Posttranslational Modifications Drive Protein Stability to Control the Dynamic Beer Brewing Proteome

Systematic profiling of ale yeast protein dynamics across fermentation and repitching

Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is among the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout 2 fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.

Proteomics and Metabolomics Reveal that an Abundant α-Glucosidase Drives Sorghum Fermentability for Beer Brewing

Sorghum (Sorghum bicolor), a grass native to Africa, is a popular alternative to barley for brewing beer. The importance of sorghum to beer brewing is increasing because it is a naturally gluten-free cereal, and climate change is expected to cause a reduction in the production of barley over the coming decades. However, there are challenges associated with the use of sorghum instead of barley in beer brewing. Here, we used proteomics and metabolomics to gain insights into the sorghum brewing process to advise processes for efficient beer production from sorghum. We found that during malting, sorghum synthesizes the amylases and proteases necessary for brewing. Proteomics revealed that mashing with sorghum malt required higher temperatures than barley malt for efficient protein solubilization. Both α- and β-amylase were considerably less abundant in sorghum wort than in barley wort, correlating with lower maltose concentrations in sorghum wort. However, metabolomics revealed higher glucose concentrations in sorghum wort than in barley wort, consistent with the presence of an abundant α-glucosidase detected by proteomics in sorghum malt. Our results indicate that sorghum can be a viable grain for industrial fermented beverage production, but that its use requires careful process optimization for efficient production of fermentable wort and high-quality beer.

Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley

Post-translational modifications (PTMs) of biomacromolecules can be useful for understanding the processes by which a relatively small number of individual genes in a particular genome can generate enormous biological complexity in different organisms. The proteomes of barley and the brewing process were investigated by different techniques. However, their diverse and complex PTMs remain understudied. As standard analytical approaches have limitations, innovative analytical approaches need to be developed and applied in PTM studies. To make further progress in this field, it is necessary to specify the sites of modification, as well as to characterize individual isoforms with increased selectivity and sensitivity. This review summarizes advances in the PTM analysis of barley proteins, particularly those involving mass spectrometric detection. Our focus is on monitoring phosphorylation, glycation, and glycosylation, which critically influence functional behavior in metabolism and regulation in organisms.

Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching

Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is amongst the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout two fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.

Variation in quality of grains used in malting and brewing

Cereal grains have been domesticated largely from food grains to feed and malting grains. Barley (Hordeum vulgare L.) remains unparalleled in its success as a primary brewing grain. However, there is renewed interest in "alternative" grains for brewing (and distilling) due to attention being placed on flavor, quality, and health (i.e., gluten issues) aspects that they may offer. This review covers basic and general information on "alternative grains" for malting and brewing, as well as an in-depth look at several major biochemical aspects of these grains including starch, protein, polyphenols, and lipids. These traits are described in terms of their effects on processing and flavor, as well as the prospects for improvement through breeding. These aspects have been studied extensively in barley, but little is known about the functional properties in other crops for malting and brewing. In addition, the complex nature of malting and brewing produces a large number of brewing targets but requires extensive processing, laboratory analysis, and accompanying sensory analysis. However, if a better understanding of the potential of alternative crops that can be used in malting and brewing is needed, then significantly more research is required.

The Study of Mineral Elements Participation in Brewing Products Foam Structure Formation

The article is devoted to the study of the metal ion’s role in the formation of the foam colloidal structure. The nitrogenous compounds prominent role as structuring compounds of the colloidal film on the carbon dioxide bubbles surface is noted. Based on the calculation of the correlation strength between beer samples organic compounds obtained based on light and dark malts, as well as barley and corn as unmalted raw materials, the effect of Ca, Mg, Mn, Co and Na mineral ions on the foam structure was evaluated. It was shown that Ca, Mg, Mn, Na, Co ions take part in the foam structure formation in conjunction with the grain raw materials thiol nitrogen, and Ca, Mg, Mn ions in conjunction with catechins of both grain and hop raw materials. High correlation coefficients between foam resistance and all ions (r-0.991÷0.998), foam resistance, catechins and Co ions (r 0.991), as well as foam resistance and Ca and Mg ions (r -0.987) ensure the elasticity of the foam structure colloidal film.

Developing colloidal structure of beer by grain organic compounds

The present article introduces the problem of determining the general structure of beer as a complex system of related biomolecules. The objective was to establish the correlation of various quantities of organic compounds in beer formulation. The research featured samples of filtered pasteurized beer obtained from a retail chain shop in Moscow (Russia). The experiment relied on standard research methods, including instrumental methods of analysis, e.g., high-performance liquid chromatography (HPLC). The obtained experimental data underwent a statistical analysis using the Statistica software (StatSoft, 2016). The research established the correlation between the type of grain (barley or wheat malt) and the content of organic compounds, e.g., β-glucan, polyphenols, soluble nitrogen, etc. The research also revealed some patterns in the distribution of proteins, which served as a framework for the system of organic compounds. The distribution of thiol proteins proved to depend on the dissolution degree of the grain and was different in barley light, barley dark, and wheat malt samples. The fraction distribution of β-glucan depended on the color of the malt. In light beer samples, it concentrated in high- and medium-molecular fractions of nitrogenous substances, in dark beer – in low-molecular fractions (≤ 63%). Initial wort density and alcohol content affected the amount of catechins and total polyphenols. Nitrogenous compounds depended on the color, initial extract, and alcohol content. The nitrogenous structure and other organic compounds of beer proved to depend on protein substances. The research also revealed a number of factors that affected the fraction distribution of biomolecules in different beer sorts.

An Integrated Proteomic and Glycoproteomic Investigation Reveals Alterations in the N-Glycoproteomic Network Induced by 2-Deoxy-D-Glucose in Colorectal Cancer Cells

As a well-known glycolysis inhibitor for anticancer treatment, 2-Deoxy-D-glucose (2DG) inhibits the growth and survival of cancer cells by interfering with the ATP produced by the metabolism of D-glucose. In addition, 2DG inhibits protein glycosylation in vivo by competing with D-mannose, leading to endoplasmic reticulum (ER) stress and unfolded protein responses in cancer cells. However, the molecular details underlying the impact of 2DG on protein glycosylation remain largely elusive. With an integrated approach to glycoproteomics and proteomics, we characterized the 2DG-induced alterations in N-glycosylation, as well as the cascading impacts on the whole proteome using the HT29 colorectal cancer cell line as a model system. More than 1700 site-specific glycoforms, represented by unique intact glycopeptides (IGPs), were identified. The treatment of 2DG had a broad effect on the N-glycoproteome, especially the high-mannose types. The glycosite occupancy of the high-mannose N-glycans decreased the most compared with the sialic acid and fucose-containing N-glycans. Many of the proteins with down-regulated high-mannose were implicated in functional networks related to response to topologically incorrect protein, integrin-mediated signaling, lysosomal transport, protein hydroxylation, vacuole, and protein N-glycosylation. The treatment of 2DG also functionally disrupted the global cellular proteome, evidenced by significant up-regulation of the proteins implicated in protein folding, endoplasmic reticulum, mitochondrial function, cellular respiration, oxidative phosphorylation, and translational termination. Taken together, these findings reveal the complex changes in protein glycosylation and expression underlying the various effects of 2DG on cancer cells, and may provide insightful clues to inform therapeutic development targeting protein glycosylation.

Proteomics and glycoproteomics of beer and wine

Beer and wine are fermented beverages that contain abundant proteins released from barley or grapes, and secreted from yeast. These proteins are associated with many quality attributes including turbidity, foamability, effervescence, flavour and colour. Many grape proteins and secreted yeast proteins are glycosylated, and barley proteins can be glycated under the high temperatures in the beer making process. The emergence of high-resolution mass spectrometry has allowed proteomic and glycoproteomic analyses of these complex mixtures of proteins towards understanding their role in determining beer and wine attributes. In this review, we summarise recent studies of proteomic and glycoproteomic analyses of beer and wine including their strategies for mass spectrometry (MS)-based identification, quantification and characterisation of the glyco/proteomes of fermented beverages to control product quality.

The Influence of Hop Phenolic Compounds on Dry Hopping Beer Quality

Background: The article considers the phenolic hop compounds’ effect on the quality indicators of finished beer. The topic under consideration is relevant since it touches on the beer matrix colloidal stability when compounds with potential destabilizing activity are introduced into it from the outside. Methods: The industrial beer samples’ quality was assessed by industry-accepted methods and using instrumental analysis methods (high-performance liquid chromatography methods—HPLC). The obtained statistical data were processed by the Statistics program (Microsoft Corporation, Redmond, WA, USA, 2006). Results: The study made it possible to make assumptions about the functional dependence of the iso-α-bitter resins and isoxanthohumol content in beer samples. Mathematical analysis indicate interactions between protein molecules and different malted grain and hop compounds are involved in beer structure, in contrast to dry hopped beer, where iso-a-bitter resins, protein, and coloring compounds were significant, with a lower coefficient of determination. The main role of rutin in the descriptor hop bitterness has been established in kettle beer hopping technology, and catechin in dry beer hopping technology, respectively. The important role of soluble nitrogen and β-glucan dextrins in the perception of sensory descriptors of various technologies’ beers, as well as phenolic compounds in relation to the formation of bitterness and astringency of beer of classical technology and cold hopping, has been shown. Conclusions: The obtained mathematical relationships allow predicting the resulting beer quality and also make it possible to create the desired flavor profiles.

Application of Mass Spectrometry-Based Proteomics to Barley Research

Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.

The post-translational modification landscape of commercial beers

Beer is one of the most popular beverages worldwide. As a product of variable agricultural ingredients and processes, beer has high molecular complexity. We used DIA/SWATH-MS to investigate the proteomic complexity and diversity of 23 commercial Australian beers. While the overall complexity of the beer proteome was modest, with contributions from barley and yeast proteins, we uncovered a very high diversity of post-translational modifications (PTMs), especially proteolysis, glycation, and glycosylation. Proteolysis was widespread throughout barley proteins, but showed clear site-specificity. Oligohexose modifications were common on lysines in barley proteins, consistent with glycation by maltooligosaccharides released from starch during malting or mashing. O-glycosylation consistent with oligomannose was abundant on secreted yeast glycoproteins. We developed and used data analysis pipelines to efficiently extract and quantify site-specific PTMs from SWATH-MS data, and showed incorporating these features into proteomic analyses extended analytical precision. We found that the key differentiator of the beer glyco/proteome was the brewery, with beer from independent breweries having a distinct profile to beer from multinational breweries. Within a given brewery, beer styles also had distinct glyco/proteomes. Targeting our analyses to beers from a single brewery, Newstead Brewing Co., allowed us to identify beer style-specific features of the glyco/proteome. Specifically, we found that proteins in darker beers tended to have low glycation and high proteolysis. Finally, we objectively quantified features of foam formation and stability, and showed that these quality properties correlated with the concentration of abundant surface-active proteins from barley and yeast.

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.

Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product

Coagulation factor IX (FIX) is a complex post-translationally modified human serum glycoprotein and high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Bioreactor operating conditions can impact rFIX production and post-translational modifications (PTMs). With the goal of optimizing rFIX production, we developed a suite of Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics methods and used these to investigate rFIX yield, γ-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. We detail the dynamics of site-specific PTM occupancy and structure on rFIX during production, which correlated with the efficiency of purification and the quality of the purified product. We identified new PTMs in rFIX near the GLA domain which could impact rFIX GLA-dependent purification and function. Our workflows are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses.

N-glycosylation on Oryza sativa root germin-like protein 1 is conserved but not required for stability or activity

Germin and germin-like proteins (GLPs) are a broad family of extracellular glycoproteins ubiquitously distributed in plants. Overexpression of Oryza sativa root germin like protein 1 (OsRGLP1) enhances superoxide dismutase (SOD) activity in transgenic plants. Here, we report bioinformatic analysis and heterologous expression of OsRGLP1 to study the role of glycosylation on OsRGLP1 protein stability and activity. Sequence analysis of OsRGLP1 homologs identified diverse N-glycosylation sequons, one of which was highly conserved. We therefore expressed OsRGLP1 in glycosylation-competent Saccharomyces cerevisiae as a Maltose Binding Protein (MBP) fusion. Mass spectrometry analysis of purified OsRGLP1 showed it was expressed by S. cerevisiae in both N-glycosylated and unmodified forms. Glycoprotein thermal profiling showed little difference in the thermal stability of the glycosylated and unmodified protein forms. Circular Dichroism spectroscopy of MBP-OsRGLP1 and a N-Q glycosylation-deficient variant showed that both glycosylated and unmodified MBP-OsRGLP1 had similar secondary structure, and both forms had equivalent SOD activity. Together, we concluded that glycosylation was not critical for OsRGLP1 protein stability or activity, and it could therefore likely be produced in Escherichia coli without glycosylation. Indeed, we found that OsRGLP1 could be efficiently expressed and purified from K12 shuffle E. coli with a specific activity of 1251 ± 70 Units/mg. In conclusion, we find that some highly conserved N-glycosylation sites are not necessarily required for protein stability or activity, and describe a suitable method for production of OsRGLP1 which paves the way for further characterization and use of this protein.

Benchtop micro-mashing: high-throughput, robust, experimental beer brewing

Brewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash, and both mash scales produced wort with equivalent fermentable sugar and free amino acid profiles. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.

Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine

Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine have not been previously investigated in detail. We analyzed the glycoproteome of sparkling wines using protein- and glycopeptide-centric approaches. We developed an automated workflow that created ion libraries to analyze sequential window acquisition of all theoretical mass spectra data-independent acquisition mass spectrometry data based on glycopeptides identified by Byonic (Protein Metrics; version 2.13.17). We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeast strains used in the liqueur de tirage for secondary fermentation. We found that aging a cuvée on lees for 24 months compared with 8 months led to a dramatic decrease in overall protein abundance and an enrichment in large glycans at specific sites in some proteins. Secondary fermentation of a Riesling wine with Saccharomyces cerevisiae yeast strain Siha4 produced more yeast proteins and glycoproteins than with S. cerevisiae yeast strain DV10. The abundance and glycosylation profiles of grape glycoproteins were also different between grape varieties. To our knowledge, this work represents the first in-depth study into protein- and peptide-specific glycosylation in sparkling wines and describes a quantitative glycoproteomic sequential window acquisition of all theoretical mass spectra/data-independent acquisition workflow that is broadly applicable to other sample types.

•

Development of an automated glycoproteomic sequential window acquisition of all theoretical mass spectra workflow.

•

Application to three pairs of commercial-scale experimental sparkling wines.

•

Decreased protein abundance in cuvée during the aging process.

•

Different yeast strains produce varying levels of yeast proteins.

Development of a Rapid Method to Assess Beer Foamability Based on Relative Protein Content Using RoboBEER and Machine Learning Modeling

Foam-related parameters are associated with beer quality and dependent, among others, on the protein content. This study aimed to develop a machine learning (ML) model to predict the pattern and presence of 54 proteins. Triplicates of 24 beer samples were analyzed through proteomics. Furthermore, samples were analyzed using the RoboBEER to evaluate 15 physical parameters (color, foam, and bubbles), and a portable near-infrared (NIR) device. Proteins were grouped according to their molecular weight (MW), and a matrix was developed to assess only the significant correlations (p < 0.05) with the physical parameters. Two ML models were developed using the NIR (Model 1), and RoboBEER (Model 2) data as inputs to predict the relative quantification of 54 proteins. Proteins in the 0–20 kDa group were negatively correlated with the maximum volume of foam (MaxVol; r = −0.57) and total lifetime of foam (TLTF; r = −0.58), while those within 20–40 kDa had a positive correlation with MaxVol (r = 0.47) and TLTF (r = 0.47). Model 1 was not as accurate (testing r = 0.68; overall r = 0.89) as Model 2 (testing r = 0.90; overall r = 0.93), which may serve as a reliable and affordable method to incorporate the relative quantification of important proteins to explain beer quality.

Glycopeptide variable window SWATH for improved data independent acquisition glycoprotein analysis

N-glycosylation plays an essential role in regulating protein folding and function in eukaryotic cells. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH) has proven useful as a data independent acquisition (DIA) MS method for analysis of glycoproteins and their glycan modifications. By separating the entire m/z range into consecutive isolation windows, DIA-MS allows comprehensive MS data acquisition and high-sensitivity detection of molecules of interest. Variable width DIA windows allow optimal analyte measurement, as peptide ions are not evenly distributed across the full m/z range. However, the m/z distribution of glycopeptides is different to that of unmodified peptides because of their large glycan structures. Here, we improved the performance of DIA glycoproteomics by using variable width windows optimized for glycopeptides. This method allocates narrow windows at m/z ranges rich in glycopeptides, improving analytical specificity and performance. We show that related glycoforms must fall in separate windows to allow accurate glycopeptide measurement. We demonstrate the utility of the method by comparing the cell wall glycoproteomes of wild-type and N-glycan biosynthesis deficient yeast and showing improved measurement of glycopeptides with different glycan structures. Our results highlight the importance of appropriately optimized DIA methods for measurement of post-translationally modified peptides.

The Brewing Industry and the Opportunities for Real-Time Quality Analysis Using Infrared Spectroscopy

Brewing is an ancient process which started in the middle east over 10,000 years ago. The style of beer varies across the globe but modern brewing is very much the same regardless of the style. While there are thousands of compounds in beer, current methods of analysis rely mostly on the content of only several important processing parameters such as gravity, bitterness, or alcohol. Near infrared and mid infrared spectroscopy offer opportunities to predict dozens to hundreds of compounds simultaneously at different stages of the brewing process. Importantly, this is an opportunity to move deeper into quality through measuring wort and beer composition, rather than just content. This includes measuring individual sugars and amino acids prior to fermentation, rather than total °Plato or free amino acids content. Portable devices and in-line probes, coupled with more complex algorithms can provide real time measurements, allowing brewers more control of the process, resulting in more consistent quality, reduced production costs and greater confidence for the future.

Phase-Variable Glycosylation in Nontypeable Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHi) is a leading cause of respiratory tract infections worldwide and continues to be a global health burden. Adhesion and colonization of host cells are crucial steps in bacterial pathogenesis, and in many strains of NTHi, the interaction with the host is mediated by the high molecular weight adhesins HMW1A and HMW2A. These adhesins are N-glycoproteins that are modified by cytoplasmic glycosyltransferases HMW1C and HMW2C. Phase variation in the number of short sequence repeats in the promoters of hmw1A and hmw2A directly affects their expression. Here, we report the presence of similar variable repeat elements in the promoters of hmw1C and hmw2C in diverse NTHi isolates. In an ex vivo assay, we systematically altered the substrate and glycosyltransferase expression and showed that both of these factors quantitatively affected the site-specific efficiency of glycosylation on HMW-A. This represents a novel mechanism through which phase variation can generate diversity in the quantitative extent of site-specific post-translational modifications on antigenic surface proteins. Glycosylation occupancy was incomplete at many sites, variable between sites, and generally lower close to the C-terminus of HMW-A. We investigated the causes of this variability. As HMW-C glycosylates HMW-A in the cytoplasm, we tested how secretion affected glycosylation on HMW-A and showed that retaining HMW-A in the cytoplasm indeed increased glycosylation occupancy across the full length of the protein. Site-directed mutagenesis showed that HMW-C had no inherent preference for glycosylating asparagines in NxS or NxT sequons. This work provides key insights into factors contributing to the heterogenous modifications of NTHi HMW-A adhesins, expands knowledge of NTHi population diversity and pathogenic capability, and is relevant to vaccine design for NTHi and related pathogens.