Nuclear Respiratory Factor 2 Induces the Expression of Many but Not All Human Proteins Acting in Mitochondrial DNA Transcription and Replication

• Published in: The Journal of biological chemistry 2010-02, Vol.285 (6), p.3939-3948
• Main Authors: Bruni, Francesco, Polosa, Paola Loguercio, Gadaleta, Maria Nicola, Cantatore, Palmiro, Roberti, Marina
• Format: Article
• Language: English
• Subjects: Base Sequence; Basic-Leucine Zipper Transcription Factors - genetics; Binding Sites - genetics; Blotting, Western; Chromatin Immunoprecipitation; DNA Helicases - genetics; DNA Polymerase beta - genetics; DNA Replication; DNA, Mitochondrial - genetics; DNA-Binding Proteins - genetics; DNA-Directed RNA Polymerases - genetics; GA-Binding Protein Transcription Factor - genetics; GA-Binding Protein Transcription Factor - metabolism; Gene Expression Regulation; HeLa Cells; Humans; Mitochondrial Proteins; Molecular Sequence Data; Oligonucleotide Probes - genetics; Oligonucleotide Probes - metabolism; Promoter Regions, Genetic - genetics; Protein Binding; Proteins - genetics; Reverse Transcriptase Polymerase Chain Reaction; RNA Interference; Sequence Homology, Nucleic Acid; Transcription, Chromatin, and Epigenetics; Transcription, Genetic
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M109.044305

In mammals, NRF-2 (nuclear respiratory factor 2), also named GA-binding protein, is an Ets family transcription factor that controls many genes involved in cell cycle progression and protein synthesis as well as in mitochondrial biogenesis. In this paper, we analyzed the role of NRF-2 in the regulation of human genes involved in mitochondrial DNA transcription and replication. By a combination of bioinformatic and biochemical approaches, we found that the factor binds in vitro and in vivo to the proximal promoter region of the genes coding for the transcription termination factor mTERF, the RNA polymerase POLRMT, the B subunit of the DNA polymerase-γ, the DNA helicase TWINKLE, and the single-stranded DNA-binding protein mtSSB. The role of NRF-2 in modulating the expression of those genes was further established by RNA interference and overexpression strategies. On the contrary, we found that NRF-2 does not control the genes for the subunit A of DNA polymerase-γ and for the transcription repressor MTERF3; we suggest that these genes are under regulatory mechanisms that do not involve NRF proteins. Since NRFs are known to positively control the expression of transcription-activating proteins, the novelty emerging from our data is that proteins playing antithetical roles in mitochondrial DNA transcription, namely activators and repressors, are under different regulatory pathways. Finally, we developed a more stringent consensus with respect to the general consensus of NRF-2/GA-binding protein when searching for NRF-2 binding sites in the promoter of mitochondrial proteins.