Changes in whey proteome with lactation stage and parity in dairy cows using a label-free proteomics approach

Gestational Diabetes Mellitus-Induced Milk Fat Globule Membrane Protein Changes of Human Mature Milk Based on TMT Proteomic Analysis

Breastfeeding by mothers with gestational diabetes mellitus (GDM) has been shown to reduce maternal insulin demands and diminish the risks of diabetes in infants, leading to improved long-term health outcomes. Milk fat globule membrane (MFGM) proteins play a crucial role in influencing the immunity and cognitive development of infants. Understanding the alterations in MFGM proteins in breastmilk from mothers with GDM is essential for enhancing their self-efficacy and increase breastfeeding rates. The objective of this study is to investigate and compare MFGM proteins in milk from mothers with GDM and without based on tandem mass tag (TMT) labeling and liquid chromatography tandem mass spectrometry (LC-MS) techniques. A total of 5402 proteins were identified, including 4 upregulated proteins and 24 downregulated proteins. These significantly altered proteins were found to be associated with human diseases, cellular processes, and metabolism pathways. Additionally, the oxidative phosphorylation pathway emerged as the predominant pathway through Gene Set Enrichment Analysis (GSEA) involving all genes.

Comparative proteomic analysis of the changes in mare milk associated with different lactation stages and management systems

Mare milk has traditionally been attributed a number of health promoting properties. However, knowledge on its composition and functionality remains scarce, with particularly limited studies on mare milk proteomics. This study deeply characterized mare milk proteome accounting for both caseins and proteins in the whey fraction, also addressing the impact of lactation stage and different management systems. Milk samples from Basque Mountain Horse breed mares belonging to three different farms and three lactation stages were analysed after in-gel and in-solution digestion using nLC-MS/MS. Among the 469 proteins identified, the content of alpha-1 antitrypsin was significantly higher in pasture-based compared to other systems. Moreover, lactation stage significantly affected the content of beta-lactoglobulin II, immunoglobulin-like domain-containing protein, interferon alpha-inducible protein 27, lactotransferrin, polypeptide N-acetylgalactosaminyltransferase, and transforming acidic coiled-coil containing protein 2. This study contributes to the deep characterization of mare milk proteome and provides new insights into the effect of different production factors.

Proteomics and Peptidomics As a Tool to Compare the Proteins and Endogenous Peptides in Human, Cow, and Donkey Milk

Cow's milk is the most widely used ingredient in infant formulas. However, its specific protein composition can cause allergic reactions. Finding alternatives to replace cow's milk and fill the nutritional gap with human milk is essential for the health of infants. Proteomic and peptidomic techniques have supported the elucidation of milk's nutritional ingredients. Recently, omics approaches have attracted increasing interest in the investigation of milk because of their high throughput, precision, sensitivity, and reproducibility. This review offers a significant overview of recent developments in proteomics and peptidomics used to study the differences in human, cow, and donkey milk. All three types of milks were identified to have critical biological functions in human health, particularly in infants. Donkey milk proteins were closer in composition to human milk, were less likely to cause allergic reactions, and may be developed as novel raw materials for formula milk powders.

Analysis and Comparison of Proteomics of Placental Proteins from Cows Using Different Proteases

Newly found biochemical characteristics of the placenta can provide new insights for further studies on the possible markers of physiological/pathological pregnancy or the function of the placenta. We compared the proteome of the dairy cow placenta after enzymatic hydrolysis by three different proteases using a label-free mass spectrometry approach. In total, 541, 136, and 86 proteins were identified in the trypsin group (TRY), pepsin group (PEP), and papain group (PAP). By comparing the proteome of the PAP and TRY, PEP and TRY, and PEP and PAP groups, 432, 421, and 136 differentially expressed proteins were identified, respectively. We compared the up-regulated DEPs and down-regulated DEPs of each comparison group. The results show that the proteins identified by papain were mostly derived from the extracellular matrix and collagen, and were enriched in the relaxin signaling pathway and AGE-RAGE signaling pathway in diabetic complications; pepsin digestion was able to identify more muscle-related proteins, which were enriched in the lysosome, platelet activation, cardiac muscle contraction, the bacterial invasion of epithelial cells, and small cell lung cancer; trypsin mainly enzymatically degraded the extracellular matrix, blood particles, and cell-surface proteins that were enriched in arginine and proline metabolism, olfactory transduction proteasome, protein processing in the endoplasmic reticulum, pyruvate metabolism, and arrhythmogenic right ventricular cardiomyopathy (ARVC). In summary, these results provide insights into the discovery of the physiological functions of dairy cow placenta and the selection of proteases in dairy cow placenta proteomics.

Proteomic profile of Trichinella spiralis infected mice with acute spinal cord injury: A 4D label-free quantitative analysis

Spinal cord injury (SCI) can cause severe loss of locomotor and sensory activities, with no ideal treatment. Emerging reports suggest that the helminth therapy is highly effective in relieving numerous inflammatory diseases. Proteomic profiling is often used to elucidate the underlying mechanism behind SCI. Herein, we systematically compared the protein expression profiles of murine SCI spinal cord and Trichinella spiralis treated murine SCI spinal cord, using a 4D label-free technique known for its elevated sensitivity. Relative to the SCI mice, the T. spiralis-treated mice exhibited marked alterations in 91 proteins (31 up- and 60 down-regulated). Based on our Gene Ontology (GO) functional analysis, the differentially expressed proteins (DEPs) were primarily enriched in the processes of metabolism, biological regulation, cellular process, antioxidant activity, and other cell functions. In addition, according to the Clusters of Orthologous Groups of protein/EuKaryotic Orthologous Groups (COG/KOG) functional stratification, proteins involved in signaling transduction mechanisms belonged to the largest category. Over-expressed DEPs were also enriched in the "NADPH oxidase complex", "superoxide anion generation", "other types of O-glycan biosynthesis", and "HIF-1 signaling pathway". Furthermore, the protein-protein interaction (PPI) network identified the leading 10 hub proteins. In conclusion, we highlighted the dynamic proteomic profiling of T. spiralis-treated SCI mice. Our findings provide significant insight into the molecular mechanism behind T. spiralis regulation of SCI.

Comparative analysis of whey proteins in yak milk from different breeds in China using a data-independent acquisition proteomics method

Yak milk is rich in essential milk proteins of nutritional and therapeutic value. In this study, whey proteins of milk from 3 yak breeds (Gannan, GN; Huanhu, HH; Maiwa, MW) in China were comprehensively identified and compared using a data-independent acquisition quantitative proteomics approach. A total of 632 proteins were identified in yak milk whey samples, in which immune-related proteins were abundant. Compared with other milks, more proteins were involved in oxidation-reduction process and with ATP binding. In addition, we identified 96, 155, and 164 differentially expressed proteins (DEP) for GN versus HH, GN versus MW, and HH versus MW, respectively. "Phagosome" and "complement and coagulation cascades" were the most significant pathways for DEP of GN versus HH and GN or HH versus MW yak milk based on the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Protein-protein interaction network analysis showed that DEP for the 3 comparisons had significant biological interactions but were associated with different functions. The results provide useful information on yak milk from different breeds in China, and elucidate the biological functions of yak milk proteins.

Quantitative phosphoproteome analysis reveals differential whey phosphoproteins of bovine milk during lactation

Whey proteins in bovine milk, as the most widely used nutritional components for infant formulae, have been paid more attention. However, the phosphorylation of proteins in bovine whey during lactation has not been thoroughly researched. In this study, a total of 185 phosphorylation sites on 72 phosphoproteins were identified in bovine whey during lactation. 45 differentially expressed whey phosphoproteins (DEWPPs) in colostrum and mature milk were focused on by bioinformatics approaches. Gene Ontology annotation indicated that blood coagulation, extractive space, and protein binding played a key role in bovine milk. The critical pathway of DEWPPs was related to the immune system according to KEGG analysis. Our study investigated the biological functions of whey proteins from a phosphorylation perspective for the first time. The results elucidate and increase our knowledge of differentially phosphorylation sites and phosphoproteins in bovine whey during lactation. Additionally, the data might offer fresh insight into the development of whey protein nutrition.

Developmental changes in proteins of casein micelles in goat milk using data-independent acquisition-based proteomics methods during the lactation cycle

Casein micelles (CM) play an important role in milk secretion, stability, and processing. The composition and content of milk proteins are affected by physiological factors, which have been widely investigated. However, the variation in CM proteins in goat milk throughout the lactation cycle has yet to be fully clarified. In the current study, milk samples were collected at d 1, 3, 30, 90, 150, and 240 of lactation from 15 dairy goats. The size of CM was determined using laser light scattering, and CM proteins were separated, digested, and identified using data-independent acquisition (DIA) and data-dependent acquisition (DDA)-based proteomics approaches. According to clustering and principal component analysis, protein profiles identified using DIA were similar to those identified using the DDA approach. Significant differences in the abundance of 115 proteins during the lactation cycle were identified using the DIA approach. Developmental changes in the CM proteome corresponding to lactation stages were revealed: levels of lecithin cholesterol acyltransferase, folate receptor α, and prominin 2 increased from 1 to 240 d, whereas levels of growth/differentiation factor 8, peptidoglycan-recognition protein, and 45 kDa calcium-binding protein decreased in the same period. In addition, lipoprotein lipase, glycoprotein IIIb, and α-lactalbumin levels increased from 1 to 90 d and then decreased to 240 d, which is consistent with the change in CM size. Protein-protein interaction analysis showed that fibronectin, albumin, and apolipoprotein E interacted more with other proteins at the central node. These findings indicate that changes in the CM proteome during lactation could be related to requirements of newborn development, as well as mammary gland development, and may thus contribute to elucidating the physical and chemical properties of CM.

BoMiProt 2.0: An update of the bovine milk protein database

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.g., whey, fat globule membranes, and exosomes). Additionally, class, architecture, topology, and homology, structural classification of proteins, known and predicted disorder, predicted transmembrane helices, and structures have been included. Each protein entry in the database is thoroughly cross-referenced, including 1392 BoMiProt defined proteins provided with secondary information, such as protein function, biochemical properties, post-translational modifications, significance in milk, domains, fold, AlphaFold predicted models and crystal structures. The proteome data in the database can be retrieved using several search parameters using protein name, accession IDs, and FASTA sequence. Overall, BoMiProt represents an extensive compilation of newer proteins, including structural, functional, and hierarchical information, to help researchers better understand mammary gland pathophysiology, including their potential application in improving the nutritional quality of dairy products.

Trypsin-Inhibitor-Aktivität im Kolostrum – eine Übersicht

Die wichtige Rolle von Kolostrum für das Immunsystem des Neonaten ist lange bekannt. Proteine und vor allem Immunglobuline müssen nach der Aufnahme den Verdauungstrakt mit seinen proteolytischen Enzymen intakt passieren, um in den neonatalen Kreislauf aufgenommen werden zu können. Aus diesem Grund weist Kolostrum eine trypsininhibitorische Aktivität auf. Die Anti-Trypsin-Aktivität wird dabei nicht nur von einem einzigen Molekül getragen, sondern ist eine generelle Eigenschaft des Erstkolostrums. Bei Paarhufern lässt sich eine hohe Trypsin-Inhibition nachweisen, die in den ersten Tagen der Laktation stark abfällt. Auch beim Pferd ist eine Trypsin-Inhibition im Kolostrum festzustellen. Die Bedeutung wird in der Literatur kontrovers diskutiert, weil die Anti-Trypsin-Aktivität im Vergleich zu den Klauentieren geringer ausgeprägt ist und weniger Stabilität im sauren Milieu zeigt. Im Kolostrum von Fleischfressern findet sich ebenfalls eine Anti-Trypsin-Aktivität, die jedoch weniger stark ausgeprägt ist als bei den Huftieren. Diese Literaturübersicht hat zum Ziel, das bekannte Wissen zur Anti-Trypsin-Aktivität im Kolostrum verschiedener Spezies zusammenzufassen.

Comprehensive Proteomic Analysis Revealed a Large Number of Newly Identified Proteins in the Small Extracellular Vesicles of Milk from Late-Stage Lactating Cows

Bovine milk contains small extracellular vesicles (sEVs) that provide proteins, miRNAs, mRNAs, DNAs, and lipids to target cells and play a role in intracellular communications. Previous studies have characterized proteins in milk sEVs from early- and mid-stage lactation. However, the proteins in milk sEVs from late-stage lactation are mostly unexplored. The aim of this study was to determine the proteomic profile of milk sEVs from late-stage lactating cows. A comprehensive nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) approach was carried out to reveal the proteins in milk sEVs. Additionally, bioinformatics analysis was carried out to interpret the molecular signatures of newly identified proteins in milk sEVs from three late-stage lactating cows. NanoLC-MS/MS analysis revealed a total of 2225 proteins in milk sEVs from cows. Notably, after comparing these identified proteins with previously deposited datasets of proteins in bovine milk sEVs, 429 proteins were detected as newly identified. Bioinformatic analysis indicated that these newly identified proteins in milk sEVs were engaged in a diverse range of molecular phenomena relevant to mammary gland physiology, milk production, immunity, and immune response. These findings suggest that the newly identified proteins could expand the inventory application of molecular cargos, nutritional status, and immune modulation of sEVs in milk during the late-stage lactation.

Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.

Comparative proteomic characterization of bovine milk containing β-casein variants A1A1 and A2A2, and their heterozygote A1A2

BACKGROUND

Genetic variants of β-casein are cosnidered to affect the components of milk. However, limited data are available on the bovine protein components correlated with β-casein variants at the proteome level. In the present study, cows producing milk containing β-casein variants (A1A1 and A2A2) and their heterozygote (A1A2) were identified using a high-resolution melting method, and milk samples were collected and tested. Comparative analyses of casein micelles, whey and milk fat globule membrane fractions in each milk variant were performed using a label-free proteomics approach.

RESULTS

The results obtained showed that ceruloplasmin and cathelicidin-2 were the most abundant proteins in milk containing variant A1A1; lactoferrin and CD5 molecule-like were the most abundant proteins in milk containing variant A2A2; and selenoprotein P and osteopontin were the most abundant proteins in milk containing heterozygote A1A2. Differences in protein components in milk containing the different β-casein variants were visualized using hierarchical clustering, and profiles were separated using principal components analysis. The differentially expressed proteins in milk containing A1A1, A2A2 or A1A2 were predominantly involved in response to stress and defense response according to their Gene Ontology annotations.

CONCLUSION

Our findings provide new insights into differentially expressed milk proteins corresponding to the presence of different β-casein variants. This knowledge will help determine their potential biological functions in dairy products and the effects on human health. © 2020 Society of Chemical Industry.

High-Resolution Mass Spectrometer-Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle

Milk serves as a mode of protection to neonate through transferring the host defense proteins from mother to offspring. It also guards the mammary gland against various types of infections. Along with the presence of six vital proteins, bovine milk (whey) contains a massive class of minor proteins, not all of which have been comprehensively reported. In this study, we performed an LC-MS/MS-based ultra-deep identification of the milk whey proteome of Indian zebu (Sahiwal) cattle. Three independent search engines that are Comet, Tandem, and Mascot-based analysis resulted in the discovery of over 6,210 non-redundant proteins commonly identified. Genome-wise mapping revealed that chromosome 1 showed a minimum expression of 14 proteins, whereas chromosome 19 expressed 250 maximum proteins in milk whey. These results demonstrate that milk proteome in Sahiwal cattle is quite complicated, and minor milk fractions play a significant role in host defense.

Label-free quantitative proteomics analysis reveals the fate of colostrum proteins in the intestine of neonatal calves

The contribution of intestinally absorbed colostral immunoglobulins to the transmission of passive immunity is widely reported in neonatal calves. However, changes in the colostral proteome in the gastrointestinal digesta remain unclear. Therefore, this study aimed to investigate changes in colostral proteome affected by gastrointestinal proteases in neonatal calves. Twenty-one neonatal Holstein calves were used in this study, including 18 colostrum-fed calves slaughtered at 8 (CI, n = 6), 24 (CII, n = 6), and 36 h (CIII, n = 6) postpartum and 3 milk-fed calves slaughtered 24 h postpartum (MI, n = 3). The ingested colostrum and milk samples were collected from the mid-jejunum segment, following the sacrifice. The undigested colostrum or milk along with their ingested colostrum or milk samples were investigated using a label-free proteomics approach. Hierarchical clustering and principal component analysis of the quantified proteins revealed that the ingested colostrum from the CII and CIII groups and the ingested mature milk from the MI group appeared to share similar patterns. Analysis of the intestinal digesta revealed a time-dependent decrease in caseins, lactoferrin, and osteopontin protein levels, and an increase in cationic trypsin, chymotrypsin, and carboxypeptidase. Several protease inhibitors, such as α-1-antiproteinase, α-2-antiplasmin, and early lactation protein, were identified in the colostrum and intestinal digesta. In addition, we detected identical levels in the intestinal digesta and colostrum for albumin, α-1-acid glycoprotein, and plasminogen. Pathway analysis indicated that proteins increased in the intestinal digesta belonged to the following categories: biosynthesis of antibiotics, carbon metabolism, and biosynthesis of amino acids. These results indicated that selected colostral proteins were digested by gastrointestinal proteases, contributing to their intestinal absorption in calves. These findings provide new insights into the fate of the colostral proteome in the gastrointestinal tract and may aid in the identification of factors contributing to health management in neonatal calves.