Chianina beef tenderness investigated through integrated Omics

Effect on the Quality of Larimichthys crocea Pretreated with Dual-Frequency Orthogonal Ultrasonic-Assisted Immersion with Different Powers during Refrigerated Storage at 4 °C

In recent years, ultrasonic pretreatment technology has been widely used in the aquatic product preservation industry. Among these technologies, dual-frequency ultrasonic refrigeration is the most common. However, in practical applications, selecting the frequency is relatively simple, and there has been less research on power selection. In this paper, the specific frequency (up and down 20 kHz, around 40 kHz), using different powers of (a) 200 W, (b) 300 W, and (c) 400 W processing, ultrasonic intermittent mode with 30 s on/30 s off cycle, and an ultrasonic processing time of 10 min was examined; the control group (CK) comprised samples without ultrasonic treatment. The samples were stored at 4 °C and then placed in a Polyethylene (PE) bag. The changes in microbiological parameters, physicochemical indices, and protein indices of the samples were monitored every two days. The results show that 400 W ultrasonic treatment can significantly inhibit the growth of TVC during storage. The rate of increase in pH, TVB-N, and TBA values decreased significantly compared with the other groups. Compared with the CK group, the shelf life of the 400 W treatment group was extended by 6 days. Therefore, the 400 W pretreatment method based on orthogonal double frequency has strong application potential for effectively extending the shelf life of refrigerated large yellow croaker.

Quality changes of Larimichthys crocea pretreated by ultrasonic-assisted immersion under cold storage at 4 °C

The effects of several ultrasonic treatments during cold storage at 4 °C on the quality of large yellow croaker (Pseudosciaena crocea) were suggested. Large yellow croaker fillets were divided into six different groups for treatment. (a) CK (without any treatment), (b) A (single frequency 20 kHz), (c) B (single frequency 40 kHz), (d) C (left and right dual frequency 20 + 40 kHz), (e) D (orthogonal dual frequency: left and right 40 kHz, upper and lower 20 kHz), and (f) E (orthogonal dual frequency: left and right 20 kHz, upper and lower 20 kHz). The samples were divided into six groups, placed in sterile PE bags, and chilled to 4 °C. In order to determine the impact of ultrasonic treatment on the quality of large yellow croaker during cold storage, microbial indicators and physical and chemical indicators were measured every 3 days. The total number of colonies, the percentage of psychrophilic bacteria, the sample's pH, and its TVB-N value were all shown to grow at a much slower pace following ultrasonic treatment. In addition, the antibacterial effect of dual frequency ultrasound was gradually better than that of single frequency ultrasound. In conclusion, Group D has a pretty excellent impact on preserving overall sample quality.

Biological function, mediate cell death pathway and their potential regulated mechanisms for post-mortem muscle tenderization of PARP1: A review

Tenderness is a key attribute of meat quality that affects consumers' willingness to purchase meat. Changes in the physiological environment of skeletal muscles following slaughter can disrupt the balance of redox homeostasis and may lead to cell death. Excessive accumulation of reactive oxygen species (ROS) in the myocytes causes DNA damage and activates poly ADP-ribose polymerase 1 (PARP1), which is involved in different intracellular metabolic pathways and is known to affect muscle tenderness during post-slaughter maturation. There is an urgent requirement to summarize the related research findings. Thus, this paper reviews the current research on the protein structure of PARP1 and its metabolism and activation, outlines the mechanisms underlying the function of PARP1 in regulating muscle tenderness through cysteine protease 3 (Caspase-3), oxidative stress, heat shock proteins (HSPs), and energy metabolism. In addition, we describe the mechanisms of PARP1 in apoptosis and necrosis pathways to provide a theoretical reference for enhancing the mature technology of post-mortem muscle tenderization.

Metabolic, proteomic and microbial changes postmortem and during beef aging

The purpose of this review is to provide an overview of the current knowledge about proteomic and metabolic changes in beef, the microbiological alteration postmortem and during aging, and observe the influence on beef quality parameters, such as tenderness, taste and flavor. This review will also focus on the different aging types (wet- and dry-aging), the aging or postmortem time of beef and their effect on the proteome and metabolome of beef. The Ca2+ homeostasis and adenosine 5'-triphosphate breakdown are the main reactions in the pre-rigor phase. After rigor mortis, the enzymatic degradation of connective tissues and breakdown of energy metabolism dominate molecular changes in beef. Important metabolic processes leading to the formation of saccharides, nucleotides, organic acids (e.g. lactic acid), creatine and fatty acids are considered in this context as possible flavor precursors or formers of beef flavor and taste. Flavor precursors are substrates for lipid oxidation, Strecker degradation and Maillard reaction during cooking or roasting. The findings presented should serve as a basis for a better understanding of beef aging and its molecular effects and are intended to contribute to meeting the challenges of improving beef quality.

Tandem mass tag labeling to assess proteome differences between intermediate and very tender beef steaks

Tenderness is considered as one of the most important quality attributes dictating consumers' overall satisfaction and future purchasing decisions of fresh beef. However, the ability to predict and manage tenderness has proven very challenging due to the numerous factors that contribute to variation in end-product tenderness. Proteomic profiling allows for global examination of differentially abundant proteins in the meat and can provide new insight into biological mechanisms related to meat tenderness. Hence, the objective of this study was to examine proteomic profiles of beef longissimus lumborum (LL) steaks varying in tenderness, with the intention to identify potential biomarkers related to tenderness. For this purpose, beef LL muscle samples were collected from 99 carcasses at 0 and 384 h postmortem. Based on Warner-Bratzler shear force values at 384 h, 16 samples with the highest (intermediate tender, IT) and lowest (very tender, VT) values were selected to be used for proteomic analysis in this study (n = 8 per category). Using tandem mass tag-based proteomics, a total of 876 proteins were identified, of which 51 proteins were differentially abundant (P < 0.05) between the tenderness categories and aging periods. The differentially identified proteins encompassed a wide array of biological processes related to muscle contraction, calcium signaling, metabolism, extracellular matrix organization, chaperone, and apoptosis. A greater (P < 0.05) relative abundance of proteins associated with carbohydrate metabolism and apoptosis, and a lower (P < 0.05) relative abundance of proteins involved in muscle contraction was observed in the VT steaks after aging compared with the IT steaks, suggesting that more proteolysis occurred in the VT steaks. This may be explained by the greater (P < 0.05) abundance of chaperonin and calcium-binding proteins in the IT steaks, which could have limited the extent of postmortem proteolysis in these steaks. In addition, a greater (P < 0.05) abundance of connective tissue proteins was also observed in the IT steaks, which likely contributed to the difference in tenderness due to added background toughness. The established proteomic database obtained in this study may provide a reference for future research regarding potential protein biomarkers that are associated with meat tenderness.

Proteomic and parallel reaction monitoring approaches to evaluate biomarkers of mutton tenderness

Intensive fattening usually results in the changes of meat quality. Tenderness is a central attribute for mutton sensory qualities and consumers' choice. Here, we reported that intensive fattening mutton was more tender than that of traditionally raised sheep. By proteomic approach, we found 49 differentially expressed proteins in longissimus dorsi muscle. After bioinformatics analysis, 5 cytoskeletal proteins, 3 protein binding proteins and 7 metabolic enzymes were identified as potential biomarkers for mutton tenderness. Finally, we verified the expression of these abundant proteins by parallel reaction monitoring (PRM). Collectively, our results reveal that the mutton of sheep raised by intensive fattening is more tender than that of traditionally raised sheep. Myosin-2, myosin-13, vimentin, carbonic anhydrase, carbonic anhydrase-2, Glutathione S-transferase and Microtubule-associated protein 4 isoform X1 can be candidate biomarkers for mutton tenderness. Our data also indicate a central role of cytoskeletal proteins and metabolic enzymes in determining mutton tenderness.

Estimation of the proteome affecting changes in tenderness of yak meat during storage by label-free mass spectrometry

Background

Tenderness is the main quality of meat products. However, the meat tenderness formation is a complex biological process, and pathways and proteins that affect the tenderness of yak meat are unknown.

Methods

Label‐free proteomics method was used to explore the effects of differentially expressed proteins on the tenderness of yak skeletal muscle (tenderloin) during post‐mortem storage (0, 3, and 7 days) at 3 ± 1°C.

Results

The tenderness of yak skeletal muscle improved significantly during storage. A total of 91 differentially expressed proteins of yak skeletal muscle during post‐mortem storage were identified by the following comparisons: day 3 versus 0, day 7 versus 0, and day 7 versus 3. NDUFS6, CYCS, COX6A2, LDB3, HSPB7, TPM4, TAGLN, COL1A1, LUM, MYH11, ACTC1, and MYOZ1 proteins showed a significant difference during yak skeletal muscle post‐mortem storage. Furthermore, bioinformatics analyses revealed that the identified proteins were related to carbon metabolism, citrate cycle, glycolysis, oxidative phosphorylation, and RNA degradation.

Conclusion

The results of the present study could provide proteomic insights into changes in yak skeletal muscle tenderness during storage and may be a valuable resource for future investigations.

Housekeeping Proteins in Meat Quality Research: Are They Reliable Markers for Internal Controls in Western Blot? A Mini Review

Advancements in technology and analytical methods enable researchers to explore the biochemical events that cause variation in meat quality. Among those, western blot techniques have been successfully used in identifying and quantifying the key proteins that have critical functions in the development of meat quality. Housekeeping proteins, like β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and tubulins are often used as internal controls in western blots to normalize the abundance of the protein of interest. However, there are increasing concerns about using housekeeping proteins for western blot normalization, as these proteins do not demonstrate any loading differences above the relatively small total protein loading amounts of 10μg. In addition, the interaction between these housekeeping proteins and programmed cell death processes highlights the concerns about using the housekeeping protein as the internal control in meat quality research. Moreover, recent proteomic research has indicated that the abundance of some housekeeping proteins, like β-actin, GAPDH, and tubulin, can be altered by preslaughter stress, dietary supplementation, sex, slaughter method, genotype, breed, aging period, muscle type, and muscle portion. Furthermore, these housekeeping proteins could have differential expression in meat with differing color stability, tenderness, and water holding capacity. Therefore, this review aims to examine the realities of using housekeeping proteins as the loading control in meat quality research and introduce some alternative methods that can be used for western blot normalization.

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

Beef quality is the first deciding factor for consumers to consider before purchasing. The aim of this study was to evaluate the effects of suspension and aging time on beef quality. We compared the differences in pH, drip loss, cooking loss, color, shear force, myofibril fragmentation index (MFI), and electron microscope of three muscle tissues between Achilles tendon (AT) and neck-arm restraint (NR) suspensions during seven aging periods (days 0, 1, 2, 3, 7, 14, and 21) after slaughter using the carcasses of six Xinjiang brown cattle. We found that NR suspension could significantly increase the water loss rate and MFI, as well as reduce the shear force compared to AT suspension. The muscle fiber structure with NR suspension was more severely damaged. The proteomics of longissimus dorsi was checked for the post-mortem days 1, 7, and 14. We detected 50, 26, and 29 differentially expressed proteins between NR and AT suspension at post-mortem days 1, 7, and 14, respectively. These proteins were involved in metabolic and muscle structure associated pathways and contributed to a comprehensive understanding of suspension-dependent meat quality regulation by proteins in beef cattle. To conclude, NR suspension can accelerate the aging time of beef carcasses, which will reduce the cost of carcass suspension and bring more benefits in the beef industry.

Proteomics discovery of protein biomarkers linked to yak meat tenderness as determined by label-free mass spectrometry

Tenderness is one of the most important qualities in meat. A proteomic approach is a suitable way to ensure meat tenderness. Thirty-six tenderloin samples from yak were classified as exhibiting high (n = 12) or low (n = 12) tenderness and were evaluated using label-free proteomics for the identification of the proteins and pathways most influential in tenderness variability. Between the two groups, proteomic changes were mainly caused by 33 differentially expressed proteins as displayed in reference patterns in heat maps. The expression of ENO2, SUCLG2, ETFDH, PGM1, TNNT3, TNNT1, HSDL2, GPI, ALAD, and COL1A1 proteins was very different between yak meats with high and low tenderness, and therefore, they are candidate biomarkers of yak meat tenderness. Furthermore, bioinformatics analyses revealed that the identified proteins are related to pentose phosphate, glycolysis, the citrate cycle, fatty acid metabolism, and the calcium signaling pathway.

Multi-frequency ultrasound:A potential method to improve the effects of surface decontamination and structural characteristics on large yellow croaker (Pseudosciaena crocea) during refrigerated storage

The effects of multi-frequency ultrasound on surface decontamination and structural characteristics of large yellow croaker (Pseudosciaena crocea) during refrigerated storage were evaluated. The results of total viable counts (TVCs) and psychrophilic bacteria counts (PBCs) demonstrated that multi-frequency ultrasound retarded the growth of microorganisms. The bacteriostatic effect was positively correlated with the increase of ultrasound frequencies. However, compared with triple-frequency ultrasound (TUS, 20/28/40 kHz) treatment, dual-frequency ultrasound (DUS, 20/28 kHz) treatment had higher water-holding capacity (WHC) and immobilized water content, better texture characteristics, lower pH and total volatile basic nitrogen (TVB-N). Through the results of myofibrillar fragmentation index (MFI), intrinsic fluorescence intensity (IFI) and atomic force microscope (AFM), multi-frequency ultrasound could effectively stabilize the myofibrillar protein structure of refrigerated large yellow croaker, which could maintain better texture characteristics. The effects of DUS were the most significant. Therefore, multi-frequency ultrasound treatment could inhibit the growth of microorganisms and improve the structural characteristics of large yellow croaker during refrigerated storage.

Current State of Metabolomics Research in Meat Quality Analysis and Authentication

In the past decades, as an emerging omic, metabolomics has been widely used in meat science research, showing promise in meat quality analysis and meat authentication. This review first provides a brief overview of the concept, analytical techniques, and analysis workflow of metabolomics. Additionally, the metabolomics research in quality analysis and authentication of meat is comprehensively described. Finally, the limitations, challenges, and future trends of metabolomics application in meat quality analysis and meat authentication are critically discussed. We hope to provide valuable insights for further research in meat quality.

The differences of muscle proteins between neon flying squid (Ommastrephes bartramii) and jumbo squid (Dosidicus gigas) mantles via physicochemical and proteomic analyses

Neon flying squid (OB) and jumbo squid (DG) mantles were evaluated to reveal the similarities and differences in their physicochemical features and protein abundances. Microstructural results indicated that the OB mantle exhibited numerous myofibril fragments and disordered microstructures after frozen storage compared with DG tissues. Chemical analysis suggested that freezing resulted in a rapid decrease in myofibrillar protein (MP) content, Ca²⁺-ATPase activity, and total sulfhydryl content, and promoted the increase in carbonyl content of MPs in both OB and DG. While, DG presented better MP stability than OB muscle after 120 days of frozen storage. Label-free proteomic analysis detected 24 down- and 33 up-regulated differentially abundant proteins (DAPs) in OB and DG mantles. Identified DAPs including isocitrate dehydrogenase and malic enzyme initiated a rapid decrease in the MP properties in OB samples. Moreover, DAPs were related to cytoskeleton function, including paramyosin, tropomyosin, and troponin C, which improved the stability of DG in response to freezing-induced changes.

Relationship Between Meat Quality, Carcass Characteristics, and Protein Abundance of HSPβ1, HSPA, and DJ1 in Beef Longissimus thoracis Pre-Rigor or After 14 Days’ Aging

This study evaluated associations of heat shock proteins (HSP) and an oxidative stress protein, protein deglycase (DJ1), with beef quality and tenderness. Samples from the longissimus thoracis (N = 99) were collected pre-rigor (day 0) and after 14-d aging. Warner-Bratzler shear force (WBSF), myofibrillar fragmentation index (MFI), and a trained sensory panel were used to determine meat quality. Protein abundance of DJ1 and 2 HSP—HSPβ1 and HSPA—were assessed. Regression analyses demonstrated that DJ1 abundance after 14 d of aging is a predictor of WBSF (P &lt; 0.001), MFI (P = 0.02), and sensory panel tenderness (P &lt; 0.001). Abundance of HSPβ1 after 14 d of aging is also a predictor of MFI (P = 0.03). Additionally, abundance of both HSPβ1 and DJ1 pre-rigor are predictors of juiciness (P &lt; 0.05). Abundance of HSPβ1 pre-rigor was correlated with WBSF (R = 0.67), sensory panel tenderness (R = −0.44), juiciness (R = −0.30), and umami (R = −0.20). Abundance of DJ1 pre-rigor was also correlated with WBSF (R = 0.72), sensory panel tenderness (R = −0.44), juiciness (R = − 0.24), and umami (R = −0.31). After 14-d aging, HSP β 1 abundance was cor- related with WBSF (R = 0.66), sensory panel tenderness (R = −0.34), juiciness (R = −0.34), umami (R = −0.33), and brown/ roasted (R = −0.30). Abundance of DJ1 after 14-d aging was also correlated with WBSF (R = 0.68), sensory panel tenderness (R = −0.41), juiciness (R = −0.21), and umami (R = −0.28). These results demonstrate that abundance of HSPβ1 and DJ1 both pre-rigor and after 14 d of aging are correlated with meat tenderness and end-product quality as assessed by a trained sensory panel. Regression analyses further reveal that abundance of DJ1 and HSPβ1 after 14 d of aging is causative in development of beef tenderness and juiciness, respectively. Taken together, these results suggest that abundance of DJ1 is a predictor of tenderness, whereas abundance of HSPβ1 is related to meat quality but cannot be used to predict tenderness.

Effects of protein posttranslational modifications on meat quality: A review

Meat quality plays an important role in the purchase decision of consumers, affecting producers and retailers. The formation mechanisms determining meat quality are intricate, as several endogenous and exogenous factors contribute during antemortem and postmortem periods. Abundant research has been performed on meat quality; however, unexpected variation in meat quality remains an issue in the meat industry. Protein posttranslational modifications (PTMs) regulate structures and functions of proteins in living tissues, and recent reports confirmed their importance in meat quality. The objective of this review was to provide a summary of the research on the effects of PTMs on meat quality. The effects of four common PTMs, namely, protein phosphorylation, acetylation, S-nitrosylation, and ubiquitination, on meat quality were discussed, with emphasis on the effects of protein phosphorylation on meat tenderness, color, and water holding capacity. The mechanisms and factors that may affect the function of protein phosphorylation are also discussed. The current research confirms that meat quality traits are regulated by multiple PTMs. Cross talk between different PTMs and interactions of PTMs with postmortem biochemical processes need to be explored to improve our understanding on factors affecting meat quality.

Molecular signatures of beef tenderness: Underlying mechanisms based on integromics of protein biomarkers from multi-platform proteomics studies

Over the last two decades, proteomics have been employed to decipher the underlying factors contributing to variation in the quality of muscle foods, including beef tenderness. One such approach is the application of high-throughput protein analytical platforms in the identification of meat quality biomarkers. To broaden our understanding about the biological mechanisms underpinning meat tenderization across a large number of studies, an integromics study was performed to review the current status of protein biomarker discovery targeting beef tenderness. This meta-analysis is the first to gather and propose a comprehensive list of 124 putative protein biomarkers derived from 28 independent proteomics-based experiments, from which 33 robust candidates were identified worthy of evaluation using targeted or untargeted data-independent acquisition proteomic methods. We further provide an overview of the interconnectedness of the main biological pathways impacting tenderness determination after multistep analyses including Gene Ontology annotations, pathway and process enrichment and literature mining, and specifically discuss the major proteins and pathways most often reported in proteomics research.

Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction

This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner-Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers. Irrespective of the statistical method and quality trait, seven biomarkers were related with both WBSF and IMF, including three small HSPs (CRYAB, HSP20 and HSP27), two metabolic enzymes from the oxidative pathway (MDH1: Malate dehydrogenase and ALDH1A1: Retinal dehydrogenase 1), the structural protein MYH1 (Myosin heavy chain-IIx) and the multifunctional protein FHL1 (four and a half LIM domains 1). Further, three more proteins were retained for tenderness whatever the statistical method, among which two were structural proteins (MYL1: Myosin light chain 1/3 and TNNT1: Troponin T, slow skeletal muscle) and one was glycolytic enzyme (ENO3: β-enolase 3). For IMF, two proteins were, in this trial, specific for marbling whatever the statistical method: TRIM72 (Tripartite motif protein 72, negative) and PRDX6 (Peroxiredoxin 6, positive). From the 20 proteins, this trial allowed us to qualify 10 and 9 proteins respectively as strongly related with beef tenderness and marbling in PDO Maine-Anjou cows.

Muscle Fiber Properties in Cattle and Their Relationships with Meat Qualities: An Overview

The control of meat quality traits constitutes an important target for any farm animal production, including cattle. Therefore, better understanding of the biochemical properties that drive muscle development and final outcomes constitutes one of the main challenging topics of animal production and meat science. Accordingly, this review has focused on skeletal muscle fibers in cattle and their relationships with beef qualities. It aimed to describe the chemical and structural properties of muscle fibers as well as a comprehensive review of their contractile and metabolic characteristics during the life of the animal. The existing methods for the classification of muscle fibers were reviewed, compared, and discussed. Then, the different stages of myogenesis in cattle were defined. The main factors regulating fetal and postnatal growth and the plasticity of muscle fibers were evidenced, especially the role of myostatin growth factor and the impact of nutritional factors. This review highlights that the knowledge about muscle fibers is paramount for a better understanding of how to control the muscle properties throughout the life of the animal for better management of the final eating qualities of beef. Accordingly, the associations between bovine muscle fibers and different meat eating qualities such as tenderness, pH decline, and color traits were further presented.

Gene and protein expression of myosin heavy chain in Nellore cattle comparing growth or meat tenderness traits

The objective was to investigate gene and protein expression of myosin heavy chain (MyHC) in Nellore cattle slaughtered at different weights (BW) or degrees of meat tenderness. Ninety animals with initial BW 370 ± 37 kg, 24 months of age, were slaughtered after 95 days on feed. We evaluated shear force (SF), myofibrillar fragmentation index, ribeye area, backfat thickness, marbling, color, and cooking losses. Subsequently, 24 animals were selected and divided into four contrasting groups, in which light (BW = 504.58 ± 32.36 kg) versus heavy animals (BW = 604.83 ± 42.97 kg) and animals with tender (SF = 3.88 ± 0.57 kg) versus tough meat (SF = 7.95 ± 1.04 kg) were compared. The MYH7, MYH2 and MYH1 genes were analyzed by real-time PCR. The MyHC isoforms (MyHC-I, MyHC-IIa, and MyHC-IIx) were quantified by SDS-PAGE electrophoresis. We found lower expression of MYH2 and MYH1 genes in heavy compared to light animals and a higher amount of MyHC-I isoform in the tough meat group compared to the tender meat group. Protein expression of MyHC-IIa was higher in the tender meat group. A negative correlation was found of this protein and SF (tenderness), suggesting MyHC-IIa as a biomarker of meat quality.

The first evidence of global meat phosphoproteome changes in response to pre-slaughter stress

BACKGROUND

Pre-slaughter stress (PSS) impairs animal welfare and meat quality. Dark, firm and dry (DFD) are terms used to designate poor quality meats induced by PSS. Protein phosphorylation can be a potentially significant mechanism to explain rapid and multiple physiological and biochemical changes linked to PSS-dependent muscle-to-meat conversion. However, the role of reversible phosphorylation in the response to PSS is still little known. In this study, we report a comparative phosphoproteomic analysis of DFD and normal meats at 24 h post-mortem from the longissimus thoracis (LT) bovine muscle of male calves of the Rubia Gallega breed. For this purpose, two-dimensional gel electrophoresis (2-DE), in-gel multiplex identification of phosphoproteins with PRO-Q Diamond phosphoprotein-specific stain, tandem (MALDI-TOF/TOF) mass spectrometry (MS), novel quantitative phosphoproteomic statistics and bioinformatic tools were used.

RESULTS

Noticeable and statistically significant differences in the extent of protein phosphorylation were detected between sample groups at the qualitative and quantitative levels. Overall phosphorylation rates across significantly changed phosphoproteins were about three times higher in DFD than in normal meat. Significantly changed phosphoproteins involved a variable number of isoforms of 13 myofibrillar and sarcoplasmic nonredundant proteins. However, fast skeletal myosin light chain 2 followed by troponin T, F-actin-capping and small heat shock proteins showed the greatest phosphorylation change, and therefore they were the most important phosphoproteins underlying LT muscle conversion to DFD meat in the Rubia Gallega breed.

CONCLUSIONS

This is the first study reporting global meat phosphoproteome changes in response to PSS. The results show that reversible phosphorylation is a relevant mechanism underlying PSS response and downstream effects on meat quality. This research opens up novel horizons to unravel the complex molecular puzzle underlying muscle-to-meat conversion in response to PSS.

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.

Cattle production practices and the incidence of dark cutting beef

The effects of cattle sex, production system, growth promotant use, slaughter season, carcass phenotype, and pre-slaughter cattle management on the incidence of beef carcasses grading Canada B4 (dark cutting) were investigated using two data sets (A, n = 2009, and B, n = 86,408) containing data from cattle that produced Canada Prime, AAA, AA, A, and B4 carcasses. The probability of producing a Canada B4 carcass was greater (P < .0001) for heifers than steers in both data sets, with the likelihood of dark cutting decreasing with increased carcass weight in heifers in data set B. The incidence of dark cutting was increased (P < .0001) in Winter-born calf-fed (WC) and Fall-born calf-fed (FC) heifers. Production system and phenotype appear to interact to influence the incidence of dark cutting.

Differential protein profiles in duck meat during the early postmortem storage period

The present study was designed to investigate proteomic differences in duck breast muscle during the early postmortem storage period. The meat quality was evaluated at 0 hr and 24 hr postmortem at 4°C in Pekin ducks, black Muscovy ducks and Mule ducks. Differentially expressed proteins were detected by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/TOF MS) at 0 hr and 24 hr postmortem in the three duck breeds. The results showed that 53 proteins spots were differentially expressed at 0 hr and 24 hr postmortem at 4°C in Pekin ducks, 75 spots in black Muscovy ducks, and 72 spots in Mule ducks. A total of 30 (10 spots for each breed) were selected for identification by mass spectrometry. Seven proteins were identified in Pekin ducks, eight in black Muscovy ducks and seven in Mule ducks. Moreover, the above results obtained by 2-DE and MALDI-TOF/TOF MS were confirmed by western blotting. To our knowledge, this study is the first to provide insights into the protein profiles of ducks during postmortem storage and provides a better understanding of the biochemical processes that contribute to duck meat quality.

MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness

Background

MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness.

Results

Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system.

Conclusion

The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.

Electronic supplementary material

The online version of this article (10.1186/s12867-018-0118-3) contains supplementary material, which is available to authorized users.

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle

Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer’s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.

The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed

In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.

Dephosphorylation enhances postmortem degradation of myofibrillar proteins

Protein degradation is primarily responsible for postmortem meat tenderization, which might be affected by phosphorylation. The objective of this study was to investigate the effect of phosphorylation on myofibrillar proteins degradation in muscle during postmortem. Here we modulated the phosphorylation status of protein by protein kinase inhibitor and phosphatase inhibitor, and the effect of these inhibitors on myofibrillar protein degradation was evaluated. Generally, myofibril fragmentation index of samples with lower phosphorylation level was higher. Troponin T and heat shock protein 27 were degraded faster in protein kinase inhibited (low phosphorylation level) muscle, compared with the other two groups, while the degradation of desmin was not affected by inhibitors. Meanwhile, myosin heavy chain, actin and tropomyosin showed limited degradation in postmortem muscle. This study showed that dephosphorylation enhances the degradation of some myofibrillar proteins, indicating that protein phosphorylation may play an important role in postmortem meat tenderization.

Effect of inhibition of μ-calpain on the myofibril structure and myofibrillar protein degradation in postmortem ovine muscle

BACKGROUND

Tenderness is considered to be one of the most important attributes of meat quality. Myofibrillar protein degradation contributes to meat tenderization during postmortem ageing. In this process, calpain is the primary enzyme catalyzing the proteolysis. To further understand the action of calpain in meat tenderization, a μ-calpain inhibitor, MDL-28170, was used and its effects on sarcomere structure and myofibrillar protein degradation were determined.

RESULTS

The results of the present study showed that inhibition of μ-calpain significantly reduced muscle myofibrillar fragmentation compared to the group without μ-calpain inhibitor. Meanwhile, the sarcomere structure of the μ-calpain inhibited muscle was only slightly broken and largely remained integral 48 h postmortem. Myosin heavy chain, actin, desmin, troponin T and troponin I were identified to be substrates of μ-calpain by liquid chromatography-tandem mass spectrocopy and western blotting, and were detected with a higher degradation degree in the control group compared to the μ-calpain inhibition group.

CONCLUSION

Comparatively, myosin heavy chain and actin were found to be less sensitive to μ-calpain compared to desmin, troponin T and troponin I. These findings provide a better understanding of the contribution of μ-calpain to the myofibril structure and myofibrillar protein degradation of ovine muscle. © 2016 Society of Chemical Industry.

Differences in Beef Quality between Angus (Bos taurus taurus) and Nellore (Bos taurus indicus) Cattle through a Proteomic and Phosphoproteomic Approach

Proteins are the major constituents of muscle and are key molecules regulating the metabolic changes during conversion of muscle to meat. Brazil is one of the largest exporters of beef and most Brazilian cattle are composed by zebu (Nellore) genotype. Bos indicus beef is generally leaner and tougher than Bos taurus such as Angus. The aim of this study was to compare the muscle proteomic and phosphoproteomic profile of Angus and Nellore. Seven animals of each breed previously subjected the same growth management were confined for 84 days. Proteins were extracted from Longissimus lumborum samples collected immediately after slaughter and separated by two-dimensional electrophoresis. Pro-Q Diamond stain was used in phosphoproteomics. Proteins identification was performed using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Tropomyosin alpha-1 chain, troponin-T, myosin light chain-1 fragment, cytoplasmic malate dehydrogenase, alpha-enolase and 78 kDa glucose-regulated protein were more abundant in Nellore, while myosin light chain 3, prohibitin, mitochondrial stress-70 protein and heat shock 70 kDa protein 6 were more abundant in Angus (P<0.05). Nellore had higher phosphorylation of myosin regulatory light chain-2, alpha actin-1, triosephosphate isomerase and 14-3-3 protein epsilon. However, Angus had greater phosphorylation of phosphoglucomutase-1 and troponin-T (P<0.05). Therefore, proteins involved in contraction and muscle organization, myofilaments expressed in fast or slow-twitch fibers and heat shock proteins localized in mitochondria or sarcoplasmic reticulum and involved in cell flux of calcium and apoptosis might be associated with differences in beef quality between Angus and Nellore. Furthermore, prohibitin appears to be a potential biomarker of intramuscular fat in cattle. Additionally, differences in phosphorylation of myofilaments and glycolytic enzymes could be involved with differences in muscle contraction force, susceptibility to calpain, apoptosis and postmortem glycolysis, which might also be related to differences in beef quality among Angus and Nellore.

Phosphorylation prevents in vitro myofibrillar proteins degradation by μ-calpain

Myofibrillar proteins degradation contributes to meat tenderisation during post-mortem ageing. Protein phosphorylation has been revealed to be associated with meat tenderness in recent years. This study was undertaken to determine the impact of myofibrillar proteins phosphorylation on the degradation susceptibility by μ-calpain. Myofibrillar proteins were first incubated with protein kinase A (PKA) or alkaline phosphatase (AP) to increase or decrease the phosphorylation level, following μ-calpain hydrolysis. Myosin heavy chain, actin, desmin and troponin T showed different levels of degradation in control, AP and PKA groups under different Ca²⁺ concentrations. Generally, more degradation products were detected with the increase of Ca²⁺ concentration. Compared to the control, the protein degradation was higher in AP-treated group and lower in PKA-treated group. This study shows that phosphorylation prevents proteolytic susceptibility of myofibrillar proteins to degradation by μ-calpain, indicating that protein phosphorylation plays an important role in meat tenderisation during post-mortem ageing.