Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines

A comparative analysis of label-free liquid chromatography-mass spectrometry liver proteomic profiles highlights metabolic differences between pig breeds

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.

Gender influence on the salivary protein profile of finishing pigs

A study on gender differences in the normal range of biomarkers in porcine saliva samples has the scope for further attention. In the present study, the salivary protein profiles of age-matched healthy male and female finishing pigs were compared. The levels of salivary adenosine deaminase (ADA) activity, haptoglobin (Hp) and C-reactive protein (CRP) have been quantified in 32 male and 32 female pigs to ensure the presence of gender effect on the median levels of salivary biomarkers. Moreover, the total salivary protein content was quantified and compared. The overall salivary protein distribution was compared with SDS-PAGE in 14 male and 14 female pigs and the possible gender influence in the salivary protein profile was analysed by 2DE in 6 male and 6 female pigs. Statistically significant differences were observed in the median values of Hp, CRP, and ADA between male and female pigs (p<0.005). Although the total salivary protein content was not different between the sexes, the salivary protein distribution and profile showed specific gender differences in three proteins of the lipocalin family: the odorant-binding protein, salivary lipocalin and lipocalin 1. These proteins have been related to animal immune status and should be further explored as possible porcine salivary biomarkers.

SIGNIFICANCE

The biological relevance of the reported research is based on the possible gender influence on the discovery of salivary biomarkers in porcine production. As differences have been reported in the salivary protein distribution in male pigs in comparison to that of female pigs, the normal-range values, according to gender, of the newly discovered biomarkers should be explored and defined prior to its application in the porcine production system. A hormonal sexual influence is highly hypothesized.

Gender proteomics I. Which proteins in non-sexual organs

Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved.

SIGNIFICANCE

As our knowledge, and the methods to build it, get refined, gender differences need to receive more and more attention, as they influence the outcome of all aspects in lifestyle, including diet, exercise and environmental factors. In turn this background modulates a differential susceptibility to some disease, or a different pathogenetic mechanism, depending on gender, and a different response to pharmacological therapy. Preparing this review we meant to raise awareness about the gender issue. We anticipate that more and more often, in the future, separate evaluations will be carried out on male and female subjects as an alternative - and an upgrade - to the current approach of reference and test groups being 'matched for age and sex'.

iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs

Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated. Functional annotation suggested that 28 DEPs were related to muscle growth and 15 to lipid deposition. Protein interaction network predictions indicated that differences in muscle growth and muscle fibre between TP-DSP and YY-LL groups were regulated by ALDOC, ENO3, PGK1, PGK2, TNNT1, TNNT3, TPM1, TPM2, TPM3, MYL3, MYH4, and TNNC2, whereas differences in lipid deposition ability were regulated by LPL, APOA1, APOC3, ACADM, FABP3, ACADVL, ACAA2, ACAT1, HADH, and PECI. Twelve DEPs were analysed using parallel reaction monitoring to confirm the reliability of the iTRAQ analysis. Our findings provide new insights into key proteins involved in muscle growth and lipid deposition in the pig.

Comparative carcass and tissue nutrient composition of transgenic Yorkshire pigs expressing phytase in the saliva and conventional Yorkshire pigs

A transgenic line of Yorkshire (YK) pigs named the Cassie (CA) line was produced with a low copy number phytase transgene inserted in the genome. The transgenic line efficiently digests P, Ca, and other major minerals of plant dietary origin. The objectives of this study were to 1) compare carcass and tissue nutrient composition and meat quality traits for third generation hemizygous CA line market BW finisher pigs (n = 24) with age-matched conventional YK finisher pigs (n = 24) and 2) examine effects of outbreeding with high-index conventional YK boars on modifying carcass leanness from the third to sixth generations in CA line finisher boars (n = 73) and gilts (n = 103). Cassie boars (n = 12) and CA gilts (n = 12) were fed diets without supplemental P and comparable numbers of age-matched YK boars and gilts fed diets containing supplement P were raised throughout the finisher phase. The pigs were slaughtered and then fabricated into commercial pork primals before meat composition and quality evaluation. Proximate and major micronutrient composition was determined on tissues including fat, kidney, lean, liver, and skin. The main difference observed was greater (P = 0.033) crude fat content in CA boar carcasses and increased (P < 0.04) leaf lard in both CA boars and gilts but no differences were observed (P = 0.895 and P = 0.223, respectively) in carcass backfat thickness as compared with YK pigs. There were no substantive differences in tissue composition, except for CA boar kidneys. Numerous changes in the mineral, fatty acid, and indispensable AA composition for CA boar kidneys were not apparent in CA gilts. These changes may point to adaptive physiological changes in the boar kidney necessary for homeostatic regulation of mineral retention related to phytase action rather than to insertion of the transgene. However, from a meat composition perspective, transgenic expression of phytase in the CA line of YK pigs had little overall effect on meat composition. Outbreeding of high-index CA gilts with high-index commercial YK boars linearly reduced (P = 0.002) back fat thickness with a corresponding linear increase (P = 0.001) in lean yield in finisher CA gilts, although no change in these parameters was observed in CA finisher boars. The increase in lean yield in CA gilts by selective breeding without affecting the level of salivary phytase activity documents the value of conventional genetic selection in conjunction with genetic modification.

Proteomic analysis of liver development of lean Pekin duck (Anas platyrhynchos domestica)

The liver plays vital roles in digestion, metabolism and immune defense. To elucidate the molecular mechanism of nutrient metabolism and antioxidation of lean Pekin duck liver from hatching to slaughter, the proteome changes were investigated using 2-DE, MS, quantitative real-time PCR and bioinformatics. A total of 59 differentially expressed proteins were identified. Proteins involved in transportation were highly up-regulated in newborn ducks whereas 37 proteins associated with metabolism, defense and antioxidation were up-regulated in adult ducks. The over-expression of proteins at the last developmental stage presumably occurs to fulfill the needs of multiple functions of the liver. However, the over-expressed proteins related to transportation during the first developmental stage are involved in maintaining the high basal metabolism of newborn ducks. The functional enrichment analysis also confirmed these results. Furthermore, the protein interaction network predicted 28 proteins acting as key nodes for liver development. The validated expression between proteins and genes provides us target genes for future genetic analyses to improve the health and performance of these ducks. These significant advanced proteome data expand our knowledge on the physiology of the duck liver, thereby providing a potentially valuable foundation for molecular breeding to enhance feed efficiency and immunity and for optimizing the feeding strategy.

Precision genetics for complex objectives in animal agriculture

Indirect modification of animal genomes by interspecific hybridization, cross-breeding, and selection has produced an enormous spectrum of phenotypic diversity over more than 10,000 yr of animal domestication. Using these established technologies, the farming community has successfully increased the yield and efficiency of production in most agricultural species while utilizing land resources that are often unsuitable for other agricultural purposes. Moving forward, animal well-being and agricultural sustainability are moral and economic priorities of consumers and producers alike. Therefore, these considerations will be included in any strategy designed to meet the challenges produced by global climate change and an expanding world population. Improvements in the efficiency and precision of genetic technologies will enable a timely response to meet the multifaceted food requirements of a rapidly increasing world population.