Research Interests

Mitochondrial gene expression, mitochondrial biogenesis and mitochondrial disease

Mitochondria contain a small (16.5 kb) double-stranded circular genome that in mammals encodes 13 polypeptides. Expression of this genome depends on a molecular genetic system that is distinct from the nuclear gene expression machinery. Defects in mitochondrial gene expression, often resulting from the inheritance of genetic mutations, result in mitochondrial dysfunction. Insufficient mitochondrial function is the cause of mitochondrial disease and many other pathologies, including neurodegenerative and cardiovascular diseases, diabetes and cancer. Many FDA-approved drugs to treat some of these conditions likely exert at least some of their therapeutic effects by stimulating mitochondrial biogenesis, and selective modulation of mitochondrial biogenesis is a promising therapeutic strategy to overcome mitochondrial dysfunction. Our reseach aims to understand the mechanisms that control mitochondrial gene expression in mitochondria, and how deficiencies in these processes are related to human disease.

Mechanisms of mitochondrial transcription

Mitochondrial transcription is a carefully regulated process that is crucial to generate the tRNAs, rRNAs and mRNAs necessary for mitochondrial protein production, but is also essential to initiate replication of the mitochondrial genome. How this process is specifically organized and regulated is still a matter of debate, but it involves the RNA polymerase, at least two transcription factors and no more than two or three promoters that generate polycistronic transcripts that are subsequently processed. Understanding the mechanisms by which the cell controls differential initiation at these promoters is key to understand how the transcription process is regulated. We are studying the process of transcription initiation taking advantage of a robust reconstituted in vitro system and a combination of single-particle electron microscopy, small-angle x-ray scattering and biochemical and biophysical measurements.

Transcription termination and MTERF proteins

Another aspect of mitochondrial transcription that we are investigating is the mechanism of transcription termination at a specific site downstream of the rRNA genes. This termination event is dependent on a protein called MTERF1, for Mitochondrial TERmination Factor 1, and it was postulated to be important to determine the ratio of mitochondrial rRNAs to mRNAs, although this is still a subject of debate. We have demonstrated that MTERF1 belongs to a class of modular proteins characterized by an all-alpha-helical fold. We also found that MTERF1 utilizes an extremely unusual DNA binding mechanism that involves active distortion of the DNA molecule and demonstrated that several disease-associated mitochondrial DNA mutations can interfere with this binding mode, severely impairing the termination process. This suggests that their effect on MTERF1 function might be related to the pathogenic mechanism.

Mitochondrial rRNA modifications

We are studying the process of rRNA modification in mitochondria. Although the functional significance of these modifications is unclear, they are essential for mitochondrial function. We have studied the roles in this process of MTERF4, an MTERF family member, and TFB1M, a methyltransferase responsible for adenine dimethylation in a conserved stem-loop near the 3’-end of the 12S rRNA.

DNA synthesis and DNA repair

The nuclear replication process in humans is extremely complex and only partially understood. The accuracy of this process is essential to avoid deleterious mutagenesis. The proteins mainly responsible for this accuracy are DNA polymerases, the enzymes responsible for DNA synthesis. There are at least 15 different DNA polymerases in human cells, and except for a few their functions are largely unknown. Structural analysis of DNA polymerases has made a significant contribution to our understanding of DNA polymerase fidelity and substrate specificity, and this information is precious to understand their biological function. We are particularly interested in DNA polymerases responsible for smaller patches of DNA synthesis that mainly take place during DNA repair. We are studying how these enzymes contribute to genome stability, in particular in response to DNA damage, and how their function can be affected by different environmental exposures.

List of references