Proteogenomics Provides Evidence of Enhanced Ribosome Assembly, and Protein Translation in Muscle of High vs Low Feed Efficiency Pedigree Broiler Males

Global gene (cDNA microarray, RNAseq) and protein expression (shotgun proteomics) analyses have been conducted on breast muscle samples obtained from pedigree broiler males exhibiting high and low feed efficiency (FE) phenotypes. In this analysis, using the original entire datasets (not using cutoffs for P value or fold difference in expression) we first counted the number of genes or proteins that were expressed numerically higher or lower in the high FE phenotype for key terms; e.g. ribosomal, mitochondrial ribosomal, tRNA, RNA binding motif, RNA polymerase, small nuclear ribonucleoprotein, and protein tyrosine phosphatase. We then conducted Chi square analysis on the numbers of higher or lower expressed genes and proteins in these various categories from the global expression datasets. Chi square analysis on individual or combined data revealed a significant number of molecules that were higher in all of these categories in the high FE compared to the low FE phenotype with P values ranging from P < 0.05 to P< 1 x 10^-6.. In contrast the numbers of proteins or genes associated with protein tyrosine phosphatase activity were lower in the high FE phenotype (Chi Sq P value < 1 x 10^-6). These results suggest that processes of ribosomal construction, activity, and protein translation would be enhanced in high FE breast muscle and that phosphorylation of tyrosine moeities of proteins could be prolonged in the high compared to low FE phenotype. We feel these results are important in generating hypotheses to be tested regarding fundamental mechanisms contribution to the cellular efficiency in muscle tissue. Funding provided by USDA-NIFA (#2013-01953), Arkansas Biosciences Institute (Little Rock, AR) and the Agricultural Experiment Station (Univ. of Arkansas).