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. 1990 Jan 11;18(1):173–180. doi: 10.1093/nar/18.1.173

Nucleotide sequence of the mitochondrial genome of Paramecium.

A E Pritchard 1, J J Seilhamer 1, R Mahalingam 1, C L Sable 1, S E Venuti 1, D J Cummings 1
PMCID: PMC330218  PMID: 2308823

Abstract

The nucleotide sequence for 40,469 bp of the linear Paramecium aurelia mitochondrial (mt) genome is presented with the locations of the known genes, presumed ORFs, and their transcripts. Many of the genes commonly encoded in mt DNA of other organisms have been identified in the Paramecium mt genome but several unusual genes have been found. Ribosomal protein genes rps14, rps12, and rpl2 are clustered in a region that also contains two other genes usually found in chloroplasts, but rpl14 is over 16 kbp away. The ATP synthase gene, atp9, is encoded in this mt genome, but the atp6, atp8, and COIII genes have not been identified. All of the identified genes are transcribed. Many mono- and poly- cistronic transcripts have been detected which cover most of the genome, including large regions where genes have yet to be identified. Based on sequence comparisons with known tRNAs, only those for phe, trp, and tyr are encoded in Paramecium mt DNA.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Anderson S., de Bruijn M. H., Coulson A. R., Eperon I. C., Sanger F., Young I. G. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol. 1982 Apr 25;156(4):683–717. doi: 10.1016/0022-2836(82)90137-1. [DOI] [PubMed] [Google Scholar]
  3. Arnberg A. C., Van Bruggen E. F., Clegg R. A., Upholt W. B., Borst P. An analysis by electron microscopy of intermediates in the replication of linear Tetrahymena mitochondrial DNA. Biochim Biophys Acta. 1974 Sep 13;361(3):266–276. doi: 10.1016/0005-2787(74)90370-0. [DOI] [PubMed] [Google Scholar]
  4. Benne R., Sloof P. Evolution of the mitochondrial protein synthetic machinery. Biosystems. 1987;21(1):51–68. doi: 10.1016/0303-2647(87)90006-2. [DOI] [PubMed] [Google Scholar]
  5. Bibb M. J., Findlay P. R., Johnson M. W. The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene. 1984 Oct;30(1-3):157–166. doi: 10.1016/0378-1119(84)90116-1. [DOI] [PubMed] [Google Scholar]
  6. Bibb M. J., Van Etten R. A., Wright C. T., Walberg M. W., Clayton D. A. Sequence and gene organization of mouse mitochondrial DNA. Cell. 1981 Oct;26(2 Pt 2):167–180. doi: 10.1016/0092-8674(81)90300-7. [DOI] [PubMed] [Google Scholar]
  7. Boer P. H., Gray M. W. Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria. Curr Genet. 1988 Dec;14(6):583–590. doi: 10.1007/BF00434084. [DOI] [PubMed] [Google Scholar]
  8. Brown T. A., Waring R. B., Scazzocchio C., Davies R. W. The Aspergillus nidulans mitochondrial genome. Curr Genet. 1985;9(2):113–117. doi: 10.1007/BF00436957. [DOI] [PubMed] [Google Scholar]
  9. Chomyn A., Mariottini P., Cleeter M. W., Ragan C. I., Matsuno-Yagi A., Hatefi Y., Doolittle R. F., Attardi G. Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase. Nature. 1985 Apr 18;314(6012):592–597. doi: 10.1038/314592a0. [DOI] [PubMed] [Google Scholar]
  10. Clary D. O., Wolstenholme D. R. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22(3):252–271. doi: 10.1007/BF02099755. [DOI] [PubMed] [Google Scholar]
  11. Crick F. H. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. doi: 10.1016/s0022-2836(66)80022-0. [DOI] [PubMed] [Google Scholar]
  12. Cummings D. J., Domenico J. M. Sequence analysis of mitochondrial DNA from Podospora anserina. Pervasiveness of a class I intron in three separate genes. J Mol Biol. 1988 Dec 20;204(4):815–839. doi: 10.1016/0022-2836(88)90044-7. [DOI] [PubMed] [Google Scholar]
  13. Cummings D. J., Laping J. L. Organization and closing of mitochondrial deoxyribonucleic acid from Paramecium tetraaurelia and Paramecium primaurelia. Mol Cell Biol. 1981 Nov;1(11):972–982. doi: 10.1128/mcb.1.11.972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dewey R. E., Schuster A. M., Levings C. S., Timothy D. H. Nucleotide sequence of F(0)-ATPase proteolipid (subunit 9) gene of maize mitochondria. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1015–1019. doi: 10.1073/pnas.82.4.1015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Feagin J. E., Abraham J. M., Stuart K. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell. 1988 May 6;53(3):413–422. doi: 10.1016/0092-8674(88)90161-4. [DOI] [PubMed] [Google Scholar]
  16. Fearnley I. M., Runswick M. J., Walker J. E. A homologue of the nuclear coded 49 kd subunit of bovine mitochondrial NADH-ubiquinone reductase is coded in chloroplast DNA. EMBO J. 1989 Mar;8(3):665–672. doi: 10.1002/j.1460-2075.1989.tb03424.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fearnley I. M., Walker J. E. Two overlapping genes in bovine mitochondrial DNA encode membrane components of ATP synthase. EMBO J. 1986 Aug;5(8):2003–2008. doi: 10.1002/j.1460-2075.1986.tb04456.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Fickett J. W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 1982 Sep 11;10(17):5303–5318. doi: 10.1093/nar/10.17.5303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gray M. W., Sankoff D., Cedergren R. J. On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res. 1984 Jul 25;12(14):5837–5852. doi: 10.1093/nar/12.14.5837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Heckman J. E., Sarnoff J., Alzner-DeWeerd B., Yin S., RajBhandary U. L. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3159–3163. doi: 10.1073/pnas.77.6.3159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Heinonen T. Y., Schnare M. N., Young P. G., Gray M. W. Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J Biol Chem. 1987 Feb 25;262(6):2879–2887. [PubMed] [Google Scholar]
  22. Horowitz S., Gorovsky M. A. An unusual genetic code in nuclear genes of Tetrahymena. Proc Natl Acad Sci U S A. 1985 Apr;82(8):2452–2455. doi: 10.1073/pnas.82.8.2452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jacobs H. T., Elliott D. J., Math V. B., Farquharson A. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol. 1988 Jul 20;202(2):185–217. doi: 10.1016/0022-2836(88)90452-4. [DOI] [PubMed] [Google Scholar]
  24. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  25. Macino G., Tzagoloff A. Assembly of the mitochondrial membrane system. The DNA sequence of a mitochondrial ATPase gene in Saccharomyces cerevisiae. J Biol Chem. 1979 Jun 10;254(11):4617–4623. [PubMed] [Google Scholar]
  26. Mahalingam R., Seilhamer J. J., Pritchard A. E., Cummings D. J. Identification of Paramecium mitochondrial proteins using antibodies raised against fused mitochondrial gene products. Gene. 1986;49(1):129–138. doi: 10.1016/0378-1119(86)90392-6. [DOI] [PubMed] [Google Scholar]
  27. Maréchal-Drouard L., Weil J. H., Guillemaut P. Import of several tRNAs from the cytoplasm into the mitochondria in bean Phaseolus vulgaris. Nucleic Acids Res. 1988 Jun 10;16(11):4777–4788. doi: 10.1093/nar/16.11.4777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Matsubayashi T., Wakasugi T., Shinozaki K., Yamaguchi-Shinozaki K., Zaita N., Hidaka T., Meng B. Y., Ohto C., Tanaka M., Kato A. Six chloroplast genes (ndhA-F) homologous to human mitochondrial genes encoding components of the respiratory chain NADH dehydrogenase are actively expressed: determination of the splice sites in ndhA and ndhB pre-mRNAs. Mol Gen Genet. 1987 Dec;210(3):385–393. doi: 10.1007/BF00327187. [DOI] [PubMed] [Google Scholar]
  29. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  30. Nixon P. J., Gounaris K., Coomber S. A., Hunter C. N., Dyer T. A., Barber J. psbG is not a photosystem two gene but may be an ndh gene. J Biol Chem. 1989 Aug 25;264(24):14129–14135. [PubMed] [Google Scholar]
  31. Palmer J. D., Herbon L. A. Unicircular structure of the Brassica hirta mitochondrial genome. Curr Genet. 1987;11(6-7):565–570. doi: 10.1007/BF00384620. [DOI] [PubMed] [Google Scholar]
  32. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Preer J. R., Jr, Preer L. B., Rudman B. M., Barnett A. J. Deviation from the universal code shown by the gene for surface protein 51A in Paramecium. Nature. 1985 Mar 14;314(6007):188–190. doi: 10.1038/314188a0. [DOI] [PubMed] [Google Scholar]
  34. Pritchard A. E., Laping J. L., Seilhamer J. J., Cummings D. J. Inter-species sequence diversity in the replication initiation region of Paramecium mitochondrial DNA. J Mol Biol. 1983 Feb 15;164(1):1–15. doi: 10.1016/0022-2836(83)90084-0. [DOI] [PubMed] [Google Scholar]
  35. Pritchard A. E., Sable C. L., Venuti S. E., Cummings D. J. Analysis of NADH dehydrogenase proteins, ATPase subunit 9, cytochrome b, and ribosomal protein L14 encoded in the mitochondrial DNA of Paramecium. Nucleic Acids Res. 1990 Jan 11;18(1):163–171. doi: 10.1093/nar/18.1.163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pritchard A. E., Seilhamer J. J., Cummings D. J. Paramecium mitochondrial DNA sequences and RNA transcripts for cytochrome oxidase subunit I, URF1, and three ORFs adjacent to the replication origin. Gene. 1986;44(2-3):243–253. doi: 10.1016/0378-1119(86)90188-5. [DOI] [PubMed] [Google Scholar]
  37. Pritchard A. E., Venuti S. E., Ghalambor M. A., Sable C. L., Cummings D. J. An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes. Gene. 1989 May 15;78(1):121–134. doi: 10.1016/0378-1119(89)90320-x. [DOI] [PubMed] [Google Scholar]
  38. Rich A., RajBhandary U. L. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. doi: 10.1146/annurev.bi.45.070176.004105. [DOI] [PubMed] [Google Scholar]
  39. Roe B. A., Ma D. P., Wilson R. K., Wong J. F. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem. 1985 Aug 15;260(17):9759–9774. [PubMed] [Google Scholar]
  40. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Schnare M. N., Heinonen T. Y., Young P. G., Gray M. W. A discontinuous small subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J Biol Chem. 1986 Apr 15;261(11):5187–5193. [PubMed] [Google Scholar]
  42. Seilhamer J. J., Cummings D. J. Altered genetic code in Paramecium mitochondria: possible evolutionary trends. Mol Gen Genet. 1982;187(2):236–239. doi: 10.1007/BF00331123. [DOI] [PubMed] [Google Scholar]
  43. Seilhamer J. J., Cummings D. J. Structure and sequence of the mitochondrial 20S rRNA and tRNA tyr gene of Paramecium primaurelia. Nucleic Acids Res. 1981 Dec 11;9(23):6391–6406. doi: 10.1093/nar/9.23.6391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Seilhamer J. J., Gutell R. R., Cummings D. J. Paramecium mitochondrial genes. II. Large subunit rRNA gene sequence and microevolution. J Biol Chem. 1984 Apr 25;259(8):5173–5181. [PubMed] [Google Scholar]
  45. Seilhamer J. J., Olsen G. J., Cummings D. J. Paramecium mitochondrial genes. I. Small subunit rRNA gene sequence and microevolution. J Biol Chem. 1984 Apr 25;259(8):5167–5172. [PubMed] [Google Scholar]
  46. Simpson A. M., Suyama Y., Dewes H., Campbell D. A., Simpson L. Kinetoplastid mitochondria contain functional tRNAs which are encoded in nuclear DNA and also contain small minicircle and maxicircle transcripts of unknown function. Nucleic Acids Res. 1989 Jul 25;17(14):5427–5445. doi: 10.1093/nar/17.14.5427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Simpson L., Neckelmann N., de la Cruz V. F., Simpson A. M., Feagin J. E., Jasmer D. P., Stuart K. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J Biol Chem. 1987 May 5;262(13):6182–6196. [PubMed] [Google Scholar]
  48. Simpson L., Neckelmann N., de la Cruz V. F., Simpson A. M., Feagin J. E., Jasmer D. P., Stuart K. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J Biol Chem. 1987 May 5;262(13):6182–6196. [PubMed] [Google Scholar]
  49. Simpson L. The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution. Annu Rev Microbiol. 1987;41:363–382. doi: 10.1146/annurev.mi.41.100187.002051. [DOI] [PubMed] [Google Scholar]
  50. Steinmetz A. A., Castroviejo M., Sayre R. T., Bogorad L. Protein PSII-G. An additional component of photosystem II identified through its plastid gene in maize. J Biol Chem. 1986 Feb 25;261(6):2485–2488. [PubMed] [Google Scholar]
  51. Steinmüller K., Ley A. C., Steinmetz A. A., Sayre R. T., Bogorad L. Characterization of the ndhC-psbG-ORF157/159 operon of maize plastid DNA and of the cyanobacterium Synechocystis sp. PCC6803. Mol Gen Genet. 1989 Mar;216(1):60–69. doi: 10.1007/BF00332231. [DOI] [PubMed] [Google Scholar]
  52. Suyama Y., Fukuhara H., Sor F. A fine restriction map of the linear mitochondrial DNA of Tetrahymena pyriformis: genome size, map locations of rRNA and tRNA genes, terminal inversion repeat, and restriction site polymorphism. Curr Genet. 1985;9(6):479–493. doi: 10.1007/BF00434053. [DOI] [PubMed] [Google Scholar]
  53. Suyama Y., Jenney F. The tRNAglu (anticodon TTU) gene and its upstream sequence coding for a homolog of the E. coli large ribosome-subunit protein L14 in the Tetrahymena mitochondrial genome. Nucleic Acids Res. 1989 Jan 25;17(2):803–803. doi: 10.1093/nar/17.2.803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Suyama Y. Two dimensional polyacrylamide gel electrophoresis analysis of Tetrahymena mitochondrial tRNA. Curr Genet. 1986;10(5):411–420. doi: 10.1007/BF00418415. [DOI] [PubMed] [Google Scholar]
  55. Wahleithner J. A., Wolstenholme D. R. Ribosomal protein S14 genes in broad bean mitochondrial DNA. Nucleic Acids Res. 1988 Jul 25;16(14B):6897–6913. doi: 10.1093/nar/16.14.6897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Yang D., Oyaizu Y., Oyaizu H., Olsen G. J., Woese C. R. Mitochondrial origins. Proc Natl Acad Sci U S A. 1985 Jul;82(13):4443–4447. doi: 10.1073/pnas.82.13.4443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Ziaie Z., Suyama Y. The cytochrome oxidase subunit I gene of Tetrahymena: a 57 amino acid NH2-terminal extension and a 108 amino acid insert. Curr Genet. 1987;12(5):357–368. doi: 10.1007/BF00405758. [DOI] [PubMed] [Google Scholar]
  58. de Zamaroczy M., Bernardi G. The primary structure of the mitochondrial genome of Saccharomyces cerevisiae--a review. Gene. 1986;47(2-3):155–177. doi: 10.1016/0378-1119(86)90060-0. [DOI] [PubMed] [Google Scholar]

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