Evaluation of Extraction Solutions for Biochemical Analyses of the Proteins in Rice Grains

Protein content prediction of rice grains based on hyperspectral imaging

This study utilized hyperspectral imaging technology combined with mathematical modeling methods to predict the protein content of rice grains. Firstly, the Kjeldahl method was used to determine the protein content of rice grains, and different preprocessing techniques were applied to the spectral information. Then, a prediction model for rice grain protein content was developed by combining the spectral data with the protein content. After performing multiplicative scatter correction (MSC) preprocessing and selecting feature wavelengths based on successive projections algorithm (SPA), the multivariate linear regression (MLR) model showed the best prediction performance, with a calibration set R2C of 0.9393, a validation set R2V of 0.8998, an RMSEV of 0.1725, and an RPD of 3.16. Finally, the quantitative protein content model was mapped pixel by pixel to visualize the distribution of rice protein, providing possibilities for non-destructive protein content detection.

Wheat-Based Glues in Conservation and Cultural Heritage: (Dis)solving the Proteome of Flour and Starch Pastes and Their Adhering Properties

Plant-based adhesives, such as those made from wheat, have been prominently used for books and paper-based objects and are also used as conservation adhesives. Starch paste originates from starch granules, whereas flour paste encompasses the entire wheat endosperm proteome, offering strong adhesive properties due to gluten proteins. From a conservation perspective, understanding the precise nature of the adhesive is vital as the longevity, resilience, and reaction to environmental changes can differ substantially between starch- and flour-based pastes. We devised a proteomics method to discern the protein content of these pastes. Protocols involved extracting soluble proteins using 0.5 M NaCl and 30 mM Tris-HCl solutions and then targeting insoluble proteins, such as gliadins and glutenins, with a buffer containing 7 M urea, 2 M thiourea, 4% CHAPS, 40 mM Tris, and 75 mM DTT. Flour paste's proteome is diverse (1942 proteins across 759 groups), contrasting with starch paste's predominant starch-associated protein makeup (218 proteins in 58 groups). Transformation into pastes reduces proteomes' complexity. Testing on historical bookbindings confirmed the use of flour-based glue, which is rich in gluten and serpins. High levels of deamidation were detected, particularly for glutamine residues, which can impact the solubility and stability of the glue over time. The mass spectrometry proteomics data have been deposited to the ProteomeXchange, Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the data set identifier MSV000093372 (ftp://MSV000093372@massive.ucsd.edu).

Effects of endogenous proteins on rice digestion during small intestine (in vitro) digestion

Rices with higher protein contents are nutritionally desirable. This study investigates the effects of endosperm proteins on starch in vitro digestibility in cooked and uncooked rice, and the mechanisms underlying any changes. The composition of rice endosperm proteins and the morphologies of proteins and starch granules were determined by SDS-PAGE and confocal microscopy. Starch molecular fine structure was examined using size-exclusion chromatography. In vitro digestion showed that the digestion rate coefficients (k) of cooked rice flour were significantly lower than those of isolated starch or of a starch-protein mixture. (e.g for samples from SWR4, k is 9.6, 12.9 and 11.6 × 10^-2 min^-1 for cooked rice flour, isolated starch and starch-protein mixture, respectively). For uncooked samples, digestion rate coefficients were 1.4, 1.5 and 1.8 × 10^-2 min^-1 for flour, starch-protein mixture and starch, respectively. The digestion rates in cooked samples were higher than those in uncooked samples. This suggests that, in cooked samples, starch digestion rates are more affected by the protein physical barrier than by some chemical effect (e.g. hydrogen bonding between protein and starch), while in uncooked samples, a chemical effect from protein is more pronounced than a physical barrier from protein.

Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

BACKGROUND

Wheat grain avenin-like proteins (ALPs) belong to a recently discovered class of wheat grain storage protein. ALPs in wheat grains not only have beneficial effects on dough quality but also display antifungal activities, which is a novel observation for wheat storage proteins. Previous studies have shown that ALPs are likely present in the albumin/globulin fractions of total protein extract from wheat flour. However, the accumulation characteristics of these ALPs in the mature wheat grain remains unknown.

RESULTS

In the present study, a total of 13 ALPs homologs were isolated and characterized in the albumin/globulin fractions of the wheat protein extract. A combination of multiple techniques including RP-HPLC, SDS-PAGE, MALDI-TOF and peptide sequencing were used for accurate separation and identification of individual ALP homolog. The C-terminal TaALP-by-4AL/7DS, TaALP-by-4AL/7AS/7DS, TaALP-bx/4AL/7AS/7DS, TaALP-ay-7DS, TaALP-ay-4AL, TaALP-ax-4AL, TaALP-ax-7AS, and TaALP-ax-7DS, were separated as individual protein bands from wheat flour for the first time. These unique ALPs peptides were mapped to the latest wheat genome assembly in the IWGSC database. The characteristic defence related proteins present in albumin and globulin fractions, such as protein disulfide-isomerase (PDI), grain softness protein (GSP), alpha-amylase inhibitors (AAIs) and endogenous alpha-amylase/subtilisin inhibitor were also found to co-segregate with these identified ALPs, avenin-3 and α-gliadins. The molecular weight range and the electrophoresis segregation properties of ALPs were characterised in comparison with the proteins containing the tryp_alpha_amyl domain (PF00234) and the gliadin domain (PF13016), which play a role in plant immunity and grain quality. We examined the phylogenetic relationships of the AAIs, GSP, avenin-3, α-gliadins and ALPs, based on the alignment of their functional domains. MALDI-TOF profiling indicated the occurrence of certain post-translations modifications (PTMs) in some ALP subunits.

CONCLUSIONS

We reported for the first time the complete profiling of ALPs present in the albumin/globulin fractions of wheat grain protein extracts. We concluded that majority of the ALPs homologs are expressed in wheat grains. We found clear evidence of PTMs in several ALPs peptides. The identification of both gliadin domain (PF13016) and Tryp_alpha_amyl domain (PF00234) in the mature forms of ALPs highlighted the multiple functional properties of ALPs in grain quality and disease resistance.

Absolute Quantification of Allergen Glb33 in Rice by Liquid Chromatography-Mass Spectrometry using Two Isotope-Labeled Standard Peptides

Allergen Glb33 is an important allergen in rice that can cause allergic reactions such as asthma and atopic dermatitis. However, knowledge of the content in rice is sparse. In the present work, an absolute protein quantification method was established for allergen Glb33 in rice samples using liquid chromatography-tandem mass spectrometry. After extraction of allergen Glb33 from rice grains using salt solution, the isotope-labeled peptide internal standard was added to the extract, followed by enzymatic digestion with trypsin. The signature peptide and its isotope-labeled analogue from the tryptic hydrolysates of allergen Glb33 and the internal standard were detected by liquid chromatography-tandem mass spectrometry. The quantitative bias caused by tryptic efficiency and matrix effect was corrected by using two isotope-labeled standard peptides. The method exhibited good linearity in the range of 1-200 nM, with coefficients of determination of R² > 0.998. A high sensitivity was observed, with a limit of quantification of 0.97 nM. Mean recoveries obtained from different rice matrices ranged from 82.7%-98.1% with precision <8.5% in intraday trials ( n = 6), while mean recoveries were from 75.1%-107.4% with precision <14.6% in interday trials ( n = 14). The developed method was successfully applied to the analysis of allergen Glb33 in 24 different rice cultivars.

Unexpected synergistic HIV neutralization by a triple microbicide produced in rice endosperm

Our paper provides an approach for the durable deployment of anti-HIV agents in the developing world. We developed a transgenic rice line expressing three microbicidal proteins (the HIV-neutralizing antibody 2G12 and the lectins griffithsin and cyanovirin-N). Simultaneous expression in the same plant allows the crude seed extract to be used directly as a topical microbicide cocktail, avoiding the costs of multiple downstream processes. This groundbreaking strategy is realistically the only way that microbicidal cocktails can be manufactured at a cost low enough for the developing world, where HIV prophylaxis is most in demand.

The transmission of HIV can be prevented by the application of neutralizing monoclonal antibodies and lectins. Traditional recombinant protein manufacturing platforms lack sufficient capacity and are too expensive for developing countries, which suffer the greatest disease burden. Plants offer an inexpensive and scalable alternative manufacturing platform that can produce multiple components in a single plant, which is important because multiple components are required to avoid the rapid emergence of HIV-1 strains resistant to single microbicides. Furthermore, crude extracts can be used directly for prophylaxis to avoid the massive costs of downstream processing and purification. We investigated whether rice could simultaneously produce three functional HIV-neutralizing proteins (the monoclonal antibody 2G12, and the lectins griffithsin and cyanovirin-N). Preliminary in vitro tests showed that the cocktail of three proteins bound to gp120 and achieved HIV-1 neutralization. Remarkably, when we mixed the components with crude extracts of wild-type rice endosperm, we observed enhanced binding to gp120 in vitro and synergistic neutralization when all three components were present. Extracts of transgenic plants expressing all three proteins also showed enhanced in vitro binding to gp120 and synergistic HIV-1 neutralization. Fractionation of the rice extracts suggested that the enhanced gp120 binding was dependent on rice proteins, primarily the globulin fraction. Therefore, the production of HIV-1 microbicides in rice may not only reduce costs compared to traditional platforms but may also provide functional benefits in terms of microbicidal potency.

Inter-laboratory optimization of protein extraction, separation, and fluorescent detection of endogenous rice allergens

In rice, several allergens have been identified such as the non-specific lipid transfer protein-1, the α-amylase/trypsin-inhibitors, the α-globulin, the 33 kDa glyoxalase I (Gly I), the 52-63 kDa globulin, and the granule-bound starch synthetase. The goal of the present study was to define optimal rice extraction and detection methods that would allow a sensitive and reproducible measure of several classes of known rice allergens. In a three-laboratory ring-trial experiment, several protein extraction methods were first compared and analyzed by 1D multiplexed SDS-PAGE. In a second phase, an inter-laboratory validation of 2D-DIGE analysis was conducted in five independent laboratories, focusing on three rice allergens (52 kDa globulin, 33 kDa glyoxalase I, and 14-16 kDa α-amylase/trypsin inhibitor family members). The results of the present study indicate that a combination of 1D multiplexed SDS-PAGE and 2D-DIGE methods would be recommended to quantify the various rice allergens.

Rice protein-induced enterocolitis syndrome with transient specific IgE to boiled rice but not to retort-processed rice

Described herein is the case of an 8-month-old girl with atypical food protein-induced enterocolitis syndrome due to rice. She presented with vomiting and poor general activity 2 h after ingestion of boiled rice. Oral food challenge test using high-pressure retort-processed rice was negative, but re-exposure to boiled rice elicited gastrointestinal symptoms. On western blot analysis the patient's serum was found to contain IgE bound to crude protein extracts from rice seed or boiled rice, but not from retort-processed rice. The major protein bands were not detected in the electrophoresed gel of retort-processed rice extracts, suggesting decomposition by high-temperature and high-pressure processing. Oral food challenge for diagnosing rice allergy should be performed with boiled rice to avoid a false negative. Additionally, some patients with rice allergy might be able to ingest retort-processed rice as a substitute for boiled rice.

Differential analysis of protein expression in RNA-binding-protein transgenic and parental rice seeds cultivated under salt stress

Transgenic plants tolerant to various environmental stresses are being developed to ensure a consistent food supply. We used a transgenic rice cultivar with high saline tolerance by introducing an RNA-binding protein (RBP) from the ice plant (Mesembryanthemum crystallinum); differences in salt-soluble protein expression between nontransgenic (NT) and RBP rice seeds were analyzed by 2D difference gel electrophoresis (2D-DIGE), a gel-based proteomic method. To identify RBP-related changes in protein expression under salt stress, NT and RBP rice were cultured with or without 200 mM sodium chloride. Only two protein spots differed between NT and RBP rice seeds cultured under normal conditions, one of which was identified as a putative abscisic acid-induced protein. In NT rice seeds, 91 spots significantly differed between normal and salt-stress conditions. Two allergenic proteins of NT rice seeds, RAG1 and RAG2, were induced by high salt. In contrast, RBP rice seeds yielded seven spots and no allergen spots with significant differences in protein expression between normal and salt-stress conditions. Therefore, expression of fewer proteins was altered in RBP rice seeds by high salt than those in NT rice seeds.