“Muscle to meat” molecular events and technological transformations: The proteomics insight

MeRIP sequencing reveals the regulation of N6-methyladenosine in muscle development between hypertrophic and leaner broilers

Meat production performance is the most important economic trait in broilers, and skeletal muscle, as the largest organ in animals, is directly related to meat production during embryonic and postnatal growth and development. N6-Methyladenosine (m6A) is a chemical modification occurs on RNA adenosine that has been reported to participate in a variety of biological processes in all species. However, there are still few reports on the regulatory role of muscle growth and development in poultry after birth. This study aims to reveal the distribution of m6A modification sites in chicken pectoralis major muscle after birth and find out the regulatory relationship between m6A and muscle development. As representatives of leaner (Xinghua chicken [XH]) and hypertrophic (White Recessive Rock chicken [WRR]) broilers, there are significant differences in body weight, muscle fiber diameter, and muscle fiber cross-sectional area between XH and WRR chickens. RNA sequencing detected a total of 397 differentially expressed genes (DEG) in the pectoralis major muscle of XH and WRR chicken, and these DEGs were mainly enriched in catalytic activity and metabolic pathways. MeRIP sequencing results showed that among all 6,476 differentially modified m6A peaks, about 90% peaks (5,823) were differentially down regulated in XH chickens. The joint analysis of the mRNA and MeRIP sequencing data found 145 DEGs with differential m6A peak, ALKBH5 as a m6A demethylase, was also included. The highly expression of ALKBH5 in the muscle tissue of poultry and differential expression between XH and WRR chickens suggest that ALKBH5 may play a crucial role in regulating muscle development. Our results revealed that there were significant differences in growth rate, body weight, muscle fiber diameter, and fiber cross-section area between WRR and XH chicken, as well as significant differences in m6A methylation level and muscle metabolism level.

Protein Post-Translational Modifications Based on Proteomics: A Potential Regulatory Role in Animal Science

Genomic studies in animal breeding have provided a wide range of references; however, it is important to note that genes and mRNA alone do not fully capture the complexity of living organisms. Protein post-translational modification, which involves covalent modifications regulated by genetic and environmental factors, serves as a fundamental epigenetic mechanism that modulates protein structure, activity, and function. In this review, we comprehensively summarize various phosphorylation and acylation modifications on metabolic enzymes relevant to energy metabolism in animals, including acetylation, succinylation, crotonylation, β-hydroxybutylation, acetoacetylation, and lactylation. It is worth noting that research on animal energy metabolism and modification regulation lags behind the demands for growth and development in animal breeding compared to human studies. Therefore, this review provides a novel research perspective by exploring unreported types of modifications in livestock based on relevant findings from human or animal models.

Physicochemical properties and sensory profile of some breeds of rabbits in Algeria

The objective of this study was to compare physicochemical traits and sensory profile of meat from rabbits of both sexes belonging to two genotypes, local population and new line (ITELV 2006) which exhibited better characteristics due to its genetic potential. A total of 60 rabbits at 90 days of age were used in the experiment. At slaughter, meat physicochemical and sensory characteristics were measured on Longissimus lumborum muscle. Differences related to genotype were found in most of the physicochemical characteristics studied like Cooking Losses (P < 0.001), Percentage of Released Water (P < 0.001), Myofibril Fragmentation Index (P < 0.001) and a* value (P < 0.001). However, in some of the traits, the differences were related to interaction of sex and genotype (S*G) as in the case of Cooking Losses (P < 0.001) and b* value (P < 0.01). Regarding SDS-PAGE analysis results, the comparison between two breeds has not shown any particular distinction in the myofibrillar and sarcoplasmic protein profiles in relation to the number and the intensity of bands. No significant differences in the sensory characteristics of the meat were noted (P > 0.05). Interestingly, no relevant differences were found between meat from male and female rabbits in all the variables studied (P > 0.05). It was concluded that meat quality was mainly affected by genotype. Thus, the new line exhibited good physicochemical characteristics compared to the local one. This study is the first to analyse and compare the physicochemical and sensory properties of Algerian rabbit meat.

Relationship between peptides and the change in quality characteristics of beef strip loin (M. longissimus lumborum) and tenderloin (M. psoas major)

Peptides in fresh and aged beef strip loin (M. longissimus lumborum) and tenderloin (M. psoas major) were quantified to investigate the relationship between proteolysis-induced peptides and beef quality characteristics. A total of 409 and 450 peptides were quantified from strip loin and tenderloin, respectively, and found to be significantly correlated to beef quality characteristics. Changes in redness and yellowness were significantly correlated to the peptides derived from G3P, ENOB, and KCRM in both muscles during 14 days of storage. The peptides produced from MYG, ENOB, HBA, PGK1, and TPIS were strongly associated with improved tenderness, while those derived from major myofibrillar proteins, such as MYH1, MYH2, ACTS, and DESM, were associated with changes in tenderloin color. These results improve our understanding of the association between peptides and changes in meat quality during cold storage, indicating that proteolysis-induced peptides can be indicators of the quality characteristics of fresh and aged meat.

Study of emerging chicken meat quality defects using OMICs: What do we know?

Starting in approximately 2010, broiler breast meat myopathies, specifically woody breast meat, white striping, spaghetti meat, and gaping have increased in prevalence in the broiler meat industry. Omic methods have been used to elucidate compositional, genetic, and biochemical differences between myopathic and normal breast meat and have provided information on the factors that contribute to these myopathies. This review paper focuses on the genomic, transcriptomic, proteomic, metabolomic, and other omics research that has been conducted to unravel the molecular mechanisms involved in the development of these myopathies and their associated factors and potential causes. SIGNIFICANCE: This review manuscript summarizes poultry meat quality defects, also referred to as myopathies, that have been evaluated using omics methods. Genomics, transcriptomics, proteomics, metabolomics and other methodologies have been used to understand the genetic predisposition, the protein expression, and the biochemical pathways that are associated with the expression of woody breast meat, white striping, and other myopathies. This has allowed researchers and the industry to differentiate between chicken breast meat with and without myopathic muscle as well as the environmental and genetic conditions that contribute to differences in biochemical pathways and lead to the phenotypes associate with these different myopathies.

Improving animal welfare status and meat quality through assessment of stress biomarkers: A critical review

Stress induces various physiological and biochemical alterations in the animal body, which are used to assess the stress status of animals. Blood profiles, serum hormones, enzymes, and physiological conditions such as body temperature, heart, and breathing rate of animals are the most commonly used stress biomarkers in the livestock sector. Previous exposure, genetics, stress adaptation, intensity, duration, and rearing practices result in wide intra- and inter-animal variations in the expression of various stress biomarkers. The use of meat proteomics by adequately analyzing the expression of various muscle proteins such as heat shock proteins (HSPs), acute phase proteins (APPs), texture, and tenderness biomarkers help predict meat quality and stress in animals before slaughter. Thus, there is a need to identify non-invasive, rapid, and accurate stress biomarkers that can objectively assess stress in animals. The present manuscript critically reviews various aspects of stress biomarkers in animals and their application in mitigating preslaughter stress in meat production.

Application of 2-D DIGE to study the effect of ageing on horse meat myofibrillar sub-proteome

Considering the high relevance of meat tenderness for consumer acceptability, the aim of this study was to investigate post-mortem changes in myofibrillar sub-proteome in steaks from longissimus thoracis et lumborum muscle of six Hispano-Bretón horses. Indeed, the ageing process that leads to meat tenderization has been scarcely studied in this species. Steaks (n = 24) were aged (4 °C) in the dark under vacuum for 0, 7, 14 and 21 days and the myofibrillar sub-proteome was extracted. Using 2-D DIGE minimal labelling, 35 spots that were differentially abundant between 0 and 21 days aged meat were detected. Of them, 24 were analysed by LC-MS/MS, identifying a total of 29 equine proteins. These were structural and metabolic proteins, and among them, four (Actin, Troponin T and Myosin binding proteins 1 and 2) were selected for Western blot analysis, reporting changes in their abundance after 0, 7, 14 and 21 days of ageing. Results revealed that they should be further studied as potential protein biomarkers of horse meat tenderization. Additionally, several protein fragments increased after ageing, as was the case of glyceraldehyde-3-phosphate dehydrogenase. Fragments of this protein were present in four protein spots, and their study could be useful for monitoring horse meat tenderization. SIGNIFICANCE: Tenderization during ageing has been widely studied in meat from several farm animal species; however, both research and standardized ageing practices are lacking for the particular case of horse meat. In this regard, this study presents novel proteomic findings related to post-mortem evolution of horse muscle proteins. Acquired knowledge would support the development and optimization of efficient ageing practices by horse meat industry.

The potential of proteomics in the study of processed meat products

Proteomics is a field that has grown rapidly since its emergence in the mid-1990s, reaching many disciplines such as food technology. The application of proteomic techniques in the study of complex biological samples such as foods, specifically meat products, allows scientists to decipher the underlying cellular mechanisms behind different quality traits. Lately, much emphasis has been placed on the discovery of biomarkers that facilitate the prediction of biochemical transformations of the product and provide key information on parameters associated with traceability and food safety. This review study focuses on the contribution of proteomics in the improvement of processed meat products. Different techniques and strategies have recently been successfully carried out in the study of the proteome of these products that can help the development of foods with a higher sensory quality, while ensuring consumer safety through early detection of microbiological contamination and fraud. SIGNIFICANCE: The food industry and the academic world work together with the aim of responding to market demands, always seeking excellence. In particular, the meat industry has to face a series of challenges such as, achieving sensory attributes in accordance with the standards required by the consumer and maintaining a high level of safety and transparency, avoiding deliver adulterated and/or contaminated products. This review work exposes how the aforementioned challenges are attempted to be solved through proteomic technology, discussing the latest and most outstanding research in this regard, which undoubtedly contribute to improving the quality, in all the extension of the word, of meat products, providing relevant knowledge in the field of proteomic research.

Integrated Omics analysis of pig muscle metabolism under the effects of dietary Chlorella vulgaris and exogenous enzymes

Monogastric feeding is dependent on costly conventional feedstuffs. Microalgae such as Chlorella vulgaris are a sustainable alternative; however, its recalcitrant cell wall hinders monogastric digestion. Carbohydrate Active Enzyme (CAZyme) supplementation is a possible solution. The objective of this work was to evaluate the effect of 5% dietary C. vulgaris (CV) and enzymatic supplementation (CV + R-Rovabio® Excel AP; CV + M-four CAZyme mix) on muscle transcriptome and proteome of finishing pigs, in an integrated approach. Control pigs increased the abundance of contractile apparatus (MYH1, MYH2, MYH4) and energy metabolism (CKMT1, NDUFS3) proteins, demonstrating increased nutrient availability. They had increased expression of SCD, characteristic of increased glucose availability, via the activation of SREBP-1c and ChREBP. CV and CV + R pigs upregulated proteolytic and apoptotic genes (BAX, DDA1), whilst increasing the abundance of glucose (UQCRFS1) and fatty acid catabolism (ACADS) proteins. CV + R pigs upregulated ACOT8 and SIRT3 genes as a response to reduced nutrient availability, maintaining energy homeostasis. The cell wall specific CAZyme mix, CV + M, was able to comparatively reduce Omics alterations in the muscle, thereby reducing endogenous nutrient catabolism compared to the CV + R and CV.

Effect of dietary Spirulina (Arthrospira platensis) on the intestinal function of post-weaned piglet: An approach combining proteomics, metabolomics and histological studies

The effect of dietary Spirulina (Arthrospira platensis) and CAZyme supplementation was assessed on the gut of weaned piglets, using an integrated NMR-metabolomics approach combined with Tandem Mass Tag labelled proteomics. Thirty weaned male piglets were assigned to one of the three following diets (n = 10): cereal and soybean meal basal diet (Control), basal diet with 10% Spirulina inclusion (SP) and SP diet supplemented with 0.01% lysozyme (SP + L). The experiment lasted 4 weeks and, upon slaughter, small intestine samples were collected for histological, metabolomic and proteomic analysis. No significant differences were found for the histology and metabolomics analysis between the three experimental groups. Lactate, glutamate, glycine and myo-inositol were the most abundant metabolites. Proteomics results showed 1502 proteins identified in the intestine tissue. A total of 23, 78, 27 differentially abundant proteins were detected respectively for the SP vs. Control, SP + L vs. Control and SP + L vs. SP comparisons. The incorporation of Spirulina and supplementation of lysozyme in the piglet's diets is associated to intestinal proteomic changes. These include increased protein synthesis and abundance of contractile apparatus proteins, related with increased nutrient availability, which has beneficial (increased glucose uptake) and detrimental (increased digesta viscosity) metabolic effects. SIGNIFICANCE: The use of conventional feedstuffs becomes increasingly prohibitive due to its environmental toll. To increase the sustainability of the livestock sector, novel feedstuffs such as microalgae need to be considered. However, its recalcitrant cell wall has antinutritional effects that can inhibit high dietary inclusion levels. The supplementation with CAZymes is a possible solution to this issue. The small intestine is a central piece in monogastric digestion and of particular importance for the weaned piglet. Studying the effect of dietary Spirulina and CAZyme supplementation on its histomorphology, metabolome and proteome allows studying relevant physiological adaptations to these diets.

The Influence of Vacuum Packaging of Hot-Boned Lamb at Early Postmortem Time on Meat Quality during Postmortem Chilled Storage

To evaluate the effects of early postmortem vacuum packaging (VP) on meat quality during postmortem chilled storage, hot-boned lamb was vacuum-packaged at 1, 6, 12, 24, and 48 h postmortem and stored around 2°C until 168 h postmortem, with lamb packaged in plastic wrap as the control (aerobic packaging). Intramuscular pH decline was delayed when lamb was vacuum packaged at 1, 6, and 12 h postmortem (p<0.05). The lamb vacuum-packaged at 1 h postmortem (VP-1h group) had significantly lower shear force values and purge losses accompanied by lower free thiol group values than other treatments during postmortem storage and was also higher in extractable calpain-1 activity by 6 h postmortem (p<0.05). Free thiol group concentrations were significantly higher after VP at 6 and 12 h postmortem (p<0.05). Packaging lamb under vacuum very early postmortem produced the lowest shear force and purge loss, likely by slowing heat loss and muscle temperature decline, implying that lamb quality is improved by VP when applied very early postmortem. This was at the expense of protein oxidation, which was unrelated to other meat quality measurements, most likely because potential contracture during hot boning confounded its impact. Further research is required to understand the implications of the interaction between protein oxidation, VP, and hot boning on the acceptability of lamb.

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.

Proteomic Profile of M. Longissimus Thoracis from Commercial Lambs Reared in Different Forage Systems

This study compared the protein composition of M. longissimus thoracis of lambs from six commercial forage production systems in New Zealand. A total of 286 proteins were identified based on liquid chromatography-tandem mass spectrometry. First, a binomial model showed that different production groups could be distinguished based on abundances of 16 proteins. Second, pair-wise comparisons were performed to search for protein abundance differences in meat due to animal sex (ewe vs. wether), diet (perennial ryegrass vs. chicory), and age (4 vs. 6–8 months old). Greater abundance of some myofibrillar and sarcoplasmic proteins were observed in lamb loins from ewes compared to wethers. Chicory diet and older age at slaughter were associated with meat with lower abundance of some myofibrillar proteins, possibly due to a greater proportion of muscle glycolytic fibres. The proteins that showed significant differences in their abundances due to production factors could be further investigated to understand their influence on meat quality.

Proteomics and metabolomics combined study on endopathic changes of water-soluble precursors in Tan lamb during postmortem aging

Tan lamb is highly recommended breed in China. It is of great significance to understand the underlying mechanism of how water‐soluble flavor precursors metabolize in Tan lamb muscles during the postmortem aging period. In this study, we investigated the muscle pH, lactate dehydrogenase (LDH) activity, and the variations in water‐soluble flavor‐related metabolites. The proteome changes were profiled to provide insights into the biochemical changes affecting accumulation of water‐soluble flavor precursors in different aging stages (days 0, 4, and 8). The results indicated that pH value considerably decreased from day 0 to day 4, and increased from day 4 to day 8 (p < .05). The activity of LDH significantly increased from day 0 to day 4, and decreased from day 4 to day 8 (p < .05). Postmortem glycolysis was activated in 4 days, which directly affected the variations in metabolic enzymes and triggered the accumulation of flavor‐related carbohydrates. The free amino acids accumulated due to hydrolysis of structural proteins, with 3‐hydroxy‐L‐proline, aspartic acid, and methionine increasing from day 0 to day 4, and aspartic acid, serine, threonine, tyrosine, phenylalanine, and D‐phenylalanine from day 4 to day 8. The inosine and hypoxanthine accumulated due to the degradation of ATP. The results of the present study provide insightful information, revealing the differences in biochemical attributes in Tan lamb muscles caused by postmortem aging.

The effect of postmortem pH decline rate on caspase-3 activation and tenderness of bovine skeletal muscle during aging

This study aimed to investigate the effect of postmortem pH decline rate on caspase-3 activity and bovine muscle tenderness during aging. Protein denaturation, reactive oxygen species (ROS) levels, mitochondrial apoptosis factors, and shear force were assessed in bovine muscles with different pH decline rates. The results showed that, compared with the slow group, the fast pH decline group had a 1.79% and 1.39% higher sarcoplasmic protein denaturation at 6 and 12 h, respectively (p < .05), and a significantly or extremely significantly higher ROS levels at 6-24 (p < .05, p < .01). Moreover, the fast group had a 14.05%, 22.39%,18.34%, and 25.28% of higher mitochondrial dysfunction at 6, 12, 24, and 72 h, respectively (p < .05); a 16.71%, 23.39%, 17.05%, and 26.61% of lower cytochrome c reduction levels at 6, 12, 24, and 120 h, respectively (p < .05); a significantly increased caspase-3 activity and proportion of apoptotic nuclei at 12-168 and 24-168 h, respectively (p < .05); and a 5.70%, 7.24%, 12.16%, 10.10% and 10.49% decreased shear force at 12, 24, 72,120, and 168 h, respectively (p < .05). These results demonstrated that the fast postmortem pH decline enhanced caspase-3 activation and bovine muscle tenderization by mitochondrial dysfunction-induced apoptosis during aging. PRACTICAL APPLICATIONS: Beef tenderness has long been one of the most important concerns for consumers and the meat industry. To date, the postmortem aging process has been an effective way to improve the tenderness of chilled beef. However, changes in many of the elements in a cattle's muscle after slaughter might actually determine the final tenderness of the meat. The present study suggested that the fast postmortem pH decline could promote the activation of caspase-3 and improve the tenderness of beef during aging. This finding can provide a basis for the meat processing industry to produce beef with high tenderness. In the future, beef tenderness could even be improved by adjusting the glycolytic rate and pH of muscle for a short time after slaughter.

Proteomic Technologies and their Application for Ensuring Meat Quality, Safety and Authenticity

:

Proteomic tools were extensively used to understand the relationship between muscle proteome and conversion of muscle to meat, post-mortem proteolysis, meat texture, and variation in meat color. Developments in proteomic tools have also resulted in their application for addressing the safety and authenticity issues including meat species identification, detection of animal byproducts, non-meat ingredients and tissues in meat products, traceability, identification of genetically modified ingredients, chemical residues and other harmful substances. Proteomic tools are also being used in some of the potential areas like understanding the effect of animal transportation, stunning, slaughter stress, halal authentication and issues related to animal welfare. Emerging advances in proteomic and peptidomic technologies and their application in traceability, meat microbiology, safety and authentication are taking a major stride as an interesting and complementary alternative to DNA-based methods currently in use. Future research in meat science need to be linked to emerging metabolomic, lipidomic and other omic technologies for ensuring integrated meat quality and safety management. In this paper, a comprehensive overview of the use of proteomics for the assessment of quality and safety in the meat value chain and their potential application is discussed.

Metabolites Analysis on Water-Holding Capacity in Beef Longissimus lumborum Muscle during Postmortem Aging

Currently, the metabolomic research on water-holding capacity (WHC) of beef during postmortem aging is still insufficient. In this paper, the kit method was adopted for energy metabolites testing, the ultra-high-performance liquid chromatography (UHPLC) system was used for sample separation, and the mass spectrometer was applied to collect the primary and secondary spectra of the samples. The results showed that lactic acid reached saturation at day 2 postmortem, while energy metabolites changed significantly within day 2 postmortem (p < 0.05). Based on these findings, it was suggested that the energy metabolism qualities of the beef had already achieved a largely stable state at around day 2 postmortem. Then, through metabolomic analysis, 25 compounds were differentially abundant at days 0, 0.5, 1, and 2 during postmortem aging. Within the period of day 0−2 postmortem, the purine metabolism in beef was relatively active until 0.5 d postmortem, while glycolysis metabolism remained active until day 2 postmortem. The functions of the identified metabolites contribute to a more detailed molecular view of the processes behind WHC and are a valuable resource for future investigations into the flavor of postmortem beef.

The Quality Changes and Proteomic Analysis of Cattle Muscle Postmortem during Rigor Mortis

Rigor mortis occurs in a relatively early postmortem period and is a complex biochemical process in the conversion of muscle to meat. Understanding the quality changes and biomarkers during rigor mortis can provide a theoretical basis for maintaining and improving meat quality. Herein, a tandem mass tag proteomic method is used to investigate the effects of differentially expressed proteins on the meat quality of cattle Longissimus lumborum muscle postmortem (0, 6, and 24 h). The pH, total sulfhydryl content and sarcomere length decrease significantly during storage. In contrast, meat color values (L*, a*, and b*) and the myofibril fragmentation index increase significantly. Altogether, 147 differentially expressed proteins are identified, most being categorized as metabolic enzymes, mitochondrial proteins, necroptosis and ferroptosis proteins and structural proteins. The results also reveal additional proteins that are potentially involved in rigor mortis, such as cardiac phospholamban, acetyl-coenzyme A acyltransferase, and ankyrin repeat domain 2. The current results provide proteomic insights into the changes in meat quality during rigor mortis.

Peptidomic analysis characterising proteolysis in thaw-aging of beef short plate

Recent studies have suggested that thaw-aging can improve sensory attributes of freeze-thawed meat. Acceleration of proteolysis is expected to promote tenderisation and improve taste; however, the details of protein degradation, including substrate proteins and cleavage sites, remain unclear. Here, we report a time course overview of the peptidome of beef short plates during thaw-aging. The accelerated degradation of key proteins for meat tenderisation, such as troponin T and desmin, was confirmed. Additionally, 11 cleavage sites in troponin T related to taste-active peptide generation were identified. Terminome analysis showed that the contribution of each protease varies depending on the substrate proteins and the thaw-aging period. Based on our results; proteases, not only calpains, but also others contributed to the degradation of myofibrillar proteins. The techniques employed indicate that meat proteolysis during thaw-aging is not constant but dynamic.

Dietary Germinated Paddy Rice and Stocking Density Affect Egg Performance, Serum Biochemical Properties, and Proteomic and Transcriptomic Response of Laying Hens Exposed to Chronic Heat Stress

Germinated paddy rice (GPR) could be a good alternative feed source for poultry with stocking density and heat stress problems. A total of 72 Hy-line Brown laying hens raised under low (LSD, 0.12 m2/bird) and high stocking densities (HSD, 0.06 m2/bird) were investigated. Three dietary GPR levels (0, 74 and 148 g/kg) were used. It was found that average daily feed intake, hen-day egg production, and egg mass significantly decreased in the HSD group. The levels of serum glucose (GLU), phosphorous (P), corticosterone (CORT), total Ig, lysozyme (LZY), and superoxide dismutase activities (SOD) in the HSD group were higher than those in the LSD group. Dietary GPR significantly affected GLU, P, alternative complement haemolytic 50 (ACH50), total Ig, and LZY. Moreover, CORT level significantly decreased in 74 and 148 g/kg dietary GPR groups, whereas SOD significantly increased only in the 148 g/kg dietary GPR group. Serum samples were analyzed using liquid chromatography-tandem mass spectrometry, and 8607 proteins were identified. Proteome analysis revealed 19 proteins which were enriched in different stocking densities and dietary GPR levels. Quantitative real-time reverse transcription-PCR technique was successfully used to verify the differentiated abundant protein profile changes. The proteins identified in this study could serve as appropriate biomarkers.

Protein Biomarkers of Bovine Defective Meats at a Glance: Gel-Free Hybrid Quadrupole-Orbitrap Analysis for Rapid Screening

An understanding of biological mechanisms that could be involved in the stress response of animal cattle prior to slaughter is critical to create effective strategies aiming at the production of high-quality meat. The sarcoplasmic proteome of directly extracted samples from normal and high ultimate pH (pHu) meat groups was studied through a straightforward gel-free strategy supported by liquid chromatography hybrid quadrupole-Orbitrap high-resolution mass spectrometry (LC-HRMS) analysis. A stepped proteomic pipeline combining rapid biomarker hunting supported by qualitative protein Mascot scores followed by targeted label-free peptide quantification revealed 26 descriptors that characterized meat groups assayed. The functional study of the proposed biomarkers suggested their relevant role in metabolic, chaperone/stress-related, muscle contractility/fiber organization, and transport activities. The efficiency, flexibility, rapidity, and easiness of the methodology proposed can positively contribute to the creation of innovative proteomic alternatives addressing meat quality assessment.

Applied Proteomics in 'One Health'

‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.

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

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

Comprehensive Proteomic Characterization of the Pectoralis Major at Three Chronological Ages in Beijing-You Chicken

Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the chronological age of 90, 120, and 150 days. Each chronological age contained 3 pooling samples or 15 birds (five birds per pooling sample). A total of 1,413 proteins were identified in chicken breast muscle with FDR < 1% and 197 of them were differentially expressed (fold change ≥1.2 or ≤0.83 and p < 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. In summary, these results provided some candidate protein-coding genes for further functional validation and contribute to a comprehensive understanding of muscle development and age-dependent meat quality regulation by proteins in chickens.

The Effect of Dietary Lycopene Supplementation on Drip Loss during Storage of Lamb Meat by iTRAQ Analysis

This study was designed to investigate the impact of dietary lycopene (antioxidant extracted from tomato) supplementation on postmortem antioxidant capacity, drip loss and protein expression profiles of lamb meat during storage. Thirty male Hu lambs were randomly divided into three treatment groups and housed in individual pens and received 0, 200 or 400 mg·kg⁻¹ lycopene in their diet, respectively. All lambs were slaughtered after 3 months of fattening, and the longissimus thoracis (LT) muscle was collected for analyses. The results indicated that drip loss of LT muscle increased with storage days (P < 0.05). After storage for 7 days, significantly lower drip loss of meat was found in fed the lycopene-supplemented diet (P < 0.05). Dietary lycopene supplementation increased the activity of antioxidant enzymes (total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT)) (P < 0.05) and decreased the thiobarbituric acid reactive substance (TBARS) and carbonyl contents (P < 0.05). During the storage period (days 0, 5 and 7), a number of differentially abundant proteins (DAPs), including oxidases, metabolic enzymes, calcium channels and structural proteins, were identified based on iTRAQ data, with roles predominantly in carbon metabolism, oxidative phosphorylation, cardiac muscle contraction and proteasome pathways, and which contribute to decreased drip loss of lamb meat during storage. It can be concluded that dietary lycopene supplementation increased antioxidant capacity after slaughter, and the decreased drip loss during postmortem storage might occur by changing the expression of proteins related to enzyme activity and cellular structure in lamb muscle.

Proteomic analysis reveals changes in energy metabolism of skeletal muscle in beef cattle supplemented with vitamin A

BACKGROUND

Vitamin A has been reported as a factor influencing marbling deposition in meat from animals. Although the mechanisms by which vitamin A regulates lipid metabolism in mature adipocytes are already well-established, information regarding molecular mechanisms underlying the effects of vitamin A on the regulation of intramuscular fat deposition in beef cattle still remains limited. The present study aimed to assess the molecular mechanisms involved in the intramuscular fat deposition in beef cattle supplemented with vitamin A during the fattening phase using a proteomic approach.

RESULTS

Vitamin A supplementation during the fattening phase decreased intramuscular fat deposition in beef cattle. Proteome and phospho-proteome analysis together with biological and networking analysis of the protein differentially abundant between treatments indicated that Vitamin A supplementation affects the overall energy metabolism of skeletal muscle, impairing lipid biosynthesis in skeletal muscle.

CONCLUSION

Vitamin A supplementation at fattening phase impairs intramuscular fat deposition in beef cattle likely by changing the energy metabolism of skeletal muscle. The interaction of retinoic acid and heat shock 70-kDa protein may play a pivotal role in intramuscular fat deposition as a consequence of vitamin A supplementation by impairing de novo fatty acid synthesis as a result of a possible decrease in insulin sensitivity in the skeletal muscle. © 2020 Society of Chemical Industry.

The effects of improving low dietary protein utilization on the proteome of lamb tissues

Cistus ladanifer L. is a common shrub endemic to the Mediterranean region with high levels of condensed tannins (CT). CT form complexes with dietary protein resisting microbial degradation in the rumen, which enhances dietary protein utilization in ruminant diets. The objective of this study was to evaluate the utilization of CT in the diet of lambs on the proteomes of muscle, hepatic and adipose tissues. Twenty-four Merino Branco ram lambs were randomly allocated to three treatments (n = 8): C - control (160 g crude protein (CP)) per kg DM, RP - reduced protein (120 g CP/kg DM); and RPCT - reduced protein (120 g CP/kg DM) treated with CT extract. At the end of the trial, lambs were slaughtered and the longissimus lumborum muscle, hepatic and peri-renal adipose tissues sampled. A two-way approach was used for proteomic analysis: 2D-DIGE and nanoLC-MS. In the muscle, C lambs had lower abundance proteins that partake in the glycolysis pathway than the lambs of other treatments. Control lambs had lower abundance of Fe-carrying proteins in the hepatic tissue than RP and RPCT lambs. The latter lambs had highest abundance of hepatic flavin reductase. In the adipose tissue, C lambs had lowest abundance of fatty-acid synthase. SIGNIFICANCE: soybean meal is an expensive feedstuff in which intensive animal production systems heavily rely on. It is a source of protein extensively degraded in the rumen, leading to efficiency losses on dietary protein utilization during digestion. Protection of dietary protein from extensive ruminal degradation throughout the use of plants or extracts rich in CT allow an increase in the digestive utilization of feed proteins. In addition to enhance the protein digestive utilization, dietary CT may induce other beneficial effects in ruminants such as the improvement of the antioxidant status.

Is the protein profile of pig Longissimus dorsi affected by gender and diet?

The impact of gender and diet on the proteome of Longissimus dorsi was addressed by 2D-PAGE analysis of male and female pigs, fed with a barley-based control diet and a diet enriched with extruded linseed and plant extracts. No statistically significant difference in protein number between female and male samples was found. Furthermore, PCA excluded gender-dependent protein clusters. For both the control and enriched diet, several spots exhibited at least a 1.5-fold intensity difference, but none showed a statistically relevant variation. Protein profiles PCA for both diets indicated that the first two principal components account up to 47% of total variance, with two diet-dependent separated clusters. Among 176 common spots, 29 exhibited >1.5 fold change, mostly more abundant in the control diet. PMF identified 14 distinct proteins, including myofibrillar proteins, glycolytic enzymes and myoglobin, thus suggesting a diet-dependent meat quality. A statistically significant increase in carbonylated proteins of enriched diet samples was detected using the 2,4-dinitrophenylhydrazine method but not using fluorescein-5-thiosemicarbazide-labeled bands. ROS induction and DNA oxidative damage, detected in a human cell line exposed to digested meat from both diets, further support the notion that the enriched diet does not protect against oxidative stress. SIGNIFICANCE: The comparison of the protein profile of female and male Longissimus dorsi from pigs fed by a control diet and a diet enriched with polyphenols, indicate no gender effect, whereas diet affects the abundance of several proteins, possibly linked to meat quality. Protein carbonylation was statistically higher in meat from the enriched diet, suggesting that polyphenols at the concentration present in the diet did not exert a protective effect against oxidation.

Evaluation of WBSF, Color, Cooking Loss of Longissimus Lumborum Muscle with Fiber Optic Near-Infrared Spectroscopy (FT-NIR), Depending on Aging Time

Near-infrared spectroscopy is a known technique for assessing the quality of compounds found in food products. However, it is still not widely used for predicting physical properties of meat using the online system. This study aims to assess the possibility of application of a NIR equipped with fiber optic system as an online measurement system to predict Warner⁻Bratzler shear force (WBSF) value, cooking loss (CL), and color of longissimus lumborum muscle, depending on aging time. The prediction model satisfactorily estimated the WBSF on day 1 and day 7 of aging as well as a* color parameter on day one and CL on day 21. This could be explained by the fact that during beef aging, the physicochemical structure of meat becomes more uniform and less differentiation of raw data is observed. There is still a challenge to obtain a verifiable model for the prediction of physical properties, using NIR, by utilizing more varied raw data.

Coupling of Rigor Mortis and Intestinal Necrosis during C. elegans Organismal Death

Organismal death is a process of systemic collapse whose mechanisms are less well understood than those of cell death. We previously reported that death in C. elegans is accompanied by a calcium-propagated wave of intestinal necrosis, marked by a wave of blue autofluorescence (death fluorescence). Here, we describe another feature of organismal death, a wave of body wall muscle contraction, or death contraction (DC). This phenomenon is accompanied by a wave of intramuscular Ca2+ release and, subsequently, of intestinal necrosis. Correlation of directions of the DC and intestinal necrosis waves implies coupling of these death processes. Long-lived insulin/IGF-1-signaling mutants show reduced DC and delayed intestinal necrosis, suggesting possible resistance to organismal death. DC resembles mammalian rigor mortis, a postmortem necrosis-related process in which Ca2+ influx promotes muscle hyper-contraction. In contrast to mammals, DC is an early rather than a late event in C. elegans organismal death. VIDEO ABSTRACT.

Intramuscular variations of proteome and muscle fiber type distribution in semimembranosus and semitendinosus muscles associated with pork quality

Proteome analysis was performed to understand intramuscular variations in muscle fiber distribution in semimembranosus (SM) and semitendinosus (ST) muscles associated with pork quality. Fifteen SM and ST muscles were separated into dark and light portions. The relative area of oxidative fiber was higher (P < .0001) in dark portion than that in light portion, while glycolytic fiber types were distributed primarily (P < .01) in light portions regardless of muscle types. Myosin-1, myosin-4, troponin complex (fast), myosin light chains, and metabolic enzymes responsible for fast-twitch glycolytic types were overexpressed in light portions (P < .05). However, myosin-2, myosin-7, myoglobin, and mitochondrial oxidative metabolic enzymes were closely related to slow-twitch oxidative fibers. These resulted in high pH, redness, and tenderness but low lightness and drip loss of pork quality. In conclusion, differentially expressed muscle proteins are associated with fiber type (oxidative vs. glycolytic) distribution, resulting in intramuscular variations of pork quality.

A comparative analysis of phosphoproteome in ovine muscle at early postmortem in relationship to tenderness

BACKGROUND

Tenderness is considered to be the most important quality characteristic of meat as it is the main cause of unacceptability of meat. Post-translational modification regulates protein functions that involve in postmortem changes in muscle and meat quality formation. Specifically, phosphorylation was proved to regulate postmortem glycolytic rates and meat tenderisation. However, the relationship between protein phosphorylation and meat tenderness remains unclear. This study examined the phosphoproteomes found in ovine muscle with different degrees of tenderness over time (at 0.5 h, 4 h, and 24 h postmortem).

RESULTS

This study detected five, eight and nine phosphoprotein spots (>two-fold change, P < 0.05) at each respective time point. The different phosphoproteins found included glyceraldehyde-3-phosphate dehydrogenase, tropomyosin α-1 chain, pyruvate kinase, myosin binding protein H, glycogen phosphorylase, α-actinin-3, and an uncharacterised protein (GN, myosin-binding protein C2, MYBPC2). Most of the different phosphoproteins maintained sarcomeric functions, or were involved in glycometabolism.

CONCLUSION

Phosphorylation levels of multiple proteins that are involved in glycolysis, muscle contraction or sarcomeric structure integrity were identified in ovine muscles with different tenderness. The differential phosphorylation of these proteins explains in part the difference in meat tenderness. © 2017 Society of Chemical Industry.

Proteomics of Parma Dry-Cured Ham: Analysis of Salting Exudates

The production of Parma dry-cured ham involves the steps of salting, drying, and ripening. Although sea salt is the only preserving agent, there are strategies being developed with the goal of reducing salt content in order to decrease its negative impact on consumer health. A 24 h pressure treatment was applied before salting to reduce thickness and inequalities in shape. To evaluate the potential impact of the pressure step on the process outcome, differential proteomic analyses by complementary 2D-PAGE and LC-MS/MS were carried out on exudates collected at day 1, 5, and 18 of the salting phase for hams treated or untreated with pressure. Specific proteins were found differentially abundant in exudates from pressed vs unpressed hams and as a function of time. These changes include glycolytic enzymes and several myofibrillar proteins. These findings indicate that pressure causes a faster loosening of the myofibrillar structure with the release of specific groups of proteins.

Proteomic approach to characterize biochemistry of meat quality defects

Proteomics can be used to characterize quality defects including pale, soft, and exudative (PSE) meat (pork and poultry), woody broiler breast meat, reddish catfish fillets, meat toughness, and beef myoglobin oxidation. PSE broiler meat was characterized by 15 proteins that differed in abundance in comparison to normal broiler breast meat, and eight proteins were differentially expressed in woody breast meat in comparison to normal breast meat. Hemoglobin was the only protein that was differentially expressed between red and normal catfish fillets. However, inducing low oxygen and/or heat stress conditions to catfish fillets did not lead to the production of red fillets. Proteomic data provided information pertaining to the protein differences that exist in meat quality defects. However, these data need to be evaluated in conjunction with information pertaining to genetics, nutrition, environment of the live animal, muscle to meat conversion, meat quality analyses and sensory attributes to understand causality, protein biomarkers, and ultimately how to prevent quality defects.

Proteome Analysis Using Isobaric Tags for Relative and Absolute Analysis Quantitation (iTRAQ) Reveals Alterations in Stress-Induced Dysfunctional Chicken Muscle

The current study was designed to investigate changes in the protein profiles of pale, soft, and exudative (PSE)-like muscles of broilers subjected to transportation under high-temperature conditions, using isobaric tags for relative and absolute analysis quantitation (iTRAQ). Arbor Acres chickens (n = 112) were randomly divided into two treatments: unstressed control (CON) and 0.5 h of transport (T). Birds were transported according to a designed protocol. Pectoralis major (PM) muscle samples in the T group were collected and classified as normal (T-NOR) or PSE-like (T-PSE). Plasma activities of stress indicators, muscle microstructure, and proteome were measured. Results indicated that broilers in the T-PSE group exhibited higher activities of plasma stress indicators. The microstructure of T-PSE group showed a looser network and larger intercellular spaces in comparison to the other groups. Proteomic analysis, based on iTRAQ, revealed 29 differentially expressed proteins in the T-NOR and T-PSE groups that were involved in protein turnover, signal transduction, stress and defense, calcium handling, cell structure, and metabolism. In particular, proteins relating to the glycolysis pathway, calcium signaling, and molecular chaperones exhibited significant differences that may contribute to the inferior post-mortem meat quality. Overall, the proteomic results provide a further understanding of the mechanism of meat quality changes in response to stress.

Beef Tenderness Improvement by Dietary Vitamin D3 Supplementation in the Last Stage of Fattening of Cattle

Tenderness is the most important characteristic of meat, determining consumer approval. There are numerous methods of its improvement, although of diverse effectiveness. addition of vitamin D₃ to the feed for a short period before slaughter (7–10 days) is one of the natural ways to enhance the tenderness. Vitamin D₃ is responsible for Ca²⁺ mobilisation in serum and increase in activity of proteolytic enzymes belonging to calpains, which results in significant improvement of beef tenderness and reduction of ageing time. The use of vitamin D₃ is an application tool determining tenderness improvement of beef with substantial reduction in processing costs. Moreover, shorter post mortem ageing process will exceed the retail display time, which will consequently reduce losses due to unsold meat being returned from shops to the manufacturers. Based on the results of studies conducted over the last 15 years, this paper presents the possibility and the effects of the use of vitamin D₃ to improve beef tenderness.