Artificial selection at the extremes of a trait concentrates contrasting allelic variation from one generation to the next and can produce informative genetic models. In particular, selection on running capacity has created rat phenotypes of intrinsically low capacity runners (LCR) and high capacity runners (HCR). Previous studies demonstrate that HCR exhibit enhanced cardiac and skeletal muscle function and are relatively protected from disease, whereas, LCR are dyslipidaemic, insulin resistant, hypertensive and relatively susceptible to cardiac ischaemia.

Molecular differences that regress with the divergence in running capacity may be mechanistically responsible for the differences in correlated traits and disease risk. We performed proteomic analysis on the hearts of HCR and LCR rats (n = 6, in each group) from generation 23. Homogenates of left ventricle were labelled with cyanine minimal fluorescence dyes Cy2, Cy3 or Cy5. HCR and LCR samples and a pooled internal standard were combined equivalently and resolved using large-format 2-dimensional electrophoresis (i.e. Difference in-gel electrophoresis; DIGE). Gel spots were robotically excised from preparative gels and proteins identified using database searches of their tryptic peptide mass fingerprint and fragment ion spectra collected by matrix-assisted laser desorption ionisation tandem time of flight (MALDI-TOF/TOF) mass spectrometry.

Consistent with earlier reports using this model, the intrinsic running capacity of HCR was 4-fold greater than LCR. DIGE resolved 957 gel spots and protein expression profiling detected 68 statistically significant (P<0.05; false discovery rate <10 %, calculated using q-values) differences between HCR and LCR hearts. Proteins were unambiguously identified in 369 gel spots, including 54 of the spots differentially expressed between HCR and LCR. The proteomic analysis identified robust differences in the expression of proteins involved in mitochondrial metabolism and oxidative stress response. This agrees closely with previous microarray data, but the majority of gene products were resolved as multiple isoelectric species. Thus, some of the differences in spot expression represent changes in post-translational modification not evident in microarray investigations. The 54 gel spots differentially expressed between HCR and LCR represent 37 gene products, 20 of which are associated with metabolism. In particular, there was robust modulation of isoelectric species of each enzyme of the beta-oxidation pathway.

Our data suggest that artificial selection on low running capacity altered the metabolic profile of the heart, diminishing its utilisation of fatty acids. The fact that some enzymes of beta-oxidation were modified at the post-translational level suggests novel mechanisms may exist that regulate mitochondrial fatty acid metabolism.