Transcriptional profiling of mRNAs, microRNAs and mitochondrialnuclear crosstalk in porcine muscle fibers, mitochondrial respiratory and metabolic enzyme activities

Abstract

Skeletal muscle is a highly metabolically active tissue and has market value in meat-producing farm animals. The overall aim of this thesis is to deeply investigate the biological functions and pathways associated with muscle fiber types, mitochondrial respiration, glycolytic and oxidative enzyme activities in porcine muscle. Firstly, the transcriptional profile of longissimus biopsies 24h <em>ante mortem</em> was investigated in malignant hyperthermia syndrome (MHS)-negative Duroc and Pietrain (PiNN) pigs significantly distinct in muscle fiber types and mitochondrial respiration. Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) revealed clear differences in muscle metabolic properties between two breeds and identified many biological pathways associated with fiber types and metabolic enzyme activities. To explore the regulatory role of microRNAs (miRNAs) in energy metabolism, the miRNA expression profiles were investigated in the same muscle samples. The miRNA-mRNA regulatory networks related to muscle fiber type, metabolic enzyme activity and ATP production were modelled based on <em>in silico</em> prediction of target mRNAs and correlation of expression and phenotypic measurements of muscles in Duroc and PiNN pigs. These complex networks may contribute to the muscle phenotypic variations by fine-tuning gene expressions. Next, the expression profiles of pathway-focused genes related to oxidative and glycolytic pathways were analyzed in conjunction with phenotypic measurements in four pig breeds with distinct metabolic types including Duroc, PiNN, Pietrain homozygous-positive for MHS (PiPP) and an F2 Duroc-Pietrain crossbred homozygous-negative for MHS (DuPi) using longissimus biopsies. At transcript level, lactate dehydrogenase B showed breed specificity, with significantly lower expression in PiPP pigs. A similar mRNA expression pattern was observed for several subunits of oxidative phosphorylation (OXPHOS) complexes, including complex I, complex II, complex IV and ATP synthase. The expressions of these pathway-focused genes were well correlated to their enzyme activities and muscle fiber composition in a breed-dependent manner. These results stressed the importance of transcriptional regulation of genes involved in metabolic pathways especially OXPHOS system in muscle fibers. Finally, in order to address the role of mitochondria, early <em>post mortem</em> longissimus samples taken from the same four breeds were used to investigate mitochondrial DNA content, haplotypes and gene expressions of OXPHOS subunits. PiPP pigs carried only one haplotype (Haplotype 8) and showed the lowest absolute mtDNA copy number, the lowest abundance of transcripts of many mitochondrial and nuclear encoded OXPHOS subunits among all four breeds. The results were informative for the understanding of haplotype and breed-specific mitochondrial content variation and molecular basis of OXPHOS pathway. The co-expression pattern of OXPHOS genes supported the mitochondrial-nuclear crosstalk and their complexity contributed to muscular metabolism. This part of the study highlighted the importance of mitochondrial-nuclear crosstalk, haplotype and copy number variation underlying muscle phenotype differences. In summary, muscle energy metabolism was investigated in this thesis by the whole genome transcriptional profiling of mRNAs and miRNAs followed by a focus on OXPHOS system at the level of both nuclear and mitochondrial DNA contributing to phenotypic variations in different pig breeds. These findings provided insights into the molecular regulatory patterns involved muscular energy metabolism which may be used as biomarkers to predict meat quality and/or diagnose muscular diseases.