Journal of Molecular Evolution

, Volume 63, Issue 5, pp 707–717 | Cite as

Evidence for an Early Gene Duplication Event in the Evolution of the Mitochondrial Transcription Factor B Family and Maintenance of rRNA Methyltransferase Activity in Human mtTFB1 and mtTFB2

  • Justin Cotney
  • Gerald S. ShadelEmail author


Most metazoans have two nuclear genes encoding orthologues of the well-characterized Saccharomyces cerevisiae mitochondrial transcription factor B (sc-mtTFB). This class of transcription factors is homologous to the bacterial KsgA family of rRNA methyltransferases, which in Escherichia coli dimethylates adjacent adenine residues in a stem-loop of the 16S rRNA. This posttranscriptional modification is conserved in most metazoan cytoplasmic and mitochondrial rRNAs. Homo sapiens mitochondrial transcription factor B1 (h-mtTFB1) possesses this enzymatic activity, implicating it as a dual-function protein involved in mitochondrial transcription and translation. Here we demonstrate that h-mtTFB2 also has rRNA methyltransferase activity but is a less efficient enzyme than h-mtTFB1. In contrast, sc-mtTFB has no detectable rRNA methyltransferase activity, correlating with the lack of the corresponding modification in the mitochondrial rRNA of budding yeast. Based on these results, and reports that Drosophila melanogaster mtTFB1 and mtTFB2 do not have completely overlapping functions, we propose a model for human mtDNA regulation that takes into account h-mtTFB1 and h-mtTFB2 likely having partially redundant transcription factor and rRNA methyltransferase functions. Finally, phylogenetic analyses of this family of proteins strongly suggest that the presence of two mtTFB homologues in metazoans is the result of a gene duplication event that occurred early in eukaryotic evolution prior to the divergence of fungi and metazoans. This model suggests that, after the gene duplication event, differential selective pressures on the rRNA methyltransferase and transcription factor activities of mtTFB genes occurred, with extreme cases culminating in the loss of one of the paralogous genes in certain species.


Mitochondria Transcription mtTFB TFB1M TFB2M MTF1 rRNA Methylation Gene Expression KsgA 



This work was supported by NIH Grant HL-59655 from the National Heart, Lung and Blood Institute awarded to G.S.S. The authors wish to thank Dr. A. Vila-Sanjurjo for providing the E. coli ksgA mutant strain used in this study and Nick Bonawitz and Tim Shutt for providing critical insights and comments on the manuscript.

Supplementary material

supp.pdf (181 kb)
Supplementary material


  1. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780PubMedCrossRefGoogle Scholar
  2. Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: anything goes. Trends Genet 19:709–716PubMedCrossRefGoogle Scholar
  3. Carrodeguas JA, Yun S, Shadel GS, Clayton DA, Bogenhagen DF (1996) Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Expr 6:219–230PubMedGoogle Scholar
  4. Cermakian N, Ikeda TM, Cedergren R, Gray MW (1996) Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage. Nucleic Acids Res 24:648–654PubMedCrossRefGoogle Scholar
  5. Dairaghi DJ, Shadel GS, Clayton DA (1995) Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator. J Mol Biol 249:11–28PubMedCrossRefGoogle Scholar
  6. Diffley JF, Stillman B (1991) A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc Natl Acad Sci USA 88:7864–7868PubMedCrossRefGoogle Scholar
  7. Falkenberg M, Gaspari M, Rantanen A, Trifunovic A, Larsson NG, Gustafsson CM (2002) Mitochondrial transcription factors B1 and B2 activate transcription of human mtDNA. Nat Genet 31:289–294PubMedCrossRefGoogle Scholar
  8. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.65. Distributed by author, Department of Genome Sciences, University of Washington, Seattle; available at:
  9. Fisher RP, Clayton DA (1988) Purification and characterization of human mitochondrial transcription factor 1. Mol Cell Biol 8:3496–3509PubMedGoogle Scholar
  10. Gleyzer N, Vercauteren K, Scarpulla RC (2005) Control of mitochondrial transcription specificity factors (TFB1M and TFB2M) by nuclear respiratory factors (NRF-1 and NRF-2) and PGC-1 family coactivators. Mol Cell Biol 25:1354–1366PubMedCrossRefGoogle Scholar
  11. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283:1476–1481PubMedCrossRefGoogle Scholar
  12. Greenleaf AL, Kelly JL, Lehman IR (1986) Yeast RPO41 gene product is required for transcription and maintenance of the mitochondrial genome. Proc Natl Acad Sci USA 83:3391–3394PubMedCrossRefGoogle Scholar
  13. Hall T (2005) BioEdit version 7.05. Distributed by author, Carlsbad, CA; available at:
  14. Helser TL, Davies JE, Dahlberg JE (1972) Mechanism of kasugamycin resistance in Escherichia coli. Nat New Biol 235:6–9PubMedGoogle Scholar
  15. Jang SH, Jaehning JA (1991) The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J Biol Chem 266:22671–22677PubMedGoogle Scholar
  16. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282PubMedGoogle Scholar
  17. Klootwijk J, Klein I, Grivell LA (1975) Minimal post-transcriptional modification of yeast mitochondrial ribosomal RNA. J Mol Biol 97:337–350PubMedCrossRefGoogle Scholar
  18. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150–163PubMedCrossRefGoogle Scholar
  19. Lafontaine DL, Preiss T, Tollervey D (1998) Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis? Mol Cell Biol 18:2360–2370PubMedGoogle Scholar
  20. Lang BF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351–397PubMedCrossRefGoogle Scholar
  21. Lisowsky T, Michaelis G (1988) A nuclear gene essential for mitochondrial replication suppresses a defect of mitochondrial transcription in Saccharomyces cerevisiae. Mol Gen Genet 214:218–223PubMedCrossRefGoogle Scholar
  22. Lisowsky T, Michaelis G (1989) Mutations in the genes for mitochondrial RNA polymerase and a second mitochondrial transcription factor of Saccharomyces cerevisiae. Mol Gen Genet 219:125–128PubMedCrossRefGoogle Scholar
  23. Masters BS, Stohl LL, Clayton DA (1987) Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51:89–99PubMedCrossRefGoogle Scholar
  24. Matsushima Y, Garesse R, Kaguni LS (2004) Drosophila mitochondrial transcription factor B2 regulates mitochondrial DNA copy number and transcription in schneider cells. J Biol Chem 279:26900–26905PubMedCrossRefGoogle Scholar
  25. Matsushima Y, Adan C, Garesse R, Kaguni LS (2005) Drosophila mitochondrial transcription factor B1 modulates mitochondrial translation but not transcription or DNA copy number in Schneider cells. J Biol Chem 280:16815–16820PubMedCrossRefGoogle Scholar
  26. McCulloch V, Shadel GS (2003) Human mitochondrial transcription factor B1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity. Mol Cell Biol 23:5816–5824PubMedCrossRefGoogle Scholar
  27. McCulloch V, Seidel-Rogol BL, Shadel GS (2002) A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. Mol Cell Biol 22:1116–1125PubMedCrossRefGoogle Scholar
  28. O’Farrell HC, Scarsdale JN, Rife JP (2004) Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J Mol Biol 339:337–353PubMedCrossRefGoogle Scholar
  29. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  30. Parisi MA, Clayton DA (1991) Similarity of human mitochondrial transcription factor 1 to high mobility group proteins. Science 252:965–969PubMedCrossRefGoogle Scholar
  31. Rantanen A, Gaspari M, Falkenberg M, Gustafsson CM, Larsson NG (2003) Characterization of the mouse genes for mitochondrial transcription factors B1 and B2. Mammal Genome 14:1–6CrossRefGoogle Scholar
  32. Schinkel AH, Koerkamp MJ, Touw EP, Tabak HF (1987) Specificity factor of yeast mitochondrial RNA polymerase. Purification and interaction with core RNA polymerase. J Biol Chem 262:12785–12791PubMedGoogle Scholar
  33. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504PubMedCrossRefGoogle Scholar
  34. Schubot FD, Chen CJ, Rose JP, Dailey TA, Dailey HA, Wang BC (2001) Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription. Protein Sci 10:1980–1988PubMedCrossRefGoogle Scholar
  35. Seidel-Rogol BL, McCulloch V, Shadel GS (2003) Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop. Nat Genet 33:23–24PubMedCrossRefGoogle Scholar
  36. Shadel GS (2004) Coupling the mitochondrial transcription machinery to human disease. Trends Genet 20:513–519PubMedCrossRefGoogle Scholar
  37. Shadel GS, Clayton DA (1995) A Saccharomyces cerevisiae mitochondrial transcription factor, sc-mtTFB, shares features with sigma factors but is functionally distinct. Mol Cell Biol 15:2101–2108PubMedGoogle Scholar
  38. Shutt TE, Gray MW (2006) Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethlyadenosine methyltransferase of the mitochondrial endosymbiont. Mol Biol Evol 23:1169–1179PubMedCrossRefGoogle Scholar
  39. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  40. van Buul CP, van Knippenberg PH (1985) Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene 38:65–72PubMedCrossRefGoogle Scholar
  41. Vila-Sanjurjo A, Squires CL, Dahlberg AE (1999) Isolation of kasugamycin resistant mutants in the 16 S ribosomal RNA of Escherichia coli. J Mol Biol 293:1–8PubMedCrossRefGoogle Scholar
  42. Xu B, Clayton DA (1992) Assignment of a yeast protein necessary for mitochondrial transcription initiation. Nucleic Acids Res 20:1053–1059PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  1. 1.Department of PathologyYale University School of MedicineNew HavenUSA
  2. 2.Graduate Program in Genetics and Molecular BiologyEmory University School of MedicineAtlantaUSA

Personalised recommendations