Global gene expression profiles in developing soybean seeds.

The gene expression profiles in soybean (Glycine max L.) seeds at 4 stages of development, namely, pod, 2-mm bean, 5-mm bean, and full-size bean, were examined by DNA microarray analysis. The total genes of each sample were classified into 4 clusters based on stage of development. Gene expression was strictly controlled by seed size, which coincides with the development stage. First, stage specific gene expression was examined. Many transcription factors were expressed in pod, 2-mm bean and 5-mm bean. In contrast, storage proteins were mainly expressed in full-size bean. Next, we extracted the genes that are differentially expressed genes (DEGs) that were extracted using the Rank products method of the Bioconductor software package. These DEGs were sorted into 8 groups using the hclust function according to gene expression patterns. Three of the groups across which the expression levels progressively increased included 100 genes, while 3 groups across which the levels decreased contained 47 genes. Storage proteins, seed-maturation proteins, some protease inhibitors, and the allergen Gly m Bd 28K were classified into the former groups. Lipoxygenase (LOX) family members were present in both the groups, indicating the multi-functionality with different expression patterns.

Expression of the stress-related genes for glutathione S-transferase and ascorbate peroxidase in the most-glycinin-deficient soybean cultivar Tousan205 during seed maturation.

Global analysis of gene expression profiles in most-glycinin-deficient cultivar Tousan205, was performed by DNA microarray analysis. It was confirmed that Tousan205 lacks mRNA expression of three glycinin subunit precursor genes, G1 (A1aB1x), G2 (A2B1a), and G5 (A3B4), and lacks G4 (A5A4B3) protein. Most glycinin subunits were deficient in mature seeds of Tousan205. We compared the gene expression of Tousan205 with those of parent cultivar, Tamahomare, which was used for crossbreeding of Tousan205. As a result, Tousan205 exhibited higher expression of some seed maturation proteins, and stress-related genes such as glutathione S-transferase and ascorbate peroxidase. This result indicates the possibility that the decrease of main storage protein, glycinin causes stress in soybean.

QTL analysis of seed-flooding tolerance in soybean (Glycine max [L.] Merr.).

In soybean (Glycine max [L.] Merr.), varieties with seed-flooding tolerance at the geminating stage are desirable for breeding in countries with much rainfall at sowing time. Our study revealed great intervarietal variation in seed-flooding tolerance as evaluated by germination rate (GR) and normal seedling rate (NS). Pigmented seed coat and small seed weight tended to give a positive effect on seed-flooding tolerance. Subsequently, QTL analysis of GR and NS were performed and a total of four QTLs were detected. Among them, Sft1 on the linkage group H (LG_H) exhibited a large effect on GR after a 24-h treatment; however, Sft2 near the I locus on LG_A2 involved in seed coat pigmentation exhibited the largest effect on seed-flooding tolerance. Sft1, Sft3 and Sft4 were independent of seed coat color and seed weight. Based on the results, we discussed the physiological effects of genetic factors responsible for seed-flooding tolerance in soybean.

Relationship between protein composition and coagulation reactivity, particulate formation, and incorporation of lipids in soymilk.

Many studies have suggested that the 11S/7S ratio in soybeans affects the coagulation reaction at the first step. In this study, the 11S/7S ratio in soybeans showed significantly negative correlation with MgCl(2) concentrations for the maximum breaking stress of tofu for six Japanese varieties. To determine the effect of the 11S/7S ratio, soymilk was fractionated by centrifugation after the addition of MgCl(2), and the distribution of lipids and proteins was studied. The amount of precipitate increased as the MgCl(2) concentration or the 11S/7S ratio increased. More triglyceride was incorporated into the precipitate as the MgCl(2) concentration or the 11S/7S ratio increased. The stain intensity of bands after sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) indicated that the ratio of oleosin, a membrane protein of the oil body, increased in the precipitate as the MgCl(2) concentration or the 11S/7S ratio increased, while the ratios of glycinin and beta-conglycinin were less variable. These results indicate that the 11S/7S ratio and coagulant concentration may have an effect on the amount of coagulum and the concentration of oil globules in the coagulum at the beginning of coagulation.

Structure-physicochemical function relationships of soybean glycinin at subunit levels assessed by using mutant lines.

Glycinin is a hexameric protein composed of five kinds of subunits. The subunits are classified into two groups, group I (A1aB1b, A1bB2, and A2B1a) and group II (A3B4 and A5A4B3). We purified four mutant glycinins composed of only group I subunits (group I-glycinin), only group II subunits (group II-glycinin), only A3B4 (A3B4-glycinin), and only A5A4B3 (A5A4B3-glycinin) from mutant soybean lines. The physicochemical properties of these glycinin samples were compared with those of the normal glycinin (11S) composed of five kinds of subunits. The thermal stabilities (as measured by thermal denaturation midpoint temperatures) of 11S, group I-glycinin, and group II-glycinin were similar to each other, although that of A3B4-glycinin was significantly lower than those of the others. The orders of aromatic and aliphatic surface hydrophobicities were the same: A3B4-glycinin > group II-glycinin > A5A4B3-glycinin > 11S > group I-glycinin. The solubility of 11S as a function of pH at mu = 0.5 was governed by that of group I-glycinin and followed this order at acidic pH: 11S = group I-glycinin > A3B4-glycinin > group II-glycinin = A5A4B3-glycinin. The order of emulsifying abilities was A5A4B3-glycinin > group II-glycinin > A3B4-glycinin > 11S > group I-glycinin. This order was consistent with that of the length of their hypervariable regions. Except for this relationship, there was no significant relationship among the other physicochemical properties of the mutant glycinins.

The composition of newly synthesized proteins in the endoplasmic reticulum determines the transport pathways of soybean seed storage proteins.

Glycinin (11S) and beta-conglycinin (7S) are major storage proteins in soybean (Glycine max L.) seeds and accumulate in the protein storage vacuole (PSV). These proteins are synthesized in the endoplasmic reticulum (ER) and transported to the PSV by vesicles. Electron microscopic analysis of developing soybean cotyledons of the wild type and mutants with storage protein composition different from that of the wild type showed that there are two transport pathways: one is via the Golgi and the other bypasses it. Golgi-derived vesicles were observed in all lines used in this study and formed smooth dense bodies with a diameter of 0.5 to several micrometers. ER-derived protein bodies (PBs) with a diameter of 0.3-0.5 microm were observed at high frequency in the mutants containing higher amount of 11S group I subunit than the wild type, whereas they were hardly observed in the mutants lacking 11S group I subunit. These indicate that pro11S group I may affect the formation of PBs. Thus, the composition of newly synthesized proteins in the ER is important in the selection of the transport pathways.

Gelling properties of soybean beta-conglycinin having different subunit compositions.

The effects of protein concentration, and heating temperature and time on the gelling properties of soybean beta-conglycinin (7S globulins) lacking the alpha or alpha' subunit were compared with those of 7S containing all three subunits (alpha, alpha', and beta) to determine whether each subunit contributes equally. In most of the conditions, the relative order of gel hardness was alpha'-lacking > 7S > alpha-lacking. From Fourier transform infrared studies, the secondary structure change after heating was very similar among the three samples; thus, the secondary structural change is not the reason for the differences in gel hardness. By using scanning electron microscopy, we observed differences in strand thickness and the density of the gel network among the three samples. These differences correlated well with the differences in gel hardness.

Changes in characters of soybean glycinin groups I, IIa, and IIb caused by heating.

Soybean glycinin groups I, IIa, and IIb were purified from soybeans composed of only glycinin groups I, IIa, and IIb, respectively. When these protein solutions were heated, the amount of the particulate protein formed in these solutions was greatest in the order of groups IIa, IIb, and I. The protein solubilities decreased upon the addition of magnesium chloride in the order of groups IIa, IIb, and I. It was determined by differential scanning calorimetry analysis that the denaturation temperatures of groups I, IIa, and IIb were 92.8, 96.0, and 97.9 degrees C, and that the enthalpies of their transitions were 24.2, 27.4, and 28.1 J g(-)(1), respectively. The alpha-helix rates of groups I, IIa, and IIb in aqueous solution were analyzed by circular dichroism and were 19, 16, and 15%, respectively. The beta-sheet rates of groups I, IIa, and IIb were 44, 38, and 39%, respectively. In all group proteins, the alpha-helix rates were decreased by heating and the beta-sheet rates were increased. The surface hydrophobicity of these group proteins increased as a result of heating, and those of groups IIa and IIb were larger than that of group I. The surface hydrophobicity of these protein groups increased by heating, and those of groups IIa and IIb were larger than that of group I and beta-conglycinin. Breaking stress of curds prepared from these group proteins containing more than 1 of beta-conglycinin ration showed similar values, but the order of those containing less than 1 in strength was groups I, IIb and IIa. These results suggest that the increase of particulate contents and the curd formation are related to the increase of surface hydrophobicity by heating.

Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer.

Most plant seeds contain 11S globulins as major storage proteins for their nutrition. Soybean glycinin belongs to the 11S globulin family and consists of five kinds of subunits. We determined the crystal structure of a homohexamer of the glycinin A3B4 subunit at 2.1-A resolution. The crystal structure shows that the hexamer has 32-point group symmetry formed by face-to-face stacking of two trimers. The interface buries the highly conserved interchain disulfide. Based on the structure, we propose that an ingenious face-to-face mechanism controls the hexamer formation of the 11S globulin by movement of a mobile disordered region to the side of the trimer after posttranslational processing. Electrostatic analysis of the faces suggests that the interchain disulfide-containing face has high positive potential at acidic pH, which induces dissociation of the hexamer into trimers that may be susceptible to proteinases after seed imbibition. This dissociation might result in the degradation and mobilization of 11S globulins as storage proteins in embryos during germination and seedling growth.

Accumulation of high levels of free amino acids in soybean seeds through integration of mutations conferring seed protein deficiency.

Soybean ( Glycine max [L.] Merr.) seeds are rich in protein, most of which is contributed by the major storage proteins glycinin (11S globulin) and beta-conglycinin (7S globulin). Null mutations for each of the subunits of these storage proteins were integrated by crossbreeding to yield a soybean line that lacks both glycinin and beta-conglycinin components. In spite of the absence of these two major storage proteins, the mutant line grew and reproduced normally, and the nitrogen content of its dry seed was similar to that for wild-type cultivars. However, protein bodies appeared underdeveloped in the cotyledons of the integrated mutant line. Furthermore, whereas free amino acids contribute only 0.3-0.8% of the seed nitrogen content of wild-type varieties, they constituted 4.5-8.2% of the seed nitrogen content in the integrated mutant line, with arginine (Arg) being especially enriched in the mutant seeds. Seeds of the integrated mutant line thus appeared to compensate for the reduced nitrogen content in the form of glycinin and beta-conglycinin by accumulating free amino acids as well as by increasing the expression of certain other seed proteins. These results indicate that soybean seeds are able to store nitrogen mostly in the form of either proteins or free amino acids.

Structure-physicochemical function relationships of soybean beta-conglycinin heterotrimers.

We purified four single molecular species of beta-conglycinin heterotrimers consisting of the alpha and beta subunits or the alpha' and beta subunits from mutant soybean cultivars lacking the alpha or alpha' subunit, respectively, and examined their structural features and physicochemical functions. The extent of the hydrophobicities of the heterotrimers was related to the number of the alpha or alpha' subunit. The thermal stabilities of the heterotrimers were mainly conferred by the subunit which had lower thermal stability. Solubilities at low ionic strength (mu = 0.08) of the heterotrimers containing the alpha or alpha' subunit were very similar to those of the alpha and alpha' homotrimers, respectively. Emulsifying abilities and heat-induced associations of the heterotrimers containing one beta subunit were similar to those of the alpha or alpha' homotrimer, whereas those of the heterotrimers containing two beta subunits were similar to those of the beta homotrimer.