Molecular mechanism of protein dynamic change for Hengshan goat meat during freezing storage based on high-throughput proteomics

Investigation of the protective mechanisms of liquid nitrogen spray freezing and TGase cross-linking on the structural characteristics of surimi gels during frozen storage

This study explored the mechanism of liquid nitrogen spray freezing and transglutaminase cross-linking in maintaining surimi gels' structure during storage. Results revealed that structure changes were, on the one hand, related to the growth and recrystallization of ice crystals during storage. Low cross-linking gels with air freezing exhibited minimum value after 20 days of storage, with hardness decreasing by 38.02 %, while -80 °C liquid nitrogen spray freezing combined with 62.99 % cross-linked effectively preserved structure by maintaining uniform ice crystal distribution and preventing microstructural fractures, limiting the hardness decrease to 18.32 %. On the other hand, structure changes were closely associated with protein variations. There were 766 differential proteins identified in the CKb vs. CKa comparison. The enhanced texture retention of 62.99 % cross-linked during storage, in contrast to low cross-linked gel, was probably associated with higher concentrations of structural proteins like A0A3N0XRS8 and A0A3N0YCS0 as well as calcium-related proteins like A0A3N0XCW2 and A0A3N0Y0G9.

Analysis of the influencing mechanism of low-frequency alternating magnetic field-assisted freezing on oxidative and structural attributes of pork myofibrillar proteins based on proteomic changes

Using quantitative proteomics, the study investigated the effects of low-frequency alternating magnetic field-assisted freezing (LF-MFF) on the oxidative status and structural integrity of porcine myofibrillar proteins (MPs). LF-MFF, especially at 3 mT (LF-MFF-3) and 4 mT (LF-MFF-4), significantly reduced MPs' oxidation compared to refrigerator freezing (RF) (P < 0.05). The spectroscopic analysis confirmed better structural preservation with LF-MFF-4. We identified 126 differentially abundant proteins (DAPs) associated with key metabolic pathways, including amino acid biosynthesis and oxidative phosphorylation, potentially affecting Adenosine Triphosphate (ATP) metabolism and contributing to freeze-induced protein damage and oxidative denaturation of MPs. Through correlation analysis, among the 52 DAPs in the LF-MFF-4 vs RF comparison, eight proteins with variable importance in projection (VIP) > 1.1 were identified as potential biomarkers for porcine MPs. These findings enhance our understanding of the oxidative and structural changes in MPs following LF-MFF, suggesting its potential for improving pork quality and meat preservation.

TMT-based quantitative proteomics reveals the effects of electromagnetic field and freezing preservation techniques on mutton quality

This study investigated the effects of electromagnetic field preservation (EP) and freezing storage (FS) on the quality of northern Qianbei Ma mutton. Using tandem mass tagging (TMT)-labeled quantitative proteomics and bioinformatics, it was observed that EP more effectively inhibited pH increase and maintained a* and b* values compared to FS. Furthermore, the EP group was able to better maintain the water-holding capacity and tenderness of the mutton under prolonged storage. Proteomics analysis identified 397 differentially expressed proteins (DEPs) between the two storage methods at the same storage duration. GO and KEGG enrichment analyses indicated that proteins such as A0A452DSW4, A0A452E8M7, and D3JYV6 were involved in energy metabolism and redox processes, while A0A452EJ66, A0A452DSW4, and A0A452FJE8 played significant roles in protein binding. Overall, EP technology demonstrated superior benefits for maintaining mutton quality, suggesting a novel approach for mutton preservation.

TMT quantitative proteomics analysis reveals molecular mechanism of ferroptosis during beef refrigeration

Ferroptosis is a recently identified cell death process in refrigerated beef, and its mediated protein oxidation and cell death may reduce muscle quality, but the mechanism of ferroptosis is unclear. In the study, free iron accumulation reached 19.670 ± 0.482 μg/g after 6 days refrigeration, the levels of apoptosis, ROS, and lipid peroxidation increased significantly (P < 0.05), and muscle tissue cells exhibited typical ferroptosis characteristics. A total of 377 differentially expressed proteins (DEPs) were identified by TMT quantitative proteomics. 15 DEPs, including transferrin, ferritin, glutathione peroxidase (GPX) 4, and heme oxygenase 1, were involved in lipid peroxidation, Fe2+ and Fe3+ conversion, iron ion accumulation, and mitochondrial oxidative stress to induce ferroptosis. In addition, signalling pathways, such as chemical carcinogenesis-ROS, glutathione metabolism, HIF-1, and PPAR may promote ferroptosis by affecting free iron overload and GPX4 inactivation.

Investigating comprehensive effects of depuration salinity and duration on posterior anhydrous living-preservation of Pacific oyster (Crassostrea gigas)

Depuration and anhydrous living-preservation are two important and consecutive steps during the circulation of Pacific oyster (Crassostrea gigas), and two main factors in depuration, salinity and duration, are pivotal to posterior anhydrous living-preservation of C. gigas. In this work, the comprehensive effects of depuration salinity (26-38 g/L) and duration (0-72 h) on anhydrous living-preservation at 4 °C for 7 days were investigated in regard of mortality, biochemical indexes (fatty acids profile analysis, glycogen) and proteome changes as well. The results showed that the mortality of C. gigas increased obviously with 72 h depuration and especially with 20 % salinity fluctuation, concomitantly accompanying metabolism disorder. Furthermore, alterations in salinity and duration resulted in 381 different expression proteins (DEPs), which were gotten more involved in the pathways related to amino acid metabolism. Taken together, it was suggested that duration < 48 h and salinity fluctuations lower than 10 % were the preferred conditions for anhydrous living-preservation.

Effects of Quality Enhancement of Frozen Tuna Fillets Using Ultrasound-Assisted Salting: Physicochemical Properties, Histology, and Proteomics

Salting pretreatment is an effective method to improve the quality of frozen fish. This study investigated the quality changes and proteomic profile differences of frozen yellowfin tuna fillets pretreated with ultrasound-assisted salting (UAS) and static salting (SS). This study was centered on three aspects: physicochemical indicators' determination, histological observation, and proteomic analysis. The results showed that UAS significantly increased yield, salt content, and water-holding capacity (WHC), decreased total volatile base nitrogen (TVBN) compared to SS (p < 0.05), and significantly increased water in the protein matrix within myofibrils. Histological observations showed that the tissue cells in the UAS group were less affected by frozen damage, with a more swollen structure and rougher surface of myofibrils observed. Furthermore, 4D label-free proteomics revealed 56 differentially abundant proteins (DAPs) in UAS vs. NT comparison, mainly structural proteins, metabolic enzymes, proteasomes, and their subunits, which are associated with metabolic pathways such as calcium signaling pathway, gap junction, actin cytoskeletal regulation, and necroptosis, which are intimately associated with quality changes in freeze-stored tuna fillets. In brief, UAS enhances the potential for the application of salting pretreatment to improve frozen meat quality, and 4D label-free proteomics provides knowledge to reveal the potential links between quality and molecular changes in processed frozen meat to optimize future UAS meat processing.

Tandem Mass Tag Proteomics Provides Insights into the Underlying Mechanism of Flesh Quality Degradation of Litopenaeus vannamei during Refrigerated Waterless Transport at 12 °C

Refrigerated waterless transport at 12 °C of live shrimp (Litopenaeus vannamei) causes flesh quality deterioration, and the underlying mechanism remains unknown. Herein, proteomics and bioinformatics analyses were used to elucidate the molecular mechanism of flesh quality changes. The result showed that 33 and 44 of the differentially abundant proteins (DAPs) were, respectively, identified in the acute cold (AC) group and the combined stress of acute cold and waterless duration (AC+WD) group, which were mostly involved in the metabolism processes and cellular structure of animal tissues, and notably enriched in biological pathways such as lysosome, glycolysis/gluconeogenesis, and focal adhesion. Furthermore, the changes in color and texture properties were closely associated with tubulin, gelsolin, laminin, trypsin-1, dipeptidyl peptidase, triosephosphate isomerase, and aldehyde dehydrogenase. Therefore, these DAPs could be used as potential biomarkers to monitor the deterioration of shrimp flesh quality during refrigerated waterless transportation.

A Role of Multi-Omics Technologies in Sheep and Goat Meats: Progress and Way Ahead

Sheep and goat meats are increasingly popular worldwide due to their superior nutritional properties and distinctive flavor profiles. In recent decades, substantial progress in meat science has facilitated in-depth examinations of ovine and caprine muscle development during the antemortem phase, as well as post-mortem changes influencing meat attributes. To elucidate the intrinsic molecular mechanisms and identify potential biomarkers associated with meat quality, the methodologies employed have evolved from traditional physicochemical parameters (such as color, tenderness, water holding capacity, flavor, and pH) to some cutting-edge omics technologies, including transcriptomics, proteomics, and metabolomics approaches. This review provides a comprehensive analysis of multi-omics techniques and their applications in unraveling sheep and goat meat quality attributes. In addition, the challenges and future perspectives associated with implementing multi-omics technologies in this area of study are discussed. Multi-omics tools can contribute to deciphering the molecular mechanism responsible for the altered the meat quality of sheep and goats across transcriptomic, proteomic, and metabolomic dimensions. The application of multi-omics technologies holds great potential in exploring and identifying biomarkers for meat quality and quality control, thereby promoting the optimization of production processes in the sheep and goat meat industry.

First insights into the dynamic protein changes in goat Semitendinosus muscle during the post-mortem period using high-throughput proteomics

Proteomics plays a key and insightful role in meat research in the post-genomic era. This study aimed to unveil using a shotgun proteomics approach the temporal dynamic changes in early post-mortem proteome of goat Semitendinosus muscle. Therefore, the evolution and comparison of the muscle proteome over three post-mortem times (1, 8, and 24 h) was assessed. The temporal proteomics profiling quantified 748 proteins, from which 174 were differentially abundant (DAPs): n = 55 between 1 h versus 8 h, n = 52 between 8 h versus 24 h, and n = 154 between 1 h versus 24 h. The DAPs belong to myriad interconnected pathways. Binding, transport and calcium homeostasis, as well as muscle contraction and structure, exhibited an equivalent contribution during post-mortem, demonstrating their central role. Catalytic, metabolism and ATP metabolic process, and proteolysis were active pathways from the first hours of animal bleeding. Conversely, oxidative stress, response to hypoxia and cell redox homeostasis along chaperones and heat shock proteins accounted for the large proportion of the biochemical processes, more importantly after 8 h post-mortem. Overall, the conversion of muscle into meat is largely orchestrated by energy production as well as mitochondrial metabolism and homeostasis through calcium and permeability transition regulation. The study further evidenced the role of ribosomal proteins in goat post-mortem muscle, signifying that several proteins experiencing changes during storage, also undergo splicing modifications, which is for instance a mechanism known for mitochondrial proteins. Overall, temporal proteomics profiling of early post-mortem muscle proteome offers an unparalleled view of the sophisticated post-mortem biochemical and proteolytic events associated with goat meat quality determination.

A strategy to link the changes in the quality traits of Japanese sea bass (Lateolabrax japonicus) muscle and proteins in its exudate during cold storage using mass spectrometry

In this study, Japanese sea bass (Lateolabrax japonicus) was used as a model to link the changes in the quality traits of fish muscle during storage to the change of protein in muscle exudate. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) combined with variables importance in projection (VIP) analysis, and high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), were applied to identify the proteins by analyzing the enzymatic hydrolysates of exudates of fish muscle. The link in the identified proteins to the change in the quality traits of fish muscle during storage was explored using pyramid diagrams. Nine proteins were identified from the exudate of Japanese sea bass muscle during 12 days of storage at 4 °C. Of these, four proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), heat shock protein 90 (HSP90), and peroxiredoxin 1 (PRX1), and beta-actin were found to be responsible for the changes in the quality traits of fish muscle. It is promising to correlate the changes in the quality traits of fish muscle and proteins in muscle exudate via MS-based protein identification and the construction of a relationship diagram to understand the mechanism of muscle change at the molecular level.

Unraveling propylene glycol-induced lipolysis of the biosynthesis pathway in ultra-high temperature milk using high resolution mass spectrometry untargeted lipidomics and proteomics

In July 2022, the food safety accident that excessive propylene glycol was detected in milk processing factory raised widespread concerns about quality and nutrition of milk with illegal additive. To the best of our knowledge, the influences of propylene glycol to lipids in milk had not been systematically explored. Therefore, spatiotemporal distributions of lipids related to propylene glycol reaction and changes of sensory quality were investigated by food exogenous. Briefly, 10 subclasses (Cer, DG, HexCer, LPC, LPE, PC, PE, PI, SPH and TG) included 147 lipids and 38 pivotal enzymes were annotated. Propylene glycol altered lysophospholipidase and phospholipase A₂ through altering structural order in lipids domains surrounding proteins to inhibit glycerophospholipid metabolism and initiated obvious changes in PC (10.45-27.91 mg kg^-1) and PE (12.92-49.02 mg kg^-1). This study offered insights into influences of propylene glycol doses and storage time on milk metabolism at molecular level to assess the quality of milk.

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.

Freezing-induced denaturation of myofibrillar proteins in frozen meat

Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

The visual appearance of the fish fillet is a significant determinant of consumers' purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15'-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15'-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.

Proteomic changes involved in water holding capacity of frozen bovine longissimus dorsi muscles based on DIA strategy

As freeze/thaw procedure leads to inevitable drip loss, elucidation of mechanism on dynamic changes in water holding capacity (WHC) of muscle is urgently needed. In this study, the proteomic profile by DIA-based strategy, muscle microstructure, water mobility, and WHC indices of bovine longissimus dorsi muscles were investigated under different freezing conditions as well as the correlations among them. Results indicated that slow freezing (SF) sample exhibited significantly higher water mobility, thaw loss, total loss, and shear force value than the samples subjected to fast freezing (FF) and non-frozen control (CON). According to the protein profile, we have identified 272 differential abundance proteins (DAPs), in which more significant proteome changes were found in SF/CON samples as compared with FF/CON. Among the 132 DAPs in FF/SF comparison, correlation analysis revealed that MYL3, DES, SYNE2, EXR, RPL35A, RPS6, and Hsp40 were closely correlated with T₂₃ , thaw loss, and total loss. Accordingly, we considered those seven proteins as potential biomarkers related to WHC of frozen muscle. Our study should give a further understanding on mechanisms behind the various WHC of muscle when subjected to different freezing conditions. PRACTICAL APPLICATIONS: Freezing plays a key role in the preservation method for meat and meat products. However, the drip loss during freezing and subsequent thawing procedure causes considerable economic and nutritional losses. To minimize the losses, elucidation of mechanism on the mechanism of thaw loss formation is urgently needed. DIA-based proteomics is a novel, robust method that provides further understanding on the mechanisms behind the dynamic changes in water holding capacity of muscle. The screened protein biomarkers in frozen muscle would play key roles in the development of WHC, especially for the thaw loss formation. Through this perspective, we can explain the origin of thaw loss and the variation under different freezing conditions, which should provide the meat industries with theoretical basis for reducing losses.

The Investigation of Protein Profile and Meat Quality in Bovine Longissimus thoracic Frozen under Different Temperatures by Data-Independent Acquisition (DIA) Strategy

The influence of freezing on the protein profile and quality traits in bovine Longissimus thoracic (LT) muscle was investigated by the data-independent acquisition (DIA) technique. Compared to fresh meat, a total of 262 proteins were identified as differential abundance proteins (DAPs) in four frozen groups (−12 °C, −18 °C, −38 °C, and −80 °C). According to the bioinformatics analysis, most of the DAPs in the significant Go terms and the KEGG pathway were structure proteins and enzymes. Proteome changes in the frozen bovine muscle at −12 °C and −18 °C were more significant than those at −38 °C and −80 °C. The result was consistent with the deterioration trend of the meat quality. The correlation analysis revealed that 17 proteins were correlated closely with the color, shear force, thawing loss, and cooking loss of the frozen meat, which could be used as putative biomarkers for frozen meat quality. MYO18A and ME3 are newly discovered proteins that are associated with frozen beef quality. In addition, CTTN and SERPINB6 were identified in frozen groups, which exhibited a significant inverse correlation with thawing loss (p < 0.01). These findings reveal the quality changes induced by freezing at the protein molecular level and provide new insights into the control of quality deterioration.

Molecular mechanism of protein dynamic change in Pacific oyster (Crassostrea gigas) during depuration at different salinities uncovered by mass spectrometry-based proteomics combined with bioinformatics

Salinity stress during depuration of Pacific oysters (Crassostrea gigas) leads to degradation in quality; therefore, an understanding of the molecular mechanisms regulating dynamic changes during depuration is needed. Here, C. gigas was depurated for 72 h at salinities ranging from 26 to 38 g/L, a ± 10-20% fluctuation from that in the production area, and the gill proteomes were analyzed by sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS). Of the 1218 proteins analyzed, 241 were differentiating proteins (DPs). Salinity stress led to increased levels of DPs associated with glycolysis and the extracellular matrix-receptor interaction pathway, and decreased levels of DPs associated with the citric acid cycle, lipid metabolism, genetic information processing, and cell transformation, especially in oysters exposed to 38 g/L salinity (+20%). Controlling salinity fluctuation within ± 10% of the production area during depuration was conducive to maintaining quality in C. gigas.

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.

Proteomics analysis to investigate the impact of diversified thermal processing on meat tenderness in Hengshan goat meat

During the thermal processing, proteins of Hengshan goat meat undergo structural modifications such as degradation, oxidation and denaturation, ultimately affect the palatability and acceptability. The results of several objective metrics demonstrated that thermal processing exhibited significant impacts on the tenderness of goat meat. The 551, 84, 72, and 121 proteins were identified in the control and thermal processed groups (boiled, steamed, and roasted), respectively. Compared with the control group, the 101, 98, and 109 differentially-expressed proteins were explored in the treatment groups. Furthermore, the functions of metabolic and skeletal muscle proteome were investigated and discussed. Sensory evaluation and proteomics analysis showed that steaming and boiling treatment had no significant effect on the tenderness of goat meat, while roasting significantly reduced the tenderness, indicating that the available thermal processing methods to ensure the tenderness of goat meat were steaming and boiling treatments. Thus, the established proteomics database of goat meat provided the valuable reference for rational selection of thermal processing methods.