Comparison of Activity, Expression, and S-Nitrosylation of Calcium Transfer Proteins between Pale, Soft, and Exudative and Red, Firm, and Non-exudative Pork during Post-Mortem Aging

S-nitrosoproteomics profiling elucidates the regulatory mechanism of S-nitrosylation on beef quality

This study aimed to quantitively profile the S-nitrosylation in beef semimembranosus (SM) with different treatments (nitric oxide donor or nitric oxide synthase inhibitor) by applying iodoTMT-based nitrosoproteomics. Results showed that 2096 S-nitrosylated cysteine sites in 368 proteins were detected in beef SM. Besides, differential SNO-modified proteins were screened, some of which were involved in crucial biochemical pathways, including calcium-releasing-related proteins, energy metabolic enzymes, myofibrils, and cytoskeletal proteins. GO analysis indicated that differential proteins were localized in a wide range of cellular compartments, such as cytoplasm, organelle, and mitochondrion, providing a prerequisite for S-nitrosylation exerting broad roles in post-mortem muscles. Furthermore, KEGG analysis validated that these proteins participated in the regulation of diverse post-mortem metabolic processes, especially glycolysis. To conclude, changes of S-nitrosylation levels in post-mortem muscles could impact the structure and function of crucial muscle proteins, which lead to different levels of muscle metabolism and ultimately affect beef quality.

3D-MPEA: A Graph Attention Model-Guided Computational Approach for Annotating Unknown Metabolites in Interactomics via Mass Spectrometry-Focused Multilayer Molecular Networking

The spectral matching strategy of MS2 fragment spectrograms serves as a ubiquitous method for compound characterization within the matrix. Nevertheless, challenges arise due to the deficiency of distinctions in spectra across instruments caused by coelution peak-derived fragments and incompleteness of the current spectral reference database, leading to dilemma of multidimensional omics annotation. The graph attention model embedded with long short-term memory was proposed as an optimized approach involving integrating similar MS2 spectra into molecular networks according to the isotopic ion peak cluster spacing features to collapse diverse ion species and expand the spectral reference library, which efficiently evaluated the substance capture capacity to 123.1% than classic substance perception tactics. The versatility and utility of the established annotation procedure were showcased in a study on the stimulation of pork mediated by 2,2-bis(4-hydroxyphenyl)propane and enabled the global metabolite annotation from knowns to unknowns at metabolite-lipid-protein level. On the spectra for which in silico extended spectral library search provided a group truth, 83.5-117.1% accuracy surpassed 1.2-14.3% precision after manual validation. β-Ala-His dipeptidase was first evidenced as the critical node related to the transformation of α-helical (36.57 to 35.74%) to random coil (41.53 to 42.36%) mediated by 2,2-bis(4-hydroxyphenyl)propane, ultimately triggering an augment of catalytic performance, inducing a series of oxidative stress, and further intervening in the availability of animal-derived substrates. The integration of ionic fragment feature networks and long short-term memory models allows the effective annotation of recurrent unknowns in organisms and the deciphering of unacquainted matter in multiomics.

Integration of transcriptome and machine learning to identify the potential key genes and regulatory networks affecting drip loss in pork

Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL in muscles postmortem, 12 Duroc × (Landrace × Yorkshire) pigs with extremely high (n = 6, H group) and low (n = 6, L group) DL at both 24 and 48 h postmortem were selected for transcriptome sequencing. The analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA) were performed to find the overlapping genes using the transcriptome data, and functional enrichment and protein-protein interaction (PPI) network analysis were conducted using the overlapping genes. Moreover, we used machine learning to identify the key genes and regulatory networks related to DL based on the interactive genes of the PPI network. Finally, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, the insulin signaling pathway, and the calcium signaling pathway were identified, and a single-gene set enrichment analysis (GSEA) was performed to further annotate the functions of these potential key genes. The GSEA results showed that these genes are mainly related to ubiquitin-mediated proteolysis and oxidative reactions. Taken together, our results indicate that the potential key genes influencing DL are mainly related to insulin signaling mediated differences in glycolysis and ubiquitin-mediated changes in muscle structure and improve the understanding of gene expression and regulation related to DL and contribute to future molecular breeding for improving pork quality.

Modification-Specific Proteomic Analysis Reveals Cysteine S-Nitrosylation Mediated the Effect of Preslaughter Transport Stress on Pork Quality Development

This study aimed to explore the effects of preslaughter transport stress on protein S-nitrosylation levels and S-nitrosylated proteome in post-mortem pork longissimus thoracis (LT) muscle. Pigs (N= 16) were randomly divided into 3 h transport (high-stress group, HS) and 3 h transport followed by 3 h resting treatments (low-stress control group, LS). Results demonstrated that high transport stress levels induced nitric oxide (NO) overproduction by promoting NO synthase (NOS) activity and neuronal NOS (nNOS) expression, which thereby notably increased protein S-nitrosylation levels in post-mortem muscle (p < 0.05). Proteomic analysis indicated that 133 S-nitrosylation-modified cysteines belonging to 85 proteins were significantly differential, of which 101 cysteines of 63 proteins were higher in the HS group (p < 0.05). Differential proteins including cytoskeletal and calcium-handling proteins, glycolytic enzymes, and oxidoreductase were mainly involved in the regulation of muscle contraction and energy metabolism that might together mediate meat quality development. Overall, this study provided direct evidence for changes in S-nitrosylation levels and proteome in post-mortem muscle in response to preslaughter transport stress and revealed the potential impact of S-nitrosylated proteins on meat quality.

Mitochondrial dysfunction and calcium dyshomeostasis in the pectoralis major muscle of broiler chickens with wooden breast myopathy

The incidence of wooden breast (WB) meat of commercial broiler chicken has been increasing in recent years. Histological examination found that the occurrence of WB myopathy was accompanied by the pectoralis major (PM) muscle damage. So far, the potential mechanisms are not fully understood. This study aimed to explore the underlying mechanism of the damage of WB-affected PM muscle caused by changes in mitochondrial function, mitochondrial redox status and Ca2+ homeostasis. A total of 80 market-age Arbor Acres male broiler chickens were sampled and categorized into control (CON) and WB groups based on the evaluation of myopathic lesions. PM muscle samples were collected (n = 8 in each group) for histopathological evaluation and biochemical analyses. Ultrastructural examination and histopathological changes suggested the occurrence of PM muscle damage in broiler chickens with WB myopathy. The WB group showed an increased level of reactive oxygen species and enhanced antioxidant capacities in mitochondria of PM muscle. These changes were related to impaired mitochondria morphology and mitochondrial dysfunction. In addition, abnormal expressions of Ca2+ channels led to substantial Ca2+ loss in SR and cytoplasmic Ca2+ overload, as well as Ca2+ accumulation in mitochondria, resulting in Ca2+ dyshomeostasis in PM muscle of broiler chickens with WB myopathy. Combined, these findings indicate that WB myopathy is related to mitochondrial dysfunction, mitochondrial redox status imbalance and Ca2+ dyshomeostasis, leading to WB-affected PM muscle damage.

Intracellular Calcium Overload and Activation of CaMKK/AMPK Signaling Are Related to the Acceleration of Muscle Glycolysis of Broiler Chickens Subjected to Acute Stress

The current study investigated the effect of preslaughter transport on stress response and meat quality of broilers and explored the underlying mechanisms involved in the regulation of muscle glycolysis through calcium/calmodulin-dependent protein kinase kinase (CaMKK)/AMP-activated protein kinase (AMPK) signaling. Results suggested that transport induced stress responses of broilers and caused PSE-like syndrome of pectoralis major muscle. Preslaughter transport enhanced the mRNA expressions of glycogen phosphorylase and glucose transporters, as well as the activities of glycolytic enzymes, which accelerated the breakdown of glycolytic substrates and the accumulation of lactic acid. In addition, acute stress induced abnormal intracellular calcium homeostasis by disrupting calcium channels on the cell membrane and sarcoplasmic reticulum, which led to the activation of CaMKK and promoted AMPK phosphorylation. This study provides evidence that the intracellular calcium overload and the enhancement of CaMKK/AMPK signaling are related to the accelerated muscle glycolysis of broiler chickens subjected to acute stress.

Targeted energy metabolomics analysis of postmortem pork in an in vitro model as influenced by protein S-nitrosylation

For exploring the effect of protein S-nitrosylation on the energy metabolism of early postmortem pork (within 24 h postmortem), the six Longissimus thoracis (LT) muscle homogenates were treated with nitric oxide donor (NOR-3, (±)-(E)-4-Ethyl-2-(E)-hydroxyimino-5-nitro-3-hexenamide), nitric oxide synthase (NOS) inhibitor (L-NAME, Nω-nitro-L-arginine methyl ester hydrochloride) and control (0.1 M K₂HPO₄, pH 7.4) in the in vitro buffer system for 24 h, respectively. The western blotting result showed that NOR-3 treatment led to a greater level of protein S-nitrosylation (p < 0.05). However, S-nitrosylation levels had no significant difference between L-NAME and control groups (p > 0.05). In addition, results showed that 16 significantly differential energy metabolites were identified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and clearly separated among three groups in the principal component analysis. Four pathways (glycolysis, tricarboxylic acid cycle, purine metabolism and pentose phosphate pathway) related to energy metabolism were significantly influenced by different levels of protein S-nitrosylation. Furthermore, the correlation analysis of metabolites demonstrated that metabolites were in dynamic equilibrium with each other. These results indicate that protein S-nitrosylation can participate in and regulate energy metabolism postmortem pork through glycolysis and tricarboxylic acid (TCA) cycle.

Protein S-Nitrosylation Regulates Postmortem Beef Apoptosis through the Intrinsic Mitochondrial Pathway

The objective of the present study was to investigate the regulatory mechanism of protein S-nitrosylation on early postmortem beef muscle apoptosis. Beef semimembranosus (SM) muscles at 45 min postmortem were treated with nitric oxide (NO) donor, control (NaCl solution), or nitric oxide synthase (NOS) inhibitor for 24 h at 4 °C. Bcl-2 expression and mitochondrial membrane potential were significantly increased by the NO donor treatment at 6 h postmortem, while the NOS inhibitor group exhibited a lower Bcl-2 level and mitochondrial membrane potential in comparison with the control (P < 0.05). The cytochrome c expression analysis highlighted that NO donor incubation repressed cytochrome c release from mitochondria to the cytoplasm. Further, S-nitrosylation levels of caspase-3 and caspase-9 were elevated after incubation with the NO donor (P < 0.05), leading to decreased caspase-3 and caspase-9 activities (P < 0.05). The aforementioned findings imply that protein S-nitrosylation mediates postmortem apoptosis of beef SM through the mitochondrial apoptotic pathway.

Meat tenderness: advances in biology, biochemistry, molecular mechanisms and new technologies

Meat tenderness is an important quality trait critical to consumer acceptance, and determines satisfaction, repeat purchase and willingness-to-pay premium prices. Recent advances in tenderness research from a variety of perspectives are presented. Our understanding of molecular factors influencing tenderization are discussed in relation to glycolysis, calcium release, protease activation, apoptosis and heat shock proteins, the use of proteomic analysis for monitoring changes, proteomic biomarkers and oxidative/nitrosative stress. Each of these structural, metabolic and molecular determinants of meat tenderness are then discussed in greater detail in relation to animal variation, postmortem influences, and changes during cooking, with a focus on recent advances. Innovations in postmortem technologies and enzymes for meat tenderization are discussed including their potential commercial application. Continued success of the meat industry relies on ongoing advances in our understanding, and in industry innovation. The recent advances in fundamental and applied research on meat tenderness in relation to the various sectors of the supply chain will enable such innovation.

Comparative Study on Pale, Soft and Exudative (PSE) and Red, Firm and Non-Exudative (RFN) Pork: Protein Changes during Aging and the Differential Protein Expression of the Myofibrillar Fraction at 1 h Postmortem

In this paper, the protein changes during aging and the differences in the myofibrillar protein fraction at 1 h postmortem of pale, soft and exudative (PSE), and red, firm and non-exudative (RFN) pork longissimus thoracis (LT) were comparatively studied. The PSE and RFN groups were screened out based on the differences in their pH and lightness (L*) at 1 h, and their purge loss at 24 h postmortem. Based on the measured MFI, desmin degradation, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, PSE meat presented more significant changes in the myofibrillar protein fraction compared to RFN meat during postmortem aging. Through liquid chromatograph-mass spectrometer/mass spectrometer (LC-MS/MS) analysis, a total of 172 differential proteins were identified, among which 151 were up-regulated and 21 were down-regulated in the PSE group. The differential proteins were muscle contraction, motor proteins, microfilaments, microtubules, glycolysis, glycogen metabolism, energy metabolism, molecular chaperones, transport, and enzyme proteins. The AMP activated protein kinase (AMPK) signaling pathway, HIF-1 signaling pathway, calcium signaling pathway, and PI3K-Akt signaling pathway were identified as the significant pathways related to meat quality. This study suggested that the different changes of the myofibrillar protein fraction were involved in the biochemical metabolism in postmortem muscle, which may contribute to the molecular understanding of PSE meat formation.

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.

Involvement of protein S-nitrosylation in regulating beef apoptosis during postmortem aging

This study was the first attempt to explore the effect of protein S-nitrosylation on the progress of apoptosis in postmortem beef semimembranosus muscle (SM). Five beef SM were incubated with S-nitrosoglutathione (GSNO, nitric oxide donor), control, or Nω-nitro-l-arginine methyl ester hydrochloride (l-NAME, nitric oxide synthase inhibitor). Results suggest that compared to the control, more chromatin condensation, nucleusfragmentation, apoptoticbody formation, and mitochondrialswelling were observed in the l-NAME group while these apoptosis-related morphological changes were retarded in the GSNO group. Notably, there were fewer apoptotic nuclei in the GSNO group and more apoptotic nuclei in the l-NAME group compared to the control (P < 0.05). Additionally, caspase-3 and -9 activities and caspase-3 activation were greatly decreased by GSNO treatment and increased by l-NAME treatment (P < 0.05). The morphological and biochemical results indicate that protein S-nitrosylation could play a negative regulatory role in beef apoptosis during postmortem aging.

Comparison of activity, expression and S-nitrosylation of glycolytic enzymes between pale, soft and exudative and red, firm and non-exudative pork during post-mortem aging

The activity, expression and S-nitrosylation of glycogen phosphorylase (GP), phosphofructokinase (PFK) and pyruvate kinase (PK) was compared between pale, soft and exudative (PSE) and red, firm and non-exudative (RFN) pork. The nitric oxide synthase (NOS) activity of RFN pork was higher than PSE pork (P < 0.05). Glycogen and lactic acid content were significantly different between PSE and RFN samples at 1 h postmortem (P < 0.05). Compared to PSE pork, RFN pork had lower activities and higher S-nitrosylation levels of GP, PFK and PK (P < 0.05). Moreover, GP expression in RFN pork was lower (P < 0.05) while no significant differences of PFK and PK expression were observed between these two groups. These data suggest that protein S-nitrosylation can presumably regulate glycolysis by modulating glycolytic enzymes activities and then regulate the development of PSE pork.