Skip to main content
Log in

Mitochondrial transcription initiation: promoter structures and RNA polymerases

  • Review
  • Published:
Current Genetics Aims and scope Submit manuscript

Summary

A diversity of promoter structures

It is evident that tremendous diversity exists between the modes of mitochondrial transcription initiation in the different eukaryotic kingdoms, at least in terms of promoter structures. Within vertebrates, a single promoter for each strand exists, which may be unidirectional or bidirectional. In fungi and plants, multiple promoters are found, and in each case, both the extent and the primary sequences of promoters are distinct. Promoter multiplicity in fungi, plants and trypanosomes reflects the larger genome size and scattering of genes relative to animals. However, the dual roles of certain promoters in transcription and replication, at least in yeast, raises the interesting question of how the relative amounts of RNA versus DNA synthesis are regulated, possibly via cis-elements downstream from the promoters.

Mitochondrial RNA polymerases

With respect to mitochondrial RNA polymerases, characterization of human, mouse, Xenopus and yeast enzymes suggest a marked degree of conservation in their behaviur and protein composition. In general, these systems consist of a relatively non-selective core enzyme, which itself is unable to recognize promoters, and at least one dissociable specificity factor, which confers selectivity to the core subunit. In most of these systems, components of the RNA polymerase have been shown to induce a conformational change in their respective promoters and have also been assigned the role of a primase in the replication of mtDNA. While studies of the yeast RNA polymerase have suggested it has both eubacterial (mtTFB) and bacteriophage (RPO41) orgins, it is not yet clear whether these characteristics will be conserved in the mitochondrial RNA polymerases of all eukaryotes.

mtTFA-mtTFB; conserved but dissimilar functions

With respect to transcription factors, mtTFA has been found in both vertebrates and yeast, and may be a ubiquitous protein in mitochondria. However, the divergence in non-HMG portions of the proteins, combined with differences in promoter structure, has apparently relegated mtTFA to alternative, or at least non-identical, physiological roles in vertebrates and fungi. The relative ease with which mtTFA can be purified (Fisher et al. 1991) suggests that, where present, it should be facile to detect. mtTFB may represent a eubacterial sigma factor adapted for interaction with the mitochondrial RNA polymerase. In plants, sigma-like factors capable of interacting with a eubacterial polymerase are found in chloroplasts (Lerbs et al. 1988; Tiller and Link 1993; Troxler et al. 1994) raising the possibility that a gene family in plants contributes transcriptional factors to both mitochondria and chloroplasts. In coming years, we can expect a more detailed analysis of RNA polymerases, accessory factors and promoter structures, which will lead to a better understanding of the different modes of mitochondrial transcription initiation in eukaryotic species and the evolutionary relationships between them.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Attardi G, Schatz G (1988) Bigenesis of mitochondria. Annu Rev Cell Biol 4:289–333

    Google Scholar 

  • Barat-Gueride M, Dufresne C, Rickwood D (1989) Effect of DNA conformation on the transcription of mitochondrial DNA. Eur J Biochem 183:297–302

    Google Scholar 

  • Benne R (1985) Mitochondrial genes in trypanosomes. Trends Genet 1:117–121

    Google Scholar 

  • Benne R (1994) RNA editing in trypanosomes. Eur J Biochem 221:9–23

    Google Scholar 

  • Bennett JL, Jeung Yu S, Clayton DA (1992) Characterization of a Xenopus laevis ribonucleoprotein endoribonuclease: isolation of the RNA component and its expression during development. J Biol Chem 267:21765–21772

    Google Scholar 

  • Bhat GJ, Souza AE, Feagin JE, Stuart K (1992) Transcript-specific developmental regulation of polyadenylation in Trypanosoma brucei mitochondria. Mol Biochem Parasitol 52:231–240

    Google Scholar 

  • Binder S, Brennicke A (1993a) Transcription initiation sites in mitochondria of Oenothera berteriana. J Biol Chem 268: 7849–7855

    Google Scholar 

  • Binder S, Brennicke A (1993b) A tRNA gene-transcription initiation site is similar to mRNA and rRNA promoters in plant mitochondria. Nucleic Acids Res 21:5012–5019

    Google Scholar 

  • Biswas TK, Getz GS (1986) Nucleotides flanking the promoter sequence influence the transcription of the yeast mitochondrial gene coding for ATPase subunit 9. Proc Natl Acad Sci USA 83:270–274

    Google Scholar 

  • Biswas TK, Edwards JC, Rabinowitz M, Getz GS (1985) Characterization of a yeast mitochondrial promoter by deletion mutagenesis. Proc Natl Acad Sci USA 82:1954–1958

    Google Scholar 

  • Biswas TK, Baruch T, Getz GS (1987) In vitro characterization of the yeast mitochondrial promoter using single-base substitution mutants. J Biol Chem 262:13690–13696

    Google Scholar 

  • Bogenhagen DF, Insdorf NF (1988) Purification of Xenopus laevis mitochondrial RNA polymerase and identification of a dissociable factor required for specific transcription. Mol Cell Biol 8:2910–2916

    Google Scholar 

  • Bogenhagen DF, Romanelli MF (1988) Template sequences required for transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters. Mol Cell Biol 8:2917–2924

    Google Scholar 

  • Bogenhagen DF, Yoza BK (1986) Accurate in vitro transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters. Mol Cell Biol 6:2543–2550

    Google Scholar 

  • Bogenhagen DF, Yoza BK, Cairns SS (1986) Identification of initiation sites for transcription of Xenopus laevis mitochondrial DNA. J Biol Chem 261:8488–8494

    Google Scholar 

  • Brown GG, Auchincloss AH, Colello PS, Gray MW, Menassa R, Singh M (1991) Characterization of transcription initiation sites in the soybean mitochondrial genome allows identification of a transcription-associated sequence motif. Mol Gen Genet 228:345–355

    Google Scholar 

  • Carlson JE, Brown GL, Kemble RJ (1986) In organello mitochondrial DNA and RNA synthesis in fertile and cytoplasmic male-sterile Zea mays L.. Curr Genet 11:151–160

    Google Scholar 

  • Chang DD, Clayton DA (1984) Precise identification of individual promoters for transcription of each strand of human mitochondrial DNA. Cell 36:635–643

    Google Scholar 

  • Chang DD, Clayton DA (1986a) Identification of primary transcriptional start sites of mouse mitochondrial DNA:accurate in vitro initiation of both heavy and light-strand transcripts. Mol Cell Biol 6:1446–1453

    Google Scholar 

  • Chang DD, Clayton DA (1986b) Precise assignment of the heavy strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcription initiation. Mol Cell Biol 6:3262–3267

    Google Scholar 

  • Chang DD, Clayton DA (1986c) Precise assignment of the lightstrand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains. Mol Cell Biol 6:3253–3261

    Google Scholar 

  • Chomyn A, Attardi G (1987) Mitochondrial gene products. Curr Top Bioenerg 15:295–329

    Google Scholar 

  • Christianson T, Rabinowitz M (1983) Identification of multiple transcriptional initiation sites on the yeast mitochondrial genome by in vitro capping with guanylyltransferase. J Biol Chem 258:14025–14033

    Google Scholar 

  • Clark-Walker GD (1985) Basis of diversity in mitochondrial DNAs. In: Cavalier-Smith T (ed) The evolution of genome size. Wiley, New York, pp 277–297

    Google Scholar 

  • Clayton DA (1991) Replication and transcription of vertebrate mitochondrial DNA. Annu Rev Cell Biol 7:453–478

    Google Scholar 

  • Covello PS, Gray MW (1991) Sequence analysis of wheat mitochondrial transcripts capped in vitro: definitive identification of transcription-initiation sites. Curr Genet 20:245–252

    Google Scholar 

  • Daga A, Micol V, Hess D, Aebersold R, Attardi G (1993) Molecular characterization of the transcription-termination factor from human mitochondria. J Biol Chem 268:8123–8130

    Google Scholar 

  • Dairaghi DJ, Clayton DA (1993) Bovine RNAse MRP cleaves the divergent bovine mitochondrial RNA sequence at the displacement-loop region. J Mol Evol 37:338–346

    Google Scholar 

  • Diffley JFX, Stillman B (1991) A close relative of the nuclear chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc Natl Acad Sci USA 88:7864–7868

    Google Scholar 

  • Diffley JFX, Stillman B (1992) DNA-binding properties of an HMG1-related protein from yeast mitochondria. J Biol Chem 267:3368–3374

    Google Scholar 

  • Edwards JC, Levens D, Rabinowitz M (1982) Analysis of transcriptional initiation of yeast mitochondrial DNA in a homologous in vitro transcription system. Cell 31:337–346

    Google Scholar 

  • Finnegan PM, Brown GG (1990) Transcriptional and post-transcriptional regulation of RNA levels in maize mitochondria. Plant Cell 2:71–84

    Google Scholar 

  • Fisher RP, Clayton DA (1988) Purification and characterization of human mitochondrial transcription factor 1. Mol Cell Biol 8:3496–3509

    Google Scholar 

  • Fisher RP, Topper JN, Clayton DA (1987) Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements. Cell 50:247–258

    Google Scholar 

  • Fisher RP, Parisi MA, Clayton DA (1989) Flexible recognition of rapidly evolving promoter sequences by mitochondrial transcription factor 1. Genes Dev 3:2202–2217

    Google Scholar 

  • Fisher RP, Lisowsky T, Breen GAM, Clayton DA (1991) A rapid, efficient method for purifying DNA-binding proteins. J Biol Chem 266:9153–9160

    Google Scholar 

  • Fisher RP, Lisowsky T, Parisi MA, Clayton DA (1992) DNA wrapping and bending by a mitochondrial high-mobility group-like transcriptional activator protein. J Biol Chem 267:3358–3367

    Google Scholar 

  • Ghivizzani SC, Madsen CS, Hauswrith WW (1993) In organello footprinting analysis of protein binding at regulatory regions in bovine mitochondrial DNA. J Biol Chem 268:8675–8682

    Google Scholar 

  • Gray MW (1989) Origin and evolution of mitochondrial DNA. Annu Rev Cell Biol 5:25–50

    Google Scholar 

  • Gray MW (1992) The endosymbiont hypothesis revisited. Int Rev Cytol 141:233–357

    Google Scholar 

  • Gray MW, Hanic-Joyce PJ, Covello PS (1992) Transcription, processing and editing in plant mitochondria. Annu Rev Plant Physiol Plant Mol Biol 43:145–175

    Google Scholar 

  • Hanic-Joyce PJ, Gray MW (1991) Accurate transcription of a plant mitochondrial gene in vitro. Mol Cell Biol 11:2035–2039

    Google Scholar 

  • Hess WR, Prombona A, Fieder B, Subramanian AR, Borner T (1993) Chloroplast rps15 and rpoB-C1-C2 gene cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J 12:563–571

    Google Scholar 

  • Hixson JE, Clayton DA (1985) Initiation of transcription from each of the two human mitochondrial promoters requires unique nucleotides at the transcriptional start sites. Proc Natl Acad Sci USA 82:2660–2664

    Google Scholar 

  • Igloi GL, Kössel H (1992) The transcriptional apparatus of chloroplasts. Crit Rev Plant Sci 10:525–558

    Google Scholar 

  • Ikeda RA, Richardson CC (1986) Interactions of the RNA polymerase of bacteriophage T-7 with its promoter during binding and initiation of transcription. Proc Natl Acad Sci USA 83:3614–3618

    Google Scholar 

  • Jang SH, Jaehning JA (1991) The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J Biol Chem 266:22671–22677

    Google Scholar 

  • Jang SH, Jachning JA (1994) Mechanisms of mitochondrial transcription. In: Conaway RC, Conaway JW (eds) Transcription: mechanisms and regulation. Raven Press, New York, pp 171–184

    Google Scholar 

  • Kelly JL, Lehman IR (1986) Yeast mitochondrial RNA polymerase: purification and properties of the catalytic subunit. J Biol Chem 261:10340–10347

    Google Scholar 

  • Kelly JL, Greenleaf AL, Lehman IR (1986) Isolation of the nuclear gene encoding a subunit of the yeast Saccharomyces cerevisiae mitochondrial RNA polymerase. J Biol Chem 261:10348–10351

    Google Scholar 

  • Kennell JC, Lambowitz AM (1989) Development of an in vitro transcription system for Neurospora crassa mitochondrial DNA and identification of transcription initiation sites. Mol Cell Biol 9:3603–3613

    Google Scholar 

  • King TC, Low RL (1987) Mapping of control elements in the displacement-loop region of bovine mitochondrial DNA. J Biol Chem 262:6204–6213

    Google Scholar 

  • Kiss T, Filipowicz W (1992) Evidence against a mitochondrial location of the 7-2/MRP RNA in mammalian cells. Cell 70:11–16

    Google Scholar 

  • Kiss T, Marshallsay C, Filipowicz W (1992) 7-2/MRP RNAs in plant and mammalian cells: association with higher-order structures in the nucleolus. EMBO J 11:3737–3746

    Google Scholar 

  • Kubelik AR, Kennell JC, Akins RA, Lambowitz AM (1990) Identification of Neurospora mitochondrial promoters and analysis of synthesis of the mitochondrial small-ribosomal RNA in wildtype and the promoter mutant poky. J Biol Chem 265:4515–4526

    Google Scholar 

  • L'Abbé D, Duhaime JF, Lang BF, Morais R (1991) The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J Biol Chem 266:10844–10850

    Google Scholar 

  • Lakhani S, Khanna NC, Tewari KK (1992) Two distinct transcriptional activities of pea (Pisum sativum) chloroplasts share immunochemically related functional polypeptides. Biochem J 286:833–841

    Google Scholar 

  • Lerbs S, Braeutigam E, Mache R (1988) DNA-dependent RNA polymerase of spinach chloroplasts: characterization of alphalike and sigma-like polypeptides. Mol Gen Genet 211:458–464

    Google Scholar 

  • Lerbs-Mache S (1993) The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymeraseP single-subunit enzyme or catalytic core of multimeric enzyme complexes? Proc Natl Acad Sci USA 90:5509–5513

    Google Scholar 

  • Leving III CS, Brown GG (1989) Molecular biology of plant mitochondria. Cell 56:171–179

    Google Scholar 

  • Lisowsky T, Michaelis G (1988) A nuclear gene essential for mitochondrial replication suppresses a defect of mitochondrial transcription in Saccharomyces cerevisiae. Mol Gen Genet 214:218–223

    Google Scholar 

  • Lizama L, Holuigue L, Jordana X (1994) Transcription initiation sites for the potato mitochondrial gene coding for subunit 9 of ATP synthase (atp9). FEBS Lett 349:243–248

    Google Scholar 

  • Ma DP, King YT, Kim Y, Luckett WSJ, Boyle JA, Chang YF (1992) Amplification and characterization of an inverted repeat from the Chlamydomonas reinhardtii mitochondrial genome. Gene 119:253–257

    Google Scholar 

  • Magus DA, Jang SH, Jaehning JA (1994) Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J Biol Chem 269:26568–26574

    Google Scholar 

  • Masters BS, Stohl LL, Clayton DA (1987) Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51:89–99

    Google Scholar 

  • Michelotti EF, Hajduk SL (1987) Developmental regulation of trypanosome mitochondrial gene expression. J Biol Chem 262:927–932

    Google Scholar 

  • Montoya J, Christianson T, Levens D, Rabinowitz M, Attardi G (1982) Identification of initiation sites for heavy strand and light-strand transcription in human mitochondrial DNA. Proc Natl Acad Sci USA 79:7195–7199

    Google Scholar 

  • Montoya J, Gaines GL, Attardi G (1983) The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units. Cell 34:151–159

    Google Scholar 

  • Mulligan RM, Lau GT, Walbot V (1988 a) Numerous transcription initiation sites exist for the maize mitochondrial genes for subunit 9 of the ATP synthase and subunit 3 of cytochrome oxidase. Proc Natl Acad Sci USA 85:7998–8002

    Google Scholar 

  • Mulligan RM, Maloney AP, Walbot V (1988 b) RNA processing and multiple transcription initiation sites result in transcript-size heterogeneity in maize mitochondria. Mol Gen Genet 211:373–380

    Google Scholar 

  • Mulligan RM, Leon P, Walbot V (1991) Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression. Mol Cell Biol 11:533–543

    Google Scholar 

  • Newton KJ, Winberg B, Yamato K, Lupold S, Stern DB (1995) Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes. EMBO J 14:585–593

    Google Scholar 

  • Osinga KA, De Haan M, Christianson T, Tabak HF (1982) A nonanucleotide sequence involved in promotion of ribosomal RNA synthesis and RNA priming of DNA replication in yeast mitochondria. Nucleic Acids Res 10:7993–8006

    Google Scholar 

  • Parisi MA, Clayton DA (1991) Similarity of human mitochondrial transcription factor 1 to high-mobility group proteins. Science 252:965–969

    Google Scholar 

  • Parisi MA, Xu B, Clayton DA (1993) A human mitochondrial transcriptional activator can functionally replace a yeast mitochondrial HMG-box protein both in vivo and in vitro. Mol Cell Biol 13:1951–1961

    Google Scholar 

  • Perez-Martin J, Rojo F, De Lorenzo V (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58:268–290

    Google Scholar 

  • Rapp WD, Stern DB (1992) A conserved 11-nucleotide sequence contains an essential promoter element of the maize mitochondrial atp1 gene. EMBO J 11:1065–1073

    Google Scholar 

  • Rapp WD, Lupold DS, Mack S, Stern DB (1993) Architecture of the maize mitochondrial atp1 promoter as determined by linker-scanning and point mutagenesis. Mol Cell Biol 13:7232–7238

    Google Scholar 

  • Riemen G, Michaelis G (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

    Google Scholar 

  • Schinkel AH, Tabak HF (1989) Mitochondrial RNA polymerase: dual role in transcription and replication. Trends Genet 5:149–154

    Google Scholar 

  • Schinkel AH, Groot-Koerkamp MJA, Van der Horst GTJ, Touw EPW, Osinga KA, Van der Bliek AM, Veeneman GH, Van Boom JH, Tabak HF (1986) Characterization of the promoter of the large ribosomal RNA gene in yeast mitochondria and separation of mitochondrial RNA polymerase into two different functional components. EMBO J 5:1041–1047

    Google Scholar 

  • Schinkel AH, Groot-Koerkamp MJA, Touw EPW, Tabak HF (1987) Specificity factor of yeast mitochondrial RNA polymerase: purification and interaction with core RNA polymerase. J Biol Chem 262:12785–12791

    Google Scholar 

  • Schinkel AH, Groot-Koerkamp MJA, Tabak HF (1988a) Mitochondrial RNA polymerase of Saccharomyces cerevisiae: composition and mechanism of promoter recognition. EMBO J 7:3255–3262

    Google Scholar 

  • Schinkel AH, Groot-Koerkamp MJA, Teunissen AWRH, Tabak HF (1988 b) RNA polymerase induces DNA bending at yeast mitochondrial promoters. Nucleic Acids Res 16:9147–9164

    Google Scholar 

  • Schmitt ME, Clayton DA (1992) Yeast site-specific ribonucleoprotein endoribonuclease MRP contains an RNA component homologous to mammalian RNAse MRP RNA and is essential for cell viability. Genes Dev 6:1975–1985

    Google Scholar 

  • Schmitt ME, Clayton DA (1993) Nuclear RNase MRP is required for correct processing for pre-5.8S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 13:7935–7941

    Google Scholar 

  • Shadel GS, Clayton DA (1993) Mitochondrial transcription initiation. J Biol Chem 268:16083–16086

    Google Scholar 

  • 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 15:2101–2108

    Google Scholar 

  • Simpson L (1987) The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution. Annu Rev Microbiol 41:363–382

    Google Scholar 

  • Sogin ML, Gunderson JH, Elwood HJ, Alonso RA, Peattie DA (1989) Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243:75–77

    Google Scholar 

  • Stohl LL, Clayton DA (1992) Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming. Mol Cell Biol 12:2561–2569

    Google Scholar 

  • Tiller K, Link G (1993) Sigma-like transcription factors from mustard Sinapis alba L. etioplasts are similar in size to, but functionally distinct from, their chloroplast counterparts. Plant Mol Biol 21:503–513

    Google Scholar 

  • Topper JN, Bennett JL, Clayton DA (1992) A role for RNAase MRP in mitochondrial RNA processing. Cell 70:16–20

    Google Scholar 

  • Troxler RF, Zhang F, Hu J, Bogorad L (1994) Evidence that sigma factors are components of chloroplast RNA polymerase. Plant Physiol 104:753–759

    Google Scholar 

  • Tzagoloff A, Myers AM (1986) Genetics of mitochondrial biogenesis. Annu Rev Biochem 55:249–285

    Google Scholar 

  • Vahrenholz C, Riemen G, Pratje E, Dujon B, Michaelis G (1993) Mitochondrial DNA of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8-kb genome suggests mechanisms for DNA replication. Curr Genet 24:241–247

    Google Scholar 

  • Van der Vliet PC, Verrijzer CP (1993) Bending of DNA by transcription factors. Bioessays 15:25–32

    Google Scholar 

  • Walberg MW, Clayton DA (1983) In vitro transcription of human mitochondrial DNA. Identification of specific light-strand transcripts from the displacement-loop region. J Biol Chem 258:1268–1275

    Google Scholar 

  • Xu B, Clayton DA (1992) Assignment of a yeast protein necessary for mitochondrial transcription initiation. Nucleic Acids Res 20:1053–1059

    Google Scholar 

  • Yaginuma K, Kobayashi M, Taira M, Koike K (1982) A new RNA polymerase and in vitro transcription of the origin of replication from rat mitochondrial DNA. Nucleic Acids Res 10:7531–7542

    Google Scholar 

  • Yoza BK, Bogenhagen DF (1984) Identification and in vitro capping of a primary transcript of human mitochondrial DNA. J Biol Chem 259:3909–3915

    Google Scholar 

  • Zaitseva GN, Levhenko IV, Tarasov IA, Kuzmin EV (1985) DNA-dependent RNA polymerase from Crithidia oncopelti kinetoplasts. Biokhimiya 50:1463–1470

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Additional information

Communicated by L.A. Grivell

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tracy, R.L., Stern, D.B. Mitochondrial transcription initiation: promoter structures and RNA polymerases. Curr Genet 28, 205–216 (1995). https://doi.org/10.1007/BF00309779

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00309779

Keywords

Navigation