Proteome analysis of soybean hypocotyl and root under salt stress

To evaluate the response of soybean to salt stress, the related changes in protein expression were investigated using the proteomic approach. Soybean plants were exposed to 0, 50, 100, and 200 mM NaCl. Especially at 200 mM, the length and fresh weight of the hypocotyl and root reduced under salt stress, while the proline content increased. Proteins from the hypocotyl and root treated with 100 mM NaCl were extracted and separated by two-dimensional polyacrylamide gel electrophoresis; 321 protein spots were detected. In response to salt stress, seven proteins were reproducibly found to be up- or down-regulated by two to sevenfold: late embryogenesis-abundant protein, beta-conglycinin, elicitor peptide three precursor, and basic/helix-loop-helix protein were up-regulated, while protease inhibitor, lectin, and stem 31-kDa glycoprotein precursor were down-regulated. These results indicate that salinity can change the expression level of some special proteins in the hypocotyl and root of soybean that may in turn play a role in the adaptation to saline conditions.     

Identification of rice root proteins regulated by gibberellin using proteome analysis

Gibberellin (GA) promoted rice (Oryza sativa L.) root elongation in a concentration-dependent manner with roots grown in 0.1 µm GA₃ being 13.8% longer than controls. On the other hand, the roots of Tan-ginbozu, a semi-dwarf cultivar were 69.8% shorter in comparison with Nipponbare, a normal cultivar. Treatments with 10 µm uniconazole-P and 10 µm abscisic acid (ABA) caused decreases in root length in Tan-ginbozu by 44.6 and 79.2%, respectively. To investigate how GA influences rice root growth, proteome analysis techniques were applied. Extracted proteins were separated by two-dimensional polyacrylamide gel electrophoresis and analysed using an automated protein sequencer and mass spectrometer. Sixteen proteins show differences in accumulation levels as a result of treatment with GA₃, uniconazole-P and ABA treatment and/or the difference between the semi-dwarf cultivar, Tan-ginbozu, and normal cultivars. Among these proteins, fructose-bisphosphate aldolase (EC 4.1.2.13) increased in roots treated with GA₃, occurred in low levels in Tan-ginbozu roots, and decreased in roots treated with uniconazole-P or ABA. Moreover, roots from seedlings grown in 100 µm glucose were 9.1% longer than controls. These results indicate that increases in fructose-bisphosphate aldolase activity stimulate the glycolytic pathway and may play an important role in the GA-induced growth of roots.     

Characterization of post-flooding recovery-responsive enzymes in soybean root and hypocotyl

Soybean exhibits markedly reduced growth and yields under flooding stress. To determine the functional roles of four soybean proteins in post-flooding recovery, the organ/stress specificity and time-dependency of their enzymatic activities were analyzed. Peroxidase activity decreased in root and hypocotyl exposed to flooding and cold stresses, but increased during the post-stress recovery period. In contrast, its activity increased in both root and hypocotyl under drought stress. Acid phosphatase activity was suppressed in root treated with flooding and cold stresses, and slightly increased during the recovery period; however, the opposite profile was observed in hypocotyl. In response to drought stress, it did not change in root, but was decreased in hypocotyl. Beta-ketoacyl reductase activity did not change in root under flooding conditions, but was decreased in hypocotyl, although the activity increased slightly during the recovery period. In addition, it was decreased in both organs under drought and cold stresses, but again increased during the recovery period. Nucleotidylyl transferase activity was increased in root under flooding and drought stresses, but was decreased in hypocotyl. It was decreased in response to cold stress, but exhibited a slight increase during the recovery period. Furthermore, the treatment with jasmonate and salicylate suppressed the activities of peroxidase and acid phosphatase in root and hypocotyl under flooding stress; however, the activity of acid phosphatase increased during the recovery period. Nucleotidylyl transferase activity in root was also elevated by treatment with jasmonate, but gradually decreased during the recovery period. These results suggest that jasmonate-induced changes in nucleotidylyl transferase activity may facilitate soybean root recovery after flooding stress.     

Isoflavonoids in root and hypocotyl of soybean seedlings (Glycine max,Fabaceae)

Isoflavonoids, some of which are highly fluorescent, are produced by soybean [Glycine max (L.) Merr.] and serve as chemical signals for certain aspects of nitrogen fixation and microbial resistance. This study was conducted to determine whether soybean mutants with nonfluorescent roots contained abnormal concentrations of isoflavonoids. Isoflavonoids were extracted from the root and hypocotyl of 4-d-old wild-type soybean seedlings (cv. Hark) having fluorescent roots and from four nonallelic mutant, near isogenic lines of Hark having nonfluorescent roots. In addition, isoflavonoids were extracted from the root and hypocotyl of 4-d-old seedlings of near isogenic lines of Hark harboring two pairs of the mutant alleles for nonfluorescent roots. Malonyl daidzin, daidzin, malonyl genistin, and genistein were the most abundant isoflavonoids extracted from either the root or hypocotyl of seedlings with either fluorescent or nonfluorescent roots. Extracted malonyl daidzin, malonyl genistin, and malonyl glycitin decomposed readily, yielding daidzin, genistin, and glycitin, respectively. The concentrations of malonyl genistin and genistein, two highly fluorescent compounds, were similar in both fluorescent and nonfluorescent roots. Thus, root fluorescence was not correlated with abundance per se of fluorescent isoflavonoids in roots. In addition, the abundance of isoflavonoids extractable from the hypocotyl did not correlate with root fluorescence.     

Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress

Flooding is a major problem for soybean crop as it reduces the growth and grain yield. To investigate the function of the soybean cell wall in the response to flooding stress, cell wall proteins were analyzed. Cell wall proteins from roots and hypocotyls of soybeans, which were germinated for 2 days and subjected to 2 days of flooding, were purified, separated by two-dimensional polyacrylamide gel electrophoresis and stained with Coomassie brilliant blue. Sixteen out of 204 cell wall proteins showed responses to flooding stress. Of these, two lipoxygenases, four germin-like protein precursors, three stem 28/31 kDa glycoprotein precursors, and one superoxide dismutase [Cu–Zn] were downregulated. A copper amine oxidase was found to have shifted from the basic to acidic zone following flooding stress. Based on these results, it was confirmed by the lignin staining that the lignification was suppressed in the root of soybean under the flooding stress. These results suggest that the roots and hypocotyls of soybean caused the suppression of lignification through decrease of these proteins by downregulation of reactive oxygen species and jasmonate biosynthesis under flooding stress.     

大豆根系应答重金属Cd胁迫的转录组分析

重金属镉(Cd)作为一种非生命活动所需的常见污染物,在土壤中以低浓度存在时,便可以对生物体产生极强的毒性,影响农作物的生长发育.为了解大豆对重金属Cd 胁迫应答的分子机制,把发芽7 d的大豆苗在75 μmol·L^-1Cd浓度中处理0、4、8、12和48 h,然后取根进行转录组表达分析.共得到2670个表达差异基因,其中4、8、12和48 h处理组中分别有244、1545、442和1401个基因显示了表达差异.这些基因通过GO分类,可分为56类;采用COG数据库进行比对,根据其功能大致可分为25类.KEGG通路富集分析表明,差异表达基因主要富集在苯丙氨酸代谢、泛醌和其他萜类醌生物合成,以及半胱氨酸和甲硫氨酸代谢等通路中.发现3个异黄酮2′-羟化酶基因、2个异黄酮还原酶基因和1个查尔酮合成酶基因在Cd 胁迫下均表达上调.RT-PCR 检测 4个差异表达基因的表达模式与 RNA-Seq分析结果一致,证实了 RNA-Seq结果的可靠性.     

Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches

Cell wall proteins (CWPs) are important both for maintenance of cell structure and for responses to abiotic and biotic stresses. In this study, a destructive CWP purification procedure was adopted using wheat seedling roots and the purity of the CWP extract was confirmed by minimizing the activity of glucose-6-phosphate dehydrogenase, a cytoplasmic marker enzyme. To determine differentially expressed CWPs under flooding stress, gel-based proteomic and LC-MS/MS-based proteomic techniques were applied. Eighteen proteins were found to be significantly regulated in response to flood by gel-based proteomics and 15 proteins by LC MS/MS-based proteomics. Among the flooding down-regulated proteins, most were related to the glycolysis pathway and cell wall structure and modification. However, the most highly up-regulated proteins in response to flooding belong to the category of defense and disease response proteins. Among these differentially expressed proteins, only methionine synthase, β-1,3-glucanases, and β-glucosidase were consistently identified by both techniques. The down-regulation of these three proteins suggested that wheat seedlings respond to flooding stress by restricting cell growth to avoid energy consumption; by coordinating methionine assimilation and cell wall hydrolysis, CWPs played critical roles in flooding responsiveness.     

Identification of the oxidative stress proteome in the brain

The redox proteomics technique normally combines two-dimensional gel electrophoresis, mass spectrometry, and protein databases to analyze the cell proteome from various samples, thereby leading to the identification of specific targets of oxidative modification. Oxidative stress that occurs because of increased levels of reactive oxygen species and reactive nitrogen species can target most biomolecules, consequently leading to altered physiological function of the cells. Redox proteomics has identified oxidatively modified protein targets in various pathological conditions, consequently providing insight into the pathways involved in the pathogenesis of these conditions. This approach also can be used to identify possible protective mechanisms to prevent or delay these disorders.     

Isolation and culture of soybean hypocotyl protoplasts

Summary Protoplasts were isolated seedling hypocotyls of soybean (Glycine max), and cultured in both liquid and agarose-solidified, modified K8P medium. Nuclear staining revealed that only 2% of protoplasts lacked a nucleus, 93% contained a single nucleus, and 5% contained more than one. Maximum protoplast yields and subsequent division frequencies, in liquid medium, were obtained from 5 days-old seedlings. Maximum division frequencies (54%) were obtained from hypocotyl protoplasts plated at a density of 5×10⁴ ml⁻¹. Using different osmolality reduction régimes for liquid cultures, hypocotyl protoplasts developed into green, nodular callus, similar to that which has previously given rise to shoot buds in perennialGlycine species. This tissue, however, did not produce shoot buds in soybean. N. H. was supported by a SERC CASE studentship and a postdoctoral fellowship from Shell Research Ltd., Sittingbourne, Kent, UK.     

Identification of ethylene-mediated protein changes during nodulation in Medicago truncatula using proteome analysis

Ethylene has been hypothesised to be a regulator of root nodule development in legumes, but its molecular mechanisms of action remain unclear. The skl mutant is an ethylene-insensitive legume mutant showing a hypernodulation phenotype when inoculated with its symbiont Sinorhizobium meliloti. We used the skl mutant to study the ethylene-mediated protein changes during nodule development in Medicago truncatula. We compared the root proteome of the skl mutant to its wild-type in response to the ethylene precursor aminocyclopropane carboxylic acid (ACC) to study ethylene-mediated protein expression in root tissues. We then compared the proteome of skl roots to its wild-type after Sinorhizobium inoculation to identify differentially displayed proteins during nodule development at 1 and 3 days post inoculation (dpi). Six proteins (pprg-2, Kunitz proteinase inhibitor, and ACC oxidase isoforms) were down-regulated in skl roots, while three protein spots were up-regulated (trypsin inhibitor, albumin 2, and CPRD49). ACC induced stress-related proteins in wild-type roots, such as pprg-2, ACC oxidase, proteinase inhibitor, ascorbate peroxidase, and heat-shock proteins. However, the expression of stress-related proteins such as pprg-2, Kunitz proteinase inhibitor, and ACC oxidase, was down-regulated in inoculated skl roots. We hypothesize that during early nodule development, the plant induces ethylene-mediated stress responses to limit nodule numbers. When a mutant defective in ethylene signaling, such as skl, is inoculated with rhizobia, the plant stress response is reduced, resulting in increased nodule numbers.     

Comparative analysis of polyadenylated RNA complexity in soybean hypocotyl tissue and cultured suspension cells

Growth parameters of suspension culture cells of soybean (Glycine max L.) were compared between cells grown in medium with (+) auxin and without (−) auxin. Growth rates were greater for (+) auxin cells. Cells transferred to (−) auxin medium primarily expanded in size while (+) auxin cells initially divided and then expanded. Two methods were used to estimate polyadenylated RNA sequence complexity. Kinetic analysis gave a sum of component complexity values of 36,000 and 64,000 diverse poly(A) RNA sequences of about 1,400 nucleotides in (+) and (−) auxin grown cells, respectively. The most striking difference between these cell populations was the increase in the poly(A) RNA sequence complexity in cells grown in medium without auxin. RNA complexities were also determined by the saturation of `single' copy DNA by poly(A) RNAs from (+) and (−) auxin suspension cells. These saturation studies estimated the total complexity of (+) and (−) auxin suspension cells as 41,000 and 57,000 diverse sequences, respectively. Suspension cells in auxin-depleted medium produced about 20,000 more diverse sequences than (+) auxin cells. Comparisons of poly(A) complexities were also made among auxin-treated and untreated hypocotyl cells from the intact plant relative to suspension culture cells. Mixed populations of poly(A) RNA from these tissues and cells allowed the determination of shared sequences among them. When all combinations of poly(A) RNA were mixed, the percentage of `single' copy DNA that saturated was equivalent to diverse sequence complexity estimates of about 60,000. When mixed poly(A) RNA from suspension cells from (+) and (−) auxin medium were compared, they shared about 40,000 sequences and (−) auxin cells contained an additional 20,000. Both (+) and (−) tissue culture cells shared a subset of about 20,000 sequences with cells from (+) and (−) auxin treated hypocotyl. A third subset of about 20,000 sequences was shared by (−) auxin suspension cells and hypocotyl treated with or without auxin, a subset most of which were not shared by (+) auxin suspension cells. Kinetic and saturation data estimates of poly(A) RNA complexity compared favorably and indicated that exogenous auxin treatment can dramatically alter the complexity of all classes of poly(A) RNAs in cultured cells.     

Identification and comparative analysis of aluminum-induced microRNAs conferring plant tolerance to aluminum stress in soybean

Aluminum (Al) toxicity in acidic soils is a major factor restricting crop production. Although the molecular mechanisms of Al responses have been extensively investigated, microRNA (miRNA) mediated differential Al tolerance in different soybean genotypes remains largely unknown. In this study, two soybean [Glycine max (L.) Merr.] genotypes, Al-tolerant BX10 and Al-sensitive BD2, were treated with 0 and 50 μM AlCl3 and then used to construct the miRNA libraries for deep sequencing. Results revealed 453 miRNAs, whose expression patterns were affected by Al stress. We also identified 32 differentially expressed miRNAs: 19 in BX10, 7 in BD2, and 6 in both genotypes. The gene ontology analysis of their putative target genes indicated that stress-responsive genes and amino-acid-metabolism-related processes preferentially existed in BX10. Comprehensive analysis demonstrated that conserved miRNAs, such as gma-miR166k/o, gma-miR390g, and gma-miR396c/k, mediated root elongation in BX10, whereas gma-miR169r triggered oxidative stress in BD2. These processes could be regarded as important mechanisms conferring differential Al tolerance in BX10 and BD2. This study provided new insights into different Al response mechanisms in various soybean genotypes.     

Recovery of nitrogen fixation after short-term flooding of the nodulated root system of soybean

Nitrogen fixation of terrestrial legumes is strongly and rapidly diminished under flooding. Although recovery is possible with the formation of aerenchyma, information is scarce regarding recovery after draining following short-term flooding, before the appearance of morphological adaptations. This study used soybean (Glycine max) plants nodulated with Bradyrhizobium elkanii to determine xylem sap glutamine as an indication of nitrogen fixation activity during recovery from different periods of flooding. Xylem glutamine levels showed rapid recovery (within 90 min) following periods of flooding up to 4 h. Recovery was progressively slower after longer periods of flooding. After 48 h flooding very little recovery could be observed within the first 120 min after draining but recovery was possible within 48 h. Consistent with the changes in xylem glutamine, direct measurements of apparent nitrogenase activity carried out immediately on draining revealed rapid recovery after flooding for 1 h and slow recovery following 48 h of flooding. In the latter case, nitrogenase activity largely recovered 24 h after draining. Experiments with ¹⁵N₂ incorporation into amino acids exported in the xylem sap revealed that glutamine was by far the most highly labelled amino acid in sap collected over the first 30 min of exposure to the isotope. This is conclusive evidence that xylem sap glutamine is an immediate product of N₂ fixation and export. The changes in xylem sap glutamine seen on flooding (decline) and after draining (recovery) can therefore be attributed to changes in nitrogenase activity. The data show that xylem sap glutamine is a useful means for assessing changes in nitrogenase activity, especially when the root system is submersed in water and activity cannot be measured directly.     

Pools of non-structural carbohydrates in soybean root nodules during water stress

The aim of this study was to examine how the pools of non-structural carbohydrates in soybean nodules are affected under water stress conditions depending on the nature of the symbiont strains with particular emphasis on the plant-borne carbohydrates sucrose and pinitol, and on trehalose, a compatible solute synthesized by the bacteroids. Soybean ( Glycine max [L.] Merr. cv. Maple Arrow) plants were inoculated with the nitrogen-fixing strains Bradyrhizobium japonicum 61-A-101 or USDA 110 spc4 and cultivated axenically under conditions in which nodules formed in an upper soil compartment while roots for water supply grew into a compartment filled with nutrient solution. When the nodules were well established (1 month post inoculation), 10% (w/v) PEG 6000 was added to the nutrient solution. This led to a slowly progressing, moderate water stress, as determined by measuring the decrease of transpiration, and to a decrease in nitrogen fixation. The pool sizes of the major non-structural nodule carbohydrates changed during progression of water stress. Sucrose, the major soluble carbohydrate in nodules of unstressed plants (2 and 4%, respectively of nodule dry weight depending on symbiont strain), strongly increased in nodules of stressed plants, reaching nearly 10% of dry weight. The activities of two major sucrose-consuming enzymes, sucrose synthase and alkaline invertase, decreased markedly in nodules of stressed plants. Starch decreased only transiently upon water stress. Pinitol, a cyclitol serving as compatible solute in many plants, increased more than 4 times, reaching about 1% of nodule dry weight during the stress. Trehalose, the major soluble carbohydrate synthesized by the bacteroids, increased in nodules colonized by USDA 110 spc4 from about 0.2 to 0.8% of nodule dry weight, while in nodules colonized by 61-A-101 it amounted to more than 1.5% of dry weight both with and without stress.