The mitochondrial proteome: a dynamic functional program in tissues and disease states

Abstract

The nuclear DNA transcriptional programming of the mitochondria proteome varies dramatically between tissues depending on its functional requirements. This programming generally regulates all of the proteins associated with a metabolic or biosynthetic pathway associated with a given function, essentially regulating the maximum rate of the pathway while keeping the enzymes at the same molar ratio. This may permit the same regulatory mechanisms to function at low- and high-flux capacity situations. This alteration in total protein content results in rather dramatic changes in the mitochondria proteome between tissues. A tissues mitochondria proteome also changes with disease state, in Type 1 diabetes the liver mitochondrial proteome shifts to support ATP production, urea synthesis, and fatty acid oxidation. Acute flux regulation is modulated by numerous posttranslational events that also are highly variable between tissues. The most studied posttranslational modification is protein phosphorylation, which is found all of the complexes of oxidative phosphorylation and most of the major metabolic pathways. The functional significance of these modifications is currently a major area of research along with the kinase and phosphatase regulatory network. This near ubiquitous presence of protein phosphorylations, and other posttranslational events, in the matrix suggest that not all posttranslational events have functional significance. Screening methods are being introduced to detect the active or dynamic posttranslational sites to focus attention on sites that might provide insight into regulatory mechanisms.

Figure 1

2D-DIGE of mouse heart and liver mitochondria using approaches described by Johnson et al (Johnson et al. 2008). Mitochondria were isolated from mouse liver and heart and subjected to identical protein extraction conditions with the exception of the liver mitochondrial protein being stained green while the heart protein was stained red.

Figure 2

2D-DIGE of whole rat liver tissue extract from control and Type 1 Diabetic rats from Johnson et al (Johnson et al. 2008). The inserts are simply zoomed regions indicated by the arrows that represent regions where isoelectric shifts occurred. Experimental details along with protein identification are found in the original literature source.

Figure 3

Relative changes in oxidative phosphorylation Complexes content between tissues and in the diabetic liver. Porcine liver and heart data as reported by Johnson et al (Johnson et al. 2007b). Diabetes data is from matched controls of rat liver under diabetic and control conditions (Johnson et al. 2008). Data were derived from the means of experimental data taking the mean difference of all of the subunits detected within a given complex. Complex 3 was not detected in the diabetes study that was on whole tissue decreasing the sensitivity to mitochondrial proteins.

Figure 4

Protein content (upper panels) and autoradiograph (lower panels) of isolated heart and liver mitochondria. Mitochondria were exposed to 20 minutes of ³²P labeling and then extracted identically. Protein identification and method details found in Aponte et al (Aponte et al. 2009b). Some key identifications: 12: PDH, 25:SCS, 9: β subunit Complex V, 1: aconitase

Figure 5

The ³²P labeling of Complex V purified after ³²P labeling in the intact mitochondria. Energized porcine heart mitochondria were incubated for 20 minutes with ³²P. Mitochondrial proteins were extracted and Complex V purified using immuno-capture procedures. The insert is a zoom of the beta subunit autoradiogram of the beta subunit demonstrating the lack of correlation with the majority of the beta subunit protein spots. Experimental details in Aponte et al (Aponte et al. 2009b)