Phylogeny of nuclear-encoded plastid-targeted GAPDH gene supports separate origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates

Protist

Volumn 155, Issue 4, 2004, Pages 447-458

  Takishita, Kiyotaka ^a   Ishida, Ken Ichiro ^b   Maruyama, Tadashi ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b KANAZAWA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; DINOPHYCEAE; EUKARYOTA; HAPTOPHYCEAE; KARENIA; KARLODINIUM; TAKAYAMA;

EID: 10844223848     PISSN: 14344610     EISSN: None     Source Type: Journal    
DOI: 10.1078/1434461042650325     Document Type: Article

References (52)

1. Bachvaroff TR, Concepcion GT, Rogers CR, Herman EM, Delwiche CF (2004) Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155: 65-78
2. Björnland T, Liaaen-Jensen S (1989) Distribution Patterns of Carotenoids in Relation to Chromophyte Phylogeny and Systematics. In: Green JC, Leadbeater BSC, Diver WI (eds) The Chromophyte Algae: Problems and Perspectives, The Systematics Association Special Volume No. 38. Clarendon Press, Oxford, pp 37-60
3. Clermont S, Corbier C, Mely Y, Gerard D, Wonacott A, Branlant G (1993) Determinants of coenzyme specificity in glyceraldehyde-3-phosphate dehydrogenase: role of the acidic residue in the fingerprint region of the nucleotide binding fold. Biochemistry 32: 10178-10184
4. Daugbjerg N, Hansen G, Larsen J, Moestrup Ø (2000) Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of 3 new genera of unarmoured dinoflagellates. Phycologia 39: 302-317
5. de Salas MF, Bolch CJS, Botes L, Nash G, Wright SW, Hallegraeff GM (2003) Takayama gen. nov. (Gymnodiniales, Dinophyceae), a new genus of unarmored dinoflagellates with sigmoid apical grooves, including the description of two new species. J Phycol 39: 1233-1246
6. Dodge J (1975) A survey of chloroplast ultrastructure in the Dinophyceae. Phycologia 4: 253-263
7. Dodge J (1989) Phylogenetic Relationships of Dinoflagellates and their Plastids. In: Green JC, Leadbeater BSC, Diver WI (eds) The Chromophyte Algae: Problems and Perspectives, The Systematics Association Special Volume No. 38. Clarendon Press, Oxford, pp 207-227
8. Elbrächter M, Schnepf E (1996) Gymnodinium chlorophorum, a new green, bloom-forming dinoflagellate (Dinophyceae, Gymnodiniales) with a vestigial prasinophyte endosymbiont. Phycologia 35: 381-393
9. Fagan TF, Hastings WJ (2002) Phylogenetic analysis indicates multiple origins of chloroplast glyceraldehyde-3-phosphate dehydrogenase genes in dinoflagellates. Mol Biol Evol 19: 1203-1207
10. Fagan T, Hastings WJ, Morse D (1998) The phylogeny of glyceraldehyde-3-phosphate dehydrogenase indicates lateral gene transfer from cryptomonads to dinoflagellates. J Mol Evol 47: 633-639
11. Fast NM, Kissinger JC, Roos DS, Keeling PJ (2001) Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol Biol Evol 18: 418-426
12. Felsenstein J (2001) PHYLIP, Phylogeny Inference Package (Department of Genetics, University of Washington, Seattle), Version 3.6a2
13. Figge RM, Cerff R (2001) GAPDH gene diversity in spirochetes: a paradigm for genetic promiscuity. Mol Biol Evol 18: 2240-2249
14. Figge RM, Schubert M, Brinkmann H, Cerff R (1999) Glyceraldehyde-3- phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. Mol Biol Evol 16: 429-440
15. Hackett JD, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Nosenko T, Bhattacharya D (2004) Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol 14: 213-218
16. Hansen G, Daugbjerg N, Henriksen P (2000) Comparative study of Gymnodinium mikimotoi and Gymnodinium aureolum, comb. nov. (= Gyrodinium aureolum) based on morphology, pigment composition, and molecular data. J Phycol 36: 394-410
17. Harper JT, Keeling PJ (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20: 1730-1735
18. Henze K, Badr A, Wettern M, Cerff R, Martin W (1995) A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc Natl Acad Sci USA 92: 9122-9126
19. Hewes CD, Mitchell BG, Moisan TA, Vernet M, Reid FMH (1998) The phycobilin signatures of chloroplasts from three dinoflagellate species: A microanalytical study of Dinophysis caudata, D. fortii, and D. acuminata (Dinophysiales, Dinophyceae). J Phycol 34: 945-951
20. Inagaki Y, Simpson AGB, Dacks JB, Roger AJ (2004) Phylogenetic artifacts can be caused by leucine, serine and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case study. Syst Biol 53: 582-493
21. Ishida K, Green BR (2002) Second- and third-hand chloroplasts in dinoflagellates: phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont. Proc Natl Acad Sci USA 99: 9294-9299
22. Jeffrey SW (1989) Chlorophyll c Pigments and their Distribution in the Chromophyte Algae. In: Green JC, Leadbeater BSC, Diver WI (eds) The Chromophyte Algae: Problems and Perspectives, The Systematics Association Special Volume No. 38. Clarendon Press, Oxford, pp 13-36
23. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. CABIOS 8: 275-282
24. Kishore R, Muchhal US, Schwartzbach SD (1993) The presequence of Euglena LHCPII, a cytoplasmically synthesized chloroplast protein, contains a functional endoplasmic reticulum-targeting domain. Proc Natl Acad Sci USA 90: 11845-11849
25. Kite GC, Dodge JD (1988) Cell and chloroplast ultrastructure in Gyrodinium aureolum and Gymnodinium galatheanum. Two marine dinoflagellates containing an unusual carotenoid. Sarsia 73: 131-138
26. Kyte J, Doolittle R (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132
27. Liaud MF, Brandt U, Scherzinger M, Cerff R (1997) Evolutionary origin of cryptomonad microalgae: two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components. J Mol Evol 44 (Suppl): S28-37
28. Liaud MF, Lichtle C, Apt K, Martin W, Cerff R (2000) Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway. Mol Biol Evol 17: 213-223
29. Nassoury N, Cappadocia M, Morse D (2003) Plastid ultrastructure defines the protein import pathway in dinoflagellates. J Cell Sci 116: 2867-2874
30. Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst 8: 581-599
31. Qian Q, Keeling PJ (2001) Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer. Protist 152: 193-201
32. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
33. Saldarriaga JF, Taylor FJ, Keeling PJ, Cavalier-Smith T (2001) Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J Mol Evol 53: 204-213
34. Saunders GW, Hill DRA, Sexton JP, Andersen RA (1997) Small-subunit ribosomal RNA sequences from selected dinoflagellates: testing classical evolutionary hypotheses with molecular systematic methods. Plant Syst Evol (Suppl) 11: 237-259
35. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504
36. Schnepf E, Elbrächter M (1988) Cryptophycean-like double-membrane bounded chloroplast in the dinoflagellate, Dinophysis Ehrenb. Evolutionary, phylogenetic and toxicological implications. Bot Acta 101: 196-203
37. Schnepf E, Elbrächter M (1999) Dinophyte chloroplasts and phylogeny - a review. Grana 38: 81-97
38. Sulli C, Schwartzbach SD (1996) A soluble protein is imported into Euglena chloroplasts as a membrane-bound precursor. Plant Cell 8: 43-53
39. Sulli C, Fang Z, Muchhal U, Schwartzbach S (1999) Topology of Euglena chloroplast protein precursors within endoplasmic reticulum to Golgi to chloroplast transport vesicles. J Biol Chem 274: 457-463
40. Suzuki R, Ishimaru T (1992) Characteristics of photosynthetic pigment composition of Gymnodinium mikimotoi Miyake et Kominami ex Oda. J Oceanogr 48: 367-375
41. Takishita K, Ishida K, Maruyama T (2003) An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): Possible lateral gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte. Protist 154: 443-454
42. Takishita K, Nakano K, Uchida A (1999) Preliminary phylogenetic analysis of plastid-encoded genes from an anomalously pigmented dinoflagellate Gymnodinium mikimotoi (Gymnodiniales, Dinophyta). Phycol Res 47: 257-262
43. Takishita K, Nakano K, Uchida A (2000) Origin of the plastid in the anomalously pigmented dinoflagellate Gymnodinium mikimotoi (Gymnodiniales, Dinophyta) as inferred from phylogenetic analysis based on the gene encoding the large subunit of form I-type RuBisCO. Phycol Res 48: 85-89
44. Takishita K, Ishida K, Ishikura M, Maruyama T (2004) Phylogeny of the psbC gene, coding a photosystem II component CP43, suggests separate origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates. Phycologia (in press)
45. Takishita K, Koike K, Maruyama T, Ogata T (2002) Molecular evidence for plastid robbery (kleptoplastidy) in Dinophysis, a dinoflagellate causing diarrhetic shellfish poisoning. Protist 153: 293-302
46. Tangen K, Björnland T (1981) Observations on pigment and morphology of Gyrodinium aureolum Hulbert, a marine dinoflagellate containing 19′-hexanoyloxyfucoxanthin as the main carotenoid. J Plankton Res 3: 389-401
47. Tengs T, Dahlberg OJ, Shalchian-Tabrizi K, Klaveness D, Rudi K, Delwiche CF, Jakobsen KS (2000) Phylogenetic analyses indicate that the 19′hexanoyloxy-fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin. Mol Biol Evol 17: 718-729
48. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
49. van Dooren GG, Schwartzbach D, Osafune T, McFadden GI (2001) Translocation of proteins across the multiple membranes of complex plastids. Biochim Biophys Acta 1541: 34-53
50. Watanabe MM, Suda S, Inouye I, Sawaguchi T, Chichara M (1990) Lepidodinium viride gen. et sp. nov. (Gymnodiniales, Dinophyta), a green dinoflagellate with a chlorophyll a- and b-containing endosymbiont. J Phycol 26: 741-751
51. Whatley JM (1993) Chloroplast Ultrastructure. In Berner T (ed) Ultrastructure of Microalgae. CRC Press, Boca Raton, pp 135-204
52. Yoon HS, Hackett JD, Bhattacharya D (2002) A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis. Proc Natl Acad Sci USA 99:11724-11729