Journal of Molecular Evolution

, Volume 60, Issue 1, pp 113–127 | Cite as

The Origin of Dihydroorotate Dehydrogenase Genes of Kinetoplastids, with Special Reference to Their Biological Significance and Adaptation to Anaerobic, Parasitic Conditions

  • Takeshi Annoura
  • Takeshi Nara
  • Takashi Makiuchi
  • Tetsuo Hashimoto
  • Takashi Aoki
Articles

Abstract

Trypanosoma cruzi dihydroorotate dehydrogenase (DHOD), the fourth enzyme of the de novo pyrimidine biosynthetic pathway, is localized in the cytosol and utilizes fumarate as electron acceptor (fumarate reductase activity), while the enzyme from other various eukaryotes is mitochondrial membrane-linked. Here we report that DHOD-knockout T. cruzi did not express the enzyme protein and could not survive even in the presence of pyrimidine nucleosides, substrates for the potentially active salvage pathway, suggesting a vital role of fumarate reductase activity in the regulation of cellular redox balance. Cloning and phylogenetic analysis of euglenozoan DHOD genes showed that the euglenoid Euglena gracilis had a mitochondrial DHOD and that biflagellated bodonids, a sister group of trypanosomatids within kinetoplastids, harbor the cytosolic DHOD. Further, Bodo saliens, a bodonid, had an ACT/DHOD gene fusion encoding aspartate carbamoyltransferase (ACT), the second enzyme of the de novo pyrimidine pathway, and DHOD. This is the first report of this novel gene structure. These results are consistent with suggestions that an ancient common ancestor of Euglenozoa had a mitochondrial DHOD whose descendant exists in E. gracilis and that a common ancestor of kinetoplastids (bodonids and trypanosomatids) subsequently acquired a cytosolic DHOD by horizontal gene transfer. The cytosolic DHOD gene thus acquired may have contributed to adaptation to anaerobiosis in the kinetoplastid lineage and further contributed to the subsequent establishment of parasitism in a trypanosomatid ancestor. Different molecular strategies for anaerobic adaptation in pyrimidine biosynthesis, used by kinetoplastids and by euglenoids, are discussed. Evolutionary implications of the ACT/DHOD gene fusion are also discussed.

Keywords

Dihydroorotate dehydrogenase Trypanosoma cruzi Bodonid Kinetoplastid Euglenozoa Phylogenetic tree Gene fusion Horizontal gene transfer Anaerobiosis 

Notes

Acknowledgments

We express our sincere thanks to Dr. Miklós Müller for his critical reading of the manuscript, Mr. Masao Odaka and Ms. Yuko Mikami for their technical assistance, and Dr. Tomoyoshi Nozaki for plasmids p72hyg72 and p72tun72. A part of this work was supported by grants-in-aid for scientific research (Nos. 15390138, 15659102, and 13640709) from the Ministry of Education, Science, Sports, and Culture of Japan, from Ohyama Health Foundation (to T.N.), and from Kampou Science Foundation (to T.N.). T. Annoura and T. Aoki are supported by a Grant-in-Aid for 21st Century COE Research from the Ministry of Education, Science, Sports, and Culture of Japan.

References

  1. Andersen, PS, Jansen, PJ, Hammer, K 1994Two different dihydroorotate dehydrogenases in Lactococcus lactisJ Bacteriol17639753982Google Scholar
  2. Arisue, N, Hashimoto, T, Lee, JA, Moore, DV, Gordon, P, Sensen, CW, Gaasterland, T, Hasegawa, M, Müller, M 2002aThe phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2J Eukaryot Microbiol49110Google Scholar
  3. Arisue, N, Hashimoto, T, Yoshikawa, H, Nakamura, Y, Nakamura, G, Nakamura, F, Yano, TA, Hasegawa, M 2002bPhylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence dataJ Eukaryot Microbiol494253Google Scholar
  4. Arisue, N, Sánchez, LB, Weiss, LM, Müller, M, Hashimoto, T 2002cMitochondrial-type hsp70 genes of the amitochondriate protists, Giardia intestinalis, Entamoeba histolytica and two microsporidiansParasitol Int51916Google Scholar
  5. Atkins, MS, Teske, AP, Anderson, OR 2000A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approachesJ Eukaryot Microbiol47400411Google Scholar
  6. Baldauf, SL, Roger, AJ, Wenk-Siefert, I, Doolittle, WF 2000A kingdom-level phylogeny of eukaryotes based on combined protein dataScience290972977CrossRefPubMedGoogle Scholar
  7. Bapteste, E, Brinkmann, H, Lee, JA, Moore, DV, Sensen, CW, Gordon, P, Duruflé, L, Gaasterland, T, Lopez, P, Müller, M, Philippe, H 2002The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and MastigamoebaProc Natl Acad Sci USA9914141419CrossRefPubMedGoogle Scholar
  8. Cannata, JJ, Cazzulo, JJ 1984The aerobic fermentation of glucose by Trypanosoma cruziComp Biochem Physiol B79297308Google Scholar
  9. Carrey, EA 1995The shape of CADPaths Pyrimidines36872Google Scholar
  10. Cazzulo, JJ, Cazzulo, BM Franke, Engel, JC, Cannata, JJ 1985End products and enzyme levels of aerobic glucose fermentation in trypanosomatidsMol Biochem Parasitol16329343Google Scholar
  11. Chaudhuri, M, Hill, GC 1996Cloning, sequencing, and functional activity of the Trypanosoma brucei brucei alternative oxidaseMol Biochem Parasitol83125129Google Scholar
  12. Chaumont, F, Schanck, AN, Blum, JJ, Opperdoes, FR 1994Aerobic and anaerobic glucose metabolism of Phytomonas sp. isolated from Euphorbia characiasMol Biochem Parasitol67321331Google Scholar
  13. Clayton, CE, Michels, P 1996Metabolic compartmentation in African trypanosomesParasitol Today12465471Google Scholar
  14. Cooper, R, Jesus, AR, Cross, GAM 1993Deletion of an immunodominant Trypanosoma cruzi surface glycoprotein disrupts flagellum-cell adhesionJ Cell Biol122149156Google Scholar
  15. Felsenstein, J 2002PHYLIP (phylogeny inference package). Version 3.6a. Distributed by the authorUniversity of WashingtonSeattleGoogle Scholar
  16. Fernandes, AP, Nelson, K, Beverley, SM 1993Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: Perspectives on the age and origins of parasitismProc Natl Acad Sci USA901160811612Google Scholar
  17. Fichera, ME, Roos, DS 1997A plastid organelle as a drug target in apicomplexan parasitesNature390407409Google Scholar
  18. Fox, BA, Bzik, DJ 2002De novo pyrimidine biosynthesis is required for virulence of Toxoplasma gondiiNature415926929Google Scholar
  19. Gao, G, Nara, T, Nakajima-Shimada, J, Aoki, T 1999Novel organization and sequences of five genes encoding all six enzymes for de novo pyrimidine biosynthesis in Trypanosoma cruziJ Mol Biol285149161Google Scholar
  20. Gardner, MJ, Hall, N, Fung, E, White, O, Berriman, M, Hyman, RW, Carlton, JM, Pain, A, Nelson, KE, Bowman, S, Paulsen, IT, James, K, Eisen, JA, Rutherford, K, Salzberg, SL, Craig, A, Kyes, S, Chan, MS, Nene, V, Shallom, SJ, Suh, B, Peterson, J, Angiuoli, S, Pertea, M, Allen, J, Selengut, J, Haft, D, Mather, MW, Vaidya, AB, Martin, DM, Fairlamb, AH, Fraunholz, MJ, Roos, DS, Ralph, SA, McFadden, GI, Cummings, LM, Subramanian, GM, Mungall, C, Venter, JC, Carucci, DJ, Hoffman, SL, Newbold, C, Davis, RW, Fraser, CM, Barrell, B 2002Genome sequence of the human malaria parasite Plasmodium falciparumNature419498511CrossRefPubMedGoogle Scholar
  21. Gutteridge, WE, Gaborak, M 1979A re-examination of purine and pyrimidine synthesis in the three main forms of Trypanosoma cruziInt J Biochem10415422Google Scholar
  22. Hashimoto, T, Sanchéz, LB, Shirakura, T, Müller, M, Hasegawa, M 1998Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogenyProc Natl Acad Sci USA9568606865Google Scholar
  23. Hines, V, Keys, LD,3rd, Johnston, M 1986Purification and properties of the bovine liver mitochondrial dihydroorotate dehydrogenaseJ Biol Chem2611138611392Google Scholar
  24. Hughey, R, Krogh, A 1996Hidden Markov models for sequence analysis: extension and analysis of the basic methodComput Appl Biosci1295107Google Scholar
  25. Inui, H, Miyatake, K, Nakano, Y, Kitaoka, S 1982Wax ester fermentation in Euglena gracilisFEBS Lett1508993Google Scholar
  26. Irvine, HS, Shaw, SM, Paton, A, Carrey, EA 1997A reciprocal allosteric mechanism for efficient transfer of labile intermediates between active sites in CAD, the mammalian pyrimidine-biosynthetic multienzyme polypeptideEur J Biochem24710631073Google Scholar
  27. Jensen, KF, Björnberg, O 1998Evolutionary and functional families of dihydroorotate dehydrogenasesPaths Pyrimidines62028Google Scholar
  28. Jomaa, H, Wiesner, J, Sanderbrand, S, Altincicek, B, Weidemeyer, C, Hintz, M, Türbachova, I, Eberl, M, Zeidler, J, Lichtenthaler, HK, Soldati, D, Beck, E 1999Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugsScience28515731576Google Scholar
  29. Katinka, MD, Duprat, S, Cornillot, E, Metenier, G, Thomarat, F, Prensier, G, Barbe, V, Peyretaillade, E, Brottier, P, Wincker, P, Delbac, F, El Alaoui, H, Peyret, P, Saurin, W, Gouy, M, Weissenbach, J, Vivares, CP 2001Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculiNature414450453CrossRefPubMedGoogle Scholar
  30. Keeling, PJ 2001Parasites go the full montyNature414401402Google Scholar
  31. Kelly, JM, Ward, HM, Miles, MA, Kendall, G 1992A shuttle vector which facilitates the expression of transfected genes in Trypanosoma cruzi and LeishmaniaNucleic Acids Res2039633969Google Scholar
  32. Köhler, S, Delwiche, CF, Denny, PW, Tilney, LG, Webster, P, Wilson, RJ, Palmer, JD, Roos, DS 1997A plastid of probable green algal origin in Apicomplexan parasitesScience27514851489Google Scholar
  33. Lipscomb, WL 1994Aspartate transcarbamylase from Escherichia coli: A brief summaryPaths Pyrimidines22537Google Scholar
  34. Misset, O, Bos, OJ, Opperdoes, FR 1986Glycolytic enzymes of Trypanosoma brucei. Simultaneous purification, intraglycosomal concentrations and physical propertiesEur J Biochem157441453Google Scholar
  35. Nagy, M, Lacroute, F, Thomas, D 1992Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeastsProc Natl Acad Sci USA8989668970PubMedGoogle Scholar
  36. Nara, T, Gao, G, Yamasaki, H, Nakajima-Shimada, J, Aoki, T 1998Carbamoyl-phosphate synthetase II in kinetoplastidsBiochim Biophys Acta1387462468Google Scholar
  37. Nara, T, Hashimoto, T, Aoki, T 2000Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotesGene257209222Google Scholar
  38. Nara, T, Hirayama-Noguchi, Y, Gao, G, Murai, E, Annoura, T, Aoki, T 2003Diversity of aspartate carbamoyltransferase genes of Trypanosoma cruziInt J Parasitol33845852Google Scholar
  39. Newton, NA, Cox, GB, Gibson, F 1971The function of menaquinone (vitamin K2) in Escherichia coli K-12Biochim Biophys Acta244155166Google Scholar
  40. Nielsen, FS, Andersen, PS, Jensen, KF 1996The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centersJ Biol Chem2712935929365Google Scholar
  41. Nozaki, T, Cross, GAM 1994Functional complementation of glycoprotein 72 in a Trypanosoma cruzi glycoprotein 72 null mutantMol Biochem Parasitol6791102Google Scholar
  42. Opperdoes, FR 1987Compartmentation of carbohydrate metabolism in trypanosomesAnnu Rev Microbiol41127151Google Scholar
  43. Opperdoes, FR, Borst, P, Bakker, S, Leene, W 1977Localization of glycerol-3-phosphate oxidase in the mitochondrion and particulate NAD+-linked glycerol-3-phosphate dehydrogenase in the microbodies of the bloodstream form to Trypanosoma bruceiEur J Biochem762939Google Scholar
  44. Powls, R, Hemming, FW 1966The biosynthesis of quinones from p-hydroxybenzoic acid in Euglena gracilis var. bacillarisPhotochemistry512491255Google Scholar
  45. Schneider, T, Betz, A 1985Wax ester fermentation in Euglena gracilis. T Factors favouring the synthesis of odd-numbered fatty acids and alcoholsPlanta1666773Google Scholar
  46. Simpson, AG, Lukes, J, Roger, AJ 2002The evolutionary history of kinetoplastids and their kinetoplastsMol Biol Evol1920712083Google Scholar
  47. Simpson, L, Thiemann, OH, Savill, NJ, Alfonzo, JD, Maslov, DA 2000Evolution of RNA editing in trypanosome mitochondriaProc Natl Acad Sci USA9769866993Google Scholar
  48. Sogin, ML, Silberman, JD 1998Evolution of the protists and protistan parasites from the perspective of molecular systematicsInt J Parasitol281120CrossRefPubMedGoogle Scholar
  49. Takashima, E, Inaoka, DK, Osanai, A, Nara, T, Odaka, M, Aoki, T, Inaka, K, Harada, S, Kita, K 2002Characterization of the dihydroorotate dehydrogenase as a soluble fumarate reductase in Trypanosoma cruziMol Biochem Parasitol122189200Google Scholar
  50. Tielens, AGM, Hellemond, JJ 1998More differences in energy metabolism between TrypanosomatidaeParasitol Today14265271Google Scholar
  51. Tielens, AG, Rotte, C, Hellemond, JJ, Martin, W 2002Mitochondria as we don’t know themTrends Biochem Sci27564572Google Scholar
  52. Visser, N, Opperdoes, FR, Borst, P 1981Subcellular compartmentation of glycolytic intermediates in Trypanosoma bruceiEur J Biochem118521526Google Scholar
  53. Watanabe, Y, Gray, MW 2000Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteriaNucleic Acids Res2823422352Google Scholar
  54. Wilson, RJ, Denny, PW, Preiser, PR, Rangachari, K, Roberts, K, Roy, A, Whyte, A, Strath, M, Moore, DJ, Moore, PW, Williamson, DH 1996Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparumJ Mol Biol261155172CrossRefPubMedGoogle Scholar
  55. Yang, Z 1997PAML: A program package for phylogenetic analysis by maximum likelihoodComput Appl Biosci13555556PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Takeshi Annoura
    • 1
  • Takeshi Nara
    • 1
  • Takashi Makiuchi
    • 1
    • 2
  • Tetsuo Hashimoto
    • 3
  • Takashi Aoki
    • 1
  1. 1.Department of Molecular and Cellular ParasitologyJuntendo University School of MedicineBunkyo-kuJapan
  2. 2.Department of Molecular BiologyTokyo University of Pharmacy and Life ScienceHachiojiJapan
  3. 3.Institute of Biological SciencesUniversity of TsukubaTsukubaJapan

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