Article

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

  • Nature Ecology & Evolution 1, Article number: 0092 (2017)
  • doi:10.1038/s41559-017-0092
  • Download Citation
Received:
Accepted:
Published online:

Abstract

Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed. Here, we present a large-scale comparative transcriptomic study of MROs across a major eukaryotic group, Metamonada, examining lineage-specific gain and loss of metabolic functions in the MROs of Trichomonas, Giardia, Spironucleus and their free-living relatives. Our analyses uncover a complex history of ATP production machinery in diplomonads such as Giardia, and their closest relative, Dysnectes; and a correlation between the glycine cleavage machinery and lifestyles. Our data further suggest the existence of a previously undescribed biochemical class of MRO that generates hydrogen but is incapable of ATP synthesis.

  • Subscribe to Nature Ecology & Evolution for full access:

    $99

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    , & Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Phil. Trans. R. Soc. Lond. B 370, 20140326 (2015).

  2. 2.

    & Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate Tritrichomonas foetus, and its role in pyruvate metabolism. J. Biol. Chem. 248, 7724–7728 (1973).

  3. 3.

    et al. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76, 444–495 (2012).

  4. 4.

    et al. Hydrogenosomes in the diplomonad Spironucleus salmonicida. Nat. Commun. 4, 2493 (2013).

  5. 5.

    et al. The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis. PLoS ONE 6, e17285 (2011).

  6. 6.

    et al. A eukaryote without a mitochondrial organelle. Curr. Biol. 26, 1274–1284 (2016).

  7. 7.

    et al. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of ‘amitochondriate’ diplomonads and retortamonads. Protist 163, 344–355 (2012).

  8. 8.

    & On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata. J. Eukaryot. Microbiol. 48, 480–492 (2001).

  9. 9.

    , , & Evolution of the molecular machines for protein import into mitochondria. Science 313, 314–318 (2006).

  10. 10.

    et al. Probing the biology of Giardia intestinalis mitosomes using in vivo enzymatic tagging. Mol. Cell. Biol. 35, 2864–2874 (2015).

  11. 11.

    & Translocation of proteins into mitochondria. Annu. Rev. Biochem. 76, 723–749 (2007).

  12. 12.

    , & A yeast mutant temperature-sensitive for mitochondrial assembly is deficient in a mitochondrial protease activity that cleaves imported precursor polypeptides. EMBO J. 4, 2069–2074 (1985).

  13. 13.

    , , & , E. Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites Trichomonas vaginalis and Giardia intestinalis. PLoS Pathog. 4, e1000243 (2008).

  14. 14.

    et al. Conservation of transit peptide-independent protein import into the mitochondrial and hydrogenosomal matrix. Genome Biol. Evol. 7, 2716–2726 (2015).

  15. 15.

    The glycine cleavage system: composition, reaction mechanism, and physiological significance. Mol. Cell. Biochem. 1, 169–187 (1973).

  16. 16.

    , , & Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis. Eukaryot. Cell 5, 2062–2071 (2006).

  17. 17.

    et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317, 1921–1926 (2007).

  18. 18.

    et al. The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system. PLoS ONE 8, e55417 (2013).

  19. 19.

    et al. Genetic evidence for a mitochondriate ancestry in the ‘amitochondriate’ flagellate Trimastix pyriformis. PLoS ONE 3, e1383 (2008).

  20. 20.

    , , & OsmC and incomplete glycine decarboxylase complex mediate reductive detoxification of peroxides in hydrogenosomes of Trichomonas vaginalis. Mol. Biochem. Parasitol. 206, 29–38 (2016).

  21. 21.

    et al. On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biol. 14, 62 (2016).

  22. 22.

    , & Regulation of the glycine cleavage system in isolated rat liver mitochondria. J. Biol. Chem. 258, 2993–2999 (1983).

  23. 23.

    & Anaerobic pyruvate metabolism of Tritrichomonas foetus and Trichomonas vaginalis hydrogenosomes. Mol. Biochem. Parasitol. 20, 57–65 (1986).

  24. 24.

    , , , & Rhodoquinone and complex II of the electron transport chain in anaerobically functioning eukaryotes. J. Biol. Chem. 270, 31065–31070 (1995).

  25. 25.

    , , , & Acetate formation in the energy metabolism of parasitic helminths and protists. Int. J. Parasitol. 40, 387–397 (2010).

  26. 26.

    & Purification and characterization of the acetate forming enzyme, acetyl-CoA synthetase (ADP-forming) from the amitochondriate protist, Giardia lamblia. FEBS Lett. 378, 240–244 (1996).

  27. 27.

    et al. Metabolic capacity of mitochondrion-related organelles in the free-living anaerobic stramenopile Cantina marsupialis. Protist 166, 534–550 (2015).

  28. 28.

    , & Early lateral transfer of genes encoding malic enzyme, acetyl-CoA synthetase and alcohol dehydrogenases from anaerobic prokaryotes to Entamoeba histolytica. Mol. Microbiol. 38, 446–455 (2000).

  29. 29.

    et al. Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Mol. Biol. Evol. 32, 1039–1055 (2015).

  30. 30.

    et al. The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes. Int. J. Parasitol. 41, 1421–1434 (2011).

  31. 31.

    , , , & MPIC: a mitochondrial protein import components database for plant and non-plant species. Plant Cell Physiol. 56, e10 (2015).

  32. 32.

    et al. Marine isolates of Trimastix marina form a plesiomorphic deep-branching lineage within Preaxostyla, separate from other known Trimastigids (Paratrimastix n. gen.). Protist 166, 468–491 (2015).

  33. 33.

    et al. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Env. Microbiol. 12, 2700–2710 (2010).

  34. 34.

    et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147–1159 (2004).

  35. 35.

    et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).

  36. 36.

    et al. Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages. Mol. Phylogenet. Evol. 78, 36–42 (2014).

  37. 37.

    & MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

  38. 38.

    & BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).

  39. 39.

    , & FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).

  40. 40.

    RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

  41. 41.

    , , & IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

  42. 42.

    , & Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013).

  43. 43.

    , , & PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

  44. 44.

    , , , & CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).

  45. 45.

    , & trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

  46. 46.

    & Recent developments in the MAFFT multiple sequence alignment program. Br. Bioinform. 9, 286–298 (2008).

  47. 47.

    , , , & Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles. Mol. Phylogenet. Evol. 101, 133–141 (2016).

  48. 48.

    MitoProt, a Macintosh application for studying mitochondrial proteins. Comput. Appl. Biosci. 11, 441–447 (1995).

  49. 49.

    , , & Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2, 953–971 (2007).

  50. 50.

    et al. MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites. Mol. Cell. Proteomics 14, 1113–1126 (2015).

Download references

Acknowledgements

M.K., M.M.L. and C.W.S. were supported by a grant (MOP-142349) from the Canadian Institutes of Health Research awarded to A.J.R. This work was also supported, in part, by a grant from the JSPS Strategic Young Researcher Overseas Visits Program (awarded to R.K.), by NSERC Grant 298366-2009 to A.G.B.S., by a Czech Science Foundation grant to I.Č. (project GA14-14105S) and by grants from the Japan Society for the Promotion of Science (JSPS; nos 15H05606 and 15K14591 awarded to R.K., 23117005 and 15H05231 awarded to T.H., and 23117006 awarded to Y.I.). We thank A. A. Heiss for his help with Trimastix marina data generation, and N. Ros for her comments on the manuscript.

Author information

Author notes

    • Michelle M. Leger
    • , Martin Kolisko
    •  & Ryoma Kamikawa

    These authors contributed equally to this work.

    • Michelle M. Leger
    • , Martin Kolisko
    • , Courtney W. Stairs
    •  & Laura Eme

    Present addresses: Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain (M.M.L.); Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budĕjovice, Czech Republic (M.K.); Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden (C.W.S. and L.E.)

Affiliations

  1. Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, PO Box 15000, Halifax, Nova Scotia B3H 4R2, Canada

    • Michelle M. Leger
    • , Martin Kolisko
    • , Courtney W. Stairs
    • , Laura Eme
    •  & Andrew J. Roger
  2. Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan

    • Ryoma Kamikawa
  3. Graduate School of Life and Environmental Sciences, Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan

    • Keitaro Kume
    • , Yuji Inagaki
    •  & Tetsuo Hashimoto
  4. Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague 2, Czech Republic

    • Ivan Čepička
  5. Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA

    • Jeffrey D. Silberman
  6. Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden

    • Jan O. Andersson
    •  & Feifei Xu
  7. Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan

    • Akinori Yabuki
    •  & Kiyotaka Takishita
  8. Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, Shandong, 264003, People’s Republic of China

    • Qianqian Zhang
  9. Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan

    • Yuji Inagaki
    •  & Tetsuo Hashimoto
  10. Department of Biology, Dalhousie University, 1355 Oxford Street, PO Box 15000, Halifax, Nova Scotia B3H 4R2, Canada

    • Alastair G. B. Simpson

Authors

  1. Search for Michelle M. Leger in:

  2. Search for Martin Kolisko in:

  3. Search for Ryoma Kamikawa in:

  4. Search for Courtney W. Stairs in:

  5. Search for Keitaro Kume in:

  6. Search for Ivan Čepička in:

  7. Search for Jeffrey D. Silberman in:

  8. Search for Jan O. Andersson in:

  9. Search for Feifei Xu in:

  10. Search for Akinori Yabuki in:

  11. Search for Laura Eme in:

  12. Search for Qianqian Zhang in:

  13. Search for Kiyotaka Takishita in:

  14. Search for Yuji Inagaki in:

  15. Search for Alastair G. B. Simpson in:

  16. Search for Tetsuo Hashimoto in:

  17. Search for Andrew J. Roger in:

Contributions

M.K., R.K., J.O.A., Y.I., A.G.B.S., T.H. and A.J.R. conceived and designed the experiments; M.K., K.K., I.Č., J.D.S., F.X., A.Y. and Q.Z. performed the experiments; M.M.L., M.K., R.K., C.W.S., K.K., L.E. and Y.I. analysed the data; R.K., C.W.S., J.D.S., K.T., Y.I., A.G.B.S., T.H. and A.J.R. contributed materials and/or analysis tools; and M.M.L., M.K., R.K., A.G.B.S. and A.J.R. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Tetsuo Hashimoto or Andrew J. Roger.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1–20, Supplementary Table 1

Excel files

  1. 1.

    Supplementary Data 1

    Predicted mitochondrion-related organelle proteins, and selected predicted cytosolic proteins, in metamonads.

Text files

  1. 1.

    Supplementary Data 2

    File containing the raw phylogenetic trees depicted in Supplementary Figs 4–20, including bootstrap support values, in Newick format.