Barley germination: Spatio-temporal considerations for designing and interpreting ‘omics’ experiments

Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley (Hordeum vulgare L.)

The conversion of raw barley (Hordeum vulgare L.) to malt requires a process of controlled germination, where the grain is submerged in water to raise the moisture content to >40%. The transmembrane proteins, aquaporins, influence water uptake during the initial stage of controlled germination, yet little is known of their involvement in malting. With the current focus on sustainability, understanding the mechanisms of water uptake and usage during the initial stages of malting has become vital in improving efficient malting practices. In this study, we used quantitative proteomics analysis of two malting barley genotypes demonstrating differing water-uptake phenotypes in the initial stages of malting. Our study quantified 19 transmembrane proteins from nine families, including seven distinct aquaporin isoforms, including the plasma intrinsic proteins (PIPs) PIP1;1, PIP2;1, and PIP2;4 and the tonoplast intrinsic proteins (TIPs) TIP1;1, TIP2;3, TIP3;1, and TIP3;2. Our findings suggest that the presence of TIP1;1, TIP3;1, and TIP3;2 in the mature barley grain proteome is essential for facilitating water uptake, influencing cell turgor and the formation of large central lytic vacuoles aiding storage reserve hydrolysis and endosperm modification efficiency. This study proposes that TIP3s mediate water uptake in malting barley grain, offering potential breeding targets for improving sustainable malting practices.

Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.

Comparison of structural and functional properties of maize starch produced with commercial or endogenous enzymes

To explore an effective and economic method to prepare higher contents of resistant starch (RS), different enzyme treatments including single pullulanase (PUL), commercial α-amylase (AA) or/and β-amylase (BA) with PUL, and malt endogenous amylase (MA) with PUL were used and the structural, physicochemical properties and digestibility of all modified starches (MS) were compared. All the enzyme-treated starches displayed a mixture of B and V-type diffraction patterns. The MA/PUL-MS showed higher V-type diffraction peak intensity as compared to other modified starches. Compared to the combination of commercial enzyme treatment, the combination of malt enzyme treatment led to higher apparent amylose contents (45.56%), RS content (53.93%) and thermal stability (302 °C), whereas it possessed lower solubility indices and predicted glycaemic index. The apparent viscosity and shear resistance of MA/PUL-MS were lower than that of AA/PUL-MS, whereas that of MA/PUL-MS was higher than that of BA/PUL-MS and BA/AA/PUL-MS. These findings would provide a theoretical and applicative basis to produce foods with lower GI in industrial production.

Corn starch modification during endogenous malt amylases: The impact of synergistic hydrolysis time of α-amylase and β-amylase and limit dextrinase

To expand the utility of barley malts and decrease the cost of enzyme-modified starch production, the structural and physicochemical characteristics of corn starch modified with fresh barley malts at different hydrolysis time were investigated. The results indicated that compared to native starch, A chain (DP 6-12) of the enzyme-treated starches increased at hydrolysis time (≤12 h), but it decreased at hydrolysis time (>12 h). Inversely, B chains (DP > 13) decreased at hydrolysis time (≤12 h) and they generally increased at hydrolysis time (>12 h). The relative crystallinity decreased from 25.63% to 21.38% and 1047 cm^-1/1022 cm^-1 reduced from 1.042 to 0.942 after endogenous malt amylases at hydrolysis time from 0 to 72 h, and the thermal degradation temperatures decreased from 323.19 to 295.94 °C, whereas the gelatinization temperatures slightly increased. The gel strength decreased at hydrolysis time less than 12 h, but it increased at hydrolysis time more than 12 h. The outcomings would provide a theoretical and applicative basis about how endogenous malt amylases with lower price modify starches to obtain desirable starch derivatives and industrial production.

Description and functional analysis of the transcriptome from malting barley

The present study aimed to establish an early model of the malting barley transcriptome, which describes the expression of genes and their ontologies, identify the period during malting with the largest dynamic shift in gene expression for future investigation, and to determine the expression patterns of all starch degrading enzyme genes relevant to the malting and brewing industry. Large dynamic increases in gene expression occurred early in malting with differential expressed genes enriched for cell wall and starch hydrolases amongst many malting related categories. Twenty-five of forty starch degrading enzyme genes were differentially expressed in the malting barley transcriptome including eleven α-amylase genes, six β-amylase genes, three α-glucosidase genes, and all five starch debranching enzyme genes. Four new or novel α-amylase genes, one β-amylase gene (Bmy3), three α-glucosidase genes, and two isoamylase genes had appreciable expression that requires further exploration into their potential relevance to the malting and brewing industry.

Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs

Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.

Characteristic changes in malt, wort, and beer produced from different Nigerian rice varieties as influenced by varying malting conditions

Gluten-free beer could be produced with rice, although the latter would primarily serve as adjunct in combination with barley malt in today’s brewing. However, the recent growing realisation of the potential and applications of rice malt for brewing an all-rice malt beer through varying malting conditions cannot be overlooked. In this study, therefore, the characteristic changes in malt, wort, and beer from different Nigerian rice varieties (FARO 44, FARO 57, NERICA 7) as influenced by varying malting conditions (steeping duration (18, 24 and 30 h), germination periods (2, 3 and 4 days) and kilning temperatures (50 and 55 °C)), were investigated. Rice (grain) samples were examined by thousand kernel weight (TKW), germinative energy (GE), germinative capacity (GC), and degree of steeping (DoS). To ensure that rice wort/beer with unique beer style and enhanced attributes, comparable to barley wort/beer is produced, malting conditions that produced rice malts with peak diastatic power (DP), cold water extract (CWE), and hot water extract (HWE) were selected. Peak DP, CWE and HWE were obtained at FARO 44 (18 h steeping, 3 days germination, 55 °C kilning (S₁₈G₃K_55°)), FARO 57 (30 h steeping, 2 days germination, 50 °C kilning (S₃₀G₂K_50°)) and NERICA 7 (24 h steeping, 3 days germination, 55 °C kilning (S₂₄G₃K_55°)). Selected malts were further tested for moisture content, total nitrogen, malt yield and malting loss and subsequently progressed to wort and beer production. Wort’s pH, total soluble nitrogen (TSN), brix, kolbach index (KI), free amino nitrogen (FAN), dextrose equivalent (DE), original extract (OE) and sugar profile were determined, as well as beer’s pH, colour, apparent extract (AE), alcohol by volume (%ABV), turbidity and sensory attributes. Rice grain varied significantly (p < 0.05) in TKW, GE, GC and DoS across varieties. Despite wort’s pH, TSN, DE, OE as well as beer pH, colour, AE and turbidity resembling (p > 0.05) across varieties, wort’s brix, KI, FAN, sugar profile as well as beer’s %ABV, differed significantly (p < 0.05). Sensory attributes of appearance, colour, mouthfeel, and overall acceptability in beer differed noticeably (p < 0.05), except for aroma and taste (p > 0.05). Overall, the rice beer, though very slightly hazy, represented a pale yellow light lager, which is indicative of its peculiar beer style. Besides increased DP and enhanced hydrolysis, varying malting conditions of current study could serve as a pathway of reducing the cost of exogenous (commercial) enzymes or barley malt imports, together with decreasing barley’s dependency for brewing in the tropics.

Comparative de novo transcriptome analysis of barley varieties with different malting qualities

Barley is one of the most important crops in the world. Barley is used as both food and feed and is important for malt production. Demands for malting quality differ among countries and customs. Malting quality is a complex characteristic involving barley genetics, the environmental conditions during barley growth, and the technological parameters of the malting process. In this study, the hypothesis was that there were no differences between two groups of barley varieties with different but defined malting qualities, which was tested using RNA sequencing during selected stages of malting. In total, 919 differentially transcribed genes between the two barley groups were identified and annotated. Differentially expressed genes (DEGs) were primarily assigned to gene ontology (GO) terms of oxidation-reduction process - oxidoreductase activity, response to stress, carbohydrate metabolic process, and proteolysis - hydrolase activity, and metal ion binding. Genes connected with the plasma membrane and its integral components also play important roles in malting quality. DEG profiles of selected genes in the three malting stages indicate a complex character of malting quality. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were identified. SNPs and indels with the best quality were used for primer design. After optimization and validation, five molecular markers were developed for use in barley breeding.

Effect of the cleaning process on physical properties for different malting barley seed varieties

The aim of the study was to investigate the influence of the barley cleaning process in relation to physical properties. The knowledge of the range of changes in the physical parameters of processed material and their mutual relationships is required for the design and implementation of various technological processes. In this study were compared the input and output commodities in the primary postharvest cleaning process of undesirable components-occurring as admixtures of fine and coarse barley impurities as well as the barley component itself. An efficient cleaning process ensuring barley grain quality is a basic step in beer production. Therefore, seven bred varieties of brewing barley (Malz, Sebastian, Francin, KWS Irina1, KWS Irina2, Bojos, and Laudis) were tested for the qualitative assessment of the cleaning process. Physical parameters such as granulometry, bulk and tapped density, angle of repose, internal and wall friction angle, and flow functions were determined for all samples. In order to identify whether the barley variety or the sample cleaning significantly influences the determined physical properties, two-way ANOVA was applied. The results imply that barley cleaning had the main influence on wall friction angle, while the barley variety had a significant effect on effective internal friction. Moreover, the mechanical postharvest cleaning process reduces the overall wall friction.

Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain

Mobilization of reserves in germinated cereal grains is critical for early seedling vigour, global crop productivity, and hence food security. Gibberellins (GAs) are central to this process. We have developed a spatio-temporal model that describes the multifaceted mechanisms of GA regulation in germinated barley grain. The model was generated using RNA sequencing transcript data from tissues dissected from intact, germinated grain, which closely match measurements of GA hormones and their metabolites in those tissues. The data show that successful grain germination is underpinned by high concentrations of GA precursors in ungerminated grain, the use of independent metabolic pathways for the synthesis of several bioactive GAs during germination, and a capacity to abort bioactive GA biosynthesis. The most abundant bioactive form is GA1, which is synthesized in the scutellum as a glycosyl conjugate that diffuses to the aleurone, where it stimulates de novo synthesis of a GA3 conjugate and GA4. Synthesis of bioactive GAs in the aleurone provides a mechanism that ensures the hormonal signal is relayed from the scutellum to the distal tip of the grain. The transcript data set of 33 421 genes used to define GA metabolism is available as a resource to analyse other physiological processes in germinated grain.

Insights on the Proteases Involved in Barley and Wheat Grain Germination

Seed storage proteins must be hydrolyzed by proteases to deliver the amino acids essential for embryo growth and development. Several groups of proteases involved in this process have been identified in both the monocot and the dicot species. This review focuses on the implication of proteases during germination in two cereal species, barley and wheat, where proteolytic control during the germination process has considerable economic importance. Formerly, the participation of proteases during grain germination was inferred from reports of proteolytic activities, the expression of individual genes, or the presence of individual proteins and showed a prominent role for papain-like and legumain-like cysteine proteases and for serine carboxypeptidases. Nowadays, the development of new technologies and the release of the genomic sequences of wheat and barley have permitted the application of genome-scale approaches, such as those used in functional genomics and proteomics. Using these approaches, the repertoire of proteases known to be involved in germination has increased and includes members of distinct protease families. The development of novel techniques based on shotgun proteomics, activity-based protein profiling, and comparative and structural genomics will help to achieve a general view of the proteolytic process during germination.

Isolation of tissues and preservation of RNA from intact, germinated barley grain

Isolated barley (Hordeum vulgare L.) aleurone layers have been widely used as a model system for studying gene expression and hormonal regulation in germinating cereal grains. A serious technological limitation of this approach has been the inability to confidently extrapolate conclusions obtained from isolated tissues back to the whole grain, where the co-location of several living and non-living tissues results in complex tissue-tissue interactions and regulatory pathways coordinated across the multiple tissues. Here we have developed methods for isolating fragments of aleurone, starchy endosperm, embryo, scutellum, pericarp-testa, husk and crushed cell layers from germinated grain. An important step in the procedure involves the rapid fixation of the intact grain to freeze the transcriptional activity of individual tissues while dissection is effected for subsequent transcriptomic analyses. The developmental profiles of 19 611 gene transcripts were precisely defined in the purified tissues and in whole grain during the first 24 h of germination by RNA sequencing. Spatial and temporal patterns of transcription were validated against well-defined data on enzyme activities in both whole grain and isolated tissues. Transcript profiles of genes involved in mitochondrial assembly and function were used to validate the very early stages of germination, while the profiles of genes involved in starch and cell wall mobilisation matched existing data on activities of corresponding enzymes. The data will be broadly applicable for the interrogation of co-expression and differential expression patterns and for the identification of transcription factors that are important in the early stages of grain and seed germination.

Mapping Protein-Protein Interactions Using Affinity Purification and Mass Spectrometry

The mapping of protein-protein interaction (PPI) networks and their dynamics are crucial steps to deciphering the function of a protein and its role in cellular pathways, making it critical to have comprehensive knowledge of a protein's interactome. Advances in affinity purification and mass spectrometry technology (AP-MS) have provided a powerful and unbiased method to capture higher-order protein complexes and decipher dynamic PPIs. However, the unbiased calling of nonspecific interactions and the ability to detect transient interactions remains challenging when using AP-MS, thereby hampering the detection of biologically meaningful complexes. Additionally, there are plant-specific challenges with AP-MS, such as a lack of protein-specific antibodies, which must be overcome to successfully identify PPIs. Here we discuss and describe a protocol designed to bypass the traditional challenges of AP-MS and provide a roadmap to identify bona fide PPIs in plants.