Quantitative Proteomic Analysis of Tibetan Pig Livers at Different Altitudes.

In this study, the differences in protein profiles between the livers of Shannan Tibetan pigs (SNT), Linzhi Tibetan pigs (LZT) and Jiuzhaigou Tibetan pigs (JZT) were comparatively analyzed by tandem mass spectrometry-labeling quantitative proteomics. A total of 6804 proteins were identified: 6471 were quantified and 1095 were screened as differentially expressed proteins (DEPs). Bioinformatics analysis results show that, compared with JZT livers, up-regulated DEPs in SNT and LZT livers mainly promoted hepatic detoxification through steroid hormone biosynthesis and participated in lipid metabolism to maintain body energy homeostasis, immune response and immune regulation, while down-regulated DEPs were mainly involved in lipid metabolism and immune regulation. Three proteases closely related to hepatic fatty acid oxidation were down-regulated in enzymatic activity, indicating higher levels of lipid oxidation in SNT and LZT livers than in JZT livers. Down-regulation of the expression of ten immunoglobulins suggests that JZT are more susceptible to autoimmune diseases. It is highly likely that these differences in lipid metabolism and immune-related proteins are in response to the ecological environment at different altitudes, and the findings contribute to the understanding of the potential molecular link between Tibetan pig livers and the environment.

Quantitative N-Glycoproteomic Analysis of Cattle-Yak and Yak Longissimus Thoracis.

In this study, the N-glycosylated protein profiles of cattle-yak longissimus thoracis (CYLT) and yak longissimus thoracis (YLT) were comparatively analyzed using quantitative proteomics techniques. A total of 76 differential N-glycosylated proteins (DGPs) were screened from 181 quantified N-glycoproteins, indicating that differences in N-glycosylation levels are key to the differences between CYLT and YLT. In particular, a variety of N-glycoproteins involved in the extracellular matrix were differentially N-glycosylated between CYLT and YLT, mainly including fibrillin-1, fibromodulin, collagen, and laminins. In addition, the N-glycosylation levels of several lysosomal-related proteolytic enzymes (cathepsin D, dipeptidyl peptidase 1, legumain, and aminopeptidases, etc.) were significantly higher in CYLT. These results indicated that the N-glycosylation of CYLT and YLT proteins plays a crucial role in the regulation of extracellular matrix organization (muscle fiber structure) and lysosomal activity (postmortem meat tenderness). The results remind us that posttranslation modifications, especially N-glycosylation, are still icebergs beneath the surface.

Quantitative Proteomic Analysis of Yorkshire Pig Liver Reveals Its Response to High Altitude.

In this study, the protein profiles in the livers of Shannan Yorkshire pigs (SNY), Linzhi Yorkshire pigs (LZY), and Jiuzhaigou Yorkshire pigs (JZY) were comparatively analyzed using quantitative proteomics. A total of 6804 proteins were identified, of which 6471 were quantified and 774 differentially expressed proteins (DEPs) were screened. The higher level of energy metabolism in LZY livers was in response to the critical altitude environment compared to that in JZY, while the high-altitude environment suppressed energy output in SNY livers. Several key antioxidant enzymes were locally regulated in Yorkshire pig liver to balance antioxidant levels in a high-altitude, low-oxygen environment. In addition, ribosomal proteins were differentially expressed in Yorkshire pig livers in response to different altitudinal environments. These findings provide clues to the adaptation of the Yorkshire pig liver to the three altitudinal environments and the molecular links that exist between them.

Research Note: Integrated proteomic analyses of chicken egg yolk granule.

Chicken egg yolk granules (EYG) were the precipitated component of egg yolk after water dilution and centrifugation. Compared with egg yolk, EYG are rich in proteins, phospholipids, and minerals. In this study, an integrated proteomic analysis was carried out to in-depth mapping of the proteome, phosphoproteome, and N-glycoproteome of EYGs. After hydrolysis of the EYG total protein, the hydrolyzed peptides or the enriched phosphopeptides/glycopeptides were identified by liquid chromatography-tandem mass spectrometry. A total of 125 phosphorylation sites from 36 phosphoproteins and 244 N-glycosylation sites from 100 N-glycoproteins were identified in EYG. All 3 vitellogenins (precursors of egg yolk high-density lipoprotein) were heavily phosphorylated and N-glycosylated, of which 37 phosphorylation sites and 32 N-glycosylation sites were identified on vitellogenins-2. A Total of 30 N-glycosylation sites were identified on apolipoprotein-B (precursor of egg yolk low-density lipoprotein), but no phosphorylation site was identified. These phosphorylation and N-glycosylation of EYG proteins provide new insights for understanding the assembly structure and functional characteristics of EYG, thus contributing to its development and utilization.

Quantitative proteomic analysis of cattle-yak and yak longissimus thoracis provides insights into the differential mechanisms of meat quality.

In this study, proteins of cattle-yak longissimus thoracis (CYLT) and yak longissimus thoracis (YLT) were compared using tandem mass tag-labeled quantitative proteomic analysis. A total of 157 proteins were screened as differentially abundant proteins (DAPs) derived from 1551 quantitative proteins. Bioinformatics analysis revealed that the upregulated DAPs in CYLT were mainly involved in energy metabolism, oxidative stress, muscle fiber structure, and extracellular matrix (ECM), while the downregulated DAPs were mainly involved in energy metabolism and ECM function. The upregulated myoglobin, downregulation of NADH dehydrogenase, and upregulation of cytochrome oxidase indicated that CYLT initiates compensatory regulation in response to hypoxic high-altitude environments. Two differentially abundant myosins and five collagens suggested that CYLT and YLT may have distinct differences in the assembly structure of muscle fibers and connective tissue. These differences in energy metabolism and muscle structure will inevitably affect the postmortem physiology of "muscle to meat" and consequently the meat qualities. Therefore, our results will provide important clues to gain insight into the potential causes of meat quality differences between cattle-yak and yak based on high-altitude response.

Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of the longissimus thoracis of yaks.

Yaks (Bos mutus) live in the Qinghai-Tibet plateau. The quality of yak meat is unique due to its genetic and physiological characteristics. Identification of the proteome of yak muscle could help to reveal its meat-quality properties. The common proteome, phosphoproteome, and N-glycoproteome of yak longissimus thoracis (YLT) were analyzed by liquid chromatography-tandem mass spectrometry-based shotgun analysis. A total of 1812 common proteins, 1303 phosphoproteins (3918 phosphorylation sites), and 204 N-glycoproteins (285 N-glycosylation sites) were identified in YLT. The common proteins in YLT were involved mainly in myofibril structure and energy metabolism; phosphoproteins were associated primarily with myofibril organization, regulation of energy metabolism, and signaling; N-glycoproteins were engaged mainly in extracellular-matrix organization, cellular immunity, and organismal homeostasis. We reported, for the first time, the "panorama" of the YLT proteome, specifically the N-glycoproteome of YLT. Our results provide essential information for understanding post mortem physiology (rigor mortis and aging) and the quality of yak meat.