Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling

Genes expressed in mitochondria work in concert with those expressed in the nucleus to mediate oxidative phosphorylation (OXPHOS), a process that is relevant for muscle metabolism and meat quality. Mitochondrial genome activity can be efficiently studied and compared in Duroc and Pietrain pigs, which harbor different mitochondrial haplotypes and distinct muscle fiber types, mitochondrial respiratory activities, and fat content. Pietrain pigs homozygous-positive for malignant hyperthermia susceptibility (PiPP) carried only haplotype 8 and showed the lowest absolute mtDNA copy number accompanied by a decrease transcript abundance of mitochondrial-encoded subunits ND1, ND6, and ATP6 and nuclear-encoded subunits NDUFA11 and NDUFB8. In contrast, we found that haplotype 4 of Duroc pigs had significantly higher mitochondrial DNA (mtDNA) copy numbers and an increase transcript abundance of mitochondrial-encoded subunits ND1, ND6, and ATP6. These results suggest that the variation in mitochondrial and nuclear genetic background among these animals has an effect on mitochondrial content and OXPHOS system subunit expression. We observed the co-expression pattern of mitochondrial and nuclear encoded OXPHOS subunits suggesting that the mitochondrial-nuclear crosstalk functionally involves in muscle metabolism. The findings provide valuable information for understanding muscle biology processes and energy metabolism, and may direct use for breeding strategies to improve meat quality and animal health.

Section: Discussionmentioning

confidence: 96%

Mitochondrial-nuclear crosstalk, haplotype and copy number variation distinct in muscle fiber type, mitochondrial respiratory and metabolic enzyme activities

Trakooljul

Hadlich

et al. 2017

“…Expression levels of U6 served as endogenous controls for miRNA expression and were utilized to normalize the corresponding data. The 2 −ΔΔCt method was used to determine the relative mRNA and miRNA abundance 30 .…”

Section: Methodsmentioning

confidence: 99%

DNA methylation landscape of fat deposits and fatty acid composition in obese and lean pigs

Zhang

Shen

Xia³

et al. 2016

Self Cite

Obese and lean type pig breeds exhibit differences in their fat deposits and fatty acid composition. Here, we compared the effect of genome-wide DNA methylation on fatty acid metabolism between Landrace pigs (LP, leaner) and Rongchang pigs (RP, fatty). We found that LP backfat (LBF) had a higher polyunsaturated fatty acid content but a lower adipocyte volume than RP backfat (RBF). LBF exhibited higher global DNA methylation levels at the genome level than RBF. A total of 483 differentially methylated regions (DMRs) were located in promoter regions, mainly affecting olfactory and sensory activity and lipid metabolism. In LBF, the promoters of genes related to ATPase activity had significantly stronger methylation. This fact may suggest lower energy metabolism levels, which may result in less efficient lipid synthesis in LBF. Furthermore, we identified a DMR in the miR-4335 and miR-378 promoters and validated their methylation status by bisulfite sequencing PCR. The hypermethylation of the promoters of miR-4335 and miR-378 in LBF and the resulting silencing of the target genes may result in LBF's low content in saturated fatty acids and fat deposition capacity. This study provides a solid basis for exploring the epigenetic mechanisms affecting fat deposition and fatty acid composition.Animal fat is a common part of the human diet, especially in developing countries. However, it is widely accepted that the amount and type of consumed dietary fat has a direct impact on human health. For instance, an excess of dietary fat may significantly contribute to the development of type II diabetes, obesity and other diseases [1][2][3][4] . In addition, the dietary fatty acid composition is also highly related to human health. Recent studies have shown that some saturated fatty acids (SFA), but not mono-or polyunsaturated fatty acids (MUFA and PUFA, respectively), can increase plasma cholesterol levels and the risk of cardiovascular diseases 5 . However, some PUFA and MUFA are known to decrease levels of low-density lipoprotein and cholesterol and also mediate important benefits for human health by stimulating the immune system 6-8 . Additionally, the ratios between PUFA and MUFA and between n-6 PUFA and n-3 PUFA have effects on human health and are used to characterize healthy fats 9 . It is also well known that fatty acid composition directly affects the technological properties of meat products by altering the lipid melting point and fat firmness 10 . The fatty acid composition further affects the tenderness, juiciness and flavor of the meat 11 . Therefore, a better understanding of the mechanisms behind adipose tissue accumulation and fatty acid composition in pigs is of great importance for human health but simultaneously may be helpful in improving pork quality and production efficiency.In recent decades, the pork industry has focused on increasing the lean meat percentage by decreasing subcutaneous fat content, but the mechanisms behind fat deposition and fatty acid composition regulation are complex physiological proce...

“…The transcriptome data were analyzed according to method described by Shen et al . 38 with the exception that clean reads with a length of 36 nt were obtained. The following analysis was based on clean reads, which are generated by filtering raw reads.…”

Section: Methodsmentioning

confidence: 99%

Metabolic profiles of cysteine, methionine, glutamate, glutamine, arginine, aspartate, asparagine, alanine and glutathione in Streptococcus thermophilus during pH-controlled batch fermentations

Qiao

Liu

Leng

et al. 2018

Elucidating the amino acid (AA) metabolism patterns of Streptococcus thermophilus has important effects on the precise design of nitrogen sources for high-cell-density culture. Transcriptomics and metabolomics were combined to reveal the cysteine, methionine, glutamate, glutamine, arginine, aspartate, asparagine and alanine metabolic pathways in S. thermophilus MN-ZLW-002, including glutathione. The changes in the synthesis, consumption and concentration of AAs and their metabolites, as well as regulatory genes with time were revealed. The metabolism of L-cysteine, L-glutamate, L-aspartate and L-alanine generated some potential functional metabolites. The metabolism of methionine and glutamate generated potential harmful metabolites. S. thermophilus MN-ZLW-002 can synthesize glutathione. Some potential functional metabolites have similar biological functions, indicating that S. thermophilus can resist environmental stresses through multiple mechanisms. The expression of some key genes in synthesis pathway of AA indicated that cysteine, methionine, asparagine, aspartate, arginine and lysine were insufficient or imbalance between nutrient components. The accumulation of large amounts of AA metabolites might be the primary cause of the overconsumption of AAs and influence the growth of S. thermophilus. The present study revealed the metabolic profiles of abovementioned AAs as well as those of regulatory genes and metabolites. These results were beneficial to the precise design of nitrogen sources and regulation of functional metabolites for the high-cell-density culture of S. thermophilus.