Molecular Genetics and Genomics

, Volume 272, Issue 6, pp 603–615

The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants

  • Y. Sugiyama
  • Y. Watase
  • M. Nagase
  • N. Makita
  • S. Yagura
  • A. Hirai
  • M. Sugiura
Original Paper

Abstract

Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and ψrps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.

Keywords

Mitochondrial genome Multipartite organization Repeated sequence Homologous recombination  Nicotiana tabacum 

Supplementary material

supp.pdf (449 kb)
(PDF 450 KB)

References

  1. Abdelnoor RV, Yule R, Elo A, Christensen AC, Meyer-Gausen G, Mackenzie SA (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci USA 100:5968–5973CrossRefPubMedGoogle Scholar
  2. Adams KL, Daley DO, Qui Y, Whelan J, Palmer JD (2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408:354–357CrossRefPubMedGoogle Scholar
  3. Adams KL, Robenblueth M, Qiu Y, Palmer JD (2001) Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution. Genetics 158:1289–1300PubMedGoogle Scholar
  4. Adams KL, Qui Y, Stroutemyer M, Palmer JD (2002) Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 99:9905–9912CrossRefPubMedGoogle Scholar
  5. Backert S, Börner T (2000) Phage T4-like intermediates of DNA replication and recombination in the mitochondria of the higher plant Chenopodium album (L.). Curr Genet 37:304–314CrossRefPubMedGoogle Scholar
  6. Bergman P, Sdqvist J, Farbos I, Glimelius K (2000) Male-sterile tobacco displays abnormal mitochondrial atp1 transcript accumulation and reduced floral ATP/ADP ratio. Plant Mol Biol 42:531–544CrossRefPubMedGoogle Scholar
  7. Bland MM, Matzinger DF, Levings CS III (1985) Comparison of the mitochondrial genome of Nicotiana tabacum with its progenitor species. Theor Appl Genet 69:535–541Google Scholar
  8. Bland MM, Levings CS III, Matzinger DF (1986) The tobacco mitochondrial ATPase subunit 9 gene is closely linked to an open reading frame for a ribosomal protein. Mol Gen Genet 204: 8–16CrossRefPubMedGoogle Scholar
  9. Bland MM, Levings CS III, Matzinger DF (1987) The ATPase subunit 6 gene of tobacco mitochondria contains an unusual sequence. Curr Genet 12:475–481CrossRefPubMedGoogle Scholar
  10. Burger G, Franz Lang B, Braun H-P, Marx S (2003) The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b. Nucleic Acids Res 31:2353–2360CrossRefPubMedGoogle Scholar
  11. Caoile AGFS, Stern DB (1997) A conserved core element is functionally important for maize mitochondrial promoter activity in vitro. Nucleic Acids Res 25:4055–4060CrossRefPubMedGoogle Scholar
  12. Chen HC, Wintz H, Weil JH, Pillay DT (1989) Three mitochondrial tRNA genes from Arabidopsis thaliana: evidence for the conversion of a tRNAPhe gene to a tRNATyr gene. Nucleic Acids Res 17:2613–2621PubMedGoogle Scholar
  13. Ewing B, Hillier L, Wendl M, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  14. Fauron C, Casper M, Gao Y, Moor B (1995) The maize mitochondrial genome: dynamic, yet functional. Trends Genet 11:228–235Google Scholar
  15. Giegé P, Knoop V, Brennicke A (1998) Complex II subunit 4 (sdh4) homologous sequences in plant mitochondrial genomes. Curr Genet 34:313–317CrossRefPubMedGoogle Scholar
  16. Gonzalez DH, Bonnard G, Grienenberger J-M (1993) A gene involved in the biogenesis of cytochromes is co-transcribed with a ribosomal protein gene in wheat mitochondria. Curr Genet 24:248–255CrossRefPubMedGoogle Scholar
  17. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202PubMedGoogle Scholar
  18. Graham LE, Cook ME, Busse JS (2000) The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc Natl Acad Sci USA 97:4535–4540CrossRefPubMedGoogle Scholar
  19. Gray MW (1999) Evolution of organellar genomes. Curr Opin Genet Dev 9:678–687CrossRefPubMedGoogle Scholar
  20. Handa H (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed ( Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res 31:5907–5916CrossRefPubMedGoogle Scholar
  21. Hirose T, Sugiura M (2001) Involvement of a site-specific trans -acting factor and a common RNA-editing protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J 16:6804–6811CrossRefGoogle Scholar
  22. Hoffmann M, Binder S (2002) Functional importance of nucleotide identities within the pea atp9 mitochondrial promoter sequence. J Mol Biol 320:943–950CrossRefPubMedGoogle Scholar
  23. Janska H, Sarria R, Woloszynska M, Arrieta-Montiel M, Mackenzie SA (1998) Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility. Plant Cell 10:1163–1180CrossRefPubMedGoogle Scholar
  24. Joyce PBM, Gray MW (1989) Nucleotide sequence of a wheat mitochondrial glutamine tRNA gene. Nucleic Acids Res 17:5461–5476PubMedGoogle Scholar
  25. Kadowaki K, Ozawa K, Kazama S, Kubo N, Akihama T (1995) Creation of an initiation codon by RNA editing in the coxI transcript from tomato mitochondria. Curr Genet 28:415–422CrossRefPubMedGoogle Scholar
  26. Kanazawa A, Tsutsumi N, Hirai A (1994) Reversible changes in the composition of the population of mtDNAs during dedifferentiation and regeneration in tobacco. Genetics 138:865–870PubMedGoogle Scholar
  27. Kenton A, Parokonny AS, Gleba YY, Bennett MD (1993) Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol Gen Genet 240:159–169CrossRefPubMedGoogle Scholar
  28. Klein M, Eckert-Ossenkopp U, Schmiedeberg I, Brandt P, Unseld M, Brennicke A, Schuster W (1994) Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones. Plant J 6:447–455CrossRefPubMedGoogle Scholar
  29. Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T (2000) The complete nucleotide sequence of the mitochondrial genome of sugar beet ( Beta vulgaris L.) reveals a novel gene for tRNAcys (GCA). Nucleic Acids Res 28:2571–2576CrossRefPubMedGoogle Scholar
  30. Kurland CG, Andersson SGE (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64:786–820Google Scholar
  31. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPUTER: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642CrossRefPubMedGoogle Scholar
  32. Lelandais C, Gutierres S, Mathieu C, Vedel F, Remacle C, Maréchal-Drouard L, Brennicke A, Binder S, Chétrit P (1996) A promoter element active in run-off transcription controls the expression of the two cistrons of nad and rps genes in Nicotiana sylvestris mitochondria. Nucleic Acids Res 24:4789-4804CrossRefGoogle Scholar
  33. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefPubMedGoogle Scholar
  34. Margulis L, Bermudes D (1985) Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis 1:101–124PubMedGoogle Scholar
  35. Marienfeld J, Unseld M, Brennicke A (1999) The mitochondrial genome of Arabidopsis is composed of both native and immigrant information. Trends Plant Sci 4:495–502CrossRefPubMedGoogle Scholar
  36. Mundel C, Schuster W (1996) Loss of RNA editing of rps1 sequences in Oenothera mitochondria. Curr Genet 30:455–460CrossRefPubMedGoogle Scholar
  37. Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G., Nakazono M, Hirai A, Kadowaki K (2002) The complete sequence of the rice ( Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics 268:434–445CrossRefPubMedGoogle Scholar
  38. Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA, a primitive form of plant mitochondrial genome. J Mol Biol 223:1–7PubMedGoogle Scholar
  39. Oldenberg DJ, Bendich AJ (1996) Size and structure of replicating mitochondrial DNA in cultured tobacco cells. Plant Cell 8:447–461CrossRefPubMedGoogle Scholar
  40. Ortega VM, Bohner JG, Chase CD (2000) The tobacco apocytochrome b gene predicts sensitivity to the respiratory inhibitors antimycin A and myxothiazol. Curr Genet 37:315–321CrossRefPubMedGoogle Scholar
  41. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu Y, Song K (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci USA 97:6960–6966CrossRefPubMedGoogle Scholar
  42. Quiñones V, Zanlungo S, Holuigue L, Litvak S, Jordana X (1995) The cox1 initiation codon is created by RNA editing in potato mitochondria. Plant Physiol 108:1327–1328CrossRefPubMedGoogle Scholar
  43. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual (3rd edn). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.Google Scholar
  44. Satoh M, Nemoto Y, Kawano S, Nagata T, Hirokawa H, Kuroiwa T (1993) Organization of heterologous mitochondrial DNA molecules in mitochondrial nuclei of cultured tobacco cells. Protoplasma 175:112–120Google Scholar
  45. Shinozaki K, et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049Google Scholar
  46. Siqueira SF, Dias SMG, Hardouin P, Pereira FRS, Lejeune B, de Souza AP (2002) Transcription of succinate dehydrogenase subunit 4 ( sdh4) gene in potato: detection of extensive RNA editing and co-transcription with cytochrome oxidase III ( cox3) gene. Curr Genet 41:282–289CrossRefPubMedGoogle Scholar
  47. Soltis PS, Soltis DE, Chase MW (1999) Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402–404CrossRefPubMedGoogle Scholar
  48. Stamper SE, Dewey RE, Bland MM, Levings CS III (1987) Characterization of the gene urf13 -T and unidentified reading frame, ORF25, in maize and tobacco mitochondria. Curr Genet 12:457–463CrossRefPubMedGoogle Scholar
  49. Sugiyama Y, Watase Y, Nagase M, Hirai A, Sugiura M (2004) Timing of tRNA gene transfer from chloroplast to mitochondrion revealed by genomic analysis of dicotyledonous plant mitochondria. Endocytobiosis Cell Res 15:77–86Google Scholar
  50. Svab Z, Maliga P (1993) High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc Natl Acad Sci USA 90:913–917PubMedGoogle Scholar
  51. 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 25:4876–4882CrossRefPubMedGoogle Scholar
  52. Turmel M, Otis C, Lemieux C (2002) The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci USA 99:11275-11280CrossRefPubMedGoogle Scholar
  53. Turmel M, Otis C, Lemieux C (2003) The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell 15:1888–1903CrossRefPubMedGoogle Scholar
  54. Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet 15:57–61PubMedGoogle Scholar
  55. Weber F, Dietrich A, Weil J-H, Marechal-Drouard L (1990) A potato mitochondrial isoleucine tRNA is coded for by a mitochondrial gene possessing a methionine anticodon. Nucleic Acids Res 18:5027–5030PubMedGoogle Scholar
  56. Zanlungo S, Quiñones V, Moenne A, Holuigue L, Jordana X (1995). Splicing and editing of rps10 transcripts in potato mitochondria. Curr Genet 27:565–571CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Y. Sugiyama
    • 1
  • Y. Watase
    • 1
  • M. Nagase
    • 1
  • N. Makita
    • 2
  • S. Yagura
    • 1
  • A. Hirai
    • 3
  • M. Sugiura
    • 2
  1. 1.Center for Gene ResearchNagoya UniversityNagoya Japan
  2. 2.Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
  3. 3.Faculty of AgricultureMeijo UniversityNagoyaJapan

Personalised recommendations