Mitochondria are the powerhouses of the cells, producing energy in the form of ATP under aerobic conditions. Although these organelles contain their own genetic material, over the course of evolution they surrendered most of their genetic makeup to the nuclear genome. Out of the thousands of genes necessary for proper mitochondrial function, only 13 are encoded by the mitochondrial genome. Therefore, anytime a cell needs to produce more mitochondria or enzymes required for oxidative processes, an intricate coordination of both nuclear and mitochondrial gene expression is necessary.
Over the last decades, several regulators of mitochondrial and nuclear gene expression have been identified. Some of these regulators are capable of inducing expression of nuclear genes that are targeted for mitochondrial function. For example, the peroxisome proliferator activated receptor gamma coactivator-1α (PGC-1α) and the NAD+ dependent protein deacetylase sirtuin 1 (SIRT1) promote the expression of a suite of nuclear encoded genes, including the mitochondrial transcription factor A (TFAM), which promotes the replication, transcription and maintenance of mitochondrial DNA. Although until now both SIRT1 and PGC-1α have only been found in the nucleus acting on nuclear gene expression, a team led by Katia Aquilano from the University of Rome and IRCCS San Raffaele in Rome postulated that these regulators could also regulate gene expression directly within the mitochondrion.
Initially, Aquilano and colleagues used microscopic staining to localize these two factors in the cell, and for the first time discovered that PGC-1α and SIRT1 colocalized with mitochondrial proteins. To confirm these results, the team further identified these proteins in purified mitochondria from both tissue cultures and mouse tissues. The group also used human platelets, cells with mitochondria that are devoid of nuclear DNA, to definitely show that both these factors were directly associated with the organelles.
Given this newly found localization, the team tackled more mechanistic questions; notably, whether these factors were associated in the mitochondrial nucleoids, submitochondrial regions packed with mitochondrial DNA and regulatory proteins. They purified nucleoids and were able to detect both SIRT1 and PGC-1α in these purified fractions. Knowing that a region of the mitochondrial DNA, the D-loop region, is where mitochondrial DNA replication and transcription originate, the team postulated that both SIRT1 and PGC-1α were associated with this region through interactions with TFAM (which specifically binds to this region). Using antibodies directed against TFAM, SIRT1 or PGC-1α, they confirmed that these factors were associated with this regulatory region of mitochondrial DNA. Further, the team unveiled the presence of large protein complexes containing these factors in purified mitochondrial extracts, suggesting a functional relationship between these regulators.
Overall, these results highlight new roles for two important regulators of mitochondrial function. Their localization within the mitochondrion and their association with TFAM, a major mitochondrial transcription factor, suggest that SIRT1 and PGC-1α have similar functions within the nucleus and the mitochondrion in promoting gene expression. Thus, although the abundance of these ‘master controllers’ has long been considered important for mitochondrial function, we now have to also consider the localization of these proteins and the ever expanding number of regulators that they can interact with.