Proteome analysis using iTRAQ reveals the differentiation between Tibetan and ordinary ovalbumin peptides

Proteomic Profiling of Thigh Meat at Different Ages of Chicken for Meat Quality and Development

Chicken age contributes to the meat characteristics; however, knowledge regarding the pathways and proteins associated with meat quality and muscle development are still scarce, especially in chicken thigh meat. Hence, the objective of this study was to elucidate the intricate relationship between these traits by liquid chromatography mass spectrometry at three different ages. A total of 341 differential expressed proteins (DEPs) were screened out (fold change ≥ 1.50 or ≤0.67 and p < 0.05) among 45 thigh meat samples (15 samples per age) of Beijing-You chicken (BYC), collected at the age of 150, 300, or 450 days (D150, D300, and D450), respectively. Subsequently, based on the protein interaction network and Markov cluster algorithm (MCL) analyses, 91 DEPs were divided into 26 MCL clusters, which were associated with pathways of lipid transporter activity, nutrient reservoir activity, signaling pathways of PPAR and MAPK, focal adhesion, ECM-receptor interaction, the cell cycle, oocyte meiosis, ribosomes, taurine and hypotaurine metabolism, glutathione metabolism, muscle contraction, calcium signaling, nucleic acid binding, and spliceosomes. Overall, our data suggest that the thigh meat of BYC at D450 presents the most desirable nutritional value in the term of free amino acids (FAAs) and intramuscular fat (IMF), and a series of proteins and pathways associated with meat quality and development were identified. These findings also provide comprehensive insight regarding these traits across a wide age spectrum.

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.

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

The disparity in fatty acids (FA) composition exhibits a significant impact on meat quality, however, the molecular regulatory mechanisms underlying this trait in chicken are far from clear. In this study, a total of 45 female Beijing-You chicken (BYC) hens, fed on the same diet, were collected at the slaughter age of 150, 300, or 450 days (D150, D300, and D450) from sexual maturation stage to culling stage (15 birds per age). Gas chromatography-mass spectrometry (GC-MS) and tandem mass tag labeling technology based on liquid chromatography mass spectrometry (TMT-LC-MS/MS) analysis strategies were applied to profile FA compositions and to compare differential expressed proteins (DEPs) between these different slaughter ages, respectively. The FA profiling showed that increasing hen ages resulted in increased contents of both saturated and unsaturated fatty acids. Proteomic analyses showed a total of 4,935 proteins in chicken breast muscle with the false discovery rate (FDR) < 1% and 664 of them were differentially expressed (fold change > 1.50 or < 0.67 and P < 0.01). There were 410 up- and 116 down-regulated proteins in D150 vs. D300 group, 32 up- and 20 down-regulated in D150 vs. D450 group, and 72 up- and 241 down-regulated in D300 vs. D450 group. A total of 57 DEPs related to FA/lipid-related metabolisms were obtained according to the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These DEPs were involved in 21 significantly enriched (P < 0.05) pathways, including well-known pathways for FA synthesis (metabolism, desaturation, and elongation) and the signaling pathways for lipid metabolism (PPAR, adipocytokine, calcium, VEGF, MAPK, and Wnt). In addition, there existed several representative DEPs (FABP, FABP3, apoA-I, apoA-IV, apoC-III, apoB, VTG1, and VTG2) involved in the regulation of FA/lipid transportation. The construction of the interaction networks indicated that HADH, ACAA2, HADHA, ACSL1, CD36, CPT1A, PPP3R1, and SPHK1 were the key core nodes. Finally, eight DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. These results expanded our understanding of how the laying age affects the FA compositions and metabolism in hen breast meat.

Comparative N-glycoproteomic analysis of Tibetan and lowland chicken fertilized eggs: Implications on proteins biofunction and species evolution

The characterization and functionality of protein glycosylation among different related species are of common interest. Herein, non-standard quantification and N-glycosylation enrichment technology combined with ultra-high liquid chromatography-tandem mass spectrometry were used to establish detailed N-glycoproteomics of fertilized eggs, and quantitatively compared between Tibetan and lowland chicken. A total of 396N-glycosites from 143 glycoproteins were found. Specifically, compared with lowland chicken egg white, 32N-glycosites of 22 glycoproteins were up-regulated and 57N-glycosites of 25 glycoproteins were down-regulated in Tibetan chicken egg white. Also, 137N-glycosites in 72 glycoproteins showed much higher-degree glycosylation and 36N-glycosites in 15 glycoproteins displayed lower-degree glycosylation in Tibetan chicken egg yolk than those in lowland chicken egg yolk. Through bioinformatic analysis, these varied glycoproteins were highly associated with antifreeze activity, hypoxia adaptation, coagulation cascade, and binding/immunity activities, which may be related to plateau hypoxia and cold stress. PRACTICAL APPLICATIONS: These findings provide a new insight on the role of biological egg N-glycoproteins related to environmental adaptation and evolution, which may be further applied in improving egg processing and human health, by developing biomolecules for food and medical industry.

Proteomic analysis of liver tissues in chicken embryo at Day 16 and Day 20 reveals antioxidant mechanisms

To investigate the mechanisms of the defense system and antioxidant defense system during chicken embryo development, protein profiling of liver tissues in chicken embryo at Day 16 and Day 20 was conducted. TMT was used to analyze the liver tissues proteomes with significantly different activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in chicken embryo. PRM was operated to validate the target differentially abundant proteins (DAPs) using the same samples. The result showed a total of 34 DAPs were identified. Among these, 9 were upregulated and 25 were downregulated. The screened DAPs strictly related to regulation of oxidoreductase activity (DDO and GAS2L1), response to stress (ERAD2 and SAA), immune system process (GAL3 and PDCD4), and lipid regulation and metabolism (ETNPPL, APOV1, LIPM, and APOA4). These analyses indicated that the antioxidant enzyme activity of chicken embryo is regulated through different pathways. Correlation analysis revealed a linear relationship between mRNA and protein expression and 12 genes (ORM1, C8B, KPNA2, CA4, C1S, SULT1B, ETNPPL, ERCC6L, DDO, SERPINF1, VAT1L, and APOA4) were detected to be differently expressed both at mRNA and protein levels. In consequence, these findings are an important resource that can be used in future studies of antioxidant mechanisms in chicken embryo. BIOLOGICAL SIGNIFICANCE: The genetic mechanisms of antioxidant activity are still unclear in chicken embryo. In the article, the combined transcriptomic and proteomic analysis is used to further explore potential signaling pathways and differentially abundant proteins related to antioxidant activity. These findings will facilitate a better understanding of the mechanism and these DAPs can be further investigated as candidate markers to predict the activity of antioxidant enzymes.

Extracellular vesicles derived from human dental pulp stem cells promote osteogenesis of adipose-derived stem cells via the MAPK pathway

Recent studies have shown that co-culture systems play an important role in bone tissue engineering. In this study, human dental pulp stem cells (hDPSCs) were co-cultured with human adipose-derived stem cells (hADSCs), and osteoblastic phenotypes were found to be enhanced in co-cultures compared with monocultures of hDPSCs or hADSCs. Furthermore, GW4869, an inhibitor of extracellular vesicle (EV) formation, suppressed the mineralization of co-cultured cells. Studies indicate that the therapeutic potential of DPSCs is realized through paracrine action, in which EVs play an important role. To study their role, we successfully obtained and identified hDPSC-derived extracellular vesicles (hDPSC-EVs), and further investigated their effects on hADSCs and the underlying mechanism. hADSCs were stimulated with hDPSC-EVs, which were found to promote the migration and mineralization of hADSCs. Moreover, hDPSC-EVs promoted osteogenic differentiation by enhancing the phosphorylation of ERK 1/2 and JNK in hADSCs. To investigate the specific proteins in EVs that might play a role in hADSC osteogenic differentiation, we performed proteomic analysis of hDPSC-EVs. We determined the top 30 enriched pathways, which notably included the insulin signaling pathway. The number of genes enriched in the insulin signaling pathway was the largest, in addition to the “protein processing in endoplasmic reticulum” term. The MAPK cascade is a typical downstream pathway mediating insulin signaling. To further study the effects of hDPSC-EVs on maxillofacial bone regeneration, we used hDPSC-EVs as a cell-free biomaterial in a model of mandibular defects in rats. To assess the therapeutic potential of EVs, we analyzed their proteome. Animal experiments demonstrated that hDPSC-EVs promoted the regeneration of bone defects. Overall, these results highlight the potential of hDPSC-EVs to induce lineage specific differentiation of hADSCs. The results also indicated the importance of considering hDPSC-EVs as biomimetic materials for clinical translation of treatments for oral maxillofacial defects.

Small RNA sequencing reveals miRNAs important for hypoxic adaptation in the Tibetan chicken

1. The Tibetan chicken, which is an indigenous breed living on the Tibetan Plateau, exhibits hypoxic adaptations to its high-altitude environment. However, the molecular mechanism behind this hypoxic adaptation is still unclear. This study aimed to investigate differentially expressed miRNAs involved in hypoxic adaptation through high-throughput RNA sequencing. 2. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differentially expressed miRNAs and their target genes in chicken embryonic heart tissues and fibroblasts. Luciferase reporter assays were performed to confirm the relationship between miRNAs and target genes. 3. The study identified 37 differentially expressed miRNAs in Tibetan chicken embryonic heart tissues, including 20 up- and 17 down-regulated miRNAs, compared to those found in lowland chickens. Differentially expressed miRNAs were mainly involved in biological processes, such as cell cycle arrest, toll-like receptor signalling pathways, and I-kappa B kinase/NF-kappa B signalling. The data showed that gga-miR-34 c-5p was significantly upregulated in Tibetan chicken tissues and hypoxic fibroblasts, while EHHADH, a target gene of gga-miR-34 c-5p, was downregulated. Moreover, gga-miR-34 c-5p dramatically decreased the luciferase activity of the wild EHHADH, whereas no effect on the mutational EHHADH was found. 4. This study identified miRNA expression profiles in the Tibetan chicken and suggested that miR-34 c-5p acts as a novel miRNA associated with hypoxic adaptation. This facilitates the understanding of molecular mechanisms that underlie long-term exposure to hypoxia.

Label-free proteomic analysis reveals the differentiation between unfertilized and fertilized Beijing-You chicken eggs

Egg fertilization is a dynamic process, including varieties of biochemical changes. To better understand the molecular mechanisms during the egg embryo development, the objective of this study was to quantify protein expression changes between fertilized and unfertilized Beijing-You chicken eggs using label-free liquid chromatography-tandem mass spectrometry method. The results showed that a total of 1241 proteins were identified from fertilized and unfertilized eggs, 229 proteins were observed difference in fertilized eggs (p < 0.05) compared with that in unfertilized eggs. The expressions of 86 proteins were up-regulated and 48 proteins were down-regulated in fertilized eggs. STRING database analysis and Gene Ontology analysis results showed that these differentially expressed proteins significantly interacted and were involved in lipid transport and inflammatory response biological processes. The mRNA and protein expression levels of most differentially expressed proteins Apolipoprotein B, Fibrinogen alpha chain, Transferrin receptor protein 1, Phospholipid transfer protein and Vimentin were validated by RT-PCR and western blot. These results could provide possible novel insights for the molecular mechanism of egg fertilization.

Optimization of Antioxidant Hydrolysate Produced from Tibetan Egg White with Papain and Its Application in Yak Milk Yogurt

The objective of the present study was to produce antioxidant hydrolysate from Tibetan egg white protein hydrolyzed with papain, and to investigate the effect of added papain egg white hydrolysate (PEWH) on the quality characteristics and amino acid profiles of yak milk yogurt. A response surface methodology (RSM) was utilized to analyze the effects of hydrolysis time (X₁), the ratio of enzymes to substrates, and enzyme dosage (X₃) on the superoxide anion radical (O₂⁻) scavenging activity of hydrolysates. The predicted maximum value of O₂⁻ scavenging activity (89.06%) was obtained an X₁ of 2.51 h, X₂ of 4.13%, and X₃ of 4500 U/g of substrate, almost approaching the experimental value (88.05 ± 1.2%). Furthermore, it was found that the addition of PEWH to yak milk can enhance acidification, sensory score, the number of lactic acid bacteria (LAB), and the amino acid content in yak milk yogurt. The results suggested that PEWH displayed an exceptional potential to be developed as a functional food ingredient that could be applied during the manufacturing process of yak milk yogurt.