Proteomics of breast muscle tissue associated with the phenotypic expression of feed efficiency within a pedigree male broiler line: I. Highlight on mitochondria

The fifth author's name is spelled incorrectly. The correct name is: Antonio Reverter. The correct citation is: Kong B-W, Lassiter K, Piekarski-Welsher A, Dridi S, Reverter A, Hudson NJ, et al. (2016) Proteomics of Breast Muscle Tissue Associated with the Phenotypic Expression of Feed Efficiency within a Pedigree Male Broiler Line: I. Highlight on Mitochondria. PLoS ONE 11(5): e0155679. doi:10.1371/journal.pone.0155679

A hierarchically clustered heat map of the 40 most differentially expressed proteins as identified by PIF.

<p>Each cell contains the normalized expression of the protein at the individual bird level. Red denotes high expression, green denotes low expression. All 8 birds discriminate into their correct treatment group of origin (HFE or LFE) and relatedness within a group is also apparent. Proteins are clustered by patterns of co-expression across the 8 birds. Strong co-expression is observed for functionally related proteins e.g. ARF1 with ARF4 and KRT3 with KRT5 and KRT14 and the muscle structural proteins, namely TPM1, TPM2 and CAPZB. Different fragment of the same protein are highly co-expressed. Note: ‘B’ are birds with a low FE phenotype whereas ‘G’ are birds with a high FE phenotype. <b>Abbreviations:</b> (RTN4), reticulon 4; (NDUFV2), NADH dehydrogenase (ubiquinone) Fe-S protein 7; (PHKG1), phosphorylase kinase gamma 1; (IDE), insulin degrading enzyme; (CACNA15), calcium channel voltage dependent 1 L type, alpha 15; (ARF), ADP ribosylation factor 4 and 1; (SAR1B), SAR1-ADP ribosylation factor, (SPEG), striated muscle preferentially expressed protein; (Gga), golgi associated gamma adaptin; (RYR3) ryanodine receptor 3; (SLC26A4), adenine nucleotide translocase 1; (MYO18A), myosin 18A; (KRT), keratin; (TPM), tropomyosin; (BAT2), large proline rich protein; (CAPZB), F-actin capping protein subunit beta; (DCTN2), dynactin 2; (ACTA1), alpha actin 1; (GSN), gelsolin; (SMYD1), myosin interacting protein; (NEB), lambda protein phosphatase; (OIH) ovoinhibitor; (UBQLN), ubituilin family proteins</p

Top canonical pathways.

<p>The top 6 canonical pathways (based on p value) generated by Ingenuity Pathway Analysis based on differentially expressed proteins in breast muscle obtained from broiler breeder males.</p

SDS-PAGE gel electrophoresis in broiler breast muscle.

<p>Protein bands prior to protein extractions of breast muscle obtained from pedigree broiler breeder males exhibiting low feed efficiency (L) or high feed efficiency (H) (n = 4 per group). From this gel, a total of 25 slices were obtained and subjected to tryptic digestion prior to conducting shotgun proteomics.</p

Upstream regulators predicted to be activated or inhibited in the proteomic dataset.

<p>Upstream regulators predicted to be activated or inhibited in the proteomic dataset.</p

The protein abundance for the difference (Minus [M] for high FE minus low FE) and protein abundance alone (A) for all proteins.

<p>The MA plot is consistent with a reduction in slow fiber subunits (TPM2, ACTC) in the high FE (HFE) and an increase in mitochondrial regulators of muscle energy supply in the form of ATP (SLC25A4) and creatine phosphate (VDAC2). GAPDH is the most abundant protein we identified. Further, the mitoproteome (highlighted in red, Fig 2A) is skewed towards the HFE consistent with a higher mitochondrial content. Highly differentially expressed proteins were identified by a metric called Phenotypic Impact Factor (PIF), with the extreme 10% highlighted in blue (Fig 2B). Abbreviations: (RTN4), reticulon 4; (PHKG1), phosphorylase kinase gamma 1; (SLC26A4), adenine nucleotide translocase 1; (ACTC), alpha actin cardiac; (Gga), golgi associated gamma adaptin; (GAPDH) glyceraldyhde 3-phosphate dehydrogenase; (TPM2), tropomyosin 2.</p