Low levels of pyrophosphate in transgenic potato plants expressing E. coli pyrophosphatase lead to decreased vitality under oxygen deficiency

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.

Identification of long noncoding RNAs involved in adaptability to chronic hypoxic by whole transcriptome sequencing

Hypoxia affects the physiology of cells and organisms; however, the mechanisms associated with hypoxia adaptation remain unknown in Tibetan chickens. In this study, we aimed to identify long noncoding RNAs (lncRNAs) involved in hypoxia adaptation in Tibetan chickens and Daheng broilers, to provide insights into the mechanisms underlying hypoxia induction. RNA sequencing results revealed that a total of 5504 lncRNAs and 16,779 microRNAs were differentially expressed in four Tibetan chickens and four Daheng broilers; 70 lncRNAs were up-regulated and 113 lncRNAs were down-regulated in the Tibetan chickens compared to the expression levels in the Daheng broilers. The differentially expressed lncRNAs (DElncRNAs) were enriched in the following Gene ontology terms: protein complex localization, small-molecule metabolic process, and RNA splicing. Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DElncRNAs were mainly enriched in pathways that regulate cell junctions and intercellular spaces and oxygen or energy metabolism, mainly involved in hypoxic adaption. Moreover, a predicted ceRNA network with five DElncRNAs interacted with three miRNAs that acted on 42 pathways through 19 target genes. Quantitative real-time polymerase chain reaction was used to verify that the expression levels of ENSGALG00000008047, ENSGALG00000050044, and ENSGALG00000053982 were significantly lower in Tibetan chickens than in the Daheng broilers, consistent with the RNA sequencing results. We obtained lncRNA expression profiles for the heart tissue of Tibetan chickens for the first time and have provided novel data that may aid research on biological adaptation to hypoxic stress.

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.

Plant proton pumping pyrophosphatase: the potential for its pyrophosphate synthesis activity to modulate plant growth

Cellular pyrophosphate (PPi) homeostasis is vital for normal plant growth and development. Plant proton-pumping pyrophosphatases (H⁺ -PPases) are enzymes with different tissue-specific functions related to the regulation of PPi homeostasis. Enhanced expression of plant H⁺ -PPases increases biomass and yield in different crop species. Here, we emphasise emerging studies utilising heterologous expression in yeast and plant vacuole electrophysiology approaches, as well as phylogenetic relationships and structural analysis, to showcase that the H⁺ -PPases possess a PPi synthesis function. We postulate this synthase activity contributes to modulating and promoting plant growth both in H⁺ -PPase-engineered crops and in wild-type plants. We propose a model where the PPi synthase activity of H⁺ -PPases maintains the PPi pool when cells adopt PPi-dependent glycolysis during high energy demands and/or low oxygen environments. We conclude by proposing experiments to further investigate the H⁺ -PPase-mediated PPi synthase role in plant growth.

Heterologous expression and kinetic characterization of the α, β and αβ blend of the PPi-dependent phosphofructokinase from Citrus sinensis

This work reports the molecular cloning and heterologous expression of the genes coding for α and β subunits of pyrophosphate-dependent phosphofructokinase (PPi-PFK) from orange. When expressed individually, both recombinant subunits were produced as highly purified monomeric proteins able to phosphorylate fructose-6-phosphate at the expenses of PPi (specific activity of 0.075 and 0.017 units. mg^-1 for α and β subunits, respectively). On the other hand, co-expression rendered a α₃β₃ hexamer with specific activity three orders of magnitude higher than the single subunits. All the conformations of the enzyme were characterized with respect to its kinetic properties and sensitivity to the regulator fructose-2,6-bisphosphate. A thorough review of current knowledge on the matter indicates that this is the first report of the recombinant production of active plant PPi-PFK and the characterization of its different conformations. This is a main contribution for future studies focused to better understand the enzyme properties and how it accomplishes its relevant role in plant metabolism.

Review: "Pyrophosphate and pyrophosphatases in plants, their involvement in stress responses and their possible relationship to secondary metabolism"

Pyrophosphate (PPi) is produced as byproduct of biosynthesis in the cytoplasm, nucleus, mitochondria and chloroplast, or in the tonoplast and Golgi by membrane-bound H⁺-pumping pyrophosphatases (PPv). Inorganic pyrophosphatases (E.C. 3.6.1.1; GO:0004427) impulse various biosynthetic reactions by recycling PPi and are essential to living cells. Soluble and membrane-bound enzymes of high specificity have evolved in different protein families and multiple pyrophosphatases are encoded in all plant genomes known to date. The soluble proteins are present in cytoplasm, extracellular space, inside chloroplasts, and perhaps inside mitochondria, nucleus or vacuoles. The cytoplasmic isoforms may compete for PPi with the PPv enzymes and how PPv and soluble activities are controlled is currently unknown, yet the cytoplasmic PPi concentration is high and fairly constant. Manipulation of the PPi metabolism impacts primary metabolism and vice versa, indicating a tight link between PPi levels and carbohydrate metabolism. These enzymes appear to play a role in germination, development and stress adaptive responses. In addition, the transgenic overexpression of PPv has been used to enhance plant tolerance to abiotic stress, but the reasons behind this tolerance are not completely understood. Finally, the relationship of PPi to stress suggest a currently unexplored link between PPi and secondary metabolism.

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.

Analysis of gene expression and proteomic profiles of clonal genotypes from Theobroma cacao subjected to soil flooding

Soil flooding causes changes in gene transcription, synthesis and degradation of proteins and cell metabolism. The main objective of this study was to understand the biological events of Theobroma cacao during soil flooding-induced stress, using the analyses of gene expression and activity of key enzymes involved in fermentation, as well as the identification of differentially expressed proteins by mass spectrometry in two contrasting genotypes for flooding tolerance (tolerant - TSA-792 and susceptible - TSH-774). Soil anoxia caused by flooding has led to changes in the expression pattern of genes associated with the biosynthesis of alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC) and lactate dehydrogenase (LDH) in leaves and roots of the two evaluated genotypes. Significant differences were observed between the enzyme activities of the two genotypes. Leaves and roots of the TSA-792 genotype showed higher ADH activity as compared to the TSH-774 genotype, whereas the activities of PDC and LDH have varied over the 96 h of soil flooding, being higher for TSA-792 genotype, at the initial stage, and TSH-774 genotype, at the final stage. Some of the identified proteins are those typical of the anaerobic metabolism-involved in glycolysis and alcoholic fermentation-and different proteins associated with photosynthesis, protein metabolism and oxidative stress. The ability to maintain glycolysis and induce fermentation was observed to play an important role in anoxia tolerance in cacao and may also serve to distinguish tolerant and susceptible genotypes in relation to this stressor.

A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1

Plant responses to biotic and abiotic stresses are often very specific, but signal transduction pathways can partially or completely overlap. Here, we demonstrate that in Arabidopsis (Arabidopsis thaliana), the transcriptional responses to phosphate starvation and oxygen deficiency stress comprise a set of commonly induced genes. While the phosphate deficiency response is systemic, under oxygen deficiency, most of the commonly induced genes are found only in illuminated shoots. This jointly induced response to the two stresses is under control of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), but not of the oxygen-sensing N-end rule pathway, and includes genes encoding proteins for the synthesis of galactolipids, which replace phospholipids in plant membranes under phosphate starvation. Despite the induction of galactolipid synthesis genes, total galactolipid content and plant survival are not severely affected by the up-regulation of galactolipid gene expression in illuminated leaves during hypoxia. However, changes in galactolipid molecular species composition point to an adaptation of lipid fluxes through the endoplasmic reticulum and chloroplast pathways during hypoxia. PHR1-mediated signaling of phosphate deprivation was also light dependent. Because a photoreceptor-mediated PHR1 activation was not detectable under hypoxia, our data suggest that a chloroplast-derived retrograde signal, potentially arising from metabolic changes, regulates PHR1 activity under both oxygen and phosphate deficiency.

Extreme flooding tolerance in Rorippa

Low oxygen stress imposed by floods creates a strong selection force shaping plant ecosystems in flood-prone areas. Plants inhabiting these environments adopt various adaptations and survival strategies to cope with increasing water depths. Two Rorippa species, R. sylvestris and R. amphibia that grow in naturally flooded areas, have high submergence tolerance achieved by the so-called quiescence and escape strategies, respectively. In order to dissect the molecular mechanisms involved in these strategies, we investigated submergence-induced changes in gene expression in flooded roots of Rorippa species. There was a higher induction of glycolysis and fermentation genes and faster carbohydrate reduction in R. amphibia, indicating a higher demand for energy potentially leading to faster mortality by starvation. Moreover, R. sylvestris showed induction of genes improving submergence tolerance, potentially enhancing survival in prolonged floods. Additionally, we compared transcript profiles of these 2 tolerant species to relatively intolerant Arabidopsis and found that only Rorippa species induced various inorganic pyrophosphate dependent genes, alternatives to ATP demanding pathways, thereby conserving energy, and potentially explaining the difference in flooding survival between Rorippa and Arabidopsis.

Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance

Complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis thaliana). We studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, Rorippa sylvestris and Rorippa amphibia. We exploited the close relationship between Rorippa species and the model species Arabidopsis by using Arabidopsis GeneChip microarrays for whole-genome transcript profiling of roots of young plants exposed to a 24-h submergence treatment or air. A probe mask was used based on hybridization of genomic DNA of both species to the arrays, so that weak probe signals due to Rorippa species/Arabidopsis mismatches were removed. Furthermore, we compared Rorippa species microarray results with those obtained for roots of submerged Arabidopsis plants. Both Rorippa species could tolerate deep submergence, with R. sylvestris surviving much longer than R. amphibia. Submergence resulted in the induction of genes involved in glycolysis and fermentation and the repression of many energy-consuming pathways, similar to the low-oxygen and submergence response of Arabidopsis and rice (Oryza sativa). The qualitative responses of both Rorippa species to submergence appeared roughly similar but differed quantitatively. Notably, glycolysis and fermentation genes and a gene encoding sucrose synthase were more strongly induced in the less tolerant R. amphibia than in R. sylvestris. A comparison with Arabidopsis microarray studies on submerged roots revealed some interesting differences and potential tolerance-related genes in Rorippa species.

Characterization of the phosphofructokinase gene family in rice and its expression under oxygen deficiency stress

Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the ATP-dependent phosphofructokinase (PFK) and the pyrophosphate-(PPi) dependent pyrophosphate-fructose-6-phosphate-phosphotransferase (PFP). During oxygen deficiency ATP levels in rice seedlings are severely reduced, and it is hypothesized that PPi is used as an alternative energy source for the phosphorylation of fructose-6-phosphate during glycolysis. In this study, we analyzed the expression of 15 phosphofructokinase-encoding genes in roots and aerial tissues of anoxia-tolerant rice seedlings in response to anoxic stress and compared our data with transcript profiles obtained from microarray analyses. Furthermore, the intracellular localization of rice PFK proteins was determined, and the PFK and PFP isoforms were grouped in a phylogenetic tree. Two PFK and two PFP transcripts accumulated during anoxic stress, whereas mRNA levels of four PFK and three PFP genes were decreased. The total specific activity of both PFK and PFP changed only slightly during a 24-h anoxia treatment. It is assumed that expression of different isoforms and their catalytic properties differ during normoxic and anoxic conditions and contribute to balanced glycolytic activity during the low-oxygen stress. These characterizations of phosphofructokinase genes and the comparison to other plant species allowed us to suggest candidate rice genes for adaptation to anoxic stress.

Low oxygen response mechanisms in green organisms

Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.

Analyzing the effect of decreasing cytosolic triosephosphate isomerase on Solanum tuberosum hairy root cells using a kinetic-metabolic model

A kinetic-metabolic model of Solanum tuberosum hairy roots is presented in the interest of understanding the effect on the plant cell metabolism of a 90% decrease in cytosolic triosephosphate isomerase (cTPI, EC 5.3.1.1) expression by antisense RNA. The model considers major metabolic pathways including glycolysis, pentose phosphate pathway, and TCA cycle, as well as anabolic reactions leading to lipids, nucleic acids, amino acids, and structural hexoses synthesis. Measurements were taken from shake flask cultures for six extracellular nutrients (sucrose, fructose, glucose, ammonia, nitrate, and inorganic phosphate) and 15 intracellular compounds including sugar phosphates (G6P, F6P, R5P, E4P) and organic acids (PYR, aKG, SUCC, FUM, MAL) and the six nutrients. From model simulations and experimental data it can be noted that plant cell metabolism redistributes metabolic fluxes to compensate for the cTPI decrease, leading to modifications in metabolites levels. Antisense roots showed increased exchanges between the pentose phosphate pathway and the glycolysis, an increased oxygen uptake and growth rate.

Magnesium and cell energetics in plants under anoxia

Stress conditions (e.g. anoxia) frequently result in a decrease of [ATP] and in an increase of [ADP] and [AMP], with a concomitant increase of [Mg2+] and other cations, e.g. Ca2+. The elevation of [Mg2+] is linked to the shift in the apparent equilibrium of adenylate kinase. As a result, enzymes that use Mg2+ as a cofactor are activated, Ca2+ activates calcium-dependent signalling pathways, and PPi can serve as an alternative energy source in its active form of MgPPi or Mg2PPi. Under anoxic conditions in plants, an important source of PPi may come as a result of combined reactions of PK (pyruvate kinase) and PPDK (pyruvate, phosphate dikinase). The PPi formed in the PPDK/PK cycle ignites glycolysis in conditions of low [ATP] by involving PPi-dependent reactions. This saves ATP and makes metabolism under stress conditions more energy efficient.

Differential regulation of vacuolar H+-ATPase and H+-PPase in Cucumis sativus roots by zinc and nickel

Zinc and nickel, as micronutrients, are essential for all organisms. We investigated the effect of 10 and 100 μM Zn and Ni on two tonoplast proton pumps, vacuolar H+-ATPase (V-ATPase) (EC 3.6.3.14) and vacuolar H+-pyrophosphatase (V-PPase) (EC 3.6.1.1), in cucumber roots. ATP-dependent proton transport as well as ATP hydrolysis, catalyzed by V-ATPase, decreased in roots after exposure of plants to both Zn and Ni under all the examined conditions. In contrast, V-PPase activities, measured as PP(i) hydrolysis and PP(i)-driven H+ transport, were stimulated by lower concentration of metals. However, at higher metal concentration, hydrolytic activity of V-PPase remained unchanged, while PP(i)-dependent proton pumping into the tonoplast vesicles was reduced. When heavy metals were introduced into the enzyme reaction medium, both V-ATPase and V-PPase activities were lowered by Zn and Ni in a similar manner. As the gene expression and immunoblot analyses depicted, observed changes in the activity of both tonoplast proton pumps in response to zinc and nickel were not due to the modification in the expression of the CsVHA-A, CsVHA-c and CsVP genes encoding V-ATPase subunit A and c, and V-PPase, respectively, in cucumber roots or in amounts of enzyme proteins. Moreover, Zn as well as Ni ions did not enhance the lipid peroxidation in the root tonoplast fractions. Comparison of ATP and pyrophosphate contents in the control roots and roots treated with heavy metals revealed that Zn and Ni do not affect the ATP amount but reduce the PP(i) level.

Application of genetic engineering in potato breeding

Potato breeding programmes worldwide are undergoing a period of rapid change. In order to be successful, breeders must adapt and incorporate the newest up-to-date techniques as they become available. Recent advances in biotechnology make it possible to develop and cultivate more and more sophisticated transgenic crops with multiple modified traits. Gene transfer methods can be used for a wide range of fundamental studies, contributing to a better understanding of the mechanisms of plant/pathogen interactions and the metabolic pathways in plants. Transgenic potato plants are being generated worldwide to investigate the impact of transgene expression on parameters as complex as yield. Historically, potato was one of the first successfully transformed crop plants. Nowadays, transgenic potatoes have been introduced into the food chain of people and animals in several countries. Some of the genetic modifications give potato plants increased resistance to biotic and abiotic environmental factors, while others lead to improved nutritional value, or cause the plants to produce proteins of the immune system of humans or animals or substances that may be used as vaccines in humans or veterinary medicine. The trend today is towards the generation of crops with output traits, e.g. modified starch or carotenoids, or the production of pharmaceuticals in tubers, whereas the early targets were input traits, e.g. herbicide resistance, pest or virus resistance. This review provides a summary of examples illustrating the versatility and applicability of transgenic biology in potato improvement.

Oxidative metabolism, ROS and NO under oxygen deprivation

Oxygen deprivation, in line with other stress conditions, is accompanied by reactive oxygen (ROS) and nitrogen species (RNS) formation and is characterised by a set of metabolic changes collectively named as the 'oxidative stress response'. The controversial induction of oxidative metabolism under the lack of oxygen is necessitated by ROS and RNS signaling in the induction of adaptive responses, and inevitably results in oxidative damage. To prevent detrimental effects of oxidative stress, the levels of ROS and NO are tightly controlled on transcriptional, translational and metabolic levels. Hypoxia triggers the induction of genes responsible for ROS and NO handling and utilization (respiratory burst oxidase, non-symbiotic hemoglobins, several cytochromes P450, mitochondrial dehydrogenases, and antioxidant-related transcripts). The level of oxygen in the tissue is also under metabolic control via multiple mechanisms: Regulation of glycolytic and fermentation pathways to manage pyruvate availability for respiration, and adjustment of mitochondrial electron flow through NO and ROS balance. Both adaptive strategies are controlled by energy status and aim to decrease the respiratory capacity and to postpone complete anoxia. Besides local oxygen concentration, ROS and RNS formation is controlled by an array of antioxidants. Hypoxic treatment leads to the upregulation of multiple transcripts associated with ascorbate, glutathione and thioredoxin metabolism. The production of ROS and NO is an integral part of the response to oxygen deprivation which encompasses several levels of metabolic regulation to sustain redox signaling and to prevent oxidative damage.

Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage

To gain better insight into how soybean roots respond to waterlogging stress, we carried out proteomic profiling combined with physiological analysis at two time points for soybean seedlings in their early vegetative stage. Seedlings at the V2 stage were subjected to 3 and 7 days of waterlogging treatments. Waterlogging stress resulted in a gradual increase of lipid peroxidation and in vivo H2O2 level in roots. Total proteins were extracted from root samples and separated by two-dimensional gel electrophoresis (2-DE). A total of 24 reproducibly resolved, differentially expressed protein spots visualized by Coomassie brilliant blue (CBB) staining were identified by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry or electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis. Of these, 14 proteins were upregulated; 5 proteins were decreased; and 5 were newly induced in waterlogged roots. The identified proteins include well-known classical anaerobically induced proteins as well as novel waterlogging-responsive proteins that were not known previously as being waterlogging responsive. The novel proteins are involved in several processes, i.e. signal transduction, programmed cell death, RNA processing, redox homeostasis and metabolisms of energy. An increase in abundance of several typical anaerobically induced proteins, such as glycolysis and fermentation pathway enzymes, suggests that plants meet energy requirement via the fermentation pathway due to lack of oxygen. Additionally, the impact of waterlogging on the several programmed cell death- and signal transduction-related proteins suggest that they have a role to play during stress. RNA gel blot analysis for three programmed cell death-related genes also revealed a differential mRNA level but did not correlate well with the protein level. These results demonstrate that the soybean plant can cope with waterlogging through the management of carbohydrate consumption and by regulating programmed cell death. The identification of novel proteins such as a translation initiation factor, apyrase, auxin-amidohydrolase and coproporphyrinogen oxidase in response to waterlogging stress may provide new insight into the molecular basis of the waterlogging-stress response of soybean.

Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses

High-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. We showed previously that Arabidopsis (Arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. To recognize low-oxygen responses that are evolutionarily conserved versus species specific, we compared the transcriptomic reconfiguration in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). Sorting of organism proteomes into clusters of putative orthologs identified broadly conserved responses associated with glycolysis, fermentation, alternative respiration, metabolite transport, reactive oxygen species amelioration, chaperone activity, and ribosome biogenesis. Differentially regulated genes involved in signaling and transcriptional regulation were poorly conserved across kingdoms. Strikingly, nearly half of the induced mRNAs of Arabidopsis seedlings encode proteins of unknown function, of which over 40% had up-regulated orthologs in poplar (Populus trichocarpa), rice (Oryza sativa), or Chlamydomonas reinhardtii. Sixteen HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes, including four that are Arabidopsis specific, were ectopically overexpressed and evaluated for their effect on seedling tolerance to oxygen deprivation. This allowed the identification of HUPs coregulated with genes associated with anaerobic metabolism and other processes that significantly enhance or reduce stress survival when ectopically overexpressed. These findings illuminate both broadly conserved and plant-specific low-oxygen stress responses and confirm that plant-specific HUPs with limited phylogenetic distribution influence low-oxygen stress endurance.

Downregulation of pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels

Analyses of transgenic sugarcane clones with 45-95% reduced cytosolic pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase (PFP, EC 2.7.1.90) activity displayed no visual phenotypical change, but significant changes were evident in in vivo metabolite levels and fluxes during internode development. In three independent transgenic lines, sucrose concentrations increased between three- and sixfold in immature internodes, compared to the levels in the wildtype control. There was an eightfold increase in the hexose-phosphate:triose-phosphate ratio in immature internodes, a significant restriction in the triose phosphate to hexose phosphate cycle and significant increase in sucrose cycling as monitored by (13)C nuclear magnetic resonance. This suggests that an increase in the hexose-phosphate concentrations resulting from a restriction in the conversion of hexose phosphates to triose phosphates drive sucrose synthesis in the young internodes. These effects became less pronounced as the tissue matured. Decreased expression of PFP also resulted in an increase of the ATP/ADP and UTP/UDP ratios, and an increase of the total uridine nucleotide and, at a later stage, the total adenine nucleotide pool, revealing strong interactions between PPi metabolism and general energy metabolism. Finally, decreased PFP leads to a reduction of PPi levels in older internodes indicating that in these developmental stages PFP acts in the gluconeogenic direction. The lowered PPi levels might also contribute to the absence of increases in sucrose contents in the more mature tissues of transgenic sugarcane with reduced PFP activity.

Altered expression of pyrophosphate: fructose-6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants

Pyrophosphate: fructose-6-phosphate 1-phosphotransferase (PFP) catalyzes the reversible interconversion of fructose-6-phosphate and fructose-1,6-bisphosphate, a key step in the regulation of the metabolic flux toward glycolysis or gluconeogenesis. To examine the role of PFP in plant growth, we have generated transgenic Arabidopsis plants that either overexpress or repress Arabidopsis PFP sub-unit genes. The overexpressing lines displayed increased PFP activity and slightly faster growth relative to wild type plants, although their photosynthetic activities and the levels of metabolites appeared not to have significantly changed. In contrast, the RNAi lines showed significantly retarded growth in parallel with the reduced PFP activity. Analysis of photosynthetic activity revealed that the growth retardation phenotype of the RNAi lines was accompanied by the reduced rates of CO(2) assimilation. Microarray analysis of our transgenic plants further revealed that the altered expression of AtPFPbeta affects the expression of several genes involved in diverse physiological processes. Our current data thus suggest that PFP is important in carbohydrate metabolism and other cellular processes.

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.

Respiration in postharvest sugarbeet roots is not limited by respiratory capacity or adenylates

Control of respiration has largely been studied with growing and/or photosynthetic tissues or organs, but has rarely been examined in harvested and stored plant products. As nongrowing, heterotrophic organs that are reliant on respiration to provide all of their metabolic needs, harvested plant products differ dramatically in their metabolism and respiratory needs from growing and photosynthetically active plant organs, and it cannot be assumed that the same mechanism controls respiration in both actively growing and harvested plant organs. To elucidate mechanisms of respiratory control for a harvested and stored plant product, sugarbeet (Beta vulgaris L.) root respiration was characterized with respect to respiratory capacity, adenylate levels and cellular energy status in roots whose respiration was altered by wounding or cold treatment (1 degrees C) and in response to potential effectors of respiration. Respiration rate was induced by wounding in roots stored at 10 degrees C and by cold temperature in roots stored at 1 degrees C for 11-13d. Alterations in respiration rate due to wounding or storage temperature were unrelated to changes in total respiratory capacity, the capacities of the cytochrome c oxidase (COX) or alternative oxidase (AOX) pathways, adenylate concentrations or cellular energy status, measured by the ATP:ADP ratio. In root tissue, respiration was induced by exogenous NADH indicating that respiratory capacity was capable of oxidizing additional electrons fed into the electron transport chain via an external NADH dehydrogenase. Respiration was not induced by addition of ADP or a respiratory uncoupler. These results suggest that respiration rate in stored sugarbeet roots is not limited by respiratory capacity, ADP availability or cellular energy status. Since respiration in plants can be regulated by substrate availability, respiratory capacity or energy status, it is likely that a substrate, other than ADP, limits respiration in stored sugarbeet roots.

Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum)

PPi has previously been implicated specifically in the co-ordination of the sucrose-starch transition and in the broader context of its role as co-factor in heterotrophic plant metabolism. In order to assess the compartmentation of pyrophosphate (PPi) metabolism in the potato tuber we analysed the effect of expressing a bacterial pyrophosphatase in the amyloplast of wild type tubers or in the cytosol or amyloplast of invertase-expressing tubers. The second and third approaches were adopted since we have previously characterized the invertase expressing lines to both exhibit highly altered sucrose metabolism and to contain elevated levels of PPi (Farré et al. (2000a) Plant Physiol 123:681) and therefore this background rendered questions concerning the level of communication between the plastidic and cytosolic pyrophosphate pools relatively facile. In this study we observed that the increase in PPi in the invertase expressing lines was mainly confined to the cytosol. Accordingly, the expression of a bacterial pyrophosphatase in the plastid of either wild type or invertase-expressing tubers did not lead to a decrease in total PPi content. However, the expression of the heterologous pyrophosphatase in the cytosol of cytosolic invertase-expressing tubers led to strong metabolic changes. These results are discussed both with respect to our previous hypotheses and to current models of the compartmentation of potato tuber metabolism.

Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum)

PPi has previously been implicated specifically in the co-ordination of the sucrose-starch transition and in the broader context of its role as co-factor in heterotrophic plant metabolism. In order to assess the compartmentation of pyrophosphate (PPi) metabolism in the potato tuber we analysed the effect of expressing a bacterial pyrophosphatase in the amyloplast of wild type tubers or in the cytosol or amyloplast of invertase-expressing tubers. The second and third approaches were adopted since we have previously characterized the invertase expressing lines to both exhibit highly altered sucrose metabolism and to contain elevated levels of PPi (Farré et al. (2000a) Plant Physiol 123:681) and therefore this background rendered questions concerning the level of communication between the plastidic and cytosolic pyrophosphate pools relatively facile. In this study we observed that the increase in PPi in the invertase expressing lines was mainly confined to the cytosol. Accordingly, the expression of a bacterial pyrophosphatase in the plastid of either wild type or invertase-expressing tubers did not lead to a decrease in total PPi content. However, the expression of the heterologous pyrophosphatase in the cytosol of cytosolic invertase-expressing tubers led to strong metabolic changes. These results are discussed both with respect to our previous hypotheses and to current models of the compartmentation of potato tuber metabolism.

Response and adaptation by plants to flooding stress

Stress on plants imposed by flooding of the soil and deeper submergence constitutes one of the major abiotic constraints on growth, species' distribution and agricultural productivity. Flooding stress is also a strong driver of adaptive evolution. This has resulted in a wide range of biochemical, molecular and morphological adaptations that sanction growth and reproductive success under episodic or permanently flooded conditions that are highly damaging to the majority of plant species. However, even seemingly poorly adapted species possess some short-term resilience that is important for overall success of these plants in various habitats. The papers contained in this Special Issue address these topics and emphasize molecular, biochemical and developmental processes that impact on flooding tolerance. Most of the articles are based on lectures given to the 8th Conference of the International Society for Plant Anaerobiosis (ISPA), held at the University of Western Australia, Perth, 20-24 September, 2004. Reviews and research papers are presented from the leading laboratories currently working on plant responses to flooding stress.