Analysis and Comparison of Proteomics of Placental Proteins from Cows Using Different Proteases

SIMPLE SUMMARY: As an organ of fetal development, the placenta has many biological functions such as anti-oxidation, anti-tumor, anti-apoptosis, immune regulation, and skin care. It was found that the protein content, trace elements, and amino acid types of bovine placenta were similar to those of human placenta—which has been widely studied, developed, and utilized—and at the same time, the waste of resources caused by the random disposal of placenta was avoided. In this study, we explored and compared the proteome of different proteases following their action on cow placenta based on marker-free mass spectrometry and performed a bioinformatics analysis, which provided valuable reference information for the subsequent proteomic analysis of pregnancy-related diseases in cows, the study of the physiological functions of cow placenta, and the development and utilization of its by-products. ABSTRACT: Newly found biochemical characteristics of the placenta can provide new insights for further studies on the possible markers of physiological/pathological pregnancy or the function of the placenta. We compared the proteome of the dairy cow placenta after enzymatic hydrolysis by three different proteases using a label-free mass spectrometry approach. In total, 541, 136, and 86 proteins were identified in the trypsin group (TRY), pepsin group (PEP), and papain group (PAP). By comparing the proteome of the PAP and TRY, PEP and TRY, and PEP and PAP groups, 432, 421, and 136 differentially expressed proteins were identified, respectively. We compared the up-regulated DEPs and down-regulated DEPs of each comparison group. The results show that the proteins identified by papain were mostly derived from the extracellular matrix and collagen, and were enriched in the relaxin signaling pathway and AGE-RAGE signaling pathway in diabetic complications; pepsin digestion was able to identify more muscle-related proteins, which were enriched in the lysosome, platelet activation, cardiac muscle contraction, the bacterial invasion of epithelial cells, and small cell lung cancer; trypsin mainly enzymatically degraded the extracellular matrix, blood particles, and cell-surface proteins that were enriched in arginine and proline metabolism, olfactory transduction proteasome, protein processing in the endoplasmic reticulum, pyruvate metabolism, and arrhythmogenic right ventricular cardiomyopathy (ARVC). In summary, these results provide insights into the discovery of the physiological functions of dairy cow placenta and the selection of proteases in dairy cow placenta proteomics.