Phloem import and storage metabolism are highly coordinated by the low oxygen concentrations within developing wheat seeds

Grain yellowness is an effective predictor of carotenoid content in global sorghum populations

Identification of high carotenoid germplasm is crucial to assist breeders in provitamin-A biofortification of sorghum (Sorghum bicolor [L.] Moench). High-performance liquid chromatography is the gold standard for carotenoid quantification, however, it is not feasible for large scale phenotyping due to its high cost and low throughput. In this study, we tested the feasibility of using grain color as a high-throughput method of carotenoid biofortification breeding. We hypothesized that visual, color-based selection can be an effective strategy to identify high-carotenoid accessions. Yellow grain had significantly higher carotenoid content than red, brown, and white grain. The degree of yellowness could distinguish the presence or absence of carotenoids, but could not distinguish carotenoid concentrations within yellow-only accessions. The degree of luminosity of the grain, however, was able to better predict carotenoid concentrations within yellow-only accessions. Genome-wide association studies identified significant marker-trait associations for qualitative and quantitative grain color traits and carotenoid concentrations near carotenoid pathway genes-ZEP, PDS, CYP97A, NCED, CCD, and LycE-three of which were common between grain color and carotenoid traits. These findings suggest that using grain color as a method for screening germplasm may be an effective high-throughput selection tool for prebreeding and early-stage breeding in carotenoid biofortification.

Nitric oxide, energy, and redox-dependent responses to hypoxia

Hypoxia occurs when oxygen levels fall below the levels required for mitochondria to support respiration. Regulated hypoxia is associated with quiescence, particularly in storage organs (seeds) and stem cell niches. In contrast, environmentally induced hypoxia poses significant challenges for metabolically active cells that are adapted to aerobic respiration. The perception of oxygen availability through cysteine oxidases, which function as oxygen-sensing enzymes in plants that control the N-degron pathway, and the regulation of hypoxia-responsive genes and processes is essential to survival. Functioning together with reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2) and reactive nitrogen species (RNS), such as nitric oxide (·NO), nitrogen dioxide (·NO2), S-nitrosothiols (SNOs), and peroxynitrite (ONOO-), hypoxia signaling pathways trigger anatomical adaptations such as formation of aerenchyma, mobilization of sugar reserves for anaerobic germination, formation of aerial adventitious roots, and the hyponastic response. NO and H2O2 participate in local and systemic signaling pathways that facilitate acclimation to changing energetic requirements, controlling glycolytic fermentation, the γ-aminobutyric acid (GABA) shunt, and amino acid synthesis. NO enhances antioxidant capacity and contributes to the recycling of redox equivalents in energy metabolism through the phytoglobin (Pgb)-NO cycle. Here, we summarize current knowledge of the central role of NO and redox regulation in adaptive responses that prevent hypoxia-induced death in challenging conditions such as flooding.

Causes and consequences of endogenous hypoxia on growth and metabolism of developing maize kernels

Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modeling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage-Dependent Anion Channel 2) and multiple signaling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm.

Climate change effects on bread wheat phenology and grain quality: A case study in the north of Italy

Increasing temperatures, heat waves, and reduction of annual precipitation are all the expressions of climate change (CC), strongly affecting bread wheat (Triticum aestivum L.) grain yield in Southern Europe. Being temperature the major driving force of plants' phenological development, these variations also have effects on wheat phenology, with possible consequences on grain quality, and gluten protein accumulation. Here, through a case study in the Bolognese Plain (North of Italy), we assessed the effects of CC in the area, the impacts on bread wheat phenological development, and the consequences on grain gluten quality. The increasing trend in mean annual air temperature in the area since 1952 was significant, with a breakpoint identified in 1989, rising from 12.7 to 14.1°C, accompanied by the signals of increasing aridity, i.e., increase in water table depth. Bread wheat phenological development was compared in two 15-year periods before and after the breakpoint, i.e., 1952-1966 (past period), and 2006-2020 (present period), the latest characterized by aridity and increased temperatures. A significant shortening of the chronological time necessary to reach the main phenological phases was observed for the present period compared to the past period, finally shortening the whole life cycle. This reduction, as well as the higher temperature regime, affected gluten accumulation during the grain-filling process, as emerged analyzing gluten composition in grain samples of the same variety harvested in the area both before and after the breakpoint in temperature. In particular, the proportion of gluten polymers (i.e., gliadins, high and low molecular weight glutenins, and their ratio) showed a strong and significant correlation with cumulative growing degree days (CGDDs) accumulated during the grain filling. Higher CGDD values during the period, typical of CC in Southern Europe, accounting for higher temperature and faster grain filling, correlated with gliadins, high molecular weight glutenins, and their proportion with low molecular weight glutenins. In summary, herein reported, data might contribute to assessing the effects of CC on wheat phenology and quality, representing a tool for both predictive purposes and decision supporting systems for farmers, as well as can guide future breeding choices for varietal innovation.

The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination

The importance of the alternative donation of electrons to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex has been demonstrated. However, the functional significance of this pathway during seed development and germination remains to be elucidated. To assess the function of this pathway, we performed a detailed metabolic and transcriptomic analysis of Arabidopsis mutants to test the molecular consequences of a dysfunctional ETF/ETFQO pathway. We demonstrate that the disruption of this pathway compromises seed germination in the absence of an external carbon source and also impacts seed size and yield. Total protein and storage protein content is reduced in dry seeds, whilst sucrose levels remain invariant. Seeds of ETFQO and related mutants were also characterized by an altered fatty acid composition. During seed development, lower levels of fatty acids and proteins accumulated in the etfqo-1 mutant as well as in mutants in the alternative electron donors isovaleryl-CoA dehydrogenase (ivdh-1) and d-2-hydroxyglutarate dehydrogenase (d2hgdh1-2). Furthermore, the content of several amino acids was increased in etfqo-1 mutants during seed development, indicating that these mutants are not using such amino acids as alternative energy source for respiration. Transcriptome analysis revealed alterations in the expression levels of several genes involved in energy and hormonal metabolism. Our findings demonstrated that the alternative pathway of respiration mediated by the ETF/ETFQO complex affects seed germination and development by directly adjusting carbon storage during seed filling. These results indicate a role for the pathway in the normal plant life cycle to complement its previously defined roles in the response to abiotic stress.

Review: Crucial role of inorganic pyrophosphate in integrating carbon metabolism from sucrose breakdown to starch synthesis in rice endosperm

The endosperm is a primary constituent of mature seeds in rice as well as in other cereal crops, serving as the major storage reserve of starch. Observations indicate that the central part of the endosperm is subject to hypoxic conditions, which require a switch of energy metabolism owing to limited mitochondrial respiration. Uniquely, this endosperm generates a large source of inorganic pyrophosphate (PPi) as a byproduct of the reaction of ADP glucose pyrophosphorylase in the cytosol. Recent results derived from examination of the mutants of cereal crops, especially rice, for PPi-utilizing enzymes clearly suggest an important role of PPi as an alternative energy currency for integrating carbon metabolism from sucrose breakdown to starch synthesis in the endosperm. Thus, the present review provides an outline of the interlaced PPi-dependent metabolic pathways, which are critical for starch synthesis in the endosperm in terms of energy metabolism, along with its application to enhance yield potential.

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.

An in situ approach to characterizing photosynthetic gas exchange of rice panicle

BACKGROUND

Photosynthesis of reproductive organs in C₃ cereals is generally regarded as important to crop yield. Whereas, photosynthetic characteristics of reproductive organs are much less understood as compared to leaf photosynthesis, mainly due to methodological limitations. To date, many indirect methods have been developed to study photosynthesis of reproductive organs and its contribution to grain yield, such as organ shading, application of herbicides and photosynthetic measurement of excised organs or tissues, which might be intrusive and cause biases. Thus, a robust and in situ approach needs to be developed.

RESULTS

Here we report the development of a custom-built panicle photosynthesis chamber (P-chamber), which can be connected to standard infrared gas analyzers to study photosynthetic/respiratory rate of a rice panicle. With the P-chamber, we measured panicle photosynthetic characteristics of seven high-yielding elite japonica, japonica-indica hybrid and indica rice cultivars. Results show that, (1) rice panicle is photosynthetically active during grain filling, and there are substantial inter-cultivar variations in panicle photosynthetic and respiratory rates, no matter on a whole panicle basis, on an area basis or on a single spikelet basis; (2) among the seven testing cultivars, whole-panicle gross photosynthetic rates are 17-54 nmol s^-1 5 days after heading under photon flux density (PFD) of 2000 μmol (photons) m^-2 s^-1, which represent some 20-38% of that of the corresponding flag leaves; (3) rice panicle photosynthesis has higher apparent CO₂ compensation point, light compensation point and apparent CO₂ saturation point, as compared to that of a typical leaf; (4) there is a strong and significant positive correlation between gross photosynthetic rate 5 days after heading on a single spikelet basis and grain setting rate at harvest (Pearson correlation coefficient r = 0.93, p value < 0.0001).

CONCLUSIONS

Rice panicle gross photosynthesis is significant, has great natural variation, and plays an underappreciated role in grain yield formation. The P-Chamber can be used as a tool to study in situ photosynthetic characteristics of irregular non-foliar plant organs, such as ears, culms, leaf sheaths, fruits and branches, which is a relatively less explored area in current cereal breeding community.

Preformed and induced mechanisms underlies the differential responses of Prunus rootstock to hypoxia

Analysis of the transcriptomic changes produced in response to hypoxia in root tissues from two rootstock Prunus genotypes differing in their sensitivity to waterlogging: resistant Myrobalan 'P.2175' (P. cerasifera Erhr.), and sensitive 'Felinem' hybrid [P. amygdalus Batsch × P. persica (L.) Batsch] revealed alterations in both metabolism and regulatory processes. Early hypoxia response in both genotypes is characterized by a molecular program aimed to adapt the cell metabolism to the new conditions. Upon hypoxia conditions, tolerant Myrobalan represses first secondary metabolism gene expression as a strategy to prevent the waste of resources/energy, and by the up-regulation of protein degradation genes probably leading to structural adaptations to long-term response to hypoxia. In response to the same conditions, sensitive 'Felinem' up-regulates a core of signal transduction and transcription factor genes. A combination of PLS-DA and qRT-PCR approaches revealed a set of transcription factors and signalling molecules as differentially regulated in the sensitive and tolerant genotypes including the peach orthologs for oxygen sensors. Apart from providing insights into the molecular processes underlying the differential response to waterlogging of two Prunus rootstocks, our approach reveals a set of candidate genes to be used expression biomarkers for biotech or breeding approaches to waterlogging tolerance.

Down-regulation of respiration in pear fruit depends on temperature

The respiration rate of plant tissues decreases when the amount of available O2 is reduced. There is, however, a debate on whether the respiration rate is controlled either by diffusion limitation of oxygen or through regulatory processes at the level of the transcriptome. We used experimental and modelling approaches to demonstrate that both diffusion limitation and metabolic regulation affect the response of respiration of bulky plant organs such as fruit to reduced O2 levels in the surrounding atmosphere. Diffusion limitation greatly affects fruit respiration at high temperature, but at low temperature respiration is reduced through a regulatory process, presumably a response to a signal generated by a plant oxygen sensor. The response of respiration to O2 is time dependent and is highly sensitive, particularly at low O2 levels in the surrounding atmosphere. Down-regulation of the respiration at low temperatures may save internal O2 and relieve hypoxic conditions in the fruit.

Starch Biosynthesis in the Developing Endosperms of Grasses and Cereals

The starch-rich endosperms of the Poaceae, which includes wild grasses and their domesticated descendents the cereals, have provided humankind and their livestock with the bulk of their daily calories since the dawn of civilization up to the present day. There are currently unprecedented pressures on global food supplies, largely resulting from population growth, loss of agricultural land that is linked to increased urbanization, and climate change. Since cereal yields essentially underpin world food and feed supply, it is critical that we understand the biological factors contributing to crop yields. In particular, it is important to understand the biochemical pathway that is involved in starch biosynthesis, since this pathway is the major yield determinant in the seeds of six out of the top seven crops grown worldwide. This review outlines the critical stages of growth and development of the endosperm tissue in the Poaceae, including discussion of carbon provision to the growing sink tissue. The main body of the review presents a current view of our understanding of storage starch biosynthesis, which occurs inside the amyloplasts of developing endosperms.

Oxygen sensing and signaling

Oxygen is an indispensable substrate for many biochemical reactions in plants, including energy metabolism (respiration). Despite its importance, plants lack an active transport mechanism to distribute oxygen to all cells. Therefore, steep oxygen gradients occur within most plant tissues, which can be exacerbated by environmental perturbations that further reduce oxygen availability. Plants possess various responses to cope with spatial and temporal variations in oxygen availability, many of which involve metabolic adaptations to deal with energy crises induced by low oxygen. Responses are induced gradually when oxygen concentrations decrease and are rapidly reversed upon reoxygenation. A direct effect of the oxygen level can be observed in the stability, and thus activity, of various transcription factors that control the expression of hypoxia-induced genes. Additional signaling pathways are activated by the impact of oxygen deficiency on mitochondrial and chloroplast functioning. Here, we describe the molecular components of the oxygen-sensing pathway.

Physical, metabolic and developmental functions of the seed coat

The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.

Redox regulation of plant development

SIGNIFICANCE

We provide a conceptual framework for the interactions between the cellular redox signaling hub and the phytohormone signaling network that controls plant growth and development to maximize plant productivity under stress-free situations, while limiting growth and altering development on exposure to stress.

RECENT ADVANCES

Enhanced cellular oxidation plays a key role in the regulation of plant growth and stress responses. Oxidative signals or cycles of oxidation and reduction are crucial for the alleviation of dormancy and quiescence, activating the cell cycle and triggering genetic and epigenetic control that underpin growth and differentiation responses to changing environmental conditions.

CRITICAL ISSUES

The redox signaling hub interfaces directly with the phytohormone network in the synergistic control of growth and its modulation in response to environmental stress, but a few components have been identified. Accumulating evidence points to a complex interplay of phytohormone and redox controls that operate at multiple levels. For simplicity, we focus here on redox-dependent processes that control root growth and development and bud burst.

FUTURE DIRECTIONS

The multiple roles of reactive oxygen species in the control of plant growth and development have been identified, but increasing emphasis should now be placed on the functions of redox-regulated proteins, along with the central roles of reductants such as NAD(P)H, thioredoxins, glutathione, glutaredoxins, peroxiredoxins, ascorbate, and reduced ferredoxin in the regulation of the genetic and epigenetic factors that modulate the growth and vigor of crop plants, particularly within an agricultural context.

Redox regulation of plant development

SIGNIFICANCE

We provide a conceptual framework for the interactions between the cellular redox signaling hub and the phytohormone signaling network that controls plant growth and development to maximize plant productivity under stress-free situations, while limiting growth and altering development on exposure to stress.

RECENT ADVANCES

Enhanced cellular oxidation plays a key role in the regulation of plant growth and stress responses. Oxidative signals or cycles of oxidation and reduction are crucial for the alleviation of dormancy and quiescence, activating the cell cycle and triggering genetic and epigenetic control that underpin growth and differentiation responses to changing environmental conditions.

CRITICAL ISSUES

The redox signaling hub interfaces directly with the phytohormone network in the synergistic control of growth and its modulation in response to environmental stress, but a few components have been identified. Accumulating evidence points to a complex interplay of phytohormone and redox controls that operate at multiple levels. For simplicity, we focus here on redox-dependent processes that control root growth and development and bud burst.

FUTURE DIRECTIONS

The multiple roles of reactive oxygen species in the control of plant growth and development have been identified, but increasing emphasis should now be placed on the functions of redox-regulated proteins, along with the central roles of reductants such as NAD(P)H, thioredoxins, glutathione, glutaredoxins, peroxiredoxins, ascorbate, and reduced ferredoxin in the regulation of the genetic and epigenetic factors that modulate the growth and vigor of crop plants, particularly within an agricultural context.

The role of photosynthesis and amino acid metabolism in the energy status during seed development

Seeds are the major organs responsible for the evolutionary upkeep of angiosperm plants. Seeds accumulate significant amounts of storage compounds used as nutrients and energy reserves during the initial stages of seed germination. The accumulation of storage compounds requires significant amounts of energy, the generation of which can be limited due to reduced penetration of oxygen and light particularly into the inner parts of seeds. In this review, we discuss the adjustment of seed metabolism to limited energy production resulting from the suboptimal penetration of oxygen into the seed tissues. We also discuss the role of photosynthesis during seed development and its contribution to the energy status of developing seeds. Finally, we describe the contribution of amino acid metabolism to the seed energy status, focusing on the Asp-family pathway that leads to the synthesis and catabolism of Lys, Thr, Met, and Ile.

A proteomic study on molecular mechanism of poor grain-filling of rice (Oryza sativa L.) inferior spikelets

Cultivars of rice (Oryza sativa L.), especially of the type with large spikelets, often fail to reach the yield potential as expected due to the poor grain-filling on the later flowering inferior spikelets (in contrast to the earlier-flowering superior spikelets). The present study showed that the size and grain weight of superior spikelets (SS) was greater than those of inferior spikelets (IS), and the carbohydrate supply should not be the major problem for the poor grain-filling because there was adequate amount of sucrose in IS at the initial grain-filling stage. High resolution two-dimensional gel electrophoresis (2-DE) in combination with Coomassie-brilliant blue (CBB) and Pro-Q Diamond phosphoprotein fluorescence stain revealed that 123 proteins in abundance and 43 phosphoproteins generated from phosphorylation were significantly different between SS and IS. These proteins and phosphoproteins were involved in different cellular and metabolic processes with a prominently functional skew toward metabolism and protein synthesis/destination. Expression analyses of the proteins and phosphoproteins associated with different functional categories/subcategories indicated that the starch synthesis, central carbon metabolism, N metabolism and cell growth/division were closely related to the poor grain-filling of IS. Functional and expression pattern studies also suggested that 14-3-3 proteins played important roles in IS poor grain-filling by regulating the activity of starch synthesis enzymes. The proteome and phosphoproteome obtained from this study provided a better understanding of the molecular mechanism of the IS poor grain-filling. They were also expected to be highly useful for improving the grain filling of rice.

Analysis of the role of the pyruvate decarboxylase gene family in Arabidopsis thaliana under low-oxygen conditions

Plants under low-oxygen conditions adapt their metabolism by inducing the fermentative pathway, with ethanol as the predominant end product. Activities of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are required for this pathway. While a single gene encodes ADH in Arabidopsis, a family of four genes codes PDC. The availability of microarray data sets enabled the relative importance of the four PDC genes under low oxygen to be assessed, and revealed that, contrary to previous published evidence, not only PDC1 but also PDC2 plays a role under hypoxic conditions. We observed a high level of expression, both at transcript and protein levels of PDCs, even under aerobic conditions when ADH is almost absent. This suggests that PDC has a role under aerobic conditions, which is not coupled to fermentative metabolism. The expression of both PDC1 and PDC2 is strongly up-regulated under low oxygen. PDC1 is predominantly present in roots, while PDC2 appears to be leaf-specific. We showed that mutations in both PDC1 and PDC2 result in lower tolerance to submergence.

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.

Identification and roles of proteins for seed development in mungbean (Vigna radiata L.) seed proteomes

Proteomic analysis of developing mungbean (Vigna radiata L.) seeds has not yet been investigated in detail. Fifty-seven proteins were separated by 2-DE, identified by nanoelectrospray mass spectrometry from the present protein databases, and categorized according to their functions. Many of the identified enzymes were involved in central carbon metabolism; thus, a pathway illustrating starch synthesis/breakdown, sugar conversion for glycolysis, and tricarboxylic acid (TCA) cycle was proposed. Quantitative comparison of the protein expression revealed that during developmental process (11-21 days after flowering, DAF), proteins involved in glycolysis, TCA cycle, and alcoholic fermentation showed a trend to be down-regulated, whereas storage proteins were generally up-regulated. The downward tendency of central carbon metabolic proteins suggests a reduction in ATP and oxygen consumption associated with accumulation of storage compounds. UDP-glucose-1-pyrophosphorylase, an upstream enzyme in the starch ADP-Glc pathway, was found as a stably expressed protein throughout the growth stage, demonstrating its importance in mungbean starch biosynthesis. The temporal expression of metabolic enzymes suggests the coordination of an acclimation mechanism and cellular processes associated with accumulation of storage compounds in seed development.

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.

Are we ready for genome-scale modeling in plants?

As it is becoming easier and faster to generate various types of high-throughput data, one would expect that by now we should have a comprehensive systems-level understanding of biology, biochemistry, and physiology at least in major prokaryotic and eukaryotic model systems. Despite the wealth of available data, we only get a glimpse of what is going on at the molecular level from the global perspective. The major reason is the high level of cellular complexity and our limited ability to identify all (or at least important) components and their interactions in virtually infinite number of internal and external conditions. Metabolism can be modeled mathematically by the use of genome-scale models (GEMs). GEMs are in silico metabolic flux models derived from available genome annotation. These models predict the combination of flux values of a defined metabolic network given the influence of internal and external signals. GEMs have been successfully implemented to model bacterial metabolism for over a decade. However, it was not until 2009 when the first GEM for Arabidopsis thaliana cell-suspension cultures was generated. Genome-scale modeling ("GEMing") in plants brings new challenges primarily due to the missing components and complexity of plant cells represented by the existence of: (i) photosynthesis; (ii) compartmentation; (iii) variety of cell and tissue types; and (iv) diverse metabolic responses to environmental and developmental cues as well as pathogens, insects, and competing weeds. This review presents a critical discussion of the advantages of existing plant GEMs, while identifies key targets for future improvements. Plant GEMs tend to be accurate in predicting qualitative changes in selected aspects of central carbon metabolism, while secondary metabolism is largely neglected mainly due to the missing (unknown) genes and metabolites. As such, these models are suitable for exploring metabolism in plants grown in favorable conditions, but not in field-grown plants that have to cope with environmental changes in complex ecosystems. AraGEM is the first GEM describing a photosynthetic and photorespiring plant cell (Arabidopsis thaliana). We demonstrate the use of AraGEM given the current (limited) knowledge of plant metabolism and reveal the unexpected robustness of AraGEM by a series of in silico simulations. The major focus of these simulations is on the assessment of the: (i) network connectivity; (ii) influence of CO₂ and photon uptake rates on cellular growth rates and production of individual biomass components; and (iii) stability of plant central carbon metabolism with internal pH changes.

Proteomic analysis of the effects of exogenous calcium on hypoxic-responsive proteins in cucumber roots

BACKGROUND

Hypoxia acts as a plant stress factor, particularly in cucumbers plants under hydroponic culture. Calcium is involved in stress signal transmission and in the growth of plants. To determine the effect of exogenous calcium on hypoxic-responsive proteins in cucumber (Cucumis sativus L. cv. Jinchun No.2) roots, proteomic analysis was performed using two-dimensional electrophoresis (2-DE) and mass spectrometry.

RESULTS

Cucumber roots were used to analyze the influence of hypoxia on plants. The expressions of 38 protein spots corresponding to enzymes were shown to change in response to hypoxia. Of these, 30 spots were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/TOF MS analysis). The proteins were categorized according to functional groups, including glycolysis, the tricarboxylic acid (TCA) cycle, fermentative metabolism, nitrogen metabolism, energy metabolism, protein synthesis and defense against stress. Exogenous calcium appeared to alleviate hypoxic stress via these metabolic and physiological systems. Western blotting was used to analyze the accumulation of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC); calcium further increased the expression of ADH and PDC under hypoxia. In addition, semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) was used to assess the transcript levels of differentially expressed proteins.

CONCLUSIONS

Exogenous calcium enhanced the expression of enzymes involved in glycolysis, the TCA cycle, fermentative metabolism, nitrogen metabolism, and reactive oxygen species (ROS) defense in plants under hypoxia. Calcium appears to induce hypoxic tolerance of cucumber seedlings. These phenomena have prompted us to further investigate the mechanisms by which cucumbers respond to exogenous calcium under hypoxia.

Soluble and filamentous proteins in Arabidopsis sieve elements

Phloem sieve elements are highly differentiated cells involved in the long-distance transport of photoassimilates. These cells contain both aggregated phloem-proteins (P-proteins) and soluble proteins, which are also translocated by mass flow. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to carry out a proteomic survey of the phloem exudate of Arabidopsis thaliana, collected by the ethylenediaminetetraacetic acid (EDTA)-facilitated method. We identified 287 proteins, a large proportion of which were enzymes involved in the metabolic precursor generation and amino acid synthesis, suggesting that sieve tubes display high levels of metabolic activity. RNA-binding proteins, defence proteins and lectins were also found. No putative P-proteins were detected in the EDTA-exudate fraction, indicating a lack of long-distance translocation of such proteins in Arabidopsis. In parallel, we investigated the organization of P-proteins, by high-resolution transmission electron microscopy, and the localization of the phloem lectin PP2, a putative P-protein component, by immunolocalization with antibodies against PP2-A1. Transmission electron microscopy observations of P-proteins revealed bundles of filaments resembling strings of beads. PP2-A1 was found weakly associated with these structures in the sieve elements and bound to plastids. These observations suggest that PP2-A1 is anchored to P-proteins and organelles rather than being a structural component of P-proteins.

Altered seed oil and glucosinolate levels in transgenic plants overexpressing the Brassica napus SHOOTMERISTEMLESS gene

SHOOTMERISTEMLESS (STM) is a homeobox gene conserved among plant species which is required for the formation and maintenance of the shoot meristem by suppressing differentiation and maintaining an undetermined cell fate within the apical pole. To assess further the role of this gene during seed storage accumulation, transgenic Brassica napus (Bn) plants overexpressing or down-regulating BnSTM under the control of the 35S promoter were generated. Overexpression of BnSTM increased seed oil content without affecting the protein and sucrose level. These changes were accompanied by the induction of genes encoding several transcription factors promoting fatty acid (FA) synthesis: LEAFY COTYLEDON1 (BnLEC1), BnLEC2, and WRINKLE1 (BnWRI1). In addition, expression of key representative enzymes involved in sucrose metabolism, glycolysis, and FA biosynthesis was up-regulated in developing seeds ectopically expressing BnSTM. These distinctive expression patterns support the view of an increased carbon flux to the FA biosynthetic pathway in developing transformed seeds. The overexpression of BnSTM also resulted in a desirable reduction of seed glucosinolate (GLS) levels ascribed to a transcriptional repression of key enzymes participating in the GLS biosynthetic pathway, and possibly to the differential utilization of common precursors for GLS and indole-3-acetic acid synthesis. No changes in oil and GLS levels were observed in lines down-regulating BnSTM. Taken together, these findings provide evidence for a novel function for BnSTM in promoting desirable changes in seed oil and GLS levels when overexpressed in B. napus plants, and demonstrate that this gene can be used as a target for genetic improvement of oilseed species.

Subcellular analysis of starch metabolism in developing barley seeds using a non-aqueous fractionation method

Compartmentation of metabolism in developing seeds is poorly understood due to the lack of data on metabolite distributions at the subcellular level. In this report, a non-aqueous fractionation method is described that allows subcellular concentrations of metabolites in developing barley endosperm to be calculated. (i) Analysis of subcellular volumes in developing endosperm using micrographs shows that plastids and cytosol occupy 50.5% and 49.9% of the total cell volume, respectively, while vacuoles and mitochondria can be neglected. (ii) By using non-aqueous fractionation, subcellular distribution between the cytosol and plastid of the levels of metabolites involved in sucrose degradation, starch synthesis, and respiration were determined. With the exception of ADP and AMP which were mainly located in the plastid, most other metabolites of carbon and energy metabolism were mainly located outside the plastid in the cytosolic compartment. (iii) In developing barley endosperm, the ultimate precursor of starch, ADPglucose (ADPGlc), was mainly located in the cytosol (80-90%), which was opposite to the situation in growing potato tubers where ADPGlc was almost exclusively located in the plastid (98%). This reflects the different subcellular distribution of ADPGlc pyrophosphorylase (AGPase) in these tissues. (iv) Cytosolic concentrations of ADPGlc were found to be close to the published K(m) values of AGPase and the ADPGlc/ADP transporter at the plastid envelope. Also the concentrations of the reaction partners glucose-1-phosphate, ATP, and inorganic pyrophosphate were close to the respective K(m) values of AGPase. (v) Knock-out of cytosolic AGPase in Riso16 mutants led to a strong decrease in ADPGlc level, in both the cytosol and plastid, whereas knock-down of the ADPGlc/ADP transporter led to a large shift in the intracellular distribution of ADPGlc. (v) The thermodynamic structure of the pathway of sucrose to starch was determined by calculating the mass-action ratios of all the steps in the pathway. The data show that AGPase is close to equilibrium, in both the cytosol and plastid, whereas the ADPGlc/ADP transporter is strongly displaced from equilibrium in vivo. This is in contrast to most other tissues, including leaves and potato tubers. (vi) Results indicate transport rather than synthesis of ADPGlc to be the major regulatory site of starch synthesis in barley endosperm. The reversibility of AGPase in the plastid has important implications for the regulation of carbon partitioning between different biosynthetic pathways.

Making sense of low oxygen sensing

Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops.

Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile

High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber.

Regulation of respiration in plants: a role for alternative metabolic pathways

Respiratory metabolism includes the reactions of glycolysis, the tricarboxylic acid cycle and the mitochondrial electron transport chain, but is also directly linked with many other metabolic pathways such as protein and lipid biosynthesis and photosynthesis via photorespiration. Furthermore, any change in respiratory activity can impact the redox status of the cell and the production of reactive oxygen species. In this review, it is discussed how respiration is regulated and what alternative pathways are known that increase the metabolic flexibility of this vital metabolic process. By looking at the adaptive responses of respiration to hypoxia or changes in the oxygen availability of a cell, the integration of regulatory responses of various pathways is illustrated.

The K (+) battery-regulating Arabidopsis K (+) channel AKT2 is under the control of multiple post-translational steps

Potassium (K (+) ) is an important nutrient for plants. It serves as a cofactor of various enzymes and as the major inorganic solute maintaining plant cell turgor. In a recent study, an as yet unknown role of K (+) in plant homeostasis was shown. It was demonstrated that K (+) gradients in vascular tissues can serve as an energy source for phloem (re)loading processes and that the voltage-gated K (+) channels of the AKT2-type play a unique role in this process. The AKT2 channel can be converted by phosphorylation of specific serine residues (S210 and S329) into a non-rectifying channel that allows a rapid efflux of K (+) from the sieve element/companion cells (SE/CC) complex. The energy of this flux is used by other transporters for phloem (re)loading processes. Nonetheless, the results do indicate that post-translational modifications at S210 and S329 alone cannot explain AKT2 regulation. Here, we discuss the existence of multiple post-translational modification steps that work in concert to convert AKT2 from an inward-rectifying into a non-rectifying K (+) channel.

Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability

• Reduced oxygen availability is not only associated with flooding, but occurs also during growth and development. It is largely unknown how hypoxia is perceived and what signaling cascade is involved in activating adaptive responses. • We analysed the expression of over 1900 transcription factors (TFs) and 180 microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots exposed to different hypoxic conditions by means of quantitative PCR. We also analysed the promoters of genes induced by hypoxia with respect to over-represented DNA elements that can act as potential TF binding sites and their in vivo interaction was verified. • We identified various subsets of TFs that responded differentially through time and in an oxygen concentration-dependent manner. The regulatory potential of selected TFs and their predicted DNA binding elements was validated. Although the expression of pri-miRNAs was differentially regulated under hypoxia, only one corresponding mature miRNA changed accordingly. Putative target transcripts of the miRNAs were not significantly affected. • Our results show that the regulation of hypoxia-induced genes is controlled via simultaneous interaction of various combinations of TFs. Under anoxic conditions, an additional set of TFs is induced. Regulation of gene expression via miRNAs appears to play a minor role during hypoxia.

Nonsymbiotic hemoglobin-2 leads to an elevated energy state and to a combined increase in polyunsaturated fatty acids and total oil content when overexpressed in developing seeds of transgenic Arabidopsis plants

Nonsymbiotic hemoglobins are ubiquitously expressed in plants and divided into two different classes based on gene expression pattern and oxygen-binding properties. Most of the published research has been on the function of class 1 hemoglobins. To investigate the role of class 2 hemoglobins, transgenic Arabidopsis (Arabidopsis thaliana) plants were generated overexpressing Arabidopsis hemoglobin-2 (AHb2) under the control of a seed-specific promoter. Overexpression of AHb2 led to a 40% increase in the total fatty acid content of developing and mature seeds in three subsequent generations. This was mainly due to an increase in the polyunsaturated C18:2 (ω-6) linoleic and C18:3 (ω-3) α-linolenic acids. Moreover, AHb2 overexpression led to an increase in the C18:2/C18:1 and C18:3/C18:2 ratios as well as in the C18:3 content in mol % of total fatty acids and in the unsaturation/saturation index of total seed lipids. The increase in fatty acid content was mainly due to a stimulation of the rate of triacylglycerol synthesis, which was attributable to a 3-fold higher energy state and a 2-fold higher sucrose content of the seeds. Under low external oxygen, AHb2 overexpression maintained an up to 5-fold higher energy state and prevented fermentation. This is consistent with AHb2 overexpression results in improved oxygen availability within developing seeds. In contrast to this, overexpression of class 1 hemoglobin did not lead to any significant increase in the metabolic performance of the seeds. These results provide evidence for a specific function of class 2 hemoglobin in seed oil production and in promoting the accumulation of polyunsaturated fatty acids by facilitating oxygen supply in developing seeds.

HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana

Plants often experience challenging hypoxic conditions imposed by soil waterlogging or complete flooding. In rice, Sub1A, a flooding-induced ethylene responsive factor (ERF) plays a crucial role in submergence tolerance. In this study, we examined two Arabidopsis Hypoxia Responsive ERF genes (HRE1 and HRE2), belonging to the same ERF group as Sub1A. Transgenic Arabidopsis plants, which over-expressed HRE1, showed an improved tolerance of anoxia, whereas a double-knockout mutant hre1hre2 was more susceptible than the wild type. HRE1 over-expressing plants showed an increased activity in the fermentative enzymes pyruvate decarboxylase and alcohol dehydrogenase together with increased ethanol production under hypoxia, but not in normoxia. Whole-genome microarray analyses suggested that an over-expression of HRE1, but not HRE2, increased the induction of most anaerobic genes under hypoxia. Real-time quantitative (q)PCR analyses confirmed a positive effect of HRE1 over-expression on several anaerobic genes, whereas the double-knockout mutant hre1hre2 showed a decreased expression in the same genes after 4 h of hypoxia. Single-knockout mutants did not show significant differences from the wild type. We found that the regulation of HRE1 and HRE2 by low oxygen relies on different mechanisms, since HRE1 requires protein synthesis to be induced while HRE2 does not. HRE2 is likely to be regulated post-transcriptionally by mRNA stabilization. We propose that HRE1 and HRE2 play a partially redundant role in low oxygen signalling in Arabidopsis thaliana, thus improving the tolerance of the plant to the stress by enhancing anaerobic gene expression and ethanolic fermentation.

Glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of Lotus japonicus

The role of nitrogen metabolism in the survival of prolonged periods of waterlogging was investigated in highly flood-tolerant, nodulated Lotus japonicus plants. Alanine production revealed to be a critical hypoxic pathway. Alanine is the only amino acid whose biosynthesis is not inhibited by nitrogen deficiency resulting from RNA interference silencing of nodular leghemoglobin. The metabolic changes that were induced following waterlogging can be best explained by the activation of alanine metabolism in combination with the modular operation of a split tricarboxylic acid pathway. The sum result of this metabolic scenario is the accumulation of alanine and succinate and the production of extra ATP under hypoxia. The importance of alanine metabolism is discussed with respect to its ability to regulate the level of pyruvate, and this and all other changes are discussed in the context of current models concerning the regulation of plant metabolism.

Regulation of respiration when the oxygen availability changes

Oxygen is a vital substrate for plant energy metabolism. Since plants do not have a sophisticated mechanism to deliver oxygen to those sites where it is actually needed, a plant cell has to continuously cope with changes of the oxygen tension within the tissue. The actual internal oxygen concentration will depend on the resistance for oxygen diffusion through the tissue, as well as on the actual respiratory activity. This paper discusses the current state of knowledge on the regulation of respiration by the oxygen availability. Contradicting opinions from the literature on plant respiration are reviewed and commented upon. Also, knowledge about the regulation of respiration in animal mitochondria is included. Apart from changes in glycolytic flux, the role of both the cytochrome-c oxidase (COX) and the alternative oxidase (AOX) in the adaptive response of respiration to changes in the oxygen availability are discussed. One hypothesis is formulated which describes an alternative or additional role for AOX. It is suggested that AOX could play a role in maintaining oxygen homeostasis within the mitochondrion. Because of the relative low affinity for oxygen of AOX as compared to COX, the alternative oxidase will not interfere with COX activity, but AOX activity will reduce the free oxygen concentration, thereby decreasing the production of reactive oxygen species (ROS) inside the mitochondrion.

Increased hexose transport in the roots of tomato plants submitted to prolonged hypoxia

We investigated the effects of prolonged hypoxia on the sugar uptake in tomato (Solanum lycopersicum L. var. MP-1) roots. Hydroponic cultures of whole tomato plants were submitted to hypoxic treatment for 1 week, and the roots were analyzed for sugar concentrations, hexose uptake and hexose transporter expression level. Contrary to what has been observed after anoxic shock or short-term hypoxic treatment, we show that sugar concentrations increase and hexose uptake is up-regulated in the roots after 1 week of hypoxic treatment. Increased hexose transport is concomitant with the induction of the hexose transporter gene LeHT2. These responses may be due either to a direct effect of low O(2) supply, or to a secondary effect associated with the increase in sugar concentrations, which, typically, develops in most hypoxic plants.

Methodology and Significance of Microsensor-based Oxygen Mapping in Plant Seeds - an Overview

Oxygen deficiency is commonplace in seeds, and limits both their development and their germination. It is, therefore, of considerable relevance to crop production. While the underlying physiological basis of seed hypoxia has been known for some time, the lack of any experimental means of measuring the global or localized oxygen concentration within the seed has hampered further progress in this research area. The development of oxygen-sensitive microsensors now offers the capability to determine the localized oxygen status within a seed, and to study its dynamic adjustment both to changes in the ambient environment, and to the seed's developmental stage. This review illustrates the use of oxygen microsensors in seed research, and presents an overview of existing data with an emphasis on crop species. Oxygen maps, both static and dynamic, should serve to increase our basic understanding of seed physiology, as well as to facilitate upcoming breeding and biotechnology-based approaches for crop improvement.

Regulation of respiration and fermentation to control the plant internal oxygen concentration

Plant internal oxygen concentrations can drop well below ambient even when the plant grows under optimal conditions. Using pea (Pisum sativum) roots, we show how amenable respiration adapts to hypoxia to save oxygen when the oxygen availability decreases. The data cannot simply be explained by oxygen being limiting as substrate but indicate the existence of a regulatory mechanism, because the oxygen concentration at which the adaptive response is initiated is independent of the actual respiratory rate. Two phases can be discerned during the adaptive reaction: an initial linear decline of respiration is followed by a nonlinear inhibition in which the respiratory rate decreased progressively faster upon decreasing oxygen availability. In contrast to the cytochrome c pathway, the inhibition of the alternative oxidase pathway shows only the linear component of the adaptive response. Feeding pyruvate to the roots led to an increase of the oxygen consumption rate, which ultimately led to anoxia. The importance of balancing the in vivo pyruvate availability in the tissue was further investigated. Using various alcohol dehydrogenase knockout lines of Arabidopsis (Arabidopsis thaliana), it was shown that even under aerobic conditions, alcohol fermentation plays an important role in the control of the level of pyruvate in the tissue. Interestingly, alcohol fermentation appeared to be primarily induced by a drop in the energy status of the tissue rather than by a low oxygen concentration, indicating that sensing the energy status is an important component of optimizing plant metabolism to changes in the oxygen availability.

The oxygen status of the developing seed

Recent applications of oxygen-sensitive microsensors have demonstrated steep oxygen gradients in developing seeds of various crops. Here, we present an overview on oxygen distribution, major determinants of the oxygen status in the developing seed and implications for seed physiology. The steady-state oxygen concentration in different seed tissues depends on developmental parameters, and is determined to a large extent by environmental factors. Photosynthetic activity of the seed significantly diminishes hypoxic constraints, and can even cause transient, local hyperoxia. Changes in oxygen availability cause rapid adjustments in mitochondrial respiration and global metabolism. We argue that nitric oxide (NO) is a key player in the oxygen balancing process in seeds, avoiding fermentation and anoxia in vivo. Molecular approaches aiming to increase oxygen availability within the seed are discussed.

Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants

BACKGROUND AND AIMS

Oxygen can fall to low concentrations within plant tissues, either because of environmental factors that decrease the external oxygen concentration or because the movement of oxygen through the plant tissues cannot keep pace with the rate of oxygen consumption. Recent studies document that plants can decrease their oxygen consumption in response to relatively small changes in oxygen concentrations to avoid internal anoxia. The molecular mechanisms underlying this response have not been identified yet. The aim of this study was to use transcript and metabolite profiling to investigate the genomic response of arabidopsis roots to a mild decrease in oxygen concentrations.

METHODS

Arabidopsis seedlings were grown on vertical agar plates at 21, 8, 4 and 1 % (v/v) external oxygen for 0.5, 2 and 48 h. Roots were analysed for changes in transcript levels using Affymetrix whole genome DNA microarrays, and for changes in metabolite levels using routine GC-MS based metabolite profiling. Root extension rates were monitored in parallel to investigate adaptive changes in growth.

KEY RESULTS

The results show that root growth was inhibited and transcript and metabolite profiles were significantly altered in response to a moderate decrease in oxygen concentrations. Low oxygen leads to a preferential up-regulation of genes that might be important to trigger adaptive responses in the plant. A small but highly specific set of genes is induced very early in response to a moderate decrease in oxygen concentrations. Genes that were down-regulated mainly encoded proteins involved in energy-consuming processes. In line with this, root extension growth was significantly decreased which will ultimately save ATP and decrease oxygen consumption. This was accompanied by a differential regulation of metabolite levels at short- and long-term incubation at low oxygen.

CONCLUSIONS

The results show that there are adaptive changes in root extension involving large-scale reprogramming of gene expression and metabolism when oxygen concentration is decreased in a very narrow range.

Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism

The accumulation of storage compounds is an important aspect of cereal seed metabolism. Due to the agronomical importance of the storage reserves of starch, protein, and oil, the understanding of storage metabolism is of scientific interest, with practical applications in agronomy and plant breeding. To get insight into storage patterning in developing cereal seed in response to environmental and genetic perturbation, a computational analysis of seed metabolism was performed. A metabolic network of primary metabolism in the developing endosperm of barley (Hordeum vulgare), a model plant for temperate cereals, was constructed that includes 257 biochemical and transport reactions across four different compartments. The model was subjected to flux balance analysis to study grain yield and metabolic flux distributions in response to oxygen depletion and enzyme deletion. In general, the simulation results were found to be in good agreement with the main biochemical properties of barley seed storage metabolism. The predicted growth rate and the active metabolic pathway patterns under anoxic, hypoxic, and aerobic conditions predicted by the model were in accordance with published experimental results. In addition, the model predictions gave insight into the potential role of inorganic pyrophosphate metabolism to maintain seed metabolism under oxygen deprivation.

The evolution of the starch biosynthetic pathway in cereals and other grasses

In most species, the precursor for starch synthesis, ADPglucose, is made exclusively in the plastids by the enzyme ADPglucose pyrophosphorylase (AGPase). However, in the endosperm of grasses, including the economically important cereals, ADPglucose is also made in the cytosol via a cytosolic form of AGPase. Cytosolic ADPglucose is imported into plastids for starch synthesis via an ADPglucose/ADP antiporter (ADPglucose transporter) in the plastid envelope. The genes encoding the two subunits of cytosolic AGPase and the ADPglucose transporter are unique to grasses. In this review, the evolutionary origins of this unique endosperm pathway of ADPglucose synthesis and its functional significance are discussed. It is proposed that the genes encoding the pathway originated from a whole-genome-duplication event in an early ancestor of the grasses.

Dynamic proteomic analysis reveals a switch between central carbon metabolism and alcoholic fermentation in rice filling grains

Accumulation of reserve materials in filling grains involves the coordination of different metabolic and cellular processes, and understanding the molecular mechanisms underlying the interconnections remains a major challenge for proteomics. Rice (Oryza sativa) is an excellent model for studying grain filling because of its importance as a staple food and the available genome sequence database. Our observations showed that embryo differentiation and endosperm cellularization in developing rice seeds were completed approximately 6 d after flowering (DAF); thereafter, the immature seeds mainly underwent cell enlargement and reached the size of mature seeds at 12 DAF. Grain filling began at 6 DAF and lasted until 20 DAF. Dynamic proteomic analyses revealed 396 protein spots differentially expressed throughout eight sequential developmental stages from 6 to 20 DAF and determined 345 identities. These proteins were involved in different cellular and metabolic processes with a prominently functional skew toward metabolism (45%) and protein synthesis/destination (20%). Expression analyses of protein groups associated with different functional categories/subcategories showed that substantially up-regulated proteins were involved in starch synthesis and alcoholic fermentation, whereas the down-regulated proteins in the process were involved in central carbon metabolism and most of the other functional categories/subcategories such as cell growth/division, protein synthesis, proteolysis, and signal transduction. The coordinated changes were consistent with the transition from cell growth and differentiation to starch synthesis and clearly indicated that a switch from central carbon metabolism to alcoholic fermentation may be important for starch synthesis and accumulation in the developmental process.

Metabolic network fluxes in heterotrophic Arabidopsis cells: stability of the flux distribution under different oxygenation conditions

Steady-state labeling experiments with [1-(13)C]Glc were used to measure multiple metabolic fluxes through the pathways of central metabolism in a heterotrophic cell suspension culture of Arabidopsis (Arabidopsis thaliana). The protocol was based on in silico modeling to establish the optimal labeled precursor, validation of the isotopic and metabolic steady state, extensive nuclear magnetic resonance analysis of the redistribution of label into soluble metabolites, starch, and protein, and a comprehensive set of biomass measurements. Following a simple modification of the cell culture procedure, cells were grown at two oxygen concentrations, and flux maps of central metabolism were constructed on the basis of replicated experiments and rigorous statistical analysis. Increased growth rate at the higher O(2) concentration was associated with an increase in fluxes throughout the network, and this was achieved without any significant change in relative fluxes despite differences in the metabolite profile of organic acids, amino acids, and carbohydrates. The balance between biosynthesis and respiration within the tricarboxylic acid cycle was unchanged, with 38% +/- 5% of carbon entering used for biosynthesis under standard O(2) conditions and 33% +/- 2% under elevated O(2). These results add to the emerging picture of the stability of the central metabolic network and its capacity to respond to physiological perturbations with the minimum of rearrangement. The lack of correlation between the change in metabolite profile, which implied significant disruption of the metabolic network following the alteration in the oxygen supply, and the unchanging flux distribution highlights a potential difficulty in the interpretation of metabolomic data.

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.

Prospects for increasing starch and sucrose yields for bioethanol production

In the short term, the production of bioethanol as a liquid transport fuel is almost entirely dependent on starch and sugars from existing food crops. The sustainability of this industry would be enhanced by increases in the yield of starch/sugar per hectare without further inputs into the crops concerned. Efforts to achieve increased yields of starch over the last three decades, in particular via manipulation of the enzyme ADPglucose pyrophosphorylase, have met with limited success. Other approaches have included manipulation of carbon partitioning within storage organs in favour of starch synthesis, and attempts to manipulate source-sink relationships. Some of the most promising results so far have come from manipulations that increase the availability of ATP for starch synthesis. Future options for achieving increased starch contents could include manipulation of starch degradation in organs in which starch turnover is occurring, and introduction of starch synthesis into the cytosol. Sucrose accumulation is much less well understood than starch synthesis, but recent results from research on sugar cane suggest that total sugar content can be greatly increased by conversion of sucrose into a non-metabolizable isomer. A better understanding of carbohydrate storage and turnover in relation to carbon assimilation and plant growth is required, both for improvement of starch and sugar crops and for attempts to increase biomass production in second-generation biofuel crops.