Spatial Distribution and Characteristics of Protein Content and Composition in Japonica Rice Grains: Implications for Sake Quality

The quantity and composition of rice proteins play a crucial role in determining taste quality of sake, Japanese rice wine. However, the spatial distribution of proteins within rice grains, especially in endosperm tissue, and the differences between rice varieties remain unclear. Here, we analyzed the crude protein contents and composition ratios of table (Nipponbare and Koshihikari) and genuine sake rice varieties (Yamadanishiki, Gohyakumangoku, Dewasansan, Dewanosato, and Yumenokaori) to elucidate their spatial distribution within the Japonica rice grain endosperm. Seven sake rice varieties were polished over five harvest years using a brewer's rice-polishing machine. We obtained fractions at 90-70% (the outermost endosperm fraction), 70-50%, 50-30%, and 30-0% (the central region of the endosperm fraction). Yamadanishiki and Dewanosato exhibited considerably lower crude protein contents than the other cultivars. After applying SDS-PAGE, the protein composition, comprising glutelin/total protein (G/TP), prolamin/TP (P/TP), and G/P ratios of these fractions was determined. In white rice (at a 90% rice-polishing ratio), the average ratio of the major protein composition was G/TP 41%, P/TP 21%, and G/P ratios of 1.97. Gohyakumangoku and Yamadanishiki had higher G/TP ratio, while Dewanosato had a lower value. Despite having lower crude protein contents, Yamadanishiki and Dewanosato exhibited significantly varying G/TP ratios. The G/TP ratio markedly varied among rice varieties, particularly in the rice grains' central region. The 50-30% fraction had the highest P/TP ratio among all tested rice varieties, suggesting spatial differences in P/TP within rice grains. Koshihikari had the lowest P/TP ratio. In addition, the 50-30% fraction had the lowest G/P ratio among all tested rice varieties, with Gohyakumangoku having the highest G/P ratio. Dewanosato had the lowest G/P value, and this value significantly differed from that of Yamadanishiki in the 30-0% fraction. We found substantial differences in protein composition within distinct spatial regions of rice grains, and larger differences among rice varieties were observed in the rice grain's central region.

QTL detection for rice grain storage protein content and genetic effect verifications

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01436-7.

Immunoanalytic investigation of grain proteins antigenic for celiac disease patients in an einkorn collection

Our study focuses on the complex characterization of a wild and cultivated einkorn collection of the Cereal Gene Bank of Agriculture Research Institute in Hungary, using proteomics, immune analytics and bioinformatics analyses. In a serological ELISA pre-screen of 208 different Triticum monococcum L. ssp. monococcum and Triticum monococcum L. ssp. aegilopoides genotypes with celiac disease samples high diversity was observed in the immune response. Based on the immune analytic results, four genotypes with significantly reduced immune reactivity were selected for detailed proteomics characterization. Our results confirm the benefits of high-throughput/large-scale pre-screening and the use of a complex examination platform to get relevant information about the genetic diversity of celiac disease-relevant proteins in the analyzed einkorn genotypes. These genotypes cannot be incorporated into the daily diet of celiac patients; however, they may represent candidates - especially in combination with enzymatic treatments - to improve the lifestyle of individuals suffering from other clinical conditions like non-celiac wheat sensitivity.

Comparison of the characteristics of prolamins among foxtail millet varieties with different palatability: Structural, morphological, and physicochemical properties

Recently, there are considerable interests in the influence of prolamins on eating quality of grains. To inquire the potential effect of prolamins on the palatability of foxtail millet, prolamin characteristics under its raw (PR) and post-cooked (PC) state among three typical varieties with high (Zhonggu, ZG), medium (Zhaonong, ZN), and low (Hongmiao, HM) palatability were compared. The distinctive differences in amino acid composition, molecular structure, physicochemical properties were found in PRs and PCs, especially for HM variety. HM-PR recorded the lowest hydrophobic amino acids and surface hydrophobicity while having the superior hydration properties. The lowest denaturation temperature was found in HM-PR, which also had the highest denaturation enthalpy (ΔH). Nevertheless, HM-PR exhibited irregularly spherical protein body with the largest mean diameter. Evidenced by the highest random coil and lower α-helix and β-sheet content, a less stable secondary structure of HM-PR was found, corresponding to the most intensified disulfide cross-linking and protein aggregations in HM upon cooking. Overall, HM-PR was presumed to greatly affect the hydro-thermal utilization efficiency of starch granules during cooking, given the steric-hindrance effect of prolamins on granules in endosperm. The Present study provided new insights into the role of prolamins on foxtail millet palatability.

Impact of condensed tannin interactions with grain proteins and non-starch polysaccharides on batter system properties

Proanthocyanidins (PA) cross-link wheat gluten proteins and dramatically enhance batter viscosity; PA could similarly affect related grains. This study aimed to determine PA effect on viscosity and pasting properties of barley, rye, and oat flours, and the relative contributions of PA interactions with proteins and non-starch polysaccharides (NSP). PA significantly increased batter viscosity, stability, and RVA peak viscosity in rye and barley flours (2.8× and 1.2×, respectively). Interestingly, viscosity peaked distinctively ~75 °C in PA-treated rye and barley flours, and their isolated protein-starch systems, indicating prolamins unravelled and complexed with PA during heating. Oat was largely unaffected by PA, likely because of its protein composition. Furthermore, water-soluble rye NSP and arabinoxylans, but not barley β-glucans, significantly increased starch pasting viscosity with PA; oxidative gelation was not a factor. Thus, rye flour viscosity dramatically increased through interactive effects of PA on rye proteins and NSP, which could expand its food applications.

Comparison of crude prolamins from seven kidney beans (Phaseolus vulgaris L.) based on composition, structure and functionality

Ethanol protocol, two-step protocol and enzymatic extraction were used to extract prolamins from seven kidney beans (P. vulgaris L.) compared with Osborne protocol. 70-80% (v/v) ethanol concentrations were beneficial to the extraction, and two-step protocol was conducive to higher prolamin content. Varied protein subunits were observed in electrophoresis profiles, and further differences in composition were identified by LC-MS/MS while potential functions were annotated. Stronger hydrophobicity was found with prolamins enrichment from light speckled kidney bean (LSKB), black speckled kidney bean (BSKB), and red kidney bean (RKB), which was negative correlation with α-helix content based on the principal component analysis (PCA). The crude prolamins from the two kinds of white kidney beans possessed higher sulfhydryl and exhibited better water holding capacity (WHC), while higher oil absorption capacity (OAC) was observed in LSKB, BSKB, and RKB. Compared with zein, kidney bean prolamins could be used as food packaging materials due to hydrophobicity.

OsERdj7 is an ER-resident J-protein involved in ER quality control in rice endosperm

OsERdj7 is one of six endoplasmic reticulum (ER)-resident J-domain-containing proteins (J-proteins) encoded by the rice genome that acts as a co-chaperone for Hsp70 and is characterized by the presence of two transmembrane domains. It is N-glycosylated and primarily exists in a dimeric form with a molecular mass of 64 kDa. When the microsomal fraction of maturing seeds was treated with alkaline, high salt or detergent compounds, OsERdj7 was solubilized, even in alkaline and high salt environments, indicating that it is not tightly integrated in the ER membrane. Next, to investigate its role during seed maturation, expression of OsERdj7 was specifically downregulated using RNA interference (RNAi) under the control of the endosperm-specific 16 kDa prolamin promoter in transgenic rice. As a result, the unfolded protein response (UPR) was induced in maturing seeds via activation of OsIRE1/OsbZIP50 and ATF6 orthologs, such as OsbZIP39 and OsbZIP60, leading to upregulation of several chaperones and folding enzymes. Furthermore, some prolamins (RM4 and RM9) were retained in the ER lumen in the form of a mesh-like structure without deposition to the inherent ER-derived protein bodies (PB-Is), although major storage protein glutelins were normally transported to protein storage vacuoles (PB-IIs). On the other hand, induction of ER associated degradation (ERAD) increased OsERdj7 expression in transgenic rice seeds in which ERAD related genes were highly expressed. Due to PDIL2-3 and OsHard3 co-immunoprecipitating with OsERdj7 in rice protoplasts, this result implicates OsERdj7 in the translocation of some seed proteins within the ER lumen and in the degradation of misfolded or unfolded proteins.

Genome-wide identification and characterization of seed storage proteins (SSPs) of foxtail millet (Setaria italica (L.) P. Beauv.)

We report the identification of 47 foxtail millet (Setaria italica (L.) P. Beauv.) seed storage proteins (SSPs) consisting of 14 albumins, 12 prolamins, 18 globulins and 3 glutelins using computational approaches and compared their essential amino acid composition with 225 SSPs of rice, barley, sorghum and maize. Comparative analysis revealed several unique foxtail millet SSPs containing high amounts of essential amino acids. These include three 2s-albumin proteins containing 11.9%, 10.9%, 9.82% lysine, one 10-kDa prolamin containing 20% methionine residues and one each 7S-globulin, 10-kDa prolamin, alpha-zein proteins containing 9.2% threonine, 9.35% phenylalanine and 2.5% tryptophan, respectively. High lysine containing albumins and high methionine containing prolamins were also detected in other cereals indicating that these SSPs are widespread in cereals. Phylogenetic studies revealed that the foxtail millet SSPs are closer to sorghum and maize. The lysine-rich albumins and the methionine-rich prolamins formed a separate cluster. Motif analysis of lysine-rich albumins displayed several lysine containing conserved motifs across cereals including foxtail millet. The 10-kDa prolamin protein containing 20% methionine was unique as it lacked the characteristic repeat motifs of methionine found in the high methionine containing zeins and kafirins. The motif "NPAAFWQQQQLL" was uniquely repeated in the foxtail millet high tryptophan prolamin protein. The findings of the present study provide new insights in foxtail millet seed storage protein characterization and their nutritional importance in terms of essential amino acid composition.

Accumulation of foreign polypeptides to rice seed protein body type I using prolamin portion sequences

Rice prolamins are accumulated in endoplasmic reticulum (ER)-derived proteins bodies, although conserved sequences retained in ER are not confirmed. We investigated portion sequences of prolamins that must accumulate in PB-Is. Rice seed prolamins are accumulated in endoplasmic reticulum (ER)-derived protein body type I (PB-I), but ER retention sequences in rice prolamin polypeptides have not been confirmed. Here we investigated the lengths of the prolamin portion sequences required for accumulation in PB-Is. Of the rice prolamins, we compared 13a and 13b prolamins because the amino acid sequences of these prolamins are quite similar except for the presence or absence of Cys-residues. We also generated and analyzed transgenic rice expressing several prolamin portion sequence-GFP fusion proteins. We observed that in 13a prolamin, when the portion sequences were extended more than the 68th amino acid residue from the initiating methionine, the prolamin portion sequence-GFP fusion proteins were accumulated in PB-Is. In 13b prolamin, when the portion sequences were extended by more than the 82nd amino acid residue from the initiating methionine, the prolamin portion sequence-GFP fusion proteins were accumulated in PB-Is. When those fusion proteins were extracted under non-reduced or reduced conditions, the 13a prolamin portion sequence-GFP fusion proteins in PB-Is were soluble under only the reduced condition. In contrast, 13b prolamin portion sequence-GFP fusion proteins were soluble under both non-reduced and reduced conditions. These results suggest that the accumulation of 13a prolamin in PB-Is is associated with the formation of disulfide bonds and/or hydrophobicity in 13a prolamin polypeptide, whereas the accumulation of 13b prolamin in PB-Is was less involved in the formation of disulfide bonds.

Deposition mode of transforming growth factor-β expressed in transgenic rice seed

Mouse TGF-β highly accumulated by expressing as a secretory homodimeric protein in transgenic rice endosperm. It was tightly deposited in ER-derived PBs by interaction with cysteine-rich prolamins. TGF-β is one of the key players involved in the induction and maintenance of mucosal immune tolerance to dietary proteins through the induction of regulatory T cells. In order to utilize rice-based TGF-β as a tool to promote oral immune tolerance induction, high production of TGF-β is essentially required. When the codon-optimized mTGF-β was expressed as a secretory protein by ligating an N-terminal signal peptide and C-terminal KDEL ER retention signal under the control of the endosperm-specific rice storage protein glutelin GluB-1 promoter, accumulation level was low in stable transgenic rice seeds. Then, to increase the accumulation level of mTGF-β, it was expressed as fusion proteins by inserting into the C terminus of acidic subunit of glutelin GluA and the variable region of 26 kDa globulin. When fused with the glutelin, it could accumulate well as visible bands by CBB staining gel, but not for the 26 kDa globulin. Unexpectedly, expression of homodimeric mTGF-β linked by a 6×Gly1×Ser linker as secretory protein resulted in higher level of accumulation. This expression level was further enhanced by reduction of some endogenous prolamins by RNA interference. The monomeric and dimeric mTGF-βs were deposited in ER-derived PBs containing prolamins. When highly produced in rice seed, it is notable that most of ER-derived PBs were distorted and granulated. Step-wise extraction of storage proteins from rice seeds suggested that the mTGF-β strongly interacted with cysteine-rich prolamins via disulfide bonds. This result was also supported by the finding that reducing agent was absolutely required for mTGF-β extraction.

Control of foreign polypeptide localization in specific layers of protein body type I in rice seed

Prolamin-GFP fusion proteins, expressed under the control of native prolamin promoters, were localized in specific layers of PB-Is. Prolamin-GFP fusion proteins were gradually digested from outside by pepsin digestion. In rice seed endosperm, protein body type I (PB-I) has a layered structure consisting of prolamin species and is the resistant to digestive juices in the intestinal tract. We propose the utilization of PB-Is as an oral vaccine carrier to induce mucosal immune response effectively. If vaccine antigens are localized in a specific layer within PB-Is, they could be protected from gastric juice and be delivered intact to the small intestine. We observed the localization of GFP fluorescence in transgenic rice endosperm expressing prolamin-GFP fusion proteins with native prolamin promoters, and we confirmed that the foreign proteins were located in specific layers of PB-Is artificially. Each prolamin-GFP fusion protein was localized in specific layers of PB-Is, such as the outer-most layer, middle layer, and core region. Furthermore, to investigate the resistance of prolamin-GFP fusion proteins against pepsin digestion, we performed in vitro pepsin treatment. Prolamin-GFP fusion proteins were gradually digested from the peripheral region and the contours of PB-Is were made rough by in vitro pepsin treatment. These findings suggested that prolamin-GFP fusion proteins accumulating specific layers of PB-Is were gradually digested and exposed from the outside by pepsin digestion.