Resolution and reconstitution of complex V of the mitochondrial oxidative phosphorylation system: properties and composition of the membrane sector

The antigenic properties of purified glycinin subunits were studied using antibodies prepared against them. Antisera against native glycinin did not react with the isolated subunits, and antibodies prepared against the purified subunits were not active against native glycinin. When native glycinin -was denatured, the antiglycinin immunoglobulins lost their ability to react with it, although the denatured complex was then recognized by antibodies against the purified subunits. Substantial structural rearrangement apparently occurred when the native complex was denatured and disaggregated. Acidic polypeptides A_1a, A_1b, and A₂ had similar determinants as judged by their reactions against A_1a and A_1a antisera. The reaction of the A₃ polypeptides with these antibodies was of lower intensity and in each case clear spurs of cross-reactivity were visible. No cross-reaction was detected between polypeptide A₄ and either anti-A_1a or A₂. Anti-A₃ antibodies reacted with each of the acidic polypeptides of glycinin, and distinct spurs of cross-reactivity were observed between A₃ vs A_1a, A₃ vs A₂, and A₃ vs A₄. B₁ Antisera developed a reaction of identity between basic polypeptides B₁ and B₂, but reacted very weakly with B₃ and B₄. The acidic and basic polypeptides of glycinin were immunologically unrelated. The results demonstrated that immunological tests would successfully differentiate some members of the family of acidic subunits, and other immunoglobulins would discriminate between members of the family of basic subunits.     

Identification and characterization of DNA clones encoding group-II glycinin subunits

Summary DNA clones that encode the group-II subunits of soybean glycinin were identified and compared with clones for group-I subunits. The group-I clones hybridize weakly to those from group-II at low stringency, but fail to hybridize with them at moderate or high stringency. The genes for the group-II subunits are contained in 13 and 9 kb EcoRI fragments of genomic DNA in cultivar CX635-1-1-1. These fragments contain genes for subunits A₅A₄B₃ and A₃B₄, respectively. The larger size of mature group-II subunits compared with group-I subunits is correlated with a larger sized mRNA. However, the gross arrangement of introns and exons within the group-II coding regions appears to be the same as for the genes which encode group-I subunits. Messenger RNA for both groups of glycinin subunits appear in the seed at the same developmental interval, and their appearance lags slightly behind that of mRNAs for the a/a subunits of -conglycinin. These data indicate that the glycinin gene family is more complex than previously thought.Abbreviations bp base pairs - kb kilobase pairs - SDS sodium dodecyl sulfate Cooperative research between USDA/ARS and the Indiana Agric. Expt. Station. This work was supported in part by grants from the USDA Competitive Grants Program and the American Soybean Association Research Foundation. This is Journal Paper No. 10,078 from the Purdue Agricultural Experiment Station     

Identification of a plant introduction soybean line with genetic lesions affecting two distinct glycinin subunits and evaluation of impacts on protein content and composition

Unlike other oilseeds, soybean (Glycine max [L.] Merr) is also valuable due to its direct conversion into human food. One notable example is the cheese-like product tofu. The quality of tofu is improved when protein subunits derived from two glycinin genes, Gy1 and Gy4, are reduced or absent. Here we report the discovery that one exotic soybean plant introduction line, PI 605781 B, has not only a previously described loss-of-expression mutation affecting one glycinin gene (gy4), but also bears an extremely rare, potentially unique, frameshift mutation in the Glycinin1 gene (gy1-a). We analyzed glycinin gene expression via qRT-PCR with mRNA from developing seeds, which revealed that the novel allele dramatically reduced Gy1 mRNA accumulation. Similarly, both A₄A₅B₃ and A_1aB_1a protein subunits were absent or at undetectable levels, as determined by two-dimensional protein fractionation. Despite the reduction in glycinin content, overall seed protein levels were unaffected. The novel gy1-a allele was found to be unique to PI 605871B in a sampling of 247 diverse germplasm lines drawn from a variety of geographic origins.     

Subunit Structure of Soybean 11S Globulin

The acidic and the basic subunits were shown to be present in equimolar amounts in the 11S globulin molecule by the densitometric scanning of the SDS gel and the molecular weight consideration. The four acidic subunits (A₁, A₂, A₃ and A₄) were found to be present in the approximate molar ratio of 1:1:2:2. Four basic subunits separated and designated as B₁, B₂, B₃ and B₄ based on the relative mobilities in the acidic gel in 7 m urea were found to be present in the approximate molar ratio of 1:1:2:2. The four basic subunits were fractionated in approximately same amounts into three different peaks, peak I (B₁ and B₂), peak II (B₃) and peak III (B₄) by CM-Sephadex C–50 column chromatography in the presence of 6 m urea. Three kinds of intermediary subunits of 11S globulin were fractionated with DEAE-Sephadex A–50 in the absence of reducing agents in 6 m urea, and disulfide bonds appeared to participate in the binding between the acidic and the basic subunits in the molar ratio of 1: 1 with the following combinations; A₁ and A₂ combined with B₃, A₃ with B₁ and B₂, and A₄ with B₄. In view of the above results and molecular weight consideration, a new model of subunit structure was proposed for 11S globulin.     

Polymorphism and Expression of cDNAs Encoding Glycinin Subunits

The nucleotide sequence of cDNA encoding the glycinin A₂B_1a subunit from var. Shirotsurunoko was determined and compared with that in the case of var. Bonminori. The comparison showed six nucleotide substitutions in the coding sequence, one of which results in one amino acid replacement, and three in the 3'-noncoding region. These differences indicate the occurrence of polymorphism of the glycinin A₂B_1a subunit gene between the cultivars. The present data together with the previous results indicating the polymorphism of the A_1aB_1b subunit gene [(Utsumi et al., J. Agric. Food Chem., 35, 210 (1987)] suggest that the polymorphism is a general property of glycinin subunit genes. The expression of cDNAs encoding the A₂B_1a and A_1aB_1b subunits was examined. The results obtained in both in vivo- and in vitro-expression experiments indicate that the resultant products were readily degraded.     

Effect of Soy Protein Subunit Composition on the Rheological Properties of Soymilk during Acidification

The effect of soy protein subunit composition on the acid-induced aggregation of soymilk was investigated by preparing soymilk from different soybean lines lacking specific glycinin and β-conglycinin subunits. Acid gelation was induced by glucono-δ-lactone (GDL) and analysis was done using diffusing wave spectroscopy and rheology. Aggregation occurred near pH 5.8 and the increase in radius corresponded to an increase in the elastic modulus measured by small deformation rheology. Diffusing wave spectroscopy was also employed to follow acid gelation, and data indicated that particle interactions start to occur at a higher pH than the pH of onset of gelation (corresponding to the start of the rapid increase in elastic modulus). The protein subunit composition significantly affected the development of structure during acidification. The onset of aggregation occurred at a higher pH for soymilk samples containing group IIb (the acidic subunit A₃) of glycinin, than for samples prepared from Harovinton (a commercial variety containing all subunits) or from genotypes null in glycinin. The gels made from lines containing group I (A₁, A₂) and group IIb (A₃) of glycinin resulted in stiffer acid gels compared to the lines containing only β-conglycinin. These results confirmed that the ratio of glycinin/β-conglycinin has a significant effect on gel structure, with an increase in glycinin causing an increase in gel stiffness. The type of glycinin subunits also affected the aggregation behavior of soymilk.     

Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers

Soybean mutant lines that differ in 11S glycinin and 7S β-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A₄ null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A_1aB₂, A₂B_1a, A_1b B_1b, and A₃B₄ subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A₄ peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A₄ (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection.     

The glycinin box: a soybean embryo factor binding motif within the quantitative regulatory region of the 11S seed storage globulin promoter

The soybean embryo factor binding sequence in the glycinin A₂B_1a gene promoter was delimited to an A/T-rich 9 bp sequence, 5-TAATAATTT-3, designated as the glycinin box, by DNA footprinting and gel mobility shift assay using synthetic oligonucleotides. It was shown that the interaction with the factor takes place at a defined DNA sequence rather than at random A/T-rich sequence blocks in the glycinin 5 flanking region. There are four glycinin boxes in the quantitative regulatory region between positions – 545 and – 378 of the glycinin A₂B_1a promoter. Multiple nonamer motifs similar to the glycinin box were also found in the equivalent regions of other glycinin and legumin promoters, suggesting that they must be conserved as a binding site for the embryo factor that activates the differential and stage-specific expression of seed 11S globulin genes in leguminous plants.     

Limited Proteolysis of Soybean Beta-conglycinin

The tryptic digestion of beta-conglycinin was studied by the pH-stat method and sodium dodecyl sulfate gel electrophoresis. The proteolysis of the protein was not affected by the change of ionic strength. This property was distinct from that of glycinin which is degraded rapidly at a low ionic strength.

Five stable fragments were generated in the degradation course. Two kinds of beta-conglycinin, one of which consisted of only the beta-subunit and the other of only the alpha’ and alpha-subunit, were isolated to elucidate the original subunit of the fragments. Two fragments (AT-1 and AT-2) from the alpha’ and alpha-subunit, and three fragments (BT-2-BT-4) from the beta-subunit were generated. The molecular weights of the fragments were similar to those of the glycinin fragments. From the fragment pattern of the beta-subunit, the presence of two types of the beta-subunit was expected.     

A complete cDNA coding for the sequence of glycinin A2B1a subunit precursor

Analysis of the A₂B_1a subunit precursor, one of the A₂-subunit family of glycinin, the main storage protein of soybean, revealed that it is composed of a signal peptide segment (18 amino acids), the A₂ acidic polypeptide (282 amino acids), followed by the B_1a basic polypeptide (185 amino acids). There was overall 63% homology between this subunit complex and pea legumin, which is an analogous protein to glycinin. As this degree of homology is rather higher than that in the A₃B₄ subunit, one of the A₃ subunit family, it seems that the genes encoding the A₂ subunit family are phylogenetically more strongly related to the legumin genes.     

Limited Tryptic Degradation of Urea Denatured Glycinin

Digestibilities of native, 5 m urea-denatured and 8 m urea-denatured glycinin were studied. Urea was removed by dialysis before digestion. The tryptic digestion of the proteins are influenced by ionic strength. Under low ionic strength condition (0 m NaCl), the proteins, even native glycinin, are well degraded. On the other hand, under high ionic strength condition (0.5 m NaCl), native glycinin resists the tryptic attack and 5 m urea-denatured glycinin is best degraded. The digestibility of 8 m urea-denatured glycinin is lower than that of 5 m urea-denatured one under the condition. The gel filtration and electrophoretic properties show that the digestion intermediate like glycinin-T (the intermediate from native glycinin) is contained in the digestion products. These suggest that the urea-denatured protein contains the almost renatured component after removal of urea. A larger amount of the glycinin-T-like protein was detected at 8 m urea denaturation than at 5 m urea. Therefore, glycinin renatures more readily from 8 m urea denaturation. Probably this is the cause of the decreased digestibility at 8 m urea denaturation.     

Purification and reconstitution of the proton-pumping ATPase of fungal and plant plasma membranes

The 11S storage protein (glycinin) of soybean [Glycine max (L.) Merr., cv. Raiden] was studied by polyacrylamide gel electrophoresis and amino acid sequence analysis. It contained the following subunits composed of acidic (A) and basic (B) polypeptides: A1aB2, A1bB1b, A2B1a, and A3B4. However, it lacked polypeptides A4, A5, and B3 which are present in many other cultivars. A new acidic polypeptide called A6 was present in a low amount and was characterized by amino acid sequence analysis. It was homologous to A4, although of a smaller apparent molecular weight. Since Raiden has an average protein content of about 40% and its glycinin fraction can be purified as a 350,000 D complex which is typical of other cultivars, the results imply polymorphism with respect to glycinin subunit composition. Because there is a wide variation in the methionine content of the various subunits, these findings suggest the possibility of genetically manipulating the nutritional quality of soybean seed protein by altering glycinin subunit composition.     

Formation of Pseudo- and Hybrid-11S Globulins from Subunits of Soybean and Broad Bean 11S Globulins

Pseudo- and hybrid-11S globulins were reconstituted from native acidic and basic subunits of soybean and broad bean 11S globulins. The subunit structures of these two globulins are known to be similar to each other. Pseudo-11S globulins were formed in combinations between glycinin acidic subunit (G-AS_{1 + 2}) and glycinin basic subunit (G-BS) and between legumin acidic subunit (L-ASII) and legumin basic subunit (L-BS). Hybrid-11S globulins were formed in combinations between G-AS_{1 + 2} and L-BS and between L-ASII and G-BS. The yields of the reconstituted 11S components of G-AS_{1 +2} + G-BS and G-AS_{1 + 2} + L-BS were lower than those of L-ASII + G-BS and L-ASII + L-BS. These pseudo- and hybrid-11S globulins were similar to native 11S globulins; they all consisted of reconstituted intermediary subunits which were composed of acidic and basic subunits linked by disufide bridges and had molecular weights similar to those of native 11S globulins. However, the dissociation-association behaviors of pseudo-glycinin and hybrid-11S globulins were different from those of native 11S globulins.     

Interaction Involving Disulfide Bridges between Subunits of Soybean Seed Globulin and between Subunits of Soybean and Sesame Seed Globulins

Native subunit proteins of glycinin, the acidic and the basic subunits designated as AS₁₊₂, AS₂₊₃, AS₄, AS₅, and AS₆ and BS, respectively, were isolated by DEAE-Sephadex A-50 column chromatography in the presence of 6 m urea and 0.2 m 2-mercaptoethanol.

Reconstitution of intermediary subunits involving a disulfide bridge from native acidic and basic subunits was investigated. Formation of the intermediary subunit was observed in combinations between BS and each acidic subunit except AS₆. The yields of the reconstituted intermediary subunits differed from one another.

Further, formation of the intermediary complexes was observed when native acidic and basic subunits of soybean glycinin and sesame 13 S globulin, respectively (or reverse combinations), were mixed under reductively denatured condition and subjected to the reconstitution procedure. Considerring the overall evidence, we may conclude that the complexes are probably a hybrid intermediary subunit.     

Purification and characterization of mRNA from soybean seeds. Identification of glycinin and beta-conglycinin precursors

Poly(A)-rich RNA was isolated from developing soybean seeds (Glycine max (L.) Merr.) and fractionated on linear log sucrose gradients. Two major fractions sedimenting at 18 S and 20 S were separated and then purified by further sucrose gradient fractionation. Both fractions were active as messengers when added to a rabbit reticulocyte lysate protein synthesis system. The 18 S fraction caused proteins migrating primarily to the 60,000-dalton region of a sodium dodecyl sulfate gel to be produced, while translation of the 20 S fraction preferentially directed the synthesis of polypeptides similar in size to the alpha and alpha' subunits of beta-conglycinin. Evidence that many of the 60,000-dalton polypeptides were related to glycinin and the high molecular weight 20 S translation products were related to beta-conglycinin was obtained by immunoprecipitation using monospecific antibodies against glycinin and beta-conglycinin, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the immunoprecipitated products revealed that the glycinin precursor region contained at least three different size components and that the family of glycinin precursors had larger apparent molecular weight (58,000-63,000) than the disulfide-linked complexes between acidic and basic glycinin subunits (57,000). Unlike the disulfide-linked glycinin complexes which were cleaved by disulfide reduction, glycinin precursors were insensitive to reducing agents. The alpha and alpha' subunits synthesized in vitro also had slightly larger apparent molecular weights than purified alpha and alpha' standards.     

Subunits of Limnodrilus erythrocruorin.

The dissociation of the erythrocruorin of the oligochaete $\text{Limnodrilus gotoi}$ was investigated using polyacrylamide gel electrophoresis at neutral pH. In the presence of 0.1% SDS, the erythrocruorin dissociated into five subunits possessing molecular weights of 13,000 (1), 20,000 (2), 23,000 (3), 25,000 (4) and 47,000 (5). In the presence of SDS and mercaptoethanol, the erythrocruorin dissociated into two subunits, whose molecular weights were 13,000 (I) and 28,000 (II). Subunit I accounts for 70–80% of the whole molecule. SDS electrophoresis of the isolated subunits 1 through 5 in the presence of mercaptoethanol showed that subunit I was derived from both subunits 1 and 5, while subunit II was derived from subunits 2–4. These results suggest that $\text{Limnodrilus}$ erythrocruorin consists of at least five polypeptide chains: two chains of 13,000 and three chains of 28,000.     

Differential Proteolysis of Glycinin and beta-Conglycinin Polypeptides during Soybean Germination and Seedling Growth

The degradation of the major seed storage globulins of the soybean (Glycine max [L.] Merrill) was examined during the first 12 days of germination and seedling growth. The appearance of glycinin and β-conglycinin degradation products was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of cotyledon extracts followed by electroblotting to nitrocellulose and immunostaining using glycinin and β-conglycinin specific antibodies. The three subunits of β-conglycinin were preferentially metabolized. Of the three subunits of β-conglycinin, the larger α and α′ subunits are rapidly degraded, generating new β-conglycinin cross-reactive polypeptides of 51,200 molecular weight soon after imbibition of the seed. After 6 days of growth the β-subunit is also hydrolyzed. At least six polypeptides, ranging from 33,100 to 24,000 molecular weight, appear as apparent degradation products of β-conglycinin. The metabolism of the glycinin acidic chains begins early in growth. The glycinin acidic chains present at day 3 have already been altered from the native form in the ungerminated seed, as evidenced by their higher mobility in an alkaline-urea polyacrylamide gel electrophoresis system. However, no change in the molecular weight of these chains is detectable by sodium dodecyl sulfate-polyarylamide gel electrophoresis. Examination of the glycinin polypeptide amino-termini by dansylation suggests that this initial modification of the acidic chains involves limited proteolysis at the carboxyl-termini, deamidation, or both. After 3 days of growth the acidic chains are rapidly hydrolyzed to a smaller (21,900 molecular weight) form. The basic polypeptides of glycinin appear to be unaltered during the first 8 days of growth, but are rapidly degraded thereafter to unidentified products. All of the original glycinin basic chains have been destroyed by day 10 of growth.     

Soybean 11S globulin polypeptides have an antigenic homology with 11S globulins from various plants

Summary Rabbit serum antibodies (AB) against glycinin acidic polypeptides were separated by cross exhausting, and the antibody fractions for each of the two subfamilies of glycinin subunits (A₁ and A₃) were obtained. The antibodies were used in the immuno blot assay with seed protein of various plant classes. Polypeptides homologous to soybean glycinin were detected. Homology with A₁ polypeptide was revealed in more cases than with A₃. Total seed protein preparations were subjected to centrifugation in sucrose density gradient, and the polypeptides, imunochemically related to glycinin, occurred only in fractions with sedimentation constant about 11S. The nativity of conservative antigenic determinants of 11S globulins is discussed.