Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs

Preparation of whey protein-chitosan edible coating modulated by cold plasma and its effect on quality and metabolites of chilled beef

The stability, safety, and sustainability of food preservation coatings have garnered increasing attention, with cold plasma modification emerging as an environmentally friendly alternative. This study developed a cold plasma (CP)-treated 1 % (w/v) whey protein isolate (WPI)/carboxymethyl chitosan (CMCS) coating (mass ratio 1:1) (CPW). The effects of CP treatment were investigated through particle size and zeta potential analyses. Further characterization using intrinsic fluorescence, confocal laser microscopy, and Fourier-transform infrared spectroscopy revealed the impact of CP treatment on WPI-CMCS polymer binding and stability within pH 4-6. Applied to beef preservation, CPW significantly inhibited color deterioration, delayed increases in TVB-N and TBARS levels, reduced total microbial counts, and maintained favorable texture properties during 4 °C storage (p < 0.05). Combined LC/MS and GC/MS analyses demonstrated that CPW treatment effectively reduced critical deterioration markers: lipid peroxidation products (13-L-hydroperoxylinoleic acid, 9(S)-HPODE, 9,10-DHOME) and protein degradation products (L-glutamic acid, L-arginine, L-phenylalanine), while regulating energy metabolism metabolites (citric acid, lactic acid). These findings indicate that CPW maintains beef quality by modulating energy metabolism, lipid peroxidation, and protein degradation pathways. This study demonstrates that CP modification enhances WPI-CMCS composites binding and stability, positioning CPW as a safe, green, and effective preservation coating with promising application prospects for chilled beef preservation, which has the potential to replace traditional chemical synthetic preservatives and mitigate the environmental pollution caused by non-biodegradable packaging.

Integrated transcriptomics and metabolomics reveal the molecular characteristics and metabolic regulatory mechanisms among different muscles in Minxian black fur sheep

BACKGROUND

Mammalian skeletal muscle is comprised of heterogeneous fibers with various contractile and metabolic properties that affect muscle flavor. Thus, it is of great significance to identify and characterize the potential molecular characteristics and metabolic regulatory mechanisms associated with muscle fiber properties.

RESULTS

In this study, the muscle samples (Biceps femoris; longissimus dorsi; and infraspinatus) from Minxian black fur sheep were used to perform transcriptome and metabolome analyses. Then, the key genes regulating the metabolism of important flavor precursors (amino acids and lipids) were explored by integrating transcriptome and metabolome. Consequently, we identified 432 differentially expressed genes, which were mainly involved in muscle development and function maintenance (e.g., myofibril, myocyte differentiation, etc.), metabolism (e.g., fatty acid metabolism, arachidonic acid metabolism, PPAR signaling pathway, and PI3K-Akt signaling pathway, etc.), and homeostasis (e.g., regulation of actin cytoskeleton, ECM-receptor interaction, calcium signaling pathway, etc.). A total of 58 key genes affecting muscle fiber properties, including MYL2, HOXA/C/D, MYBPH8, MYH8, etc., were screened, which characterized the molecular differences in muscle fiber metabolic properties between oxidative and glycolytic muscle. Meanwhile, we identified 463 differentially accumulated metabolites. Except for glycerophospholipids, most flavor metabolites were higher in oxidative muscle. Subsequently, key genes highly related to flavor amino acids were identified by weighted gene co-expression network analysis, such as ALDH6A1, BCKDHB, SLC16A7, LDHB, etc. Based on KEGG enrichment analysis, a regulatory network with both lipid metabolism and its crosstalk with other metabolic pathways was constructed.

CONCLUSIONS

In conclusion, this study provides an in-depth understanding of the molecular mechanism of differences in muscle fiber properties among different muscles of Minxian black fur sheep, and also lays a foundation for further exploration of the regulatory mechanism of key genes on flavor metabolites.

Proteomics integrated with metabolomics: Analysis of the internal mechanism underlying changes in meat quality in different muscles from bactrian camels

Knowledge about the quality of meat obtained from different muscles is crucial for developing high-quality camel meat for commercial use. Metabolomic and proteomic profiles of the longissimus thoracic (LT), semitendinosus (ST), and psoas major (PM) muscles of the bactrian camel, which significantly vary in aspects such as intramuscular fat (IMF) content and shear force, were comprehensively compared to evaluate the impact of these changes on meat quality. Compared with ST and PM muscles, LT muscles had higher IMF content, were more tender, and had a lower shear force. Proteomic analysis unveiled significant differences in metabolic enzymes and binding proteins among different muscles. Based on correlation analysis, 20 key proteins and metabolites closely related to meat quality were screened. Integration of proteomic and metabolomic data highlighted oxidative phosphorylation, TCA cycle, and glycolysis as key distinguishing pathways among different muscles. These results offer effective information for producing high-quality camel meat.

High-throughput untargeted metabolomics reveals metabolites and metabolic pathways that differentiate two divergent pig breeds

Metabolomics can describe the molecular phenome and may contribute to dissecting the biological processes linked to economically relevant traits in livestock species. Comparative analyses of metabolomic profiles in purebred pigs can provide insights into the basic biological mechanisms that may explain differences in production performances. Following this concept, this study was designed to compare, on a large scale, the plasma metabolomic profiles of two Italian heavy pig breeds (Italian Duroc and Italian Large White) to indirectly evaluate the impact of their different genetic backgrounds on the breed metabolomes. We utilised a high-throughput untargeted metabolomics approach in a total of 962 pigs that allowed us to detect and relatively quantify 722 metabolites from various biological classes. The molecular data were analysed using a bioinformatics pipeline specifically designed for identifying differentially abundant metabolites between the two breeds in a robust and statistically significant manner, including the Boruta algorithm, which is a Random Forest wrapper, and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) for feature selection. After thoroughly evaluating the impact of random components on missing value imputation, 100 discriminant metabolites were selected by Boruta and 17 discriminant metabolites (all included within the previous list) were identified with sPLS-DA. About half of the 100 discriminant metabolites had a higher concentration in one or the other breed (48 in Italian Large White pigs, with a prevalence of amino acids and peptides; 52 in Italian Duroc pigs, with a prevalence of lipids). These metabolites were from seven distinct super pathways and had an absolute mean value of percentage difference between the two breeds (|Δ|%) of 39.2 ± 32.4. Six of these metabolites had |Δ|%> 100. A general correlation network analysis based on Boruta-identified metabolites consisted of 31 singletons and 69 metabolites connected by 141 edges, with two large clusters (> 15 nodes), three medium clusters (3-6 nodes) and eight additional pairs, with most metabolites belonging to the same super pathway. The major cluster representing the lipids super-pathway included 24 metabolites, primarily sphingomyelins. Overall, this study identified metabolomic differences between Italian Duroc and Italian Large White pigs explained by the specific genetic background of the two breeds. These biomarkers can explain the biological differences between these two breeds and can have potential practical applications in pig breeding and husbandry.

Fibin is a crucial mitochondrial regulatory gene in skeletal muscle development

Fin bud initiation factor homolog (Fibin) is a secreted protein that is relatively conserved among species. It is closely related to fin bud development and can regulate a variety of cellular processes. In our previous high-throughput chromosome conformation capture (Hi-C) study of pig embryonic muscle development, it was found that Fibin has high expression and activity during the development of pig primary muscle fibers. Therefore, we speculated Fibin participated in myogenesis severely. Specific deletion of Fibin in mouse skeletal muscle resulted in abnormal primary muscle fiber development during the embryonic period and a substantial decrease in skeletal muscle mass in adulthood. In vitro, knocking out Fibin in C2C12 cells promoted cell proliferation; however, after myogenic induction, cells lacking Fibin had almost no ability to differentiate into myotubes. During myogenic differentiation, loss of Fibin disrupts the normal function of mitochondria and impairs oxidative phosphorylation, resulting in decrease of NADH and FADH in the electron transport chain. Transmission electron microscopy also showed that mitochondrial morphology of Fibin-deficient C2C12 was impaired. In conclusion, our research has unveiled a novel mechanism of myogenesis regulation in mitochondrial function and potential target Fibin, and improved understanding of a broad range of mitochondrial muscle diseases.

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.

A novel protein encoded by circKANSL1L regulates skeletal myogenesis via the Akt-FoxO3 signaling axis

Skeletal muscle is one the largest organs of the body and is involved in animal production and human health. Circular RNAs (circRNAs) have been implicated in skeletal myogenesis through largely unknown mechanisms. Herein, we report the phenotypic and metabolomic analysis of porcine longissimus dorsi muscles in Lantang and Landrace piglets, revealing a high-content of slow-oxidative fibers responsible for high-quality meat product in Lantang piglets. Using single-cell transcriptomics, we identified four myogenesis-related cell types, and the Akt-FoxO3 signaling axis was the most significantly enriched pathway in each subpopulation in the different pig breeds, as well as in fast-twitch glycolytic fibers. Using the multi-dimensional bioinformatic tools of circRNAome-seq and Ribo-seq, we identified a novel circRNA, circKANSL1L, with a protein-coding ability in porcine muscles, whose expression level correlated with myoblast proliferation and differentiation in vitro, as well as the transformation between distinct mature myofibers in vivo. The protein product of circKANSL1L could interact with Akt to decrease the phosphorylation level of FoxO3, which subsequently promoted FoxO3 transcriptional activity to regulate skeletal myogenesis. Our results established the existence of a protein encoded by circKANSL1L and demonstrated its potential functions in myogenesis.

Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs

It is well known that N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules, but many circRNA molecules have now been found to have a wide range of m6A modification sites as well. However, there are few relevant studies and information on the expression profile and functional regulatory properties of m6A-modified circRNAs (m6A-circRNAs) in longissimus dorsi. In this study, a total of 12 putative m6A-circRNAs were identified and characterized in the longissimus dorsi of Queshan Black and Large White pigs-8 of them were significantly more expressed in the longissimus dorsi of Queshan Black than in Large White pigs, while the other 4 were the opposite. These 12 putative m6A-circRNAs were also found to act as miRNA sponge molecules to regulate fat deposition by constructing the ceRNA regulatory network. Enrichment analysis also revealed that the 12 m6A-circRNAs parent genes and their adsorbed miRNA target genes were widely involved in fat deposition and cell proliferation and differentiation-related pathways, such as the HIF-1 signaling pathway, the pentose phosphate pathway, the MAPK signaling pathway, the glycosphingolipid biosynthesis-lacto and neolacto series, and the TNF signaling pathway, suggesting that the analyzed m6A-circRNAs may be largely involved in the formation of pork quality. These results provide new information to study the regulatory properties of m6A-circRNAs in the formation of pork quality.