A Human Mitochondrial Transcription Factor Is Related to RNA Adenine Methyltransferases and Binds S-Adenosylmethionine

REFERENCES

• Abad-Zapatero, C., P. Zhong, D. E. Bussiere, K. Stewart, and S. W. Muchmore. 1999. rRNA methyltransferases (ErmC" and ErmAM) and antibiotic resistance, p. 199–205. In X. Cheng and R. M. Blumenthal (ed.), S-Adenosylmethionine-dependent methyltransferases: structure and function. World Scientific Publishing, River Edge, N.J.
   Google Scholar
• Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.
   PubMed Web of Science ®Google Scholar
• Antoshechkin, I., and D. F. Bogenhagen. 1995. Distinct roles for two purified factors in transcription of Xenopus mitochondrial DNA. Mol. Cell. Biol. 15: 7032–7042.
   PubMed Web of Science ®Google Scholar
• Bogenhagen, D. F. 1996. Interaction of mtTFB and mtRNA polymerase at core promoters for transcription of Xenopus laevis mtDNA. J. Biol. Chem. 271: 12036–12041.
   PubMedGoogle Scholar
• Bussiere, D. E., S. W. Muchmore, C. G. Dealwis, G. Schluckebier, V. L. Nienaber, R. P. Edalji, K. A. Walter, U. S. Ladror, T. F. Holzman, and C. Abad-Zapatero. 1998. Crystal structure of ErmC", an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry 37: 7103–7112.
   PubMedGoogle Scholar
• Carrodeguas, J. A., and D. F. Bogenhagen. 2000. Protein sequences conserved in prokaryotic aminoacyl-tRNA synthetases are important for the activity of the processivity factor of human mitochondrial DNA polymerase. Nucleic Acids Res. 28: 1237–1244.
   PubMedGoogle Scholar
• Carrodeguas, J. A., S. Yun, G. S. Shadel, D. A. Clayton, and D. F. Bogenhagen. 1996. Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Expr. 6: 219–230.
   PubMedGoogle Scholar
• Cliften, P. F., J. Y. Park, B. P. Davis, S. H. Jang, and J. A. Jaehning. 1997. Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase. Genes Dev. 11: 2897–2909.
   PubMedGoogle Scholar
• Cliften, P. F., S. H. Jang, and J. A. Jaehning. 2000. Identifying a core RNA polymerase surface critical for interactions with a sigma-like specificity factor. Mol. Cell. Biol. 20: 7013–7023.
   PubMedGoogle Scholar
• Dairaghi, D. J., G. S. Shadel, and D. A. Clayton. 1995. Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator. J. Mol. Biol. 249: 11–28.
   PubMedGoogle Scholar
• Davenport, L., R. H. Taylor, and D. T. Dubin. 1976. Comparison of human and hamster mitochondrial transfer RNA. Physical properties and methylation status. Biochim. Biophys. Acta 447: 285–293.
   PubMed Web of Science ®Google Scholar
• Dubin, D. T. 1974. Methylated nucleotide content of mitochondrial ribosomal RNA from hamster cells. J. Mol. Biol. 84: 257–273.
   PubMed Web of Science ®Google Scholar
• Fan, L., P. C. Sanschagrin, L. S. Kaguni, and L. A. Kuhn. 1999. The accessory subunit of mtDNA polymerase shares structural homology with aminoacyl-tRNA synthetases: implications for a dual role as a primer recognition factor and processivity clamp. Proc. Natl. Acad. Sci. USA 96: 9527–9532.
   PubMed Web of Science ®Google Scholar
• Fisher, R. P., and D. A. Clayton. 1988. Purification and characterization of human mitochondrial transcription factor 1. Mol. Cell. Biol. 8: 3496–3509.
   Google Scholar
• Fisher, R. P., J. N. Topper, and D. A. Clayton. 1987. Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements. Cell 50: 247–258.
   PubMed Web of Science ®Google Scholar
• Guan, M. X., N. Fischel-Ghodsian, and G. Attardi. 1996. Biochemical evidence for nuclear gene involvement in phenotype of non-syndromic deafness associated with mitochondrial 12S rRNA mutation. Hum. Mol. Genet. 5: 963–971.
   PubMed Web of Science ®Google Scholar
• Helm, M., H. Brule, F. Degoul, C. Cepanec, J. P. Leroux, R. Giege, and C. Florentz. 1998. The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res. 26: 1636–1643.
   PubMed Web of Science ®Google Scholar
• Helser, T. L., J. E. Davies, and J. E. Dahlberg. 1972. Mechanism of kasugamycin resistance in Escherichia coli. Nat. New Biol. 235: 6–9.
   PubMedGoogle Scholar
• Holt, I. J., A. E. Harding, and J. A. Morgan-Hughes. 1988. Deletions of muscle mitochondrial DNA in patients with mitochondrial myopathies. Nature 331: 717–719.
   PubMed Web of Science ®Google Scholar
• Jang, S. H., and J. A. Jaehning. 1991. The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J. Biol. Chem. 266: 22671–22677.
   PubMedGoogle Scholar
• Lai, C. H., C. Y. Chou, L. Y. Chang, C. S. Liu, and W. Lin. 2000. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res. 10: 703–713.
   PubMed Web of Science ®Google Scholar
• Lisowsky, T., and G. Michaelis. 1988. A nuclear gene essential for mitochondrial replication suppresses a defect of mitochondrial transcription in Saccharomyces cerevisiae. Mol. Gen. Genet. 219: 125–128.
   Google Scholar
• Mangus, D. A., S. H. Jang, and J. A. Jaehning. 1994. Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J. Biol. Chem. 269: 26568–26574.
   PubMedGoogle Scholar
• Masters, B. S., L. L. Stohl, and D. A. Clayton. 1987. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51: 89–99.
   PubMed Web of Science ®Google Scholar
• Micol, V., P. Fernandez-Silva, and G. Attardi. 1996. Isolation and assay of mitochondrial transcription termination factor from human cells. Methods Enzymol. 264: 158–173.
   PubMedGoogle Scholar
• Nam, S. C., and C. Kang. 2001. Expression of cloned cDNA for the human mitochondrial RNA polymerase in Escherichia coli and purification. Protein Expr. Purif. 21: 485–491.
   PubMedGoogle Scholar
• Parisi, M. A., and D. A. Clayton. 1991. Similarity of human mitochondrial transcription factor 1 to high mobility group proteins. Science 252: 965–969.
   PubMed Web of Science ®Google Scholar
• Prezant, T. R., J. V. Agapian, M. C. Bohlman, X. Bu, S. Oztas, W. Q. Qiu, K. S. Arnos, G. A. Cortopassi, L. Jaber, J. I. Rotter, et al. 1993. Mitochondrial ribosomal RNA mutation associated with both antibiotic-induced and non-syndromic deafness. Nat. Genet. 4: 289–294.
   PubMed Web of Science ®Google Scholar
• Prieto-Martin, A., J. Montoya, and F. Martinez-Azorin. 2001. A study on the human mitochondrial RNA polymerase activity points to existence of a transcription factor B-like protein. FEBS Lett. 503: 51–55.
   PubMedGoogle Scholar
• Prince, D. L., R. M. Kotin, and D. T. Dubin. 1986. Evidence that the methylation inhibitor cycloleucine causes accumulation of a discrete ribosomal RNA precursor in hamster mitochondria. Mol. Biol. Rep. 11: 51–55.
   PubMedGoogle Scholar
• Riemen, G., and G. Michaelis. 1993. A point mutation in the core subunit gene of yeast mitochondrial RNA polymerase is suppressed by a high level of specificity factor MTF1. Mol. Gen. Genet. 237: 49–57.
   PubMedGoogle Scholar
• Rodeheffer, M. S., B. E. Boone, A. C. Bryan, and G. S. Shadel. 2001. Nam1p, a protein involved in RNA processing and translation, is coupled to transcription through an interaction with yeast mitochondrial RNA polymerase. J. Biol. Chem. 276: 8616–8622.
   PubMed Web of Science ®Google Scholar
• Schinkel, A. H., M. J. Groot Koerkamp, and H. Tabak. 1988. Mitochondrial RNA polymerase of Saccharomyces cerevisiae: composition and mechanism of promoter recognition. EMBO J. 7: 3255–3262.
   PubMedGoogle Scholar
• Schubot, F. D., C. J. Chen, J. P. Rose, T. A. Dailey, H. A. Dailey, and B. C. Wang. Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription. Protein Sci. 10:1980–1988.
   PubMedGoogle Scholar
• Shadel, G. S. 1999. Yeast as a model for human mtDNA replication. Am. J. Hum. Genet. 65: 1230–1237.
   PubMedGoogle Scholar
• Shadel, G. S., and D. A. Clayton. 1993. Mitochondrial transcription initiation. Variation and conservation. J. Biol. Chem. 268: 16083–16086.
   PubMed Web of Science ®Google Scholar
• Shadel, G. S., and D. A. Clayton. 1995. A Saccharomyces cerevisiae mitochondrial transcription factor, sc-mtTFB, shares features with sigma factors but is functionally distinct. Mol. Cell. Biol. 15: 2101–2108.
   PubMedGoogle Scholar
• Shadel, G. S., and D. A. Clayton. 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66: 409–435.
   PubMed Web of Science ®Google Scholar
• Shi, X., P. Yau, T. Jose, and P. D. Gershon. 1996. Methyltransferase-specific domains within VP39, a bi-functional protein that participates in the modification of both mRNA ends. RNA 2: 88–101.
   PubMedGoogle Scholar
• Thompson, J. D., D. J. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
   PubMed Web of Science ®Google Scholar
• Tiranti, V., A. Savoia, F. Forti, M. F. D'Apolito, M. Centra, M. Rocchi, and M. Zeviani. 1997. Identification of the gene encoding the human mitochondrial RNA polymerase (h-mtRPOL) by cyberscreening of the Expressed Sequence Tags database. Hum. Mol. Genet. 6: 615–625.
   PubMed Web of Science ®Google Scholar
• Virbasius, J. V., and R. C. Scarpulla. 1994. Activation of the human mitochondrial transcription factor A gene by nuclear respiratory factors: a potential regulatory link between nuclear and mitochondrial gene expression in organelle biogenesis. Proc. Natl. Acad. Sci. USA 91: 1309–1313.
   PubMed Web of Science ®Google Scholar
• Wallace, D. C. 1999. Mitochondrial diseases in man and mouse. Science 283: 1482–1488.
   PubMed Web of Science ®Google Scholar
• Wallace, D. C., G. Singh, M. T. Lott, J. A. Hodge, T. G. Schurr, A. M. Lezza, L. J. Elsas II, and E. K. Nikoskelainen. 1988. Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy. Science 242: 1427–1430.
   PubMed Web of Science ®Google Scholar
• Wingender, E., P. Dietze, H. Karas, and R. Knuppel. 1996. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24: 238–241.
   PubMed Web of Science ®Google Scholar
• Xu, B., and D. A. Clayton. 1992. Assignment of a yeast protein necessary for mitochondrial transcription initiation. Nucleic Acids Res. 20: 1053–1059.
   PubMedGoogle Scholar