Integrated proteomic, phosphoproteomic and N-glycoproteomic analyses of chicken eggshell matrix

N-glycoproteomic profiling reveals structural and functional alterations in yellow primary preserved egg white under saline-alkali treatment

The posttranslational N-glycosylation of food proteins is important to their structure and function. However, the N-glycoproteomics of yellow preserved egg white were rarely reported. This study explored the changes of N-glycoproteome in yellow preserved eggs white after salt and alkali treatment. A total of 213 N-glycosites were identified on 102 glycoproteins, revealing prevalent glycosylation motifs and multiple N-glycosites within proteins. Salt and alkali treatment significantly altered the glycosylation patterns, impacting major proteins differently. GO analysis indicated the roles of differentially expressed glycoproteins in responding to stimuli and biological regulation. KEGG analysis emphasized the importance of salivary secretion pathway in enzyme secretion and peptide generation. Protein domain analysis highlighted the downregulation of Serpin. Protein-protein interaction networks revealed Apolipoprotein B as central players. This study provides essential structural information on the glycosylation modifications of egg white proteins, contributing to our understanding of the mechanisms behind the functional properties of preserved eggs.

TMT-based quantitative proteomic analysis reveals eggshell matrix protein changes correlated with eggshell quality in Jing Tint 6 laying hens of different ages

The decline in eggshell quality resulting from aging hens poses a threat to the financial benefits of the egg industry. The deterioration of eggshell quality with age can be attributed to changes in its ultrastructure and chemical composition. Specific matrix proteins in eggshells have a role in controlling crystal growth and regulating structural organization. However, the variations in ultrastructure and organic matrix of eggshells in aging hens remain poorly understood. This study assessed the physical traits, mechanical quality, chemical content, as well as the microstructural and nanostructural properties of eggs from Jing Tint 6 hens at 38, 58, 78, and 108 wk of age. Subsequently, a quantitative proteomic analysis was conducted to identify differences in protein abundance in eggshells between the ages of 38 and 108 wk. The results indicated a notable decline in shell thickness, breaking strength, index, fracture toughness, and stiffness in the 108-wk-age group compared to the other groups (P < 0.05). The ultrastructure variations primarily involved an increased ratio of the mammillary layer and a reduced thickness of the effective layer of eggshell in the 108-wk-age group (P < 0.05). However, no significant differences in eggshell compositions were observed among the various age groups (P > 0.05). Proteomic analysis revealed the identification of 76 differentially expressed proteins (DEPs) in the eggshells of the 38-wk-age group and 108-wk-age group, which comprised proteins associated with biomineralization, calcium ion binding, immunity, as well as protein synthesis and folding. The downregulation of ovocleidin-116, osteopontin, and calcium-ion-related proteins, together with the upregulation of ovalbumin, lysozyme C, and antimicrobial proteins, has the potential to influence the structural organization of the eggshell. Therefore, the deterioration of eggshell quality with age may be attributed to the alterations in ultrastructure and the abundance of matrix proteins.

Comparative N-Glycoproteomic Investigation of Eggshell Cuticle and Mineralized Layer Proteins

The eggshell cuticle layer (ECL) and eggshell mineralized layer (EML) contain amounts of glycoproteins and proteoglycans. However, there were few comprehensive reports about the effect of post-translational modifications on protein structure and function which requires investigation. Therefore, we used comparative N-glycoproteomics to study glycoproteins in the ECL and EML. We identified a total of 272 glycoproteins in this experiment and found that glycoproteins located in EML were more than that in ECL. Moreover, they showed distinct functional difference between both layers. As N-glycosylation of ovocleidin-17 and ovocleidin-116 in the EML affected eggshell mineralization, some glycoproteins located in ECL, like ovotransferrin and ovostatin-like, possessed antibacterial activity. The several regulated glycoproteins in the EML may pertain to the regulation of mineralization, while glycosylated proteins in the ECL may contribute to molecular adhesion and defense against microbial invasion. This study provides new insights into the eggshell matrix protein contents of the ECL and EML.

Quantitative Proteomic Analysis of Tibetan Pig Livers at Different Altitudes

In this study, the differences in protein profiles between the livers of Shannan Tibetan pigs (SNT), Linzhi Tibetan pigs (LZT) and Jiuzhaigou Tibetan pigs (JZT) were comparatively analyzed by tandem mass spectrometry-labeling quantitative proteomics. A total of 6804 proteins were identified: 6471 were quantified and 1095 were screened as differentially expressed proteins (DEPs). Bioinformatics analysis results show that, compared with JZT livers, up-regulated DEPs in SNT and LZT livers mainly promoted hepatic detoxification through steroid hormone biosynthesis and participated in lipid metabolism to maintain body energy homeostasis, immune response and immune regulation, while down-regulated DEPs were mainly involved in lipid metabolism and immune regulation. Three proteases closely related to hepatic fatty acid oxidation were down-regulated in enzymatic activity, indicating higher levels of lipid oxidation in SNT and LZT livers than in JZT livers. Down-regulation of the expression of ten immunoglobulins suggests that JZT are more susceptible to autoimmune diseases. It is highly likely that these differences in lipid metabolism and immune-related proteins are in response to the ecological environment at different altitudes, and the findings contribute to the understanding of the potential molecular link between Tibetan pig livers and the environment.

Unveiling and application of the chicken egg proteome: An overview on a two-decade achievement

Egg proteins are not only the most complete and ideal form of protein for human or embryo nutrition but also play the vital role in the food industry. Egg proteins are subjected to many potential changes under various conditions, which may further alter the nutritional value, physicochemical-properties, and bioactivities of proteins. Recent advances in our understanding of the proteome of raw egg matrix from different species and dynamic changes occurring during storage and incubation are developing rapidly. This review provides a comprehensive overview of the main characteristics of chicken egg proteome, covering all its components and applications under various conditions, such as markers detection, egg quality evaluation, genetic and biological unknown identification, and embryonic nutritional supplementation, which not only contributes to our in-depth understanding of each constituent functionality of proteome, but also provides information to increase the value to egg industry.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Tandem mass tag-based proteomics analysis of protein changes in the freezing and thawing cycles of Trachurus murphyi

We investigated the proteome variations in Trachurus murphyi with different cycles of freezing and thawing (FT) under frozen storage. A total of 2,482 proteins were assessed quantitatively, of which 269 proteins were recognized as differential abundance proteins during the second FT cycle until the eighth FT cycle. Bioinformatics analysis on gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of Differential Analysis of Proteins (DAPs) indicated multiple DAPs engaged with the protein structure, metabolic enzymes, and protein turnover. In addition, some of the observed proteins were probably the underlying markers of protein oxidation (PO). The analysis of PO sites revealed the sites of PO, such as amino adipic semialdehydes, γ-glutamic semialdehydes, and Schiff bases. Bioinformatics analyses demonstrated the involvement of differentially expressed proteins in the Hippo signaling pathway (Ko04390), indicating strong protein degradation with greater numbers of FT cycles under frozen storage. It provides an insight into quality stability from a proteomics quality perspective at the molecular level. The results obtained have deepened our current understandings of the mechanisms that reveal variations in proteomes and quality, as well as help promote quality control of T. murphyi across the cold transportation chain. PRACTICAL APPLICATION: Temperature fluctuation is one of the core issues during frozen food storage and distribution faced by the frozen food industry. Fluctuation may result in microstructural changes, ice recrystallization, and protein change in frozen food products. Tandem mass tag-based methods were adopted to study proteome variations in Trachurus murphyi muscles under different cycles of freezing and thawing under frozen storage conditions in this paper. The results obtained have deepened our current understandings of the mechanisms that reveal variations in proteomes and quality, as well as help promote quality control of T. murphyi across the cold transportation chain.

Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of the longissimus thoracis of yaks

Yaks (Bos mutus) live in the Qinghai–Tibet plateau. The quality of yak meat is unique due to its genetic and physiological characteristics. Identification of the proteome of yak muscle could help to reveal its meat-quality properties. The common proteome, phosphoproteome, and N-glycoproteome of yak longissimus thoracis (YLT) were analyzed by liquid chromatography-tandem mass spectrometry-based shotgun analysis. A total of 1812 common proteins, 1303 phosphoproteins (3918 phosphorylation sites), and 204 N-glycoproteins (285 N-glycosylation sites) were identified in YLT. The common proteins in YLT were involved mainly in myofibril structure and energy metabolism; phosphoproteins were associated primarily with myofibril organization, regulation of energy metabolism, and signaling; N-glycoproteins were engaged mainly in extracellular-matrix organization, cellular immunity, and organismal homeostasis. We reported, for the first time, the “panorama” of the YLT proteome, specifically the N-glycoproteome of YLT. Our results provide essential information for understanding post mortem physiology (rigor mortis and aging) and the quality of yak meat.

•

A total of 2650 proteins were identified in yak longissimus thoracis.

•

Common proteins were involved mainly in myofibril structure and energy metabolism.

•

Phosphoproteins were associated with myofibrils, energy metabolism, and signaling.

•

N-glycoproteins were engaged mainly in ECM organization, immunity, and homeostasis.

Quantitative N-glycoproteome analysis of bovine milk and yogurt

Post-translational modification structure of food's proteins might be changed during processing, thereby affecting the nutritional characteristics of the food product. In this study, differences in protein N-glycosylation patterns between milk and yogurt were quantitatively compared based on glycopeptide enrichment, liquid chromatography separation, and tandem mass spectrometry analysis. A total of 181 N-glycosites were identified, among which 142 were quantified in milk and yogurt. Significant alterations in the abundance of 13 of these N-glycosites were evident after the fermentation of milk into yogurt. Overall, the N-glycosylation status of the majority of milk proteins remained relatively unchanged in yogurt, suggesting that their conformations, activities, and functions were maintained despite the fermentation process. Among the main milk proteins, N²⁴¹ of cathepsin D and N³⁵⁸ of lactoperoxidase were markedly reduced after undergoing lactic acid fermentation to produce yogurt. Furthermore, a comparative analysis of current and previously reported N-glycoproteomic data revealed heterogeneity in the N-glycosylation of milk proteins. To sum up, a quantitative comparison of the N-glycoproteomes of milk and yogurt was presented here for the first time, providing evidence that the fermentation process of yogurt could cause changes in the N-glycosylation of certain milk proteins.

•

181 N-glycosites from 118 N-glycoproteins were identified in milk and yogurt.

•

13 N-glycosites changed significantly after fermentation of milk into yogurt.

•

N²⁴¹ of cathepsin D and N³⁵⁸ of lactoperoxidase was markedly reduced in yogurt.

•

Heterogeneity of N-glycosylation of milk protein has been documented.

Quantitative proteomic analyses during formation of chicken egg yolk

A quantitative comparison of the proteomes during different periods of the formation of egg yolk, from yellow follicles (YF), small hierarchical follicles (9-12 mm, SF), and the largest hierarchical follicle (LF), was performed. The abundance of major egg yolk proteins (apolipoprotein B and vitellogenins) changed significantly during the yolk formation, and several protein hydrolases and isomerases, which may be related to the processing of egg yolk proteins, also varied significantly. The binding proteins for three vitamins (retinol, riboflavin, and vitamin D) and cholesterol were all most abundant in the LF period, suggesting that these nutrients were transported mainly at the final period of the egg yolk formation. Immunoglobulins decreased and complement proteins increased as formation progressed, indicating the dynamic nature of the egg yolk immune system. These results are helpful for understanding the nutrient composition, the formation of assembly structure, the preservation and processing properties of egg yolk.

Evolution of the Avian Eggshell Biomineralization Protein Toolkit - New Insights From Multi-Omics

The avian eggshell is a remarkable biomineral, which is essential for avian reproduction; its properties permit embryonic development in the desiccating terrestrial environment, and moreover, are critically important to preserve unfertilized egg quality for human consumption. This calcium carbonate (CaCO₃) bioceramic is made of 95% calcite and 3.5% organic matrix; it protects the egg contents against microbial penetration and mechanical damage, allows gaseous exchange, and provides calcium for development of the embryonic skeleton. In vertebrates, eggshell occurs in the Sauropsida and in a lesser extent in Mammalia taxa; avian eggshell calcification is one of the fastest known CaCO₃ biomineralization processes, and results in a material with excellent mechanical properties. Thus, its study has triggered a strong interest from the researcher community. The investigation of eggshell biomineralization in birds over the past decades has led to detailed characterization of its protein and mineral constituents. Recently, our understanding of this process has been significantly improved using high-throughput technologies (i.e., proteomics, transcriptomics, genomics, and bioinformatics). Presently, more or less complete eggshell proteomes are available for nine birds, and therefore, key proteins that comprise the eggshell biomineralization toolkit are beginning to be identified. In this article, we review current knowledge on organic matrix components from calcified eggshell. We use these data to analyze the evolution of selected matrix proteins and underline their role in the biological toolkit required for eggshell calcification in avian species. Amongst the panel of eggshell-associated proteins, key functional domains are present such as calcium-binding, vesicle-binding and protein-binding. These technical advances, combined with progress in mineral ultrastructure analyses, have opened the way for new hypotheses of mineral nucleation and crystal growth in formation of the avian eggshell, including transfer of amorphous CaCO₃ in vesicles from uterine cells to the eggshell mineralization site. The enrichment of multi-omics datasets for bird species is critical to understand the evolutionary context for development of CaCO₃ biomineralization in metazoans, leading to the acquisition of the robust eggshell in birds (and formerly dinosaurs).

Hydrophilic carrageenan functionalized magnetic carbon-based framework linked by silane coupling agent for the enrichment of N-glycopeptides from human saliva

In this work, a magnetic graphene material coated with mesoporous silica was selected as the substrate, 3-glycidoxypropyltrimethoxysilane and polyethyleneimine were sequentially bonded through chemical reactions, and then carrageenan was successfully introduced by electrostatic interaction; finally, hydrophilic nanocomposite material was prepared. Due to the large number of hydrophilic groups, and polyethyleneimine was connected by means of chemical bonds, this material exhibits good hydrophilicity and stability for glycopeptide enrichment. In the actual enrichment process, nanomaterial exhibits high selectivity (1:500), high sensitivity (2 fmol), and good repeatability (five cycles). In addition, the synthesized material also shows a good enrichment effect in the face of actual complex biological samples, which captured 40 N-glycopeptides from human saliva, indicating the application potential for enrichment of N-glycopeptides.

Avian eggshell biomineralization: an update on its structure, mineralogy and protein tool kit

BACKGROUND

The avian eggshell is a natural protective envelope that relies on the phenomenon of biomineralization for its formation. The shell is made of calcium carbonate in the form of calcite, which contains hundreds of proteins that interact with the mineral phase controlling its formation and structural organization, and thus determine the mechanical properties of the mature biomaterial. We describe its mineralogy, structure and the regulatory interactions that integrate the mineral and organic constituents during eggshell biomineralization. Main Body. We underline recent evidence for vesicular transfer of amorphous calcium carbonate (ACC), as a new pathway to ensure the active and continuous supply of the ions necessary for shell mineralization. Currently more than 900 proteins and thousands of upregulated transcripts have been identified during chicken eggshell formation. Bioinformatic predictions address their functionality during the biomineralization process. In addition, we describe matrix protein quantification to understand their role during the key spatially- and temporally- regulated events of shell mineralization. Finally, we propose an updated scheme with a global scenario encompassing the mechanisms of avian eggshell mineralization.

CONCLUSION

With this large dataset at hand, it should now be possible to determine specific motifs, domains or proteins and peptide sequences that perform a critical function during avian eggshell biomineralization. The integration of this insight with genomic data (non-synonymous single nucleotide polymorphisms) and precise phenotyping (shell biomechanical parameters) on pure selected lines will lead to consistently better-quality eggshell characteristics for improved food safety. This information will also address the question of how the evolutionary-optimized chicken eggshell matrix proteins affect and regulate calcium carbonate mineralization as a good example of biomimetic and bio-inspired material design.

Phosphoinositide signaling plays a key role in the regulation of cell wall reconstruction during the postharvest morphological development of Dictyophora indusiata

The potential signaling mechanism of Dictyophora indusiata during postharvest morphological development was investigated through quantitative phosphoproteomic analyses. A total of 1566 phosphorylation sites changed significantly (872 upregulated and 694 downregulated) in the mature stage compared with those in the peach-shaped stage of D. indusiata. Bioinformatics analysis showed that the upregulated differentially phosphorylated proteins were mainly involved in the "phosphatidylinositol signaling system" and "mitogen-activated protein kinase signaling pathway-yeast", while the downregulated differentially phosphorylated proteins were related mainly to "starch and sucrose metabolism". Further mining of the phosphoproteome data revealed that upregulated phosphoinositide signaling activated the cell wall integrity pathway and then regulated the synthesis of the main components of the cell wall. The results suggested that phosphoinositide signaling could be a potential target pathway for the regulation of the postharvest morphological development of D. indusiata.

A puzzle piece of protein N-glycosylation in chicken egg: N-glycoproteome of chicken egg vitelline membrane

The chicken egg vitelline membrane (CEVM) is an important structure for the transmembrane transport of egg yolk components, protection of the blastodisc, and separation of egg white and egg yolk. In this study, the N-glycoproteome of the CEVM was mapped and analyzed in depth. Total protein of the CEVM was digested, and the glycopeptides were enriched by a hydrophilic interaction liquid chromatography microcolumn and identified by nano liquid chromatography/tandem mass spectrometry. A total of 435 N-glycosylation sites on 208 N-glycoproteins were identified in CEVM. Gene Ontology enrichment analysis showed that CEVM N-glycoproteins are mainly involved in the regulation of proteinases/inhibitors and transmembrane transport of lipids. Mucin-5B is the primary N-glycoprotein in the CEVM. Comparison of the main N-glycoproteins between the CEVM and other egg parts revealed the tissue specificity of N-glycosylation of egg proteins. The results provide insights into protein N-glycosylation in the chicken egg, CEVM functions and underlying mechanisms.

Quantitative N-glycoproteomic analyses provide insights into the effects of thermal processes on egg white functional properties

This study tries to elucidate the different mechanisms of functional properties among pasteurized egg white (P-EW), spray-dried egg white (SD-EW) and fresh egg white (F-EW) via quantitative N-glycoproteomic analyses. The results showed that spray-drying increased the surface hydrophobicity (181.4%) and zeta potential (25.6%) of egg white, which contributed to the enhancement of emulsifying activity index (20.1%) and foaming capacity (35.2%). Pasteurization caused the disintegration of natural protein aggregates in F-EW and resulted in a "block-like" P-EW gel and higher water holding capacity (6.2%). Spray-drying caused formation of thermal aggregates and led to a "mesh-like" SD-EW gel and better cohesiveness (3.6%). Quantitative N-glycoproteomic analysis showed that the abundance of 32 N-glycosites from 18 N-glycoproteins (such as Mucin 5B) of SD-EW was significantly reduced comparing to F-EW, indicated that the N-glycans of egg white protein are likely to be covalently cross-linked during spray-drying and are involved in thermal aggregation.

Parallel reaction monitoring revealed tolerance to drought proteins in weedy rice (Oryza sativa f. spontanea)

Drought is a complicated abiotic stress factor with severe effects on rice growth and production. Weedy rice is a valuable genetic resource that possesses a strong capacity for drought tolerance, cold tolerance, and salt tolerance, and is an excellent material for studying rice tolerance. Here, according to comprehensive tolerance to drought index D, accession WR16 was selected based on strong drought tolerance among 133 studied weedy red rice germplasms. WR16 was compared with Oryza sativa ssp. Japonica. cv. IAPAR-9, a reference genotype originating from Brazil. In addition, accession WR24 was classified as moderately tolerant to drought accessions. Transcriptomic and proteomic analyses were combined to identify 38 co-upregulated proteins related to drought tolerance, and targeted parallel reaction monitoring (PRM) was used to precisely quantify and verify nine proteins in the complex backgrounds. Result showed that six proteins were significantly (Fisher's exact P value < 0.05) related to drought tolerance in accessions WR16 and WR24. Among them, OS09T0478300-01, OS09T0530300-01, and OS01T0800500-01 formed a combined defense system to respond to drought stress in weedy rice. Results of these studies provide comprehensive information for precisely identifying and verifying tolerance to drought proteins and lay a solid theoretical foundation for research on drought tolerance mechanisms.