The anaerobic response of soybean

Genome-Wide Characterization of Fructose 1,6-Bisphosphate Aldolase Genes and Expression Profile Reveals Their Regulatory Role in Abiotic Stress in Cucumber

The fructose-1,6-bisphosphate aldolase (FBA) gene family exists in higher plants, with the genes of this family playing significant roles in plant growth and development, as well as response to abiotic stresses. However, systematic reports on the FBA gene family and its functions in cucumber are lacking. In this study, we identified five cucumber FBA genes, named CsFBA1-5, that are distributed randomly across chromosomes. Phylogenetic analyses involving these cucumber FBAs, alongside eight Arabidopsis FBA proteins and eight tomato FBA proteins, were conducted to assess their homology. The CsFBAs were grouped into two clades. We also analyzed the physicochemical properties, motif composition, and gene structure of the cucumber FBAs. This analysis highlighted differences in the physicochemical properties and revealed highly conserved domains within the CsFBA family. Additionally, to explore the evolutionary relationships of the CsFBA family further, we constructed comparative syntenic maps with Arabidopsis and tomato, which showed high homology but only one segmental duplication event within the cucumber genome. Expression profiles indicated that the CsFBA gene family is responsive to various abiotic stresses, including low temperature, heat, and salt. Taken together, the results of this study provide a theoretical foundation for understanding the evolution of and future research into the functional characterization of cucumber FBA genes during plant growth and development.

Characteristics and molecular identification of glyceraldehyde-3-phosphate dehydrogenases in poplar

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an essential enzyme of the glycolysis metabolic pathway, plays a vital role in carbon metabolism, plant development, and stress resistance. As a kind of woody plant, poplars are widely cultivated for afforestation. Although the whole genome data of poplars have been published, little information is known about the GAPDH family of genes in poplar. This study performed a genome-wide identification of the poplar GAPDH family, and 13 determined PtGAPDH genes were identified from poplar genome. Phylogenetic tree showed that the PtGAPDH members were divided into PtGAPA/B, PtGAPC, PtGAPCp, and PtGAPN groups. A total of 13 PtGAPDH genes were distributed on eight chromosomes, 13 gene pairs belonging to segmented replication events were detected in poplar, and 23 collinearity gene pairs were determined between poplar and willow. The PtGAPDHcis-acting elements associated with growth and development as well as stress resistance revealed that PtGAPDHs might be involved in these processes. The phosphoglycerate kinase (PGK) and triose-phosphate isomerase (TPI) were predicted as the putative interaction proteins of PtGAPDHs. Gene ontology (GO) analysis showed that PtGAPDHs play a crucial role in the oxidation and reduction processes. PtGAPDH expression levels were induced by NaCl and PEG treatments, which implied that PtGAPDHs might be involved in stress response. Overexpression of PtGAPC1 significantly changed the contents of lipid and carbohydrate metabolites, which indicated that PtGAPC1 plays an essential role in metabolic regulation. This study highlights the characterizations and profiles of PtGAPDHs and reveals that PtGAPC1 is involved in the loop of lipid and carbohydrate metabolisms.

Uncovering the roles of hemoglobins in soybean facing water stress

Water stress drastically hinders crop yield, including soybean - one of the world's most relevant feeding crops - threatening the food security of an ever-growing global population. Hemoglobins (GLBs) are involved in water stress tolerance; however, the role they effectively play in soybean remains underexplored. In this study, in silico and in vivo analyses were performed to identify soybean GLBs, capture their transcriptional profile under water stress, and overexpress promising members to assess how soybean cope with waterlogging. Seven GLBs were found, two GLB1 (non-symbiotic) and five GLB2 (symbiotic or leghemoglobins). Three out of the seven GLBs were differentially expressed in soybean RNA-seq libraries of water stress and were evaluated by real-time PCR. Consistently, GmGLB1-1 and GmGLB1-2 were moderately and highly expressed under waterlogging, respectively. Composite plants with roots overexpressing GmGLB1-1 or GmGLB1-2 (mostly) showed higher transcript abundance of stress-defensive genes involved in anaerobic, nitrogen, carbon, and antioxidant metabolism when subjected to waterlogging. In addition, soybean bearing p35S:GmGLB1-2 had lower H2O2 root content, a reactive oxygen species (ROS), under water excess compared with the control condition. Altogether these results suggest that GmGLB1-2 is a strong candidate for soybean genetic engineering to generate waterlogging-tolerant soybean cultivars.

Effects of the Chloroplast Fructose-1,6-Bisphosphate Aldolase Gene on Growth and Low-Temperature Tolerance of Tomato

Tomato (Solanum lycopersicum) is one of the most important greenhouse vegetables, with a large cultivated area across the world. However, in northern China, tomato plants often suffer from low-temperature stress in solar greenhouse cultivation, which affects plant growth and development and results in economic losses. We previously found that a chloroplast aldolase gene in tomato, SlFBA4, plays an important role in the Calvin-Benson cycle (CBC), and its expression level and activity can be significantly altered when subjected to low-temperature stress. To further study the function of SlFBA4 in the photosynthesis and chilling tolerance of tomato, we obtained transgenic tomato plants by the over-expression and RNA interference (RNAi) of SlFBA4. The over-expression of SlFBA4 led to higher fructose-1,6-bisphosphate aldolase activity, net photosynthetic rate (Pn) and activity of other enzymes in the CBC than wild type. Opposite results were observed in the RNAi lines. Moreover, an increase in thousand-seed weight, plant height, stem diameter and germination rate in optimal and sub-optimal temperatures was observed in the over-expression lines, while opposite effects were observed in the RNAi lines. Furthermore, over-expression of SlFBA4 increased Pn and enzyme activity and decreased malonaldehyde (MDA) content under chilling conditions. On the other hand, Pn and MDA content were more severely influenced by chilling stress in the RNAi lines. These results indicate that SlFBA4 plays an important role in tomato growth and tolerance to chilling stress.

Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.

Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Alcohol dehydrogenase (ADH) is essential to the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Rosaceae fruit species. In this study, 464 ADH genes were identified in eight Rosaceae fruit species, 68 of the genes were from pear and which were classified into four subgroups. Frequent single gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those derived from other types of duplication. RNA-Seq and qRT-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds detected during fruit development.

Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions

Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.

Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean

Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.

Conservation of ethanol fermentation and its regulation in land plants

Ethanol fermentation is considered as one of the main metabolic adaptations to ensure energy production in higher plants under anaerobic conditions. Following this pathway, pyruvate is decarboxylated and reduced to ethanol with the concomitant oxidation of NADH to NAD+. Despite its acknowledgement as an essential metabolic strategy, the conservation of this pathway and its regulation throughout plant evolution have not been assessed so far. To address this question, we compared ethanol fermentation in species representing subsequent steps in plant evolution and related it to the structural features and transcriptional regulation of the two enzymes involved: pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH). We observed that, despite the conserved ability to produce ethanol upon hypoxia in distant phyla, transcriptional regulation of the enzymes involved is not conserved in ancient plant lineages, whose ADH homologues do not share structural features distinctive for acetaldehyde/ethanol-processing enzymes. Moreover, Arabidopsis mutants devoid of ADH expression exhibited enhanced PDC activity and retained substantial ethanol production under hypoxic conditions. Therefore, we concluded that, whereas ethanol production is a highly conserved adaptation to low oxygen, its catalysis and regulation in land plants probably involve components that will be identified in the future.

Proteomic analysis of the effect of plant-derived smoke on soybean during recovery from flooding stress

Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis was performed based on morphological results. Growth of soybean seedlings was inhibited under flooding stress, but it recovered after water removal following treatment with plant-derived smoke. Sucrose/starch metabolism and glycolysis were suppressed in smoke-treated flooded soybean compared to flooded soybean. The protein abundance and gene expression of O-fucosyltransferase family proteins related to the cell wall were higher in smoke-treated flooded soybean than in flooded soybean. Protein abundance and gene expression of peptidyl-prolyl cis-trans isomerase and Bowman-Birk proteinase isoinhibitor D-II were lower in smoke-treated flooded soybean than in flooded soybean. Taken together, these results suggest that plant-derived smoke enhances soybean growth during recovery from flooding stress through the balance of sucrose/starch metabolism and glycolysis. Furthermore, the accumulation of cell-wall related protein might be an important factor contributing to recovery of soybean from flooding stress.

BIOLOGICAL SIGNIFICANCE

Flooding negatively affects the growth of soybean, whereas the plant-derived smoke enhances the seedling growth of crops. To clarify the mechanism underlying the recovery from flooding stress, proteomic analysis of soybean with different treatments including normal conditions, flooding stress, and flooding stress in the presence of plant-derived smoke was performed in this study. Growth of soybean seedlings was inhibited under flooding stress, however, it recovered with plant-derived smoke treatment during recovery from flooding stress. Sucrose/starch metabolism and glycolysis were suppressed in smoke-treated flooded soybean compared to flooded soybean, which suggests altered sucrose/starch metabolism and glycolysis contribute to soybean growth recovery from flood stress. Furthermore, the protein abundance and gene expression of O-fucosyltransferase family proteins related to the cell wall was higher in smoke-treated flooded soybean than in flooded soybean, which might be an important factor contributing to the recovery of soybean from flooding stress.

Subcellular Proteomics: Application to Elucidation of Flooding-Response Mechanisms in Soybean

Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.

Proteomic analysis of soybean seedling leaf under waterlogging stress in a time-dependent manner

Leaf is sensitive to environmental changes and exhibits specific responses to abiotic stress. To identify the response mechanism in soybean leaf under waterlogging stress, a gel-free/label-free proteomic technique combined with polyethylene glycol fractionation was used. Attenuated photosynthesis by waterlogging stress in the leaf of soybean seedlings was indicated from proteomic results. Defensive mechanisms such as reactive oxygen species (ROS) scavenging was also recognized. Cluster analysis revealed that proteins that exhibit characteristic dynamics in response to waterlogging were mainly related to photosynthesis. Among the identified photorespiration-related proteins, the protein abundance and enzyme activity of hydroxypyruvate reductase were transiently increased in control plants, but were clearly decreased in response to waterlogging stress. These results suggest that waterlogging directly impairs photosynthesis and photorespiration. Furthermore, hydroxypyruvate reductase may be a critical enzyme controlling the rate of photorespiration.

Organ-specific proteomics of soybean seedlings under flooding and drought stresses

Organ-specific analyses enrich the understanding of plant growth and development under abiotic stresses. To elucidate the cellular responses in soybean seedlings exposed to flooding and drought stresses, organ-specific analysis was performed using a gel-free/label-free proteomic technique. Physiological analysis indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were markedly increased in leaf and root of plants treated with 6days of flooding and drought stresses, respectively. Proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominately affected in leaf, hypocotyl, and root in response to flooding and drought. Notably, the tricarboxylic acid cycle was suppressed in leaf and root under both stresses. Moreover, 17 proteins, including beta-glucosidase 31 and beta-amylase 5, were identified in soybean seedlings under both stresses. The protein abundances of beta-glucosidase 31 and beta-amylase 5 were increased in leaf and root under both stresses. Additionally, the gene expression of beta-amylase 5 was upregulated in leaf exposed to the flooding and drought, and the expression level was highly correlated with the protein abundance. These results suggest that beta-amylase 5 may be involved in carbohydrate mobilization to provide energy to the leaf of soybean seedlings exposed to flooding and drought.

BIOLOGICAL SIGNIFICANCE

This study examined the effects of flooding and drought on soybean seedlings in different organs using a gel-free/label-free proteomic approach. Physiological responses indicated that enzyme activities of alcohol dehydrogenase and delta-1-pyrroline-5-carboxylate synthase were increased in leaf and root of soybean seedlings exposed to flooding and drought for 6days. Functional analysis of acquired protein profiles exhibited that proteins related to photosynthesis, RNA, DNA, signaling, and the tricarboxylic acid cycle were predominated affected in leaf, hypocotyl, and root under both stresses. Moreover, the tricarboxylic acid cycle was suppressed in leaf and root of stressed soybean seedlings. Additionally, increased protein abundance of beta-amylase 5 was consistent with upregulated gene expression in the leaf under both stresses, suggesting that carbohydrate metabolism might be governed in response to flooding and drought of soybean seedlings.

Oxygen dependency of germinating Brassica seeds

Establishing plants in space, Moon or Mars requires adaptation to altered conditions, including reduced pressure and composition of atmospheres. To determine the oxygen requirements for seed germination, we imbibed Brassica rapa seeds under varying oxygen concentrations and profiled the transcription patterns of genes related to early metabolism such as starch degradation, glycolysis, and fermentation. We also analyzed the activity of lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH), and measured starch degradation. Partial oxygen pressure (pO2) greater than 10% resulted in normal germination (i.e., protrusion of radicle about 18 hours after imbibition) but lower pO2 delayed and reduced germination. Imbibition in an oxygen-free atmosphere for three days resulted in no germination but subsequent transfer to air initiated germination in 75% of the seeds and the root growth rate was transiently greater than in roots germinated under ambient pO2. In hypoxic seeds soluble sugars degraded faster but the content of starch after 24 h was higher than at ambient oxygen. Transcription of genes related to starch degradation, α-amylase (AMY) and Sucrose Synthase (SUS), was higher under ambient O2 than under hypoxia. Glycolysis and fermentation pathway-related genes, glucose phosphate isomerase (GPI), 6-phosphofructokinase (PFK), fructose 1,6-bisphosphate aldolase (ALD), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), pyruvate decarboxylase (PDC), LDH, and ADH, were induced by low pO2. The activity of LDH and ADH was the highest in anoxic seeds. Germination under low O2 conditions initiated ethanolic fermentation. Therefore, sufficient oxygen availability is important for germination before photosynthesis provides necessary oxygen and the determination of an oxygen carrying capacity is important for uniform growth in space conditions.

Gel-free/label-free proteomic analysis of root tip of soybean over time under flooding and drought stresses

Growth in the early stage of soybean is markedly inhibited under flooding and drought stresses. To explore the responsive mechanisms of soybean, temporal protein profiles of root tip under flooding and drought stresses were analyzed using gel-free/label-free proteomic technique. Root tip was analyzed because it was the most sensitive organ against flooding, and it was beneficial to root penetration under drought. UDP glucose: glycoprotein glucosyltransferase was decreased and increased in soybean root under flooding and drought, respectively. Temporal protein profiles indicated that fermentation and protein synthesis/degradation were essential in root tip under flooding and drought, respectively. In silico protein-protein interaction analysis revealed that the inductive and suppressive interactions between S-adenosylmethionine synthetase family protein and B-S glucosidase 44 under flooding and drought, respectively, which are related to carbohydrate metabolism. Furthermore, biotin/lipoyl attachment domain containing protein and Class II aminoacyl tRNA/biotin synthetases superfamily protein were repressed in the root tip during time-course stresses. These results suggest that biotin and biotinylation might be involved in energy management to cope with flooding and drought in early stage of soybean-root tip.

Proteomic analysis of flooded soybean root exposed to aluminum oxide nanoparticles

Aluminum oxide (Al2O3) nanoparticles are used in agricultural products and cause various adverse growth effects on different plant species. To study the effects of Al2O3 nanoparticles on soybean under flooding stress, a gel-free proteomic technique was used. Morphological analysis revealed that treatment with 50 ppm Al2O3 nanoparticles under flooding stress enhanced soybean growth compared to ZnO and Ag nanoparticles. A total of 172 common proteins that significantly changed in abundance among control, flooding-stressed, and flooding-stressed soybean treated with Al2O3 nanoparticles were mainly related to energy metabolism. Under Al2O3 nanoparticles the energy metabolism was decreased compared to flooding stress. Hierarchical clustering divided identified proteins into four clusters, with proteins related to glycolysis exhibiting the greatest changes in abundance. Al2O3 nanoparticle-responsive proteins were predominantly related to protein synthesis/degradation, glycolysis, and lipid metabolism. mRNA expression analysis of Al2O3 nanoparticle-responsive proteins that displayed a 5-fold change in abundance revealed that NmrA-like negative transcriptional regulator was up-regulated, and flavodoxin-like quinone reductase was down-regulated. Moreover, cell death in root including hypocotyl was less evident in flooding-stressed with Al2O3 nanoparticles compared to flooding-treated soybean. These results suggest that Al2O3 nanoparticles might promote the growth of soybean under flooding stress by regulating energy metabolism and cell death.

Characterization of proteins in soybean roots under flooding and drought stresses

Flooding and drought affect soybean growth because soybean is a stress-sensitive crop. In 2-day-old plants exposed to 2-day flooding or drought, the fresh weight of roots was markedly suppressed, although the root morphology clearly differed between two conditions. To understand the response mechanisms of soybean to flooding and drought stresses, a gel-free proteomic technique was used. A total of 97 and 48 proteins were significantly changed in response to flooding and drought stresses, respectively. Proteins involved in protein synthesis were decreased by flooding stress and increased by drought. Glycolysis-related proteins were increased in roots by both flooding and drought stresses. Fermentation, stress, and cell wall-related proteins were increased in response to flooding stress, whereas cell organization and redox-related proteins were increased under drought stress. Among the identified proteins, three S-adenosylmethionine synthetases were commonly decreased and increased in response to flooding and drought stresses, respectively. The mRNA expression levels of S-adenosylmethionine synthetase genes displayed a similar tendency to the changes in protein abundance. These results suggest that S-adenosylmethionine synthetase is involved in the regulation of stress response because it was changed in response to flooding and drought stresses.

BIOLOGICAL SIGNIFICANCE

This study reported on the response mechanisms of soybean to flooding and drought stresses using the gel-free proteomic technique. Proteins involved in protein synthesis were decreased by flooding stress and increased by drought. Glycolysis-related proteins were increased in roots by both flooding and drought stresses. Fermentation, stress, and cell wall-related proteins were increased in response to flooding stress, whereas cell organization and redox-related proteins were increased under drought stress. Among the identified proteins, three S-adenosylmethionine synthetases were commonly decreased and increased in response to flooding and drought stresses, respectively. The mRNA expression levels of S-adenosylmethionine synthetase genes displayed a similar tendency to the changes in protein abundance. These results suggest that S-adenosylmethionine synthetase is involved in the regulation of stress response because it was changed in response to flooding and drought stresses.

Analyses of flooding tolerance of soybean varieties at emergence and varietal differences in their proteomes

Flooding of fields due to heavy and/or continuous rainfall influences soybean production. To identify soybean varieties with flooding tolerance at the seedling emergence stage, 128 soybean varieties were evaluated using a flooding tolerance index, which is based on plant survival rates, the lack of apparent damage and lateral root development, and post-flooding radicle elongation rate. The soybean varieties were ranked according to their flooding tolerance index, and it was found that the tolerance levels of soybean varieties exhibit a continuum of differences between varieties. Subsequently, tolerant, moderately tolerant and sensitive varieties were selected and subjected to comparative proteomic analysis to clarify the tolerance mechanism. Proteomic analysis of the radicles, combined with correlation analysis, showed that the ratios of RNA binding/processing related proteins and flooding stress indicator proteins were significantly correlated with flooding tolerance index. The RNA binding/processing related proteins were positively correlated in untreated soybeans, whereas flooding stress indicator proteins were negatively correlated in flooded soybeans. These results suggest that flooding tolerance is regulated by mechanisms through multiple factors and is associated with abundance levels of the identified proteins.

Physiological and transcriptomic characterization of submergence and reoxygenation responses in soybean seedlings

Complete inundation at the early seedling stage is a common environmental constraint for soybean production throughout the world. As floodwaters subside, submerged seedlings are subsequently exposed to reoxygenation stress in the natural progression of a flood event. Here, we characterized the fundamental acclimation responses to submergence and reoxygenation in soybean at the seedling establishment stage. Approximately 90% of seedlings succumbed during 3 d of inundation under constant darkness, whereas 10 d of submergence were lethal to over 90% of seedlings under 12 h light/12 h dark cycles, indicating the significance of underwater photosynthesis in seedling survival. Submergence rapidly decreased the abundance of carbohydrate reserves and ATP in aerial tissue of seedlings although chlorophyll breakdown was not observed. The carbohydrate and ATP contents were recovered upon de-submergence, but sudden exposure to oxygen also induced lipid peroxidation, confirming that reoxygenation induced oxidative stress. Whole transcriptome analysis recognized genome-scale reconfiguration of gene expression that regulates various signalling and metabolic pathways under submergence and reoxygenation. Comparative analysis of differentially regulated genes in shoots and roots of soybean and other plants defines conserved, organ-specific and species-specific adjustments which enhance adaptability to submergence and reoxygenation through different metabolic pathways.

Identification of indicator proteins associated with flooding injury in soybean seedlings using label-free quantitative proteomics

Flooding injury is one of the abiotic constraints on soybean growth. An experimental system established for evaluating flooding injury in soybean seedlings indicated that the degree of injury is dependent on seedling density in floodwater. Dissolved oxygen levels in the floodwater were decreased by the seedlings and correlated with the degree of injury. To understand the molecular mechanism responsible for the injury, proteomic alterations in soybean seedlings that correlated with severity of stress were analyzed using label-free quantitative proteomics. The analysis showed that the abundance of proteins involved in cell wall modification, such as polygalacturonase inhibitor-like and expansin-like B1-like proteins, which may be associated with the defense system, increased dependence on stress at both the protein and mRNA levels in all organs during flooding. The manner of alteration in abundance of these proteins was distinct from those of other responsive proteins. Furthermore, proteins also showing specific changes in abundance in the root tip included protein phosphatase 2A subunit-like proteins, which are possibly involved in flooding-induced root tip cell death. Additionally, decreases in abundance of cell wall synthesis-related proteins, such as cinnamyl-alcohol dehydrogenase and cellulose synthase-interactive protein-like proteins, were identified in hypocotyls of seedlings grown for 3 days after flooding, and these proteins may be associated with suppression of growth after flooding. These flooding injury-associated proteins can be defined as indicator proteins for severity of flooding stress in soybean.

A comparative proteomics analysis in roots of soybean to compatible symbiotic bacteria under flooding stress

A proteomics approach was used to evaluate the effects of flooding stress on early symbiotic interaction between soybean roots and soil bacteria, Bradyrhizobium japonicum. Three-day-old soybean was inoculated with B. japonicum followed by flooding. The number of root hairs in seedlings, without or with flooding stress, was increased after 3 days of inoculation. Proteins were extracted from roots and separated by two-dimensional polyacrylamide gel electrophoresis. Out of 219 protein spots, 14 and 8 proteins were increased and decreased, respectively, by inoculation under flooding compared with without flooding. These proteins were compared in untreated and flooded seedlings. Increased level of 6 proteins in flooded seedlings compared with untreated seedlings was suppressed by inoculation in seedlings under flooding. They were related to disease/defense, protein synthesis, energy, and metabolism. Differential abundance of glucan endo-1,3-beta-glucosidase, phosphoglycerate kinase, and triosephosphate isomerase, based on their localization in middle and tip of root, indicated that they might be related to increase in number of root hairs. These results suggest that disease/defense, energy, and metabolism-related proteins may be particularly subjected to regulation in flooded soybean seedlings, when inoculated with B. japonicum and that this regulation may lead to increase in number of root hair during early symbiotic differentiation.

Analysis of response mechanism in soybean under low oxygen and flooding stresses using gel-base proteomics technique

A proteomics approach was used to analyze the response mechanism in soybean seedlings under low oxygen and flooding stresses. Three-day-old soybean seedlings were subjected to low oxygen and flooding stresses. Growth of root was suppressed in both stresses with more extent of suppression in flooded seedlings at 3 and 6 days following the treatments. Proteins were extracted from roots and separated by two-dimensional polyacrylamide gel electrophoresis. Of total 1,233 protein spots, 27 protein spots were commonly changed under low oxygen and flooding stresses; while the differential change in 4 and 18 protein spots was specific to low oxygen and flooding stresses, respectively. Proteins related to metabolism and energy were increased; while protein destination/storage related proteins were decreased commonly under low oxygen and flooding stresses. Protein specie, TCP domain class transcription factor was decreased specifically under low oxygen stress; while decrease of nine proteins related to metabolism, protein destination/storage and disease/defense was specific in flooded seedlings. The decrease in majority of the proteins related to protein destination/storage specifically in flooded seedlings implies the misfolding of proteins resulting in flooded injuries in an independent way of oxygen deprivation. These results suggest that decrease in proteins related to protein destination/storage and disease/defense causes more growth suppression in soybean seedlings under flooding stress compared to low oxygen stress.

Mass spectrometry-based analysis of proteomic changes in the root tips of flooded soybean seedlings

Flooding injury is a major problem in soybean cultivation. A proteomics approach was used to clarify the occurrence of changes in protein expression level and phosphorylation in soybeans under flooding stress. Two-day-old seedlings were flooded for 1 day, proteins were extracted from root tips of the seedlings and digested with trypsin, and their expression levels and phosphorylation states were compared to those of untreated controls using mass spectrometry-based proteomics techniques. Phosphoproteins were enriched using a phosphoprotein purification column prior to digestion and mass spectrometry. The expression of proteins involved in energy production increased as a result of flooding, while expression of proteins involved in protein folding and cell structure maintenance decreased. Flooding induced changes of phosphorylation status of proteins involved in energy generation, protein synthesis and cell structure maintenance. The response to flooding stress may be regulated by both modulation of protein expression and phosphorylation state. Energy-demanding and production-related metabolic pathways may be particularly subject to regulation by changes in protein phosphorylation during flooding.

Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots

Alcohol dehydrogenase (Adh) is the key enzyme in alcohol fermentation. We analyzed Adh expression in order to clarify the role of Adh of soybeans (Glycine max) to flooding stress. Proteome analysis confirmed that expression of Adh is significantly upregulated in 4-day-old soybean seedlings subjected to 2 days of flooding. Southern hybridization analysis and soybean genome database search revealed that soybean has at least 6 Adh genes. The GmAdh2 gene that responded to flooding was isolated from soybean cultivar Enrei. Adh2 expression was markedly increased 6 h after flooding and decreased 24 h after floodwater drainage. In situ hybridization and Western blot indicated that flooding strongly induces Adh2 expression in RNA and protein levels in the root apical meristem. Osmotic, cold, or drought stress did not induce expression of Adh2. These results indicate that Adh2 is a flooding-response specific soybean gene expressed in root tissue.

Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.

Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary

Quantitative proteomics is one of the analytical approaches used to clarify crop responses to stress conditions. Recent remarkable advances in proteomics technologies allow for the identification of a wider range of proteins than was previously possible. Current proteomic methods fall into roughly two categories: gel-based quantification methods, including conventional two-dimensional gel electrophoresis and two-dimensional fluorescence difference gel electrophoresis, and MS-based quantification methods consists of label-based and label-free protein quantification approaches. Although MS-based quantification methods have become mainstream in recent years, gel-based quantification methods are still useful for proteomic analyses. Previous studies examining crop responses to stress conditions reveal that each method has both advantages and disadvantages in regard to protein quantification in comparative proteomic analyses. Furthermore, one proteomics approach cannot be fully substituted by another technique. In this review, we discuss and highlight the basis and applications of quantitative proteomic analysis approaches in crop seedlings in response to flooding and osmotic stress as two environmental stresses.

Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques

Gel-based and gel-free proteomics techniques were used to investigate early responses to flooding stress in the roots and hypocotyls of soybean seedlings. Proteins from 2-day-old soybean seedlings flooded for 12 h were extracted and analyzed. Two mass-spectroscopy-based proteomics analyses, two-dimensional fluorescence difference gel electrophoresis, and nanoliquid chromatography identified 32 from 17 spots and 81 proteins, respectively, as responsive to flooding stress. On the basis of the number and function of proteins identified, glycolysis and fermentation enzymes and inducers of heat shock proteins were key elements in the early responses to flooding stress. Analysis of enzyme activities and carbohydrate contents in flooded seedlings showed that glucose degradation and sucrose accumulation accelerated during flooding due to activation of glycolysis and down-regulation of sucrose degrading enzymes. Additionally, the methylglyoxal pathway, which is detoxification system linked to glycolysis, was up-regulated. Furthermore, two-dimensional polyacrylamide gel electrophoresis-based phosphoproteomics analysis showed that proteins involved in protein folding and synthesis were dephosphorylated under flooding conditions. These results suggest that translational and post-translational control during flooding possibly induces an imbalance in the expression of proteins involved in several metabolic pathways including carbohydrate metabolism that might cause flooding injury of soybean seedlings.

Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture of the array of cellular responses controlled by gene expression that allow resurrection plants to survive desiccation.

Protein profile analysis of salt-responsive proteins in leaves and roots in two cultivars of creeping bentgrass differing in salinity tolerance

Knowledge of stress-responsive proteins is critical for further understanding the molecular mechanisms of stress tolerance. The objectives of this study were to establish a proteomic map for a perennial grass species, creeping bentgrass (A. stolonifera L.), and to identify differentially expressed, salt-responsive proteins in two cultivars differing in salinity tolerance. Plants of two cultivars ('Penncross' and 'Penn-A4') were irrigated daily with water (control) or NaCl solution to induce salinity stress in a growth chamber. Salinity stress was obtained by adding NaCl solution of 2, 4, 6, and 8 dS m(-1) in the soil daily for 2-day intervals at each concentration, and then by watering soil with 10 dS m(-1) solution daily for 28 days. For proteomic map, using two-dimensional electrophoresis (2-DE), approximately 420 and 300 protein spots were detected in leaves and roots, respectively. A total of 148 leaf protein spots and 40 root protein spots were excised from the 2-DE gels and subjected to mass spectrometry analysis. In total, 106 leaf protein spots and 24 root protein spots were successfully identified. Leaves had more salt-responsive proteins than roots in both cultivars. The superior salt tolerance in 'Penn-A4', indicated by shoot extension rate, relative water content, and cell membrane stability during the 28-day salinity stress could be mainly associated with its higher level of vacuolar H(+)-ATPase in roots and UDP-sulfoquinovose synthase, methionine synthase, and glucan exohydrolase in leaves, as well as increased accumulation of catalase and glutathione S-transferase in leaves. Our results suggest that salinity tolerance in creeping bentgrass could be in part controlled by an alteration of ion transport through vacuolar H(+)-ATPase in roots, maintenance of the functionality and integrity of thylakoid membranes, sustained polyamine biosynthesis, and by the activation of cell wall loosening proteins and antioxidant defense mechanisms.

The heat-inducible transcription factor HsfA2 enhances anoxia tolerance in Arabidopsis

Anoxia induces several heat shock proteins, and a mild heat pretreatment can acclimatize Arabidopsis (Arabidopsis thaliana) seedlings to subsequent anoxic treatment. In this study, we analyzed the response of Arabidopsis seedlings to anoxia, heat, and combined heat + anoxia stress. A significant overlap between the anoxic and the heat responses was observed by whole-genome microarray analysis. Among the transcription factors induced by both heat and anoxia, the heat shock factor A2 (HsfA2), known to be involved in Arabidopsis acclimation to heat and to other abiotic stresses, was strongly induced by anoxia. Heat-dependent acclimation to anoxia is lost in an HsfA2 knockout mutant (hsfa2) as well as in a double mutant for the constitutively expressed HsfA1a/HsfA1b (hsfA1a/1b), indicating that these three heat shock factors cooperate to confer anoxia tolerance. Arabidopsis seedlings that overexpress HsfA2 showed an increased expression of several known targets of this transcription factor and were markedly more tolerant to anoxia as well as to submergence. Anoxia failed to induce HsfA2 target proteins in wild-type seedlings, while overexpression of HsfA2 resulted in the production of HsfA2 targets under anoxia, correlating well with the low anoxia tolerance experiments. These results indicate that there is a considerable overlap between the molecular mechanisms of heat and anoxia tolerance and that HsfA2 is a player in these mechanisms.

A comprehensive analysis of the soybean genes and proteins expressed under flooding stress using transcriptome and proteome techniques

The inducible genes and proteins were analyzed using transcriptome and proteome techniques to explore the mechanisms underlying soybean response to flooding stress. Soybean seedlings were germinated for 2 days and subjected to flooding for 12 h, and the total RNAs and proteins were extracted from the root and hypocotyl. High-coverage gene expression profiling analysis as transcriptome technique was performed. Ninety-seven out of the 29,388 peaks observed demonstrated a greater than 25-fold change following 12 h of flood-induced stress. Furthermore, 34 proteins out of 799 proteins were changed by 12 h stress. Genes associated with alcohol fermentation, ethylene biosynthesis, pathogen defense, and cell wall loosening were significantly up-regulated. Hemoglobin, acid phosphatase, and Kunitz trypsin protease inhibitor were altered at both transcriptional and translational levels. Reactive oxygen species scavengers and chaperons were changed only at the translational level. It is suggested that the early response of soybean under flooding might be important stress adaptation to ensure survival against not only hypoxia but also the direct damage of cell by water.

Resistance of the Soybean Cultivar Archer to Pythium Damping-Off and Root Rot Caused by Several Pythium spp

Archer, a maturity group I soybean cultivar with demonstrated flood tolerance and resistance to Pythium ultimum, was compared with Hutcheson, a widely planted maturity group V cultivar in Arkansas, for resistance to P. ultimum, P. irregulare, P. aphanidermatum, P. vexans, and group HS. Emergence and establishment assays demonstrated that Archer had greater emergence and fewer disease symptoms after 10 days for all pathogenic species of Pythium than did Hutcheson. Archer also demonstrated higher root weights and fewer disease symptoms compared with Hutcheson in assays conducted for 6 weeks. Similar results were found using two different seed lots of the cultivars, suggesting that the results were not due to seed quality differences. This study indicates that resistance in Archer to Pythium damping-off and root rot compared with Hutcheson is robust, with efficacy over a number of Pythium spp. and a range of plant developmental stages.

Impact of solar ultraviolet-B on the proteome in soybean lines differing in flavonoid contents

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to systematically investigate the impact of solar ultraviolet-B (UV-B) radiation on the soybean leaf proteome. In order to investigate the protective role of flavonoids against UV-B, two isolines of the Clark cultivar (the standard line with moderate levels of flavonoids and the magenta line with reduced flavonoids) were grown in the field with or without natural levels of UV-B. The 12-day-old first trifoliates were harvested for proteomic analysis. More than 300 protein spots were reproducibly resolved and detected on each gel. Statistical analysis showed that 67 protein spots were significantly (P<0.05) affected by solar UV-B. Many more spots were altered by UV-B in the magenta line than in the standard line. Another 12 protein spots were not altered by UV-B but showed significantly (P<0.05) different accumulations between the two lines, and for most spots the line-specific differences were also observed under UV-B exclusion. Most of the differentially accumulated spots were identified by mass spectrometry. The proteins were quite diverse, and were involved in metabolism, energy, protein destination/storage, protein synthesis, disease/defense, transcription, and secondary metabolism. The results suggest that high levels of flavonoids lead to a reduction in UV-B sensitivity at the proteomic level.

Soybean Response to Flooded Soil Conditions and the Association with Soilborne Plant Pathogenic Genera

The role of soilborne pathogens in flood damage on soybeans, Glycine max, was examined using six genotypes representing a reputed range of flood tolerances. Genotypes were planted in single-row plots from 1996 to 1998 with flood treatments of no flood, flood at emergence (3-day duration), or flood at the fourth leaf node growth stage (7-day duration). Three or four days after removing each flood treatment, plant stands were estimated and 15 plants were collected from each plot, weighed, and rated for root discoloration. Roots were assayed for the presence of fungi and other filamentous eukaryotic organisms. Plant stands were reduced by flooding at emergence compared with the nonflooded control. Flooding at both growth stages caused significant increases in root discoloration compared with nonflooded soybeans. Plant weights were reduced in 2 of 3 years for flooding at emergence. Pythium was the only genus of filamentous organisms whose isolation frequency increased with flooding. Of the 60 Pythium isolates evaluated representing the different cultural groups based on appearance and growth rate on potato dextrose agar, cornmeal agar, and V8 agar, 47% were moderately to highly virulent on soybean. Pythium spp. isolated from soybean included the pathogenic species P. ultimum, P. aphanidermatum, P. irregulare, and P. vexans and Group HS. Nonpathogenic P. oligandrum also was isolated from soybean.

The Effect of Pythium ultimum and Soil Flooding on Two Soybean Cultivars

The effect of flooding and Pythium ultimum on soybean, Glycine max, was determined in a series of greenhouse experiments using the cultivars Hutcheson and Archer. Seeds were planted into pasteurized soil either not infested or infested with sand-cornmeal inoculum of P. ultimum and either flooded at emergence for 2 days or at the four leaf node stage (V4) for 5 days. A nonflooded control was included in each experiment. Seeds placed directly into infested soil resulted in little or no stand for Hutcheson regardless of flood treatment, whereas stand was reduced for Archer only in the flooded infested soil treatment. Additional experiments were conducted by placing seed onto a 2- to 5-mm layer of pathogen-free soil on top of the infested soil. Flooding at emergence reduced plant height, growth stage, and top dry weight for Hutcheson and root fresh weight for both cultivars. Greater reductions for Hutcheson in root weight, and top dry weight in P. ultimum-infested soil in the soil layer experiments, also indicated that Hutcheson was more susceptible than Archer. Flooding alone decreased root weights, and infestation with P. ultimum reduced weights further resulting in an additive effect. This also was the case for plant height, growth stage, and top dry weight for Hutcheson for flooding at emergence. Root discoloration was greatly increased for both cultivars in infested soil flooded at emergence. Similar results were found when plants were flooded at V4; however, the effect was not as great as with flooding at emergence. These studies indicate that Pythium damping-off and root rot may account for a portion of the negative response of soybean to flooding. The results also indicate that Archer has some resistance to P. ultimum.

Arabidopsis ribonucleotide reductases are critical for cell cycle progression, DNA damage repair, and plant development

Ribonucleotide reductase (RNR), comprising two large (R1) and two small (R2) subunits, catalyzes a rate-limiting step in the production of deoxyribonucleotides needed for DNA replication and repair. Previous studies in yeast and mammals indicated that defective RNR often led to cell cycle arrest, growth retardation, and p53-dependent apoptosis, whereas abnormally increased RNR activities led to higher mutation rates. Because plants are constantly exposed to environmental mutagens and plant cells are totipotent, an understanding of RNR function in plants is important. We isolated and characterized mutations in all three R2 genes (TSO2, RNR2A, and RNR2B) in Arabidopsis thaliana. tso2 mutants had reduced deoxyribonucleoside triphosphate (dNTP) levels and exhibited developmental defects, including callus-like floral organs and fasciated shoot apical meristems. tso2 single and tso2 rnr2a double mutants were more sensitive to UV-C light, and tso2 rnr2a seedlings exhibited increased DNA damage, massive programmed cell death, and release of transcriptional gene silencing. Analyses of single and double r2 mutants demonstrated that a normal dNTP pool and RNR function are critical for the plant response to mutagens and proper plant development. The correlation between DNA damage accumulation and the subsequent occurrence of apoptotic nuclei in tso2 rnr2a double mutants suggests that perhaps plants, like animals, can initiate programmed cell death upon sensing DNA damage.

Responses of soybean to oxygen deficiency and elevated root-zone carbon dioxide concentration

Root flooding is damaging to the growth of crop plants such as soybean (Glycine max L.). Field flooding for 3 d often results in leaf chlorosis, defoliation, cessation of growth and plant death. These effects have been widely attributed solely to a lack of oxygen in the root-zone. However, an additional damaging factor may be CO(2), which attains levels of 30 % (v/v) of total dissolved gases. Accordingly, the effects of root-zone CO(2) on oxygen-deficient soybean plants were investigated in hydroponic culture. Soybean plants are shown to be very tolerant of excess water and anaerobiosis. No oxygen (100 % N(2) gas) and low oxygen (non-aerated) treatments for 14 d had no effect on soybean survival or leaf greenness, but plants became severely chlorotic and stunted when the roots were exposed to no oxygen together with CO(2) concentrations similar to those in flooded fields (equilibrium concentrations of 30 %). When root-zone CO(2) was increased to 50 %, a quarter of soybean plants died. Those plants that survived showed severe symptoms of chlorosis, necrosis and root death. In contrast, rice (Oryza sativa L.) plants were not affected by the combination of no oxygen and elevated root-zone CO(2.) A concentration of 50 % CO(2) did not affect rice plant survival or leaf colour. These results suggest that the high susceptibility of soybean to soil flooding, compared with that of rice, is an outcome of its greater sensitivity to CO(2).

The metabolic response of plants to oxygen deficiency

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

Proteomic analysis of arabidopsis seed germination and priming

To better understand seed germination, a complex developmental process, we developed a proteome analysis of the model plant Arabidopsis for which complete genome sequence is now available. Among about 1,300 total seed proteins resolved in two-dimensional gels, changes in the abundance (up- and down-regulation) of 74 proteins were observed during germination sensu stricto (i.e. prior to radicle emergence) and the radicle protrusion step. This approach was also used to analyze protein changes occurring during industrial seed pretreatments such as priming that accelerate seed germination and improve seedling uniformity. Several proteins were identified by matrix-assisted laser-desorption ionization time of flight mass spectrometry. Some of them had previously been shown to play a role during germination and/or priming in several plant species, a finding that underlines the usefulness of using Arabidopsis as a model system for molecular analysis of seed quality. Furthermore, the present study, carried out at the protein level, validates previous results obtained at the level of gene expression (e.g. from quantitation of differentially expressed mRNAs or analyses of promoter/reporter constructs). Finally, this approach revealed new proteins associated with the different phases of seed germination and priming. Some of them are involved either in the imbibition process of the seeds (such as an actin isoform or a WD-40 repeat protein) or in the seed dehydration process (e.g. cytosolic glyceraldehyde-3-phosphate dehydrogenase). These facts highlight the power of proteomics to unravel specific features of complex developmental processes such as germination and to detect protein markers that can be used to characterize seed vigor of commercial seed lots and to develop and monitor priming treatments.

Differential expression of plastidic aldolase genes in Nicotiana plants under salt stress

Two homologous genes of plastidic fructose-1,6-bisphosphate aldolase (AldP) isozymes were isolated from green leaves of a salt stress-tolerant Nicotiana species, Nicotiana paniculata, by differential screening. The products of the corresponding genes, NpAldP1 and NpAldP2, were 91% identical to each other and 70-85% identical to the other known plant plastidic aldolases. Although these two genes showed similar organ-specific expression and daily cycles, their responses to salt stress differed: mRNA accumulation of NpAldP2 increased, but that of NpAldP1 slightly decreased. The mRNA accumulations of their counterparts of two other Nicotiana species, NeAldP1 and NeAldP2 (Nicotiana excelsior), and NaAldP1 and NaAldP2 (Nicotiana arentsii) were studied under the same stress condition. N. arentsii conserved accumulation profiles similar to N. paniculata, but N. excelsior did not. In N. excelsior, accumulation of NeAldP1 decreased to 50% of the control after stress and gradually recovered thereafter, whereas accumulation of NeAldP2 temporarily decreased and reached 250% of the control by the third day of stress. Southern blot analysis indicated that NpAldP1, NpAldP2, NaAldP1, and NaAldP2 include one or two closely related genes and NeAldP1 and NeAldP2 several.

Arabidopsis alcohol dehydrogenase expression in both shoots and roots is conditioned by root growth environment

It is widely accepted that the Arabidopsis Adh (alcohol dehydrogenase) gene is constitutively expressed at low levels in the roots of young plants grown on agar media, and that the expression level is greatly induced by anoxic or hypoxic stresses. We questioned whether the agar medium itself created an anaerobic environment for the roots upon their growing into the gel. beta-Glucuronidase (GUS) expression driven by the Adh promoter was examined by growing transgenic Arabidopsis plants in different growing systems. Whereas roots grown on horizontal-positioned plates showed high Adh/GUS expression levels, roots from vertical-positioned plates had no Adh/GUS expression. Additional results indicate that growth on vertical plates closely mimics the Adh/GUS expression observed for soil-grown seedlings, and that growth on horizontal plates results in induction of high Adh/GUS expression that is consistent with hypoxic or anoxic conditions within the agar of the root zone. Adh/GUS expression in the shoot apex is also highly induced by root penetration of the agar medium. This induction of Adh/GUS in shoot apex and roots is due, at least in part, to mechanisms involving Ca2+ signal transduction.

Effect of maturity and curing on peanut proteins. Changes in protein surface hydrophobicity

A hydrophobic fluorescence probe, 1,8-anilinonaphthalene sulfonate (ANS), was used to study the changes in protein surface hydrophobicity (PSH) occurring during peanut maturation and curing. PSH increased with the degree of maturity and during curing (windrow drying). The increase of PSH during curing or heating was more pronounced in immature peanuts than their mature counterparts, suggesting that more hydrophobic sites are hidden in the former proteins. PSH decreased when proteins were chemically modified with phenylglyoxal (an arginine-modifying agent), suggesting that arginine might play a role in hydrophobicity. The findings indicate that maturation and curing affect PSH, and that there is a relationship between PSH and peanut maturity. Possible factors contributing to the increase of PSH are discussed.

Evidence that the plant host synthesizes the heme moiety of leghemoglobin in root nodules

Although it is well established that the plant host encodes and synthesizes the apoprotein for leghemoglobin in root nodules, the source of the heme moiety has been uncertain. We recently found that the transcript for coproporphyrinogen III oxidase, one of the later enzymes of heme synthesis, is highly elevated in soybean (Glycine max L.) nodules compared with roots. In this study we measured enzyme activity and carried out western-blot analysis and in situ hybridization of mRNA to investigate the levels during nodulation of the plant-specific coproporphyrinogen oxidase and four other enzymes of the pathway in both soybean and pea (Pisum sativum L.). We compared them with the activity found in leaves and uninfected roots. Our results demonstrate that all of these enzymes are elevated in the infected cells of nodules. Because these are the same cells that express apoleghemoglobin, the data strongly support a role for the plant in the synthesis of the heme moiety of leghemoglobin.

OXYGEN DEFICIENCY AND ROOT METABOLISM: Injury and Acclimation Under Hypoxia and Anoxia

Oxygen deficiency in the rooting zone occurs with poor drainage after rain or irrigation, causing depressed growth and yield of dryland species, in contrast with native wetland vegetation that tolerates such conditions. This review examines how roots are injured by O2 deficiency and how metabolism changes during acclimation to low concentrations of O2. In the root apical meristem, cell survival is important for the future development; metabolic changes under anoxia help maintain cell survival by generating ATP anaerobically and minimizing the cytoplasmic acidosis associated with cell death. Behind the apex, where cells are fully expanded, ethylene-dependent death and lysis occurs under hypoxia to form continuous, gas-filled channels (aerenchyma) conveying O2 from the leaves. This selective sacrifice of cells may resemble programmed cell death and is distinct from cell death caused by anoxia. Evidence concerning alternative possible mechanisms of anoxia tolerance and avoidance is presented.

The Role of Sugars, Hexokinase, and Sucrose Synthase in the Determination of Hypoxically Induced Tolerance to Anoxia in Tomato Roots

Hypoxic pretreatment of tomato (Lycopersicon esculentum M.) roots induced an acclimation to anoxia. Survival in the absence of oxygen was improved from 10 h to more than 36 h if external sucrose was present. The energy charge value of anoxic tissues increased during the course of hypoxic acclimation, indicating an improvement of energy metabolism. In acclimated roots ethanol was produced immediately after transfer to anoxia and little lactic acid accumulated in the tissues. In nonacclimated roots significant ethanol synthesis occurred after a 1-h lag period, during which time large amounts of lactic acid accumulated in the tissues. Several enzyme activities, including that of alcohol dehydrogenase, lactate dehydrogenase, pyruvate decarboxylase, and sucrose synthase, increased during the hypoxic pretreatment. In contrast to maize, hexokinase activities did not increase and phosphorylation of hexoses was strongly inhibited during anoxia in both kinds of tomato roots. Sucrose, but not glucose or fructose, was able to sustain glycolytic flux via the sucrose synthase pathway and allowed anoxic tolerance of acclimated roots. These results are discussed in relation to cytosolic acidosis and the ability of tomato roots to survive anoxia.

Occurrence of a differential expression of the glyceraldehyde-3-phosphate dehydrogenase gene in muscle and liver from euthermic and induced hibernating jerboa (Jaculus orientalis)

A cDNA clone which contains the near-complete open reading frame (ORF) encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12) was obtained by screening a muscle cDNA library of jerboa (Jaculus orientalis), a true hibernating rodent, with a PCR-amplified 0.5-kb genomic DNA probe from an internal region of the gene. The 1.1-kb cDNA clone consists of a 927-bp ORF which codifies for 309 aa, about 93% of the original GapC gene encoding the 36-kDa protein, and a 3'-noncoding region of 167 bp. The full-length aa sequence of GAPDH was achieved by sequencing the N-terminal region of the purified protein completing the missing part in the cDNA clone. Both nt and aa sequences exhibit a high degree of homology to other mammalian GAPDHs. The expression of the GapC gene was studied in skeletal muscle and liver of euthermic and hibernating jerboas both on the mRNA level by Northern blot hybridization using the cDNA clone as a probe and on the protein level by Western blot immunodetection using an antibody raised against muscle GAPDH. A clear decrease (about threefold) in the amount of GapC mRNA, a single 1.2-kb transcript, was observed in muscle of hibernating jerboa when compared with the same tissue from the euthermic animal. This mRNA level decrease directly correlates with a reduction in both protein amount and specific activity in crude protein extracts. In contrast, both GAPDH protein and GapC mRNA levels remained unchanged in liver from euthermic and hibernating jerboas although the enzymatic activity was also about threefold lower in the hibernating tissue. These result, together with previous data obtained from protein studies [Soukri et al. (1995) Biochim. Biophys. Acta 1243, 161-168 and (1996) 1292, 177-187] indicate that jerboa GAPDH is regulated by different mechanisms during hibernation in these tissues, that is, at transcriptional level in muscle and at posttranslational level in liver. The reduced GAPDH activity should result in both cases in a decrease of the glycolytic flux that would eventually contribute to the dramatic metabolic depression of this dormant state.

Okadaic acid, a protein phosphatase inhibitor, blocks calcium changes, gene expression, and cell death induced by gibberellin in wheat aleurone cells

The cereal aleurone functions during germination by secreting hydrolases, mainly alpha-amylase, into the starchy endosperm. Multiple signal transduction pathways exist in cereal aleurone cells that enable them to modulate hydrolase production in response to both hormonal and environmental stimuli. Gibberellic acid (GA) promotes hydrolase production, whereas abscisic acid (ABA), hypoxia, and osmotic stress reduce amylase production. In an effort to identify the components of transduction pathways in aleurone cells, we have investigated the effect of okadaic acid (OA), a protein phosphatase inhibitor, on stimulus-response coupling for GA, ABA, and hypoxia. We found that OA (100 nM) completely inhibited all the GA responses that we measured, from rapid changes in cytosolic Ca2+ through changes in gene expression and accelerated cell death. OA (100 nM) partially inhibited ABA responses, as measured by changes in the level of PHAV1, a cDNA for an ABA-induced mRNA in barley. In contrast, OA had no effect on the response to hypoxia, as measured by changes in cytosolic Ca2+ and by changes in enzyme activity and RNA levels of alcohol dehydrogenase. Our data indicate that OA-sensitive protein phosphatases act early in the transduction pathway of GA but are not involved in the response to hypoxia. These data provide a basis for a model of multiple transduction pathways in which the level of cytosolic Ca2+ is a key point of convergence controlling changes in stimulus-response coupling.