Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.
Department of Statistical Sciences "Paolo Fortunati", University of Bologna, Bologna, Italy.
PLoS One. 2018 Sep 12;13(9):e0199649. doi: 10.1371/journal.pone.0199649. eCollection 2018.
The liver is a complex organ governing several physiological processes that define biological mechanisms affecting growth, feed efficiency and performance traits in all livestock species, including pig. Proteomics may contribute to a better understanding of the relationship between liver functions and complex production traits in pigs and to characterize this species as biomedical model. This study applied, for the first time, a label-free liquid chromatography-mass spectrometry (LC-MS) proteomic approach to compare the liver proteome profiles of two important heavy pig breeds, Italian Duroc and Italian Large White. Liver specimens were collected (after slaughtering) from performance tested pigs of these two breeds, raised in standard conditions. The label-free LC-MS method captured a total of 501 proteins of which 200 were subsequently considered in the between breeds comparison. A statistical pipeline based on the sparse Partial Least Squares Discriminant Analysis (sPLS-DA), coupled with stability and significance tests, was applied for the identification of up or down regulated proteins between breeds. This analysis revealed a total of 25 proteins clearly separating Italian Duroc and Italian Large White pigs. Among the top proteins differentiating the two breeds, 3-ketoacyl-CoA thiolase, mitochondrial (ACAA2) and histone H2B type 2-F (HIST2H2BF) were up-regulated in Italian Duroc pigs and carboxylesterase 3 (CES3) and ketohexokinase (KHK) were up-regulated in Italian Large White pigs. Fatty acid synthase (FASN), involved in fatty acid metabolism and encoded by a gene located in a QTL region for fatty acid composition, was up-regulated in Italian Large White pigs. The in silico protein interaction analysis showed that 16 of these proteins were connected in one big module. Bioinformatic functional analysis indicated that differentially expressed proteins were involved in several biological processes related to the metabolism of lipids, amino-acids, carbohydrates, cofactors and antibiotics/drugs, suggesting that these functions might distinguish Italian Duroc and Italian Large White pigs. This pilot comparative proteomic analysis of the porcine liver highlighted several biological factors that could determine the peculiar production potentials of these two heavy pig breeds, derived by their different genetic backgrounds.
肝脏是一个复杂的器官，它控制着几种生理过程，这些过程定义了影响所有家畜物种（包括猪）生长、饲料效率和性能特征的生物学机制。蛋白质组学可能有助于更好地理解肝脏功能与猪复杂生产特征之间的关系，并将这种物种作为生物医学模型进行特征描述。本研究首次应用无标记液相色谱-质谱（LC-MS）蛋白质组学方法比较了两个重要的重型猪品种——意大利杜洛克猪和意大利大白猪的肝脏蛋白质组图谱。从这两个品种的经过性能测试的猪只中采集了（屠宰后）肝脏标本，这些猪只在标准条件下饲养。无标记 LC-MS 方法共捕获了 501 种蛋白质，其中 200 种随后被用于品种间比较。基于稀疏偏最小二乘判别分析（sPLS-DA）的统计分析流程，结合稳定性和显著性检验，用于鉴定品种间上调或下调的蛋白质。该分析共鉴定出 25 种蛋白质可将意大利杜洛克猪和意大利大白猪清楚地区分开来。在区分这两个品种的顶级蛋白质中，3-酮酰基辅酶 A 硫解酶，线粒体（ACAA2）和组蛋白 H2B 型 2-F（HIST2H2BF）在意大利杜洛克猪中上调，而羧酸酯酶 3（CES3）和酮己糖激酶（KHK）在意大利大白猪中上调。脂肪酸合酶（FASN）参与脂肪酸代谢，由位于脂肪酸组成 QTL 区域的基因编码，在意大利大白猪中上调。蛋白质互作分析表明，这 16 种蛋白质连接成一个大模块。生物信息学功能分析表明，差异表达蛋白参与了与脂质、氨基酸、碳水化合物、辅因子和抗生素/药物代谢相关的几个生物学过程，表明这些功能可能区分意大利杜洛克猪和意大利大白猪。本研究对猪肝脏进行的初步比较蛋白质组学分析突出了几个生物学因素，这些因素可能决定了这两个重型猪品种的特殊生产潜力，这是由它们不同的遗传背景决定的。
