Analysis of the Human Casein Phosphoproteome by 2-D Electrophoresis and MALDI-TOF/TOF MS Reveals New Phosphoforms

Characteristics of casein phosphopeptides in Chinese human milk and its correlation with infant growth: A cross-sectional study

This research aimed to investigate the characteristics of casein phosphopeptides in Chinese human milk, and their potential relationship to infant growth. Using the liquid chromatography-Orbitrap-mass spectrometry technique, a total of 15 casein phosphopeptides were identified from 200 human milk samples. Also, our results indicate that casein phosphopeptides were phosphorylated with only one phosphate. The relative concentrations of casein phosphopeptides at 6 months postpartum were increased compared with milk at 2 months (FDR < 0.05). Significantly positive correlations were observed between casein phosphopeptides and infant growth, as shown by four casein phosphopeptides were positively correlated with the infants' weight-for-age Z-scores (rs range from 0.20 to 0.29), and three casein phosphopeptides were positively correlated with the infants' length-for-age Z-scores (rs range from 0.19 to 0.27). This study is the first to reveal the phosphorylated level and composition of casein phosphopeptides in Chinese human milk, and their potential relationship with infant growth.

The Aggregated and Micellar Forms of β-Casein Purified from Donkey and Bovine Milk Present Potential as Carriers for Bioactive Nutritional Compounds

In recent years, there has been a growing interest in the pure casein fraction of milk protein, particularly β-casein due to its physicochemical properties as well as its bio- and techno-functional properties. The utilization of self-assembled β-caseins from bovine origin as nanocarriers for the delivery of nutraceutical compounds or drugs has increased dramatically. Concerning β-caseins from other milk sources, the use of hypoallergenic donkey β-caseins as a potential delivery vehicle for nutraceutical hydrophobic compounds is beginning to generate interest. The present review deals with casein micelles models, bovine and donkey β-casein molecular structures, as well as their physical-chemical properties that account for their exploitation in nutraceutics and pharmaceutics. This review work suggests the possibility of developing delivery systems for hydrophobic bioactive compounds using β-casein purified from hypoallergenic donkey milk, highlighting the potential of this protein as an innovative and promising vehicle for enhancing the enrichment and bioavailability of various bioactive substances in food products.

A novel proteomic approach for the identification and relative quantification of disulfide-bridges in the human milk proteome

This study explores the disulfide bridges present in the human milk proteome by a novel approach permitting both positional identification and relative quantification of the disulfide bridges. Human milk from six donors was subjected to trypsin digestion without reduction. The digested human milk proteins were analyzed by nanoLC-timsTOF Pro combined with data analysis using xiSEARCH. A total of 85 unique disulfide bridges were identified in 25 different human milk proteins. The total relative abundance of disulfide bridge-containing peptides constituted approximately 5% of the total amount of tryptic-peptides. Seven inter-molecular disulfide bridges were identified between either α-lactalbumin and lactotransferrin (5) or αS1-casein and κ-casein (2). All cysteines involved in the observed disulfide bridges of α-lactalbumin and lactotransferrin were mapped onto protein models using AlphaFold2 Multimer to estimate the length of the observed disulfide bridges. The lengths of the disulfide bridges of lactotransferrin indicate a potential for multi- or poly-merization of lactotransferrin. The high number of intramolecular lactotransferrin disulfide bridges identified, suggests that these are more heterogeneous than previously presumed. SIGNIFICANCE: Disulfide-bridges in the human milk proteome are an often overseen post-transaltional modification. Thus, mapping the disulfide-bridges, their positions and relative abundance, are valuable new knowledge needed for an improved understanding of human milk protein behaviour. Although glycosylation and phosphorylation have been described, even less information is available on the disulfide bridges and the disulfide-bridge derived protein complexes. This is important for future work in precision fermentation for recombinant production of human milk proteins, as this will highlight which disulfide-bridges are naturally occouring in human milk proteins. Further, this knowledge would be of value for the infant formula industry as it provides more information on how to humanize bovine-milk based infant formula. The novel method developed here can be broadly applied in other biological systems as the disulfid-brigdes are important for the structure and functionality of proteins.

Evolution, diversification and function of the maternal-infant dyad in mammalian feeding

The evolution of the mother/infant dyad providing a source of nutrition for infants is essential for the origin and subsequent diversification of mammals. Despite the importance of this dyad, research on maternal and infant function is often treated independently. Our goal is to synthesize the work on maternal and infant function, discuss our own studies of suckling, and compare the origins of lactation and suckling with their ensuing diversification. Our central premise is that while extensive work has demonstrated variation across mammals in the maternal aspect of this system, very little has been done to address how this relates to infant function. We start with a discussion of the fundamental anatomy and physiology of both mother and infant. We next discuss the origin of mammary glands and milk, and infant suckling, which is distinct from their subsequent diversification. We then discuss the diversification of maternal and infant function, highlighting the evolutionary diversity present in maternal function (both anatomically and physiologically), before arguing that the diversity of infant function is unexplored, and needs to be better studied in the future. We end by discussing some of the holes in our understanding, and suggestions for future work that can address these lacunae. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Quantitative Phosphoproteome of Infant Formula: New Insights into the Difference of Phosphorylation in Milk Proteins between Bovine and Goat Species

Phosphorylation is a broad post-translational protein modification, and the level of phosphorylation of milk proteins is associated with lactation, coagulation properties, and digestibility. However, phosphoproteins in bovine milk-based and goat milk-based infant formula have not been systematically explored. Here, we have analyzed six bovine and six goat milk-based infant formula using a quantitative phosphoproteomics approach, from which we identified 200 phosphoproteins with 276 phosphorylation sites and 156 phosphorylation sites from 75 phosphoproteins, respectively. Of these, 99 phosphorylation sites from 26 shared phosphoproteins were differentially expressed between bovine and goat milk-based infant formula. Especially, CSN1S1 was the most phosphoprotein with 25 quantified phosphorylation sites. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the identified phosphoproteins not only provide nutrition to the infant but also have anti-inflammatory, antipathogenic, and other biological functions. Our results shed light on the composition, phosphorylation sites, and biological functions of phosphoproteins in bovine milk and goat milk-based infant formula, which provide new insights into the key role of protein modifications during infant development. It also helps us to better understand the differences in digestibility of infant formula from different animal milk sources and thus guides the choice of milk source for infant formula.

Molecular Characterization and Phylogenetic Analysis of Casein Gene Family in Camelus ferus

Camel milk is known for its exceptional medical uses. It has been used since ancient times to treat infant diarrhea, hepatitis, insulin-dependent diabetes (IDDM), lactose intolerance, alcohol-induced liver damage, allergies, and autism. It has the power to treat several diseases, with cancer being the most significant. This study investigated the evolutionary relationship, physiochemical characteristics, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in Camelus ferus. Molecular phylogenetics showing the camelid species clustered casein nucleotide sequences into four groups: CSN1S1, CSN2, CSN1S2, and CSN3. The casein proteins from camels were evaluated and found to be unstable, thermostable, and hydrophilic. CSN1S2, CSN2, and CSN3 were acidic, but CSN1S1 was basic. CSN1S1 showed positive selection for one amino acid (Q), CSN1S2 and CSN2 for three (T, K, Q), and CSN3 showed no positive selection. We also compared high-milk-output species such as cattle (Bos Tarus) and low-milk-yield species such as sheep (Ovies Aries) with camels (Camel ferus) and discovered that YY1 sites are more frequent in sheep than in camels and very low in cattle. We concluded that the ratio of YY1 sites in these species may affect milk production.

Effects of a Novel Infant Formula on Weight Gain, Body Composition, Safety and Tolerability to Infants: The INNOVA 2020 Study

Exclusive breastfeeding is recommended for the first six months of life to promote adequate infant growth and development, and to reduce infant morbidity and mortality. However, whenever some mothers are not able to breastfeed their infants, infant formulas mimicking human milk are needed, and the safety and efficacy of each formula should be tested. Here, we report the results of a multicenter, randomized, blinded, controlled clinical trial that aimed to evaluate a novel starting formula on weight gain and body composition of infants up to 6 and 12 months, as well as safety and tolerability. For the intervention period, infants were divided into three groups: group 1 received formula 1 (Nutribén® Innova 1 (Alter Farmacia S.A., Madrid, Spain) or INN (n = 70)), with a lower amount of protein, a lower casein to whey protein ratio by increasing the content of α-lactalbumin, and a double amount of docosahexaenoic acid/arachidonic acid than the standard formula; it also contained a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis, BPL1TM HT). Group 2 received the standard formula or formula 2 (Nutriben® Natal (Alter Farmacia S.A., Madrid, Spain) or STD (n = 70)) and the third group was exclusively breastfed for exploratory analysis and used as a reference (BFD group (n = 70)). During the study, visits were made at 21 days and 2, 4, 6, and 12 months of age. Weight gain was higher in both formula groups than in the BFD group at 6 and 12 months, whereas no differences were found between STD and INN groups either at 6 or at 12 months. Likewise, body mass index was higher in infants fed the two formulas compared with the BFD group. Regarding body composition, length, head circumference and tricipital/subscapular skinfolds were alike between groups. The INN formula was considered safe as weight gain and body composition were within the normal limits, according to WHO standards. The BFD group exhibited more liquid consistency in the stools compared to both formula groups. All groups showed similar digestive tolerance and infant behavior. However, a higher frequency of gastrointestinal symptoms was reported by the STD formula group (n = 291), followed by the INN formula (n = 282), and the BFD groups (n = 227). There were fewer respiratory, thoracic, and mediastinal disorders among BFD children. Additionally, infants receiving the INN formula experienced significantly fewer general disorders and disturbances than those receiving the STD formula. Indeed, atopic dermatitis, bronchitis, and bronchiolitis were significantly more prevalent among infants who were fed the STD formula compared to those fed the INN formula or breastfed. To evaluate whether there were significant differences between formula treatments, beyond growth parameters, it would seem necessary to examine more precise health biomarkers and to carry out long-term longitudinal studies.

Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein–protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide “molecular pictures”, which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.

Temperature-dependent dissociation of human micellar β-casein: Implications of its phosphorylation degrees and casein micelle structures

Temperature-dependent dissociation of human micellar β-casein regarding its phosphorylation degrees and micelle structures were studied. Human milk was fractionated at 25 °C into soluble (S-25 °C) and micellar (M-25 °C) fractions, and the latter was fractionated at 4 °C into soluble (S-4 °C) and micellar (M-4 °C) fractions. β-casein ratios among S-25 °C, S-4 °C and M-4 °C were 19%, 59% and 22%. β-casein isoforms were predominated by 0-P, 1-P and 2-P in S-25 °C, by 0-P, 1-P, 2-P and 4-P in S-4 °C, and by 0-P in M-4 °C. For micelles remained after dissociation of β-casein and calcium, the size increased, molar mass decreased, morphologies were maintained, and internal protein inhomogeneities disappeared, compared with micelles in M-25 °C. β-casein isoforms with lower phosphorylation degrees may form a frame mainly through hydrophobic interactions, attached with more highly phosphorylated isoforms and colloidal calcium phosphate via calcium bridges for forming human micelle.

Genetic Diversity in Casein Gene Cluster in a Dromedary Camel (C. dromedarius) Population from the United Arab Emirates

Genetic polymorphisms, causing variation in casein genes (CSN1S1, CSN1S2, CSN2, and CSN3), have been extensively studied in goats and cows, but there are only few studies reported in camels. Therefore, we aimed to identify alleles with functional roles in the United Arab Emirates dromedary camel (Camelus dromedarius) population to complement previous studies conducted on the same species. Using targeted next-generation sequencing, we sequenced all genes in the casein gene cluster in 93 female camels to identify and characterize novel gene variants. Most variants were found in noncoding introns and upstream sequences, but a few variants showed the possibility of functional impact. CSN2 was found to be most polymorphic, with total 91 different variants, followed by CSN1S1, CSN3 and CSN1S2. CSN1S1, CSN1S2 and CSN2 each had at least two variants while CSN3 had only one functional allele. In future research, the functional impact of these variants should be investigated further.

Comparative Proteomics of Human Milk From Eight Cities in China During Six Months of Lactation in the Chinese Human Milk Project Study

Human milk (HM) is the golden standard of infant nutrition that can protect immature body function and enhance nutrition metabolism to ensure infant growth. Region specificity and lactation period could change the protein composition in HM. In this research, proteomics analysis was used to compare proteomes across eight cities, namely Harbin, Lanzhou, Guangzhou, Chengdu, Jinhua, Weihai, Zhengzhou, and Beijing, which represented the northeast, northwest, southeast, southwest, east, and north and central regions of China,. Proteins varied significantly among the cities. These different proteins were mainly involved in the process of platelet degranulation, innate immune response, and triglyceride metabolic process, which might be due to different living environments. These differences also lead to variation in protection and fat metabolism from mothers to infants in different cities. Four proteins were expressed differently during 6 months of lactation, namely Dipeptidyl peptidase 1, Lysozyme C, Carbonic anhydrase 6, and Chordin-like protein 2. The changes in these proteins might be because of the change of growth needs of the infants. The findings from our results might help to improve the understanding of HM as well as to design infant formula.

Monitoring Human Milk β-Casein Phosphorylation and O-Glycosylation Over Lactation Reveals Distinct Differences between the Proteome and Endogenous Peptidome

Human milk is a vital biofluid containing a myriad of molecular components to ensure an infant’s best start at a healthy life. One key component of human milk is β-casein, a protein which is not only a structural constituent of casein micelles but also a source of bioactive, often antimicrobial, peptides contributing to milk’s endogenous peptidome. Importantly, post-translational modifications (PTMs) like phosphorylation and glycosylation typically affect the function of proteins and peptides; however, here our understanding of β-casein is critically limited. To uncover the scope of proteoforms and endogenous peptidoforms we utilized mass spectrometry (LC-MS/MS) to achieve in-depth longitudinal profiling of β-casein from human milk, studying two donors across 16 weeks of lactation. We not only observed changes in β-casein’s known protein and endogenous peptide phosphorylation, but also in previously unexplored O-glycosylation. This newly discovered PTM of β-casein may be important as it resides on known β-casein-derived antimicrobial peptide sequences.

Quantitative Phosphoproteomics of Milk Fat Globule Membrane in Human Colostrum and Mature Milk: New Insights into Changes in Protein Phosphorylation during Lactation

Phosphorylation is a widespread posttranslational protein modification and is important in various biological processes. However, milk fat globule membrane (MFGM) phosphoproteins have not been explored systematically in human milk. Here, we used quantitative phosphoproteomics to analyze phosphorylation sites in human MFGM proteins and their differences at different stages of lactation; 305 phosphorylation sites on 170 proteins and 269 phosphorylation sites on 170 proteins were identified in colostrum and mature MFGM, respectively. Among these, 71 phosphorylation sites on 48 proteins were differentially expressed between the different stages of lactation. Osteopontin in human MFGM was the most heavily phosphorylated protein, with a total of 39 identified phosphorylation sites. Our results shed light on phosphorylation sites, composition, and biological functions of MFGM phosphoproteins in human colostrum and mature milk, and provide novel insights into the crucial roles of protein phosphorylation during infant development.

Complementarity of Matrix- and Nanostructure-Assisted Laser Desorption/Ionization Approaches

In recent years, matrix-assisted laser desorption/ionization (MALDI) has become the main tool for the study of biological macromolecules, such as protein nano-machines, especially in the determination of their molecular masses, structure, and post-translational modifications. A key role in the classical process of desorption and ionization of the sample is played by a matrix, usually a low-molecular weight weak organic acid. Unfortunately, the interpretation of mass spectra in the mass range of below m/z 500 is difficult, and hence the analysis of low molecular weight compounds in a matrix-assisted system is an analytical challenge. Replacing the classical matrix with nanomaterials, e.g., silver nanoparticles, allows improvement of the selectivity and sensitivity of spectrometric measurement of biologically important small molecules. Nowadays, the nanostructure-assisted laser desorption/ionization (NALDI) approach complements the classic MALDI in the field of modern bioanalytics. In particular, the aim of this work is to review the recent advances in MALDI and NALDI approaches.

Comparative Proteomics of Whey and Milk Fat Globule Membrane Proteins of Guanzhong Goat and Holstein Cow Mature Milk

Guanzhong goat and Holstein cow milks are the major milk supply for the Chinese dairy industry. Whey proteins and milk fat globule membrane (MFGM) proteins of both milk were characterized and compared using proteomic techniques. A total of 283, 159, 593, and 349 proteins were identified, respectively, in whey and MFGM for the two species using Liquid Chromatography combined with Tandem Mass Spectrometry (LC-MS/MS). Functional categories analyses showed that both goat and cow MFGM proteins had three most abundant proteins of phosphoproteins, membrane-related and acetylation-related proteins. Gene ontology (GO) annotation revealed that whey proteins in goat and cow milk exhibited different biological processes and molecular functions while both enriched in extracellular exosome for cellular components. Both goat and cow MFGM proteins showed main biological process of oxidation-reduction, cellular component of extracellular exosome, and molecular function of poly(A) RNA binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that large number of both goat and cow whey proteins were involved in disease, metabolism, and immune pathways with different number and types. The most general pathways for goat and cow MFGM proteins were metabolism pathways and disease pathways, respectively. The results indicated that Guanzhong goat and Holstein cow milk were different in varieties of whey proteins and MFGM proteins and their functions and pathways. PRACTICAL APPLICATION: Guanzhong goat and Holstein cow milks are the major milk sources for the Chinese consumers. However, information about proteomics of whey and MFGM proteins of Guanzhong goat and Holstein cow milk is limited. Our study characterized and compared both whey and MFGM proteins using proteomic techniques. The results provide useful information for infant formula and milk protein products in the Chinese dairy industry.

Human αS1-casein induces IL-8 secretion by binding to the ecto-domain of the TLR4/MD2 receptor complex

BACKGROUND

The milk protein α_S1-casein was recently reported to induce secretion of proinflammatory cytokines via Toll-like receptor 4 (TLR4). In this study, α_S1-casein was identified as binder of theTLR4 ecto domain.

METHODS

IL-8 secretion after stimulation of TLR4/MD2 (myeloid differentiation factor 2)/CD14 (cluster of differentiation 14)-transfected HEK293 cells (TLR4⁺) and Mono Mac 6 cells (MM6) with recombinant α_S1-casein, or LPS as control was monitored. Binding of α_S1-casein to TLR4 was quantified by microscale thermophoresis (MST).

RESULTS

α_S1-casein induced secretion of IL-8 in TLR4⁺ cells and in MM6 cells with a six-times higher final IL-8 concentration in supernatants. IL-8 secretion was inhibited by intracellular TLR4-domain antagonist TAK-242 with an IC₅₀-value of 259.6 nM, by ecto-domain TLR4 antagonistic mianserin with 10-51 μM and by anti-CD14-IgA. The binding constants (K_D) of α_S1-casein to the TLR4, MD2, and CD14 were 2.8 μM, 0.3 μM and 2.7 μM, respectively. Finally, α_S1-casein showed a higher affinity to TLR4/MD2 (K_D: 2.2 μM) compared to LPS (K_D: 8.2 μM).

CONCLUSION

Human α_S1-casein induced proinflammatory effects are dependent upon binding to the TLR4 ectodomain and the presence of CD14. α_S1-casein displayed stronger TLR4 agonistic activity than LPS via a different mode of action.

GENERAL SIGNIFICANCE

Breast milk protein α_S1-casein is a proinflammatory cytokine.

A quantitative model of the bovine casein micelle: ion equilibria and calcium phosphate sequestration by individual caseins in bovine milk

The white appearance of skim milk is due to strong light scattering by colloidal particles called casein micelles. Bovine casein micelles comprise expressed proteins from four casein genes together with significant fractions of the total calcium, inorganic phosphate, magnesium and citrate ions in the milk. Thus, the milk salts are partitioned between the casein micelles, where they are mostly in the form of nanoclusters of an amorphous calcium phosphate sequestered by caseins through their phosphorylated residues, with the remainder in the continuous phase. Previously, a salt partition calculation was made assuming that the nanoclusters are sequestered only by short, highly phosphorylated casein sequences, sometimes called phosphate centres. Three of the four caseins have a proportion of their phosphorylated residues in either one or two phosphate centres and these were proposed to react with the nanoclusters equally and independently. An improved model of the partition of caseins and salts in milk is described in which all the phosphorylated residues in competent caseins act together to bind to and sequester the nanoclusters. The new model has been applied to results from a recent study of variation in salt and casein composition in the milk of individual cows. Compared to the previous model, it provides better agreement with experiment of the partition of caseins between free and bound states and equally good results for the partition of milk salts. In addition, new calculations are presented for the charge on individual caseins in their bound and free states.

Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation

Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of α-casein, β-casein, and κ-casein in human milk samples (n = 88) collected between day 1 and day 360 postpartum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37 ± 3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (α-), 0.04 to 4.42 g/L (β-), and 0.10 to 1.72 g/L (α-), with β-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, β-casein, κ-casein, total casein, and a significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.

Ser71 of αS1-Casein is Phosphorylated in Breast Milk-Evidence from Targeted Mass Analysis

SCOPE

The casein phosphoproteins in mother's milk supply calcium and phosphate ions and make them biologically available to the newborn. Human αS1-casein is of particular interest being also an autoantigen and proinflammatory cytokine. Phosphorylation of αS1-casein by casein kinase 2 completely abolishes binding to toll-like receptor 4 and proinflammatory effects. It is, however, not known, which amino acids are affected. Therefore, breast milk samples were analyzed in an effort to detect the phosphorylation sites of αS1-casein.

METHODS AND RESULTS

Breast milk samples were tryptically digested. Target tandem MS analysis confirmed the known phosphorylation sites S33 and S41; evidence for pS89 was found in some samples. Experimental support for the presence of pS31 and pS34 was weak. Phosphorylation of a new site in αS1-casein, S71, was reproducibly measured in all samples, albeit at much lower intensity than pS33 and pS41.

CONCLUSION

Phospho-occupancy rates varied greatly and could not be confidently correlated to other parameters within the cohort of 20 donors. The new phosphosite S71 is located in the neighborhood of the serine-rich region and may contribute to the cluster of high charge density at normal milk pH, likely exerting an influence on protein tertiary structure and thus function.

Large-scale label-free phosphoproteomics: from technology to data interpretation

Protein phosphorylation plays a central role in the dynamic intracellular signaling and the control of biochemical pathways in all living cells. Recent advances in high-performance MS/MS-based technology make the large-scale identification and quantification of phosphorylation sites possible. Here, we review the full data generation pipeline, starting from sample preparation methods and LC-MS detection procedures, through to data processing and analysis software tools that facilitate the systematic comparative profiling of thousands of phosphoproteins in different biological specimens in a single experiment. We emphasize current challenges and promising avenues for the mechanistic interpretation and visualization of global phosphorylation networks and their relevance to human health and disease.

In-depth phosphoproteomic analysis of royal jelly derived from western and eastern honeybee species

The proteins in royal jelly (RJ) play a pivotal role in the nutrition, immune defense, and cast determination of honeybee larvae and have a wide range of pharmacological and health-promoting functions for humans as well. Although the importance of post-translational modifications (PTMs) in protein function is known, investigation of protein phosphorylation of RJ proteins is still very limited. To this end, two complementary phosphopeptide enrichment materials (Ti(4+)-IMAC and TiO2) and high-sensitivity mass spectrometry were applied to establish a detailed phosphoproteome map and to qualitatively and quantitatively compare the phosphoproteomes of RJ produced by Apis mellifera ligustica (Aml) and Apis cerana cerana (Acc). In total, 16 phosphoproteins carrying 67 phosphorylation sites were identified in RJ derived from western bees, and nine proteins phosphorylated on 71 sites were found in RJ produced by eastern honeybees. Of which, eight phosphorylated proteins were common to both RJ samples, and the same motif ([S-x-E]) was extracted, suggesting that the function of major RJ proteins as nutrients and immune agents is evolutionary preserved in both of these honeybee species. All eight overlapping phosphoproteins showed significantly higher abundance in Acc-RJ than in Aml-RJ, and the phosphorylation of Jelleine-II (an antimicrobial peptide, TPFKLSLHL) at S(6) in Acc-RJ had stronger antimicrobial properties than that at T(1) in Aml-RJ even though the overall antimicrobial activity of Jelleine-II was found to decrease after phosphorylation. The differences in phosphosites, peptide abundance, and antimicrobial activity of the phosphorylated RJ proteins indicate that the two major honeybee species employ distinct phosphorylation strategies that align with their different biological characteristics shaped by evolution. The phosphorylation of RJ proteins are potentially driven by the activity of extracellular serine/threonine protein kinase FAM20C-like protein (FAM20C-like) through the [S-x-E] motif, which is supported by evidence that mRNA and protein expression of FAM20C-like protein kinase are both found in the highest level in the hypopharyngeal gland of nurse bees. Our data represent the first comprehensive RJ phosphorylation atlas, recording patterns of phosphorylated RJ protein abundance and antibacterial activity of some RJ proteins in two major managed honeybee species. These data constitute a firm basis for future research to better understand the biological roles of each RJ protein for honeybee biology and human health care.

The β-casein in camels: molecular characterization of the CSN2 gene, promoter analysis and genetic variability

The β-casein is the most abundant protein in camel milk and its encoding gene (CSN2) is considered in other species a 'major' gene for the presence of alleles associated to different level of expression. In the present paper, we report for the first time the characterization of the nucleotide sequence of the whole β-casein-encoding gene (CSN2) plus 2,141 bp at the 5'-flanking region in Camelus dromedarius. The promoter region and the complete cDNA are also provided for the first time in Camelus bactrianus. The gene is spread over 7.8 kb and consists of 9 exons varying in length from 24 bp (exon 5) to 519 bp (exon 7), and 8 introns from 95 bp (intron 5) to 1,950 bp (intron 1). The composite response element (CoRE) region was identified in the promoter, whereas the presence of mature microRNA sequences improves the knowledge on the factors putatively involved in the gene regulation. A total of 46 polymorphic sites have been detected. The transition g.2126A>G falls within the TATA-box of dromedary CSN2 promoter with a putative influence on the transcription factor binding activity. The frequency of the G allele is 0.35 in a population of 180 she-camels belonging to 4 different ecotypes. In the same population, a conservative SNP (g.4175C>A) was found at the codon 7 of the signal peptide, whereas a comparative analysis with a cDNA sequence available in the database evidenced a missense SNP (g.4180T(Leu)>G(Arg)) at exon 2. Four SNPs were found in the bactrian camel. The SNP c.666G>A is responsible for the amino acid change Met(201)→Ile and it represents the first missense allele at the β-casein in camels. Finally, five interspersed repeated elements were identified at intronic level, whereas the presence of putative bio-functional peptides belonging to ACE-inhibitor and anti-oxidative families confirms the potential protective role of the camel milk for the human nutrition.

Proteomic comparison of equine and bovine milks on renneting

Rennet-induced coagulation of bovine milk is a complex mechanism in which chymosin specifically hydrolyzes κ-casein, the protein responsible for the stability of the casein micelle. In equine milk, this mechanism is still unclear, and the protein targets of chymosin are unknown. To reveal the proteins involved, the rennetability of equine milk by calf chymosin was examined using gel-free and gel-based proteomic analysis and compared to bovine milk. RP-HPLC analysis of bovine and equine milks showed the release of several peptides following chymosin incubation. The hydrolyses of equine and bovine casein by chymosin were different, and the major peptides produced from equine milk were identified by mass spectrometry as fragments of β-casein. Using two-dimensional electrophoresis, equine β-casein was confirmed as the main target of calf chymosin over 24 h at 30 °C and pH 6.5. The gel-based analysis of equine milk discriminated between the different individual proteins and provided information on the range of isoforms of each protein as a result of post-translational modifications, as well as positively identified for the first time several isoforms of κ-casein. In comparison to bovine milk, κ-casein isoforms in equine milk were not involved in chymosin-induced coagulation. The intensity of equine β-casein spots decreased following chymosin addition, but at a slower rate than bovine κ-casein.

Extracellular phosphorylation and phosphorylated proteins: not just curiosities but physiologically important

Mining of the literature and high-throughput mass spectrometry data from both healthy and diseased tissues and from body fluids reveals evidence that various extracellular proteins can exist in phosphorylated states. Extracellular kinases and phosphatases (ectokinases and ectophosphatases) are active in extracellular spaces during times of sufficiently high concentrations of adenosine triphosphate. There is evidence for a role of extracellular phosphorylation in various physiological functions, including blood coagulation, immune cell activation, and the formation of neuronal networks. Ectokinase activity is increased in some diseases, including cancer, Alzheimer's disease, and some microbial infections. We summarize the literature supporting the physiological and pathological roles of extracellularly localized protein kinases, protein phosphatases, and phosphorylated proteins and provide an analysis of the available mass spectrometry data to annotate potential extracellular phosphorylated proteins.

Longitudinal analysis of protein glycosylation and β-casein phosphorylation in term and preterm human milk during the first 2 months of lactation

Human milk proteins provide term and preterm infants with both nutrition and protection. The objective of the present study was to examine longitudinal changes in the protein composition of term and preterm milk during the first 2 months of lactation, focusing on protein phosphorylation and glycosylation. Using gel electrophoresis, the relative concentration and glycosylation status of lactoferrin, secretory Ig A, β-casein, α-lactalbumin, serum albumin, bile salt-stimulated lipase, xanthine oxidoreductase, tenascin and macrophage mannose receptor 1 were measured in milk collected on days 7, 10, 14, 18, 21, 28 and 60 postpartum from preterm mothers (28-32 weeks gestation, n 17). The phosphorylation status of β-casein was also investigated. To determine if these variables differ in term and preterm milk, samples from term mothers (38-41 weeks gestation, n 8) collected on days 7, 14 and 30 of lactation were also analysed. The concentration of the abundant milk proteins decreased during lactation in term and preterm milk (P <0·05). No difference in protein glycosylation was observed, except for the glycoproteins serum albumin and tenascin. The phosphorylation of β-casein varied significantly between term and preterm milk. Further investigation is required to determine whether these modifications affect protein function and are clinically important to preterm infants.

Technical updates to basic proteins focalization using IPG strips

Background

Gel-based proteomic is a popular and versatile method of global protein separation and quantification. However, separation of basic protein still represents technical challenges with recurrent problems of resolution and reproducibility.

Results

Three different protocols of protein loading were compared using MCF7 cells proteins. In-gel rehydration, cup-loading and paper-bridge loading were first compared using 6–11 IPG strips, as attempted, in-gel rehydration gave large horizontal steaking; paper-bridge loading displayed an interesting spot resolution, but with a predominant loss of material; cup-loading was selected as the most relevant method, but still needing improvement. Twelve cup-loading protocols were compared with various strip rehydration, and cathodic wick solutions. Destreak appeared as better than DTT for strip rehydration; the use of isopropanol gave no improvement. The best 2DE separation was observed with cathodic wicks filled with rehydration solution complemented with DTT. Paper-bridge loading was finally analyzed using non-limited samples, such as bovine milk. In this case, new spots of basic milk proteins were observed, with or without paper wicks.

Conclusion

According to this technical study of basic protein focalization with IPG strips, the cup-loading protocol clearly displayed the best resolution and reproducibility: strips were first rehydrated with standard solution, then proteins were cup-loaded with destreak reagent, and focalisation was performed with cathodic wicks filled with rehydration solution and DTT. Paper-bridge loading could be as well used, but preferentially with non-limited samples.

Towards posttranslational modification proteome of royal jelly

Royal jelly (RJ) is a secretory protein from the hypopharyngeal glands of nurse honeybee workers, which contains a variety of proteins of which major royal jelly proteins (MRJPs) are some of the most important. It plays important roles both for honeybee and human. Each family of MRJP 1-5 displays a string of modified protein spots in the RJ proteome profile, which may be caused by posttranslational modifications (PTMs) of MRJPs. However, information on the RJ PTMs is still limited. Therefore, the PTM status of RJ was identified by using complementary proteome strategies of two-dimensional gel electrophoresis (2-DE), shotgun analysis in combination with high performance liquid chromatography-chip/electrospray ionization quadrupole time-of-flight/tandem mass spectrometry and bioinformatics. Phosphorylation was characterized in MRJP 1, MRJP 2 and apolipophorin-III-like protein for the first time and a new site was localized in venom protein 2 precursor. Methylation and deamidation were also identified in most of the MRJPs. The results indicate that methylation is the most important PTM of MRJPs that triggers the polymorphism of MRJP 1-5 in the RJ proteome. Our data provide a comprehensive catalog of several important PTMs in RJ and add valuable information towards assessing both the biological roles of these PTMs and deciphering the mechanisms underlying the beneficial effects of RJ for human health.

Proteomic analysis of temperature-dependent changes in stored UHT milk

Molecular changes in milk proteins during storage of UHT-treated milk have been investigated using two-dimensional electrophoresis (2-DE) coupled to MALDI-TOF mass spectrometry. UHT-treated samples were stored at three different temperatures, 4 °C, 28 °C, and 40 °C, for two months. Three main changes could be observed on 2-DE gels following storage. They were (1) the appearance of diffuse staining regions above the position of the monomeric caseins caused by nondisulfide cross-linking of α and β-caseins; (2) the appearance of additional acidic forms of proteins, predominantly of α(S1)-casein, caused by deamidation; and (3) the appearance of "stacked spots" caused by lactosylation of whey proteins. The extent of the changes increased with increased storage temperature. Mass spectrometric analysis of in-gel tryptic digests showed that the cross-linked proteins were dominated by α(S1)-casein, but a heterogeneous population of cross-linked forms with α(S2)-casein and β-casein was also observed. Tandem MS analysis was used to confirm deamidation of N(129) in α(S1)-casein. MS analysis of the stacked spots revealed lactosylation of 9/15 lysines in β-lactoglobulin and 8/12 lysines in α-lactalbumin. More extensive analysis will be required to confirm the nature of the cross-links and additional deamidation sites in α(S1)-casein as the highly phosphorylated nature of the caseins makes them challenging prospects for MS analysis.

Human milk proteins: an interactomics and updated functional overview

Milk and milk fractions are characterized by a wide array of proteins, whose concentration spans across several orders of magnitude. By exploiting a combined approach based on functional gene ontology enrichment (FatiGO/Babelomics), hierarchical clustering, and pathway and network analyses, we merged data from literature dealing with protein-oriented studies on human milk. A total of 285 entries defined a nonredundant list upon comparison with the Ingenuity Knowledge Base from the Ingenuity Pathway Analysis software. Results were compared with an inventory of bovine milk proteins gathered from dedicated proteomic studies. A protein core of 106 proteins was found, with most of the entries associated to three main biological functions, namely nutrient transport/lipid metabolism, concretization of the immune system response and cellular proliferation processes. Our analyses confirm and emphasize that the biological role of the human milk proteins is not only limited to the provision of external nutrients and defense molecules against pathogens to the suckling but also to the direct stimulation of the growth of neonate tissues/organs and to the development of a proper independent immune system, both through the induction of a number of molecular cascades associated with cell proliferation/differentiation. The latter aspects were previously investigated by single-molecule dedicated studies, missing the holistic view that results from our analysis.

Identification of de novo synthesized and relatively older proteins: accelerated oxidative damage to de novo synthesized apolipoprotein A-1 in type 1 diabetes

OBJECTIVE

The accumulation of old and damaged proteins likely contributes to complications of diabetes, but currently no methodology is available to measure the relative age of a specific protein alongside assessment of posttranslational modifications (PTM). To accomplish our goal of studying the impact of insulin deficiency and hyperglycemia in type 1 diabetes upon accumulation of old damaged isoforms of plasma apolipoprotein A-1 (ApoA-1), we sought to develop a novel methodology, which is reported here and can also be applied to other specific proteins.

RESEARCH DESIGN AND METHODS

To label newly synthesized proteins, [ring-(13)C(6)]phenylalanine was intravenously infused for 8 h in type 1 diabetic participants (n = 7) during both insulin treatment and 8 h of insulin deprivation and in nondiabetic participants (n = 7). ApoA-1 isoforms were purified by two-dimensional gel electrophoresis (2DGE) and assessment of protein identity, PTM, and [ring-(13)C(6)]phenylalanine isotopic enrichment (IE) was performed by tandem mass spectrometry.

RESULTS

Five isoforms of plasma ApoA-1 were identified by 2DGE including ApoA-1 precursor (pro-ApoA-1) that contained the relatively highest IE, whereas the older forms contained higher degrees of damage (carbonylation, deamidation) and far less IE. In type 1 diabetes, the relative ratio of IE of [ring-(13)C(6)]phenylalanine in an older isoform versus pro-ApoA-1 was higher during insulin deprivation, indicating that de novo synthesized pro-ApoA-1 more rapidly accumulated damage, converting to mature ApoA-1.

CONCLUSIONS

We developed a mass spectrometry-based methodology to identify the relative age of protein isoforms. The results demonstrated accelerated oxidative damage to plasma ApoA-1, thus offering a potential mechanism underlying the impact of poor glycemic control in type 1 diabetic patients that affects a patient's risk for vascular disease.

Label-free liquid chromatography-tandem mass spectrometry analysis with automated phosphopeptide enrichment reveals dynamic human milk protein phosphorylation during lactation

Protein phosphorylation is a critical posttranslational modification that affects cell-cell signaling and protein function. However, quantifying the relative site-specific changes of phosphorylation occupancies remains a major issue. An online enrichment of phosphopeptides using titanium dioxide incorporated in a microchip liquid chromatography device was used to analyze trypsin-digested human milk proteins with mass spectrometry. The method was validated with standards and used to determine the dynamic behavior of protein phosphorylation in human milk from the first month of lactation. α-Casein, β-casein, osteopontin, and chordin-like protein 2 phosphoproteins were shown to vary during this lactation time in an independent manner. In addition, changes in specific regions of these phosphoproteins were found to vary independently. Novel phosphorylation sites were discovered for chordin-like protein 2, α-lactalbumin, β-1,4-galactosyl transferase, and poly-Ig (immunoglobulin) receptor. Coefficients of variation for the quantitation were comparable to those in other contemporary approaches using isotopically labeled peptides, with a median value of 11% for all phosphopeptide occupancies quantified.