Application and Research Progress of Proteomics in Chicken Meat Quality and Identification: A Review

Omics based technology application in poultry meat research

Omics techniques, including genomics, transcriptomics, proteomics, metabolomics, and lipidomics, analyze entire sets of biological molecules to seek comprehensive knowledge on a particular phenotype. These approaches have been extensively utilized to identify both biomarkers and biological mechanisms for various physiological conditions in livestock and poultry. The purpose of this symposium was not only to focus on how recent omics technologies can be used to gather, integrate, and interpret data produced by various methodologies in poultry research, but also to highlight how omics and bioinformatics have increased our understanding of poultry meat quality problems and other complex traits. This Poultry Science Association symposium paper includes 5 sections that cover: 1) functional annotation of cis-regulatory elements in the genome informs genetic control of complex traits in poultry, 2) mass spectrometry for proteomics, metabolomics, and lipidomics, 3) proteomic approaches to investigate meat quality, 4) spatial transcriptomics and metabolomics studies of wooden breast disease, and 5) multiomics analyses on chicken meat quality and spaghetti meat. These topics provide insights into the molecular components that contribute to the structure, function, and dynamics of the underlying mechanisms influencing meat quality traits, including chicken breast myopathies. This information will ultimately contribute to improving the quality and composition of poultry products.

Edible Coating Based on Alginate Nanoparticles Containing Menthol and Zataria multiflora Essential Oil: Effect on the Shelf Life of Chicken Thigh in the Refrigerator

Chicken thigh is a popular and widely consumed meat product. However, its high moisture content and susceptibility to microbial spoilage limit its shelf life. To address this issue, we investigated the efficacy of an edible coating based on alginate nanoparticles (AlgNPs) containing menthol, Zataria multiflora essential oil (EO), or their combination for extending the shelf life of chicken thigh. The nanoparticles were prepared through ionic gelation methods; their particle size was obtained as 87-205 nm with PDI values of < 0.3 and SPAN values of < 1. The AlgNPs containing both menthol and the EO showed the most potent antimicrobial activity (the lowest counts of pseudomonas, aerobic mesophilic, and yeast-mold), during cold storage. This coating treatment showed also the highest antioxidant activities, with the lowest thiobarbituric acid reactive substances (TBARS), pH and total volatile basic nitrogen (TVBN) values. Moreover, this coating significantly (p < 0.05) showed the highest sensory quality of chicken thighs, as evidenced by the higher sensory scores for texture, odor, color, and overall acceptability. Therefore, the edible coating based on AlgNPs containing menthol and Z. multiflora EO is an effective and promising approach for extending the shelf life of chicken thighs.

New findings on post-mortem chicken quality changes: The ROS-influenced MAPK-JNK signaling pathway affects chicken quality by regulating muscle cell apoptosis

Research conducted previously has demonstrated that apoptosis significantly influences the chicken quality. While ROS are acknowledged as significant activators of apoptosis, the precise mechanism by which they influence muscle cell apoptosis in the post-mortem remains unclear. In this study, chicken samples were treated with rosemarinic acid and H2O2 to induce varying ROS levels, and the ROS-triggered apoptosis mechanism in chicken muscle cells in post-mortem was analyzed. The TUNEL results revealed that elevated ROS levels in chicken were associated with a greater degree of muscle cell apoptosis. Western-blot results suggested that sarcoplasmic ROS could initiate apoptosis through the mitochondrial pathway by activating the MAPK-JNK signaling pathway. Moreover, TEM and shear force results demonstrated that muscle cell apoptosis initiates myofiber fragmentation and structural damage to sarcomeres, ultimately reducing chicken tenderness. This study enhances our understanding of post-mortem muscle cell apoptosis, providing valuable insights for regulating chicken quality.

Systematic evaluation of the meat qualities of free-range chicken (Xuan-Zhou) under different ages explored the optimal slaughter age

Meat qualities of free-range chicken (Xuan-Zhou) (XZ-FRC) are closely associated with slaughter age and directly influence the economic benefits of supplier and consumer's preference. Understanding of the relationship between meat qualities and ages will be of prime important to explore a better slaughter age of XZ-FRC. In this study, the quality traits of breast and thigh muscles from XZ-FRCs at 9 to 14 wk were analyzed to establish a relatively reliable method for selecting a better slaughter age. The results showed that the effects of slaughter ages on color (CIE L*, a* and b* values), shear force, centrifugal loss, and flavor of XZ-FRCs were significant (P < 0.05). There were greater differences in meat qualities, whatever breast or thigh muscles, between same or different ages. Eleven feature indexes used for colligation evaluation of slaughter age were selected by combining the quality characteristics and data analysis. The score of colligation evaluation for XZ-FRCs at 12 wk was higher than that at 9 and 14 wk, suggesting that the 12 wk was an optimal slaughter age. This work would provide a reference method that helps the producers of livestock and poultry to select a better slaughter age.

Effects of combined treatment of electrolytic water and chitosan on the quality and proteome of large yellow croaker (Pseudosciaena crocea) during refrigerated storage

The labeled quantitative proteomic method was used to study the changes in muscle proteins of large yellow croaker (Pseudosciaena crocea) treated with electrolytic water (EW) and chitosan (CHI) combined preservation during 12 days of refrigeration storage (4 °C). The analysis indicated that the freshness instructed by total viable count (TVC), total volatile basic nitrogen (TVB-N) and K value was significantly maintained after combined preservation during storage at 4 °C for 12 days (CS12). Furthermore, 46 differentially abundant proteins (DAPs) were detected in storage at 4 °C for 12 days (S12) compared to the freshness group (F), which bioinformatics confirmed were mainly skeletal proteins and enzymes. Correlation analysis showed that 19 highly correlated DAPs could be used as potential protein markers of freshness. Changes in the relation of freshness and protein were shown in further correlative analysis of F and CS12, which were caused by combined preservation. Therefore, combined preservation is promising in the quality and stability of large yellow croakers.

Overview of omics applications in elucidating the underlying mechanisms of biochemical and biological factors associated with meat safety and nutrition

Over the years, significant technological discoveries have facilitated the improvement of meat-related research. Recent studies of complex and interactive factors contributing to variations in meat safety are increasingly focused on data-driven omics approaches such as proteomics. This review highlighted omics advances in elucidating the biochemical and biological actions on meat safety. Also, the impacts of the nutritional characteristics of meat and meat products on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers. SIGNIFICANCE OF THE REVIEW: This review highlighted omics advances in elucidating underlying mechanisms of biochemical and biological factors associated with meat safety. Also, the impacts of meat proteins on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers.

Insight into Ultrasound-Induced Modifications of the Proteome and Flavor-Related Proteins of Unsmoked Bacon by Applying Label-Free Quantitation Technology

The aim of this study was to investigate the modifications of the proteome and flavor-related proteins in unsmoked bacon resulting from ultrasound treatment with the application of label-free quantitation technology together with bioinformatics analysis. Results showed that the expression levels of 137 proteins were markedly affected by ultrasound with most of them being significantly upregulated. The proteins distributed in the cytoplasm and the cytosol, the mitochondrion, and the nucleus were more susceptible to ultrasound treatment. Meanwhile, 20 flavor-related proteins, mostly myofibrillar proteins and metabolic enzymes mainly involved in the metabolic pathways of signaling and cellular processes and environmental information processing, were screened out. In addition, the differential expressions of flavor-related proteins induced by ultrasound were verified by western blotting. This study displayed insightful information from the proteomics perspective for a better understanding of the influential effect of ultrasound treatment on meat flavor.

Physicochemical, Nutritional Properties and Metabolomics Analysis Fat Deposition Mechanism of Chahua Chicken No. 2 and Yao Chicken

Poultry is an important dietary source of animal protein, accounting for approximately 30% of global meat consumption. Because of its low price, low fat and cholesterol content, and no religious restrictions, chicken is considered a widely available healthy meat. Chahua chicken No. 2 is a synthetic breed of Chahua chicken derived from five generations of specialized strain breeding. In this study, Chahua chicken No. 2 (CH) and Yao chicken (Y) were used as the research objects to compare the differences in physicochemical and nutritional indicators of meat quality between the two chicken breeds, and metabolomics was used to analyze the differences in metabolites and lipid metabolism pathways and to explore the expression of genes involved in adipogenesis. The physical index and nutritional value of CH are better than that of Y, and the chemical index of Y is better than that of CH. However, the chemical index results of CH are also within the normal theoretical value range. Comprehensive comparison shows that the meat quality of CH is relatively good. Metabolomics analysis showed that CH and Y had 85 different metabolites, and the differential metabolites were mainly classified into eight categories. KEGG pathway enrichment analysis revealed 13 different metabolic pathways. The screened PPARG, FABP3, ACSL5, FASN, UCP3 and SC5D were negatively correlated with muscle fat deposition, while PPARα, ACACA and ACOX1 were positively correlated with muscle fat deposition. The meat quality of CH was better than Y. The metabolites and metabolic pathways obtained by metabonomics analysis mainly involved the metabolism of amino acids and fatty acids, which were consistent with the differences in meat quality between the two breeds and the contents of precursors affecting flavor. The screened genes were associated with fatty deposition in poultry.

Label-Free Mass Spectrometry-Based Proteomic Analysis in Lamb Tissues after Fish Oil, Carnosic Acid, and Inorganic Selenium Supplementation

Simple Summary

Advances in proteomics and bioinformatics analysis offer the potential to investigate nutrients’ influence on protein expression profiles, and consequently on biological processes, molecular functions, and cellular components. However, knowledge in this area, particular about the exact way selenium modulates protein expression, remains limited. Therefore, in this project, global differential proteomic experiments were carried out in order to identify changes in the expression of proteins in animal tissues obtained from lambs on a specific diet involving the addition of a combination of different supplements, namely, inorganic selenium compounds, fish oil, and carnosic acid. Following inorganic selenium supplementation, a protein-protein interaction network analysis of forty differentially-expressed proteins indicated two significant clusters.

Abstract

Selenium is an essential nutrient, building twenty five identified selenoproteins in humans known to perform several important biological functions. The small amount of selenium in the earth’s crust in certain regions along with the risk of deficiency in organisms have resulted in increasingly popular dietary supplementation in animals, implemented via, e.g., inorganic selenium compounds. Even though selenium is included in selenoproteins in the form of selenocysteine, the dietary effect of selenium may result in the expression of other proteins or genes. Very little is known about the expression effects modulated by selenium. The present study aimed to examine the significance of protein expression in lamb tissues obtained after dietary supplementation with selenium (sodium selenate) and two other feed additives, fish oil and carnosic acid. Label-free mass spectrometry-based proteomic analysis was successfully applied to examine the animal tissues. Protein-protein interaction network analysis of forty differently-expressed proteins following inorganic selenium supplementation indicated two significant clusters which are involved in cell adhesion, heart development, actin filament-based movement, plasma membrane repair, and establishment of organelle localization.

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.

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

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

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

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

Marination with citric acid, lemon, and grapefruit affects the sensory, textural, and microstructure characteristics of poultry meat

1. This study aimed to determine the effects of marination liquids prepared with citric acid (CA-0.5%), lemon (LJ-100%) and grapefruit (GJ-100%) juices on the pH, colour (L*, a*, b*, Chroma, hue angle, total colour differences), cooking loss (CL), water holding capacity (WHC) and marinade absorption (MA) of chicken breast meat. Textural, microstructure (scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM)) and sensory properties were investigated.2. As a result of marination, there was a significant (P < 0.01) decrease in the CL and pH values and an increase in WHC and MA values of marinated meat. The L*, b* and chroma values of chicken breast meats marinated with all marinades increased significantly (P < 0.01).3. While CLSM showed that LJ gave rise to a partial deterioration in muscle fibres, SEM indicated that LJ had irregular muscle fibres, some fibres were broken and separated from each other. The lowest hardness value was established in the LJ group from texture analysis. In the sensory analysis, marinated samples generally received higher scores from panellists compared with the control.

Adaptation of two-dimensional electrophoresis for muscle tissue analysis

It is important to understand the molecular mechanisms that take place in muscle tissues and to predict meat quality characteristics. One of the most popular methods is two-dimensional electrophoresis, which allows us to visualize, share and identify different molecules, including meat proteins. However, the standard conditions of this method are not universal for all types of raw material, so the authors suggest a new variation of two-dimensional electrophoresis for muscle tissue analysis. Samples were tested by the classical version of isoelectric focusing (cathode buffer in the top and anode buffer in the bottom chamber of the electrophoresis cell) and its variation (anode buffer in the top and cathode buffer in the bottom chamber of the electrophoresis cell). Next, extruded gels were incubated in two different buffer systems: the first was equilibration buffer I (6 M urea, 20% w/v glycerol, 2% w/v SDS and 1% w/v Ditiothreitol in 375 mM Tris-HCl buffer, pH 8.8) followed by equilibration buffer II (6 M urea, 20% w/v glycerol, 2% w/v SDS and 4% w/v iodoacetamide in 375 mM Tris-HCl buffer pH 8.8 and the second, buffer А, consisting of 5 M urea, 2% w/v SDS, 5% v/v mercaptoethanol, 62.5 mM Tris-HCl buffer, pH 6.8 and 0.01% w/v bromophenol blue. Electrophoretic studies of muscle tissue revealed the best protein separation after changing the direction of the current (authors' variation), while no differences were detected after changing incubation buffers.