a return to aerated conditions. Cytoplasmic pH and vacuolar pH were measured using in vivo (31)P nuclear magnetic resonance spectroscopy with 50 mM glucose in the basal perfusion medium. After 60 h in anoxia, external pH was suddenly decreased from 6.5 to 3.5, but cytoplasmic pH only decreased from 7.35 to 7.2 during the first 2 h and then remained steady for the next 16 h. During the first 3 h at pH 3.5, vacuolar pH decreased from 5.7 to 5.25 and then stabilized. After 18 h at pH 3.5, the initial values of cytoplasmic pH and vacuolar pH were rapidly restored, both upon a return to pH 6.5 while maintaining anoxia and after subsequent return to aerated solution. Summing up, rice coleoptiles exposed to a combination of anoxia and pH 3.5 retained pH regulation and cellular compartmentation, demonstrating tolerance to anoxia even during the acid load imposed by exposure to pH 3.5.

Rice germination and seedling growth in the absence of oxygen

BACKGROUND

Higher plants are aerobic organisms which suffer from the oxygen deficiency imposed by partial or total submergence. However, some plant species have developed strategies to avoid or withstand severe oxygen shortage and, in some cases, the complete absence of oxygen (tissue anoxia) for considerable periods of time.

SCOPE

Rice (Oryza sativa) is one of the few plant species that can tolerate prolonged soil flooding or complete submergence thanks to an array of adaptive mechanisms. These include an ability to elongate submerged shoot organs at faster than normal rates and to develop aerenchyma, allowing the efficient internal transport of oxygen from the re-emerged elongated shoot to submerged parts. However, rice seeds are able to germinate anaerobically by means of coleoptile elongation. This cannot be explained in terms of oxygen transport through an emerged shoot. This review provides an overview of anoxic rice germination that is mediated through coleoptile rather than root emergence.

CONCLUSIONS

Although there is still much to learn about the biochemical and molecular basis of anaerobic rice germination, the ability of rice to maintain an active fermentative metabolism (i.e. by fuelling the glycolytic pathway with readily fermentable carbohydrates) is certainly crucial. The results obtained through microarray-based transcript profiling confirm most of the previous evidence based on single-gene studies and biochemical analysis, and highlight new aspects of the molecular response of the rice coleoptile to anoxia.

Does anoxia tolerance involve altering the energy currency towards PPi?

Oxygen deficit is an important abiotic stress influencing plants, because this condition results in an 'energy crisis'. Most species only survive short periods of anoxia, but several wetland species tolerate prolonged anoxia. Transcriptomic and proteomic studies, using anoxia-tolerant rice and anoxia-intolerant Arabidopsis, have provided evidence for the selective adoption of pyrophosphate (PPi) over ATP as high-energy donor molecules, which may contribute to anoxia tolerance. The use of PPi in some tolerant plant species is similar to that observed in many anaerobic prokaryotes. Investigations are being performed to better understand the origin and regulation of reversible PPi-dependent glycolytic enzymes such as cytosolic pyruvate phosphate dikinase, as well as PPi-consuming enzymes, which are engaged during the anoxic energy crisis. This will be crucial in unraveling this currency switch and its contribution to anoxia tolerance.

The rice Mybleu transcription factor increases tolerance to oxygen deprivation in Arabidopsis plants

Mybleu is a natural incomplete transcription factor of rice (Oryza sativa), consisting of a partial Myb repeat followed by a short leucine zipper. We previously showed its localization to the apical region of rice roots and coleoptiles. Specifically, in coleoptiles, Mybleu is expressed under both aerobic and anaerobic conditions, whereas in roots, it is expressed only under aerobic conditions. Mybleu is able to dimerize with canonical leucine zippers and to activate transcription selectively. To investigate Mybleu function in vivo, we transformed Arabidopsis thaliana and evaluated several morphological, physiological and biochemical parameters. In agreement with a hypothesized role of Mybleu in cell elongation in the differentiation zone, we found that the constitutive expression of this transcription factor in Arabidopsis induced elongation in the primary roots and in the internodal region of the floral stem; we also observed a modification of the root apex morphology in transformed lines. Based on the high expression of Mybleu in anaerobic rice coleoptiles, we studied the role of this transcription factor in transgenic plants grown under low-oxygen conditions. We found that overexpression of this transcription factor increased tolerance to oxygen deficit. In transgenic plants, this effect may depend both on the maintenance of a higher metabolism during stress and on the higher expression levels of certain genes involved in the anaerobic response.

Fermentation metabolism in roots of wheat seedlings after hypoxic pre-treatment in different anoxic incubation systems

A hypoxic pre-treatment (HPT) can improve the anoxic survival of flooding sensitive plants. Here, we tested whether a 4-d HPT of wheat plants (Triticum aestivum L.) would improve their anoxic resistance, and if so, why. We found that the metabolic adjustment during prolonged HPT involved an increased lactate excretion rate, the up-regulation of glycolytic and fermentative enzymes as well as the accumulation of various sugars. Therefore, HPT wheat roots could sustain a 3 times higher ethanolic fermentation rate during an anoxic period compared to non-pre-treated (NHPT) roots. Nevertheless, the enhanced fermentation rate provided temporary relief to the energy crisis only, and both NHPT and HPT plants died after 5d of anoxia in illumination. Comparison of different low oxygen incubation systems using excised roots or roots of intact plants revealed striking differences. The benefits of intact shoots, oxygen transport as well as additional sugar supply enabled a more stable energy supply of anoxia-treated NHPT and HPT roots. However, the height of the fermentation rate was correlated with a high ATP content during dark anoxic incubation, but not in illumination.

Organ specific analysis of the anaerobic primary metabolism in rice and wheat seedlings II: light exposure reduces needs for fermentation and extends survival during anaerobiosis

Low oxygen stress in plants can occur during flooding and compromise the availability and utilization of carbohydrates in root and shoot tissues. Low-oxygen-tolerant rice and -sensitive wheat plants were analyzed under anaerobiosis in light to evaluate main factors of the primary metabolism that affect sensitivity against oxygen deprivation: activity of glycolysis and the rate of photosynthesis. Relatively stable ATP contents (93 and 58% of aerated control levels after 24 h anaerobiosis) in illuminated shoot tissues account for enhanced tolerance of rice and wheat seedlings to anaerobiosis upon light exposure in comparison to anoxia in darkness. Although the photosynthetic process was inhibited during low oxygen stress, which was partly due to CO(2) deficiency, more light-exposed than dark-incubated seedlings survived. Illuminated plants could tolerate a 70% lower anaerobic ethanol production in shoots in comparison to darkness, although still an 18-times higher ethanol production rate was determined in rice than in wheat leaves. In conclusion, light-exposed plants grown under anaerobiosis may recycle low amounts of generated oxygen between photosynthesis and dissimilation and generate additional energy not only from substrate phosphorylation during glycolysis but also from other sources like cyclic electron transport.

Organ-specific analysis of the anaerobic primary metabolism in rice and wheat seedlings. I: Dark ethanol production is dominated by the shoots

During anaerobiosis in darkness the main route for ATP production in plants is through glycolysis in combination with fermentation. We compared the organ-specific anaerobic fermentation of flooding-tolerant rice (Oryza sativa) and sensitive wheat (Triticum aestivum) seedlings. A sensitive laser-based photoacoustic trace gas detection system was used to monitor emission of ethanol and acetaldehyde by roots and shoots of intact seedlings. Dark-incubated rice seedlings released 3 times more acetaldehyde and 14 times more ethanol than wheat seedlings during anaerobiosis. Ninety percent of acetaldehyde originated from shoots of both species. In comparison to wheat shoots, the high ethanol production of rice shoots correlated with larger amounts of soluble carbohydrates, and higher activities of fermentative enzymes. After 24 h of anaerobiosis in darkness rice shoots still contained 30% of aerated ATP level, which enabled seedlings to survive this period. In contrast, ATP content declined almost to zero in wheat shoots and roots, which were irreversibly damaged after a 24-h anaerobic period. When plants were anaerobically and dark incubated for 4 h and subsequently transferred back to aeration, shoots showed a transient peak of acetaldehyde release indicating prompt re-oxidation of ethanol. Post-anoxic acetaldehyde production was lower in rice seedlings than in wheat. This observation accounts for a more effective acetaldehyde detoxification system in rice. Compared to wheat the greater tolerance of rice seedlings to transient anaerobic periods is explained by a faster fermentation rate of their shoots allowing a sufficient ATP production and an efficient suppression of toxic acetaldehyde formation in the early re-aeration period.

Apoplastic pH during low-oxygen stress in Barley

BACKGROUND AND AIMS

Anoxia leads to an energy crisis, tolerance of which varies from plant to plant. Although the apoplast represents an important storage and reaction space, and engages in the mediation of membrane transport, this extracellular compartment has not yet been granted a role during oxygen shortage. Here, an attempt is made to highlight the importance of the apoplast during oxygen stress and to test whether information about it is transferred systemically in Hordeum vulgare.

METHODS

Non-invasive ion-selective microprobes were used which, after being inserted through open stomata, directly contact the apoplastic fluid and continuously measure the apoplastic pH and changes to it.

KEY RESULTS

(a) Barley leaves respond to oxygen stress with apoplastic alkalinization and membrane depolarization. These responses are persistent under anoxia (N2; O2 < 3%) but transient under hypoxia. (b) Being applied to the root, the information 'anoxia' is signalled to the leaf as an increase in pH, whereas 'hypoxia' is not: flooding of the roots within the first 2 h has no effect on the leaf apoplastic pH, whereas anoxia (N2) or chemical anoxia (NaCN/salicylic hydroxamic acid) rapidly increase the leaf apoplastic pH. (c) Under anoxia, the proton motive force suffers a decrease by over 70 %, which impairs H(+) -driven transport.

CONCLUSIONS

Although anoxia-induced apoplastic alkalinization is a general response to stress, its impact on the proton motive force (reduction) and thus on transport mediation of energy-rich compounds is evident. It is concluded that anoxia tolerance depends on how the plant is able to hold the proton motive force and H(+) turnover at a level that guarantees sufficient energy is harvested to overcome the crisis.

Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon

DNA variation in the alcohol dehydrogenase (Adh2) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species. A dimorphic pattern was detected in the Adh2 region of O. rufipogon. The silent nucleotide diversity (pi) in the Adh2 region in O. rufipogon was 0.011, which was higher than that of the Adh1 region in O. rufipogon. Especially, a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1. Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region, indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types. On the other hand, the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region. The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region. This result suggests purifying selection on the replacement sites of the Adh2 region, as detected for the Adh1 region. Significant linkage disequilibria (16.4% of the tests) were detected between the Adh1 and Adh2 regions. Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region, significant interlocus linkage disequilibria were detected. The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations.

Manipulation of ethanol production in anoxic rice coleoptiles by exogenous glucose determines rates of ion fluxes and provides estimates of energy requirements for cell maintenance during anoxia

Ethanol production by anoxic, excised, 7-10 mm tips of rice coleoptiles was manipulated using a range of exogenous glucose concentrations. Such a dose-response curve enabled good estimates at which level of ethanol production (and hence by inference ATP production), injury commenced and also allowed assessments of energy requirements for maintenance in anoxia. Rates of net uptake or loss of K+ and P by these excised coleoptile tips were related to rates of ethanol production (r2 of 0.59 and 0.68, respectively). At 72 h anoxia, ATP levels in excised tips were similar at 0, 2.5, and 50 mol m(-3) exogenous glucose, despite large differences in the inferred rates of ATP production. At 96 h anoxia, tips without exogenous glucose had low ATP concentrations; these may be the cause or the consequence of cell injury. In tips without glucose, injury was indicated by losses of K+ and Cl- between 72-96 h anoxia, and during the first hour after re-aeration, while later than 1 h after re-aeration, rates of net uptake were substantially lower than for re-aerated tips previously in anoxia with exogenous glucose. Between 96 h and 124 h anoxia, ion losses from tips without exogenous glucose increased while recovery of net uptake after re-aeration was very sluggish and incomplete. The energy requirement for maintenance of health and survival of anoxic coleoptile tips, expressed on a fresh weight basis, was lower than for three other anoxia-tolerant plant tissues/cells, studied previously. However, the energy requirement on a protein basis was assessed at 1.4 micromol ATP mg(-1) protein h(-1) and this value is 2.6-5.4-fold higher than for the other plant tissues/cells. Yet, this requirement was still only 58-88% of the published values for aerated tissues. The reason for this relatively high ATP requirement per unit protein in anoxic rice coleoptiles remains to be elucidated.

pH regulation in anoxic plants

BACKGROUND

pH regulation is the result of a complex interaction of ion transport, H+ buffering, H+-consuming and H+-producing reactions. Cells under anoxia experience an energy crisis; an early response thereof (in most tissues) is a rapid cytoplasmic acidification of roughly half a pH unit. Depending on the degree of anoxia tolerance, this pH remains relatively stable for some time, but then drops further due to an energy shortage, which, in concert with a general breakdown of transmembrane gradients, finally leads to cell death unless the plant finds access to an energy source.

SCOPE

In this review the much-debated origin of the initial pH change and its regulation under anoxia is discussed, as well as the problem of how tissues deal with the energy crisis and to what extent pH regulation and membrane transport from and into the vacuole and the apoplast is a part thereof.

CONCLUSIONS

It is postulated that, because a foremost goal of cells under anoxia must be energy production (having an anaerobic machinery that produces insufficient amounts of ATP), a new pH is set to ensure a proper functioning of the involved enzymes. Thus, the anoxic pH is not experienced as an error signal and is therefore not reversed to the aerobic level. Although acclimated and anoxia-tolerant tissues may display higher cytoplasmic pH than non-acclimated or anoxia-intolerant tissues, evidence for an impeded pH-regulation is missing even in the anoxia-intolerant tissues. For sufficient energy production, residual H+ pumping is vital to cope with anoxia by importing energy-rich compounds; however it is not vital for pH-regulation. Whereas the initial acidification is not due to energy shortage, subsequent uncontrolled acidosis occurring in concert with a general gradient breakdown damages the cell but may not be the primary event.

Protein synthesis by rice coleoptiles during prolonged anoxia: implications for glycolysis, growth and energy utilization

BACKGROUND AND AIMS

Anoxia-tolerant plant tissues synthesize a number of proteins during anoxia, in addition to the 'classical anaerobic proteins' involved in glycolysis and fermentation. The present study used a model system of rice coleoptile tips to elucidate patterns of protein synthesis in this anoxia-tolerant plant tissue.

METHODS

Coleoptile tips 7-11 mm long were excised from intact seedlings exposed to anoxia, or excised from hypoxically pre-treated seedlings and then exposed to anoxia for 72 h. Total proteins or 35S-labelled proteins were extracted, separated using two-dimensional isoelectric focusing/SDS-polyacrylamide gel electrophoresis and analysed using mass spectrometry.

KEY RESULTS

The coleoptile tips excised after intact seedlings had been exposed to anoxia for 72 h had a similar proteome to tips that were first excised and then exposed to anoxia. After 72 h anoxia, Bowman-Birk trypsin inhibitors and a glycine-rich RNA-binding protein decreased in abundance, whereas a nucleoside diphosphate kinase and several proteins with unknown functions were strongly enhanced. Using [35S]methionine as label, proteins synthesized at high levels in anoxia, and also in aeration, included a nucleoside diphosphate kinase, a glycine-rich RNA-binding protein, a putative elicitor-inducible protein and a putative actin-depolymerizing factor. Proteins synthesized predominately in anoxia included a pyruvate orthophosphate dikinase (PPDK), alcohol dehydrogenase 1 and 2, fructose 1,6-bisphosphate aldolase and a protein of unknown function.

CONCLUSION

The induction of PPDK in anoxic rice coleoptiles might, in combination with pyruvate kinase (PK), enable operation of a 'substrate cycle' producing PPi from ATP. Production of PPi would (a) direct energy to crucial transport processes across the tonoplast (i.e. the H+-PPiase); (b) be required for sucrose hydrolysis via sucrose synthase; and (c) enable acceleration of glycolysis, via pyrophosphate:fructose 6-phosphate 1-phosphotransferase (PFP) acting in parallel with phosphofructokinase (PFK), thus enhancing ATP production in anoxic rice coleoptiles; ATP production would need to be increased if there was a substantial requirement for PPi.

Sugar utilization and anoxia tolerance in rice roots acclimated by hypoxic pretreatment

Although most cereal roots cannot elongate under anoxic conditions, primary roots of three-day-old rice (Oryza sativa L.) seedlings were able to elongate during a 24-h period of anoxia. Hypoxic pretreatment (H-PT) increased the elongation of their roots. Sucrose synthase (EC 2.4.1.13), glucokinase (EC 2.7.1.2), fructokinase (EC 2.7.1.4), pyruvate decarboxylase (EC 4.1.1.1) and alcohol dehydrogenase (EC 1.1.1.1) activities were increased by anoxia in both H-PT and non-pretreated (N-PT) roots. However, these activities were greater in the H-PT roots than in the N-PT roots. The average rate of production of ethanol for the initial 6h after the onset of anoxia was 3.7 and 1.4 micromolg(-1) fresh weight h(-1) for the H-PT and N-PT roots, respectively, suggesting that ethanolic fermentation may increase more quickly in the H-PT roots than in the N-PT roots. Roots of the seedlings lost ATP and total adenine nucleotides in anoxia, however, the H-PT roots maintained higher levels of ATP and total adenine nucleotides compared to the N-PT roots. These results show that rice roots are able to utilize the set of enzymes involved in the metabolism of soluble sugars under anoxia. The ability to maintain an active fermentative metabolism for production of ATP by fueling the glycolytic pathway with fermentable carbohydrate is probably greater in H-PT than in N-PT roots.

Anoxia tolerance in rice roots acclimated by several different periods of hypoxia

Rice (Oryza sativa L.) seedlings were subjected to hypoxic pretreatment (H-PT; incubated in 5% O2 atmosphere) for various lengths of time followed by an anoxic stress. Anoxia tolerance of rice roots was improved with increasing duration of H-PT, but longer H-PT than 12 h gave no additional improvement. Concentrations of ATP and ethanol, and activities of pyruvate decarboxylase (EC 4.1.1.1) and alcohol dehydrogenase (EC 1.1.1.1) in the roots were increased by H-PT, and the times and patterns of increasing in these concentrations and activities were similar to those of increasing in the anoxia tolerance. These results suggest that the H-PT may increase anoxia tolerance due to maintenance of ATP levels with rapid induction of ethanolic fermentation, and hypoxic acclimation may occur within 12 h.

Tolerance of crop plants to oxygen deficiency stress: fermentative activity and photosynthetic capacity of entire seedlings under hypoxia and anoxia

The study investigates the reactions of rice, wheat and maize to anoxia (plants without access to oxygen) and hypoxia (roots with very limited access to oxygen). We studied the adaptations of these intact crop plants because they are known to differ widely in their tolerance to oxygen deficiency. In hypoxia, there was an accumulation of sugars, especially in wheat and maize, although both flood-sensitive species significantly increased the activities of fermentative and glycolytic enzymes, clearly more than in rice. In rice, avoiding an oxygen limitation due to the effective aeration system (30% of root cross-sectional area) may have accounted for only a minor metabolic reaction to hypoxia. In anoxia, maize and wheat quickly lost viability and nearly all photosynthetic capacity, while most rice leaves stayed turgid and green, losing only 50% of the photosynthetic capacity. A strong metabolic arrest under anoxia was obvious for the sucrolytic, glycolytic and fermentative enzymes in all tested species, but was most pronounced in rice. Of the 14 enzymes studied, rice showed the lowest activity increase in hypoxia for 11 enzymes, and the strongest activity decrease in anoxia for 8 enzymes. However, rice was able even under anoxia to keep a 1/4 of the ATP level of the aerated control, while it was at the detection limit in maize and wheat. It appears that in anoxic rice, the switch to metabolic dormancy and maintenance of basic shoot meristems diminishes the needs for energy and substrate. Additionally, rice already has lower sugar demand under hypoxia, and sugar supply appears to be sustained under anoxia by a functioning anaerobic amylase and by the photosynthetically active shoot.

Responses by coleoptiles of intact rice seedlings to anoxia: k(+) net uptake from the external solution and translocation from the caryopses

This study evaluated the effects of anoxia on K(+) uptake and translocation in 3-4-d-old, intact, rice seedlings (Oryza sativa L. cv. Calrose). Rates of net K(+) uptake from the medium over 24 h by coleoptiles of anoxic seedlings were inhibited by 83-91 %, when compared with rates in aerated seedlings. Similar uptake rates, and degree of inhibition due to anoxia, were found for Rb(+) when supplied over 1.5-2 h, starting 22 h after imposing anoxia. The Rb(+) uptake indicated that intact coleoptiles take up ions directly from the external solution. Monovalent cation (K(+) and Rb(+)) net uptake from the solution was inhibited by anoxia to the same degree for the coleoptiles of intact seedlings and for coleoptiles excised, 'aged', and supplied with exogenous glucose. Transport of endogenous K(+) from caryopses to coleoptiles was inhibited less by anoxia than net K(+) uptake from the solution, the inhibition being 55 % rather than 87 %. Despite these inhibitions, osmotic pressures of sap (pi(sap)) expressed from coleoptiles of seedlings exposed to 48 h of anoxia, with or without exogenous K(+), were 0.66 +/- 0.03 MPa; however, the contributions of K(+) to pi(sap) were 23 and 16 %, respectively. After 24 h of anoxia, the K(+) concentrations in the basal 10 mm of the coleoptiles of seedlings with or without exogenous K(+), were similar to those in aerated seedlings with exogenous K(+). In contrast, K(+) concentrations had decreased in aerated seedlings without exogenous K(+), presumably due to 'dilution' by growth; fresh weight gains of the coleoptile being 3.6- to 4.7-fold greater in aerated than in anoxic seedlings. Deposition rates of K(+) along the axes of the coleoptiles were calculated for the anoxic seedlings only, for which we assessed the elongation zone to be only the basal 4 mm. K(+) deposition in the basal 6 mm was similar for seedlings with or without exogenous K(+), at 0.6-0.87 micro mol g(-1) f. wt h(-1). Deposition rates in zones above 6 mm from the base were greater for seedlings with, than without, exogenous K(+); the latter were sometimes negative. We conclude that for the coleoptiles of rice seedlings, anoxia inhibits net K(+) uptake from the external solution to a much larger extent than K(+) translocation from the caryopses. Furthermore, K(+) concentrations in the elongation zone of the coleoptiles of anoxic seedlings were maintained to a remarkable degree, contributing to maintenance of pi(sap) in cells of these elongating tissues.

The metabolic response of plants to oxygen deficiency

Plants, under natural or experimental conditions, can be subject to a range of O2 concentrations from normal (normoxia) through deficient (hypoxia) to total absence (anoxia). Many metabolic processes are affected by O2 deficiency but the most studied events are those related to respiration and metabolism of N. In the absence of a terminal electron acceptor for the electron transport chain, the tricarboxylic acid cycle functions only partially and in both directions. Acidification of the cytosol occurs and pyruvate, the product of glycolysis, is transformed to lactate and ethanol, which represent the main fermentation reactions in plants. Alanine is the third most important product of anaerobic metabolism, resulting from high rates of amino acid interconversion in which transaminases such as alanine aminotransferase play an important role. The role of alanine accumulation under anaerobiosis is not clear and appears to be independent of the source of N whether NO3-, NH4+ or N2. How nitrate exerts its beneficial effect on tolerance of root hypoxia in waterlogged plants is still not clearly understood. Such aspects of N metabolism pose interesting challenges for future research on metabolic responses of plants to oxygen deficiency.

Ethanol sensitivity of rice and oat coleoptiles

The ability to avoid the ethanol-induced injury was evaluated in rice (Oryza sativa L.) and oat (Avena sativa L.) coleoptiles. The growth of the rice and oat coleoptiles was inhibited by ethanol exogenously applied at concentrations greater than 200 and 30 mM, respectively. At 300 mM ethanol, oat coleoptiles were brown and flaccid but rice coleoptiles did not show any visible symptoms of toxicity. The acetaldehyde level in rice and oat coleoptiles was increased by exogenously applied ethanol and the increases were greater in oat than in rice coleoptiles under aerobic and anaerobic conditions. At 300 mM ethanol, the acetaldehyde concentrations in the rice and oat coleoptiles were 46 and 87 nmol g-1 FW under aerobic conditions, respectively, and 52 and 124 nmol g-1 FW under anaerobic conditions, respectively. The activity of alcohol dehydrogenase (ADH; EC 1.1.1.1) in the direction of ethanol to acetaldehyde was greater in oat than in rice coleoptiles and ADH protein in oat coleoptiles was more induced by exogenously applied ethanol than that in rice coleoptiles. These results suggest that in vivo conversion rate of ethanol to acetaldehyde by ADH is lower in rice than oat coleoptiles, which may be one of the reasons that ethanol sensitivity of rice is much lower than that of oat coleoptiles. The great ability of rice to avoid the ethanol-induced injuries may contribute its anoxia tolerance when glycolysis and ethanolic fermentation replace the Krebs cycle as the main source of energy under anaerobic conditions.

Metabolic regulation of pH in plant cells: role of cytoplasmic pH in defense reaction and secondary metabolism

A new biochemical pH-stat hypothesis that revised the classic hypothesis is presented to understand the metabolic regulation of intracellular pH in plant cells. Alternative pathway glycolysis, alternative pathway respiration and malate-derived lactic and alcoholic fermentation (alternative pathway fermentation), all unique to plants, are integrated into a regulatory mechanism of pH in the cytoplasm. Its uniqueness to plant kingdom is discussed from the evolutionary viewpoint: it is suggested that when the ancestors of extant terrestrial plants expanded their habitat from oceans to freshwater, they abandoned a "sodium system" and adopted a "proton system" for nutrient uptake. Validity of the new hypothesis is examined with available data on a secondary active transport, anoxia and other experimental evidence. The hypothesis predicts that biotic and abiotic stress-induced cytoplasmic acidification triggers synthesis of phytoalexins and other secondary metabolites. Possible roles of cyanide-resistant alternative pathway respiration in the secondary metabolite production, metabolic switching between primary and secondary metabolisms, and defense reactions are proposed.