Evidence for the heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase

Journal of Eukaryotic Microbiology

Volumn 43, Issue 6, 1996, Pages 475-485

  Roger, Andrew J ^a   Smith, Michael W ^b   Doolittle, Russell F ^c   Doolittle, W Ford ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b SAIC FREDERICK INC   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amoebae; endosymbiosis; eukaryotic evolution; lateral gene transfer; Mycetozoa; protein evolution; protist systematics; slime mould

Indexed keywords

EID: 0030292470     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.1996.tb04507.x     Document Type: Article

References (67)

1. Adachi, J. & Hasegawa, M. 1992. MOLPHY: Programs for Molecular Phylogenetics, Vers. 2.2. Institute of Statistical Mathematics, Tokyo, Japan.
2. Baldauf, S. L. & Palmer, J. D. 1993. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Nat. Acad. Sci. USA, 90.11558-11562
3. Berbee, M. L. 1993. Dating the evolutionary radiations of the true fungi. Can. J. Bot., 71:1114-1127.
4. Bhattacharya, D. & Ehlting, J. 1995. Actin coding regions: gene family evolution and use as a phylogenetic marker. Arch. Protistenkd., 145:155-164.
5. Blanton, R. L. 1989. Phylum Acrasea. In: Margulis, L., Corliss, J. O., Melkonian, M & Chapman, D. J. (ed.), Handbook of Protoctista. Jones & Bartlett, Boston, Massachussets. Pp. 75-87.
6. --binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase. Eur. J. Biochem., 150:61-66.
7. Brinkmann, H. & Martin, W. 1996. Plant chloroplast and cytosolic 3-phosphoglycerate kinases: a case of endosymbiotic gene replacement. Plant Mol. Biol. , 30.65-75.
8. Bruns, T. D., Vilgalys, R., Barns, S. M., Gonzalez, D., Hibbett, D. S., Lane, D. J., Simon, L., Stickel, S., Szaro, T. M., Weisburg, W. G. & Sogin, M. L. 1992. Evolutionary relationships within the fungi analyses of nuclear small subunit rRNA sequences. Mol. Phylogen. Evol., 1:231-241.
9. Cavalier-Smith, T. 1993a. Kingdom Protozoa and its 18 phyla. Microbiol. Rev., 57:953-994.
10. Cavalier-Smith, T. 1993b. Percolozoa and the symbiotic origin of the inetakaryote cell. In: Ishikawa, H., Ishida. M. & Sato, S. (ed.), Entocytobiology V., Tübingen University Press, Tübingen, Germany. Pp. 399-406.
11. Clark, C. G. 1992. DNA purification from polysaccharide-rich cells. In: Lee, J. J. & Soldo, A. (ed.), Protocols in Protozoology. Allen Press, Lawrence, Kansas. 1:D3.1-D3.2.
12. Clark, C. G. & Cross, G. A. 1988. Small-subunit ribosomal RNA sequence from Naegleria gruben supports the polyphyletic origin of amoebas Mol. Biol. Evol., 5:512-518.
13. Clark, C. G. & Roger, A. J. 1995. Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc. Nat. Acad. Sci. USA, 92:6518-6521.
14. de Bary, A. 1887. Comparative Morphology and Biology of the Fungi, Mycetozoa and Bacteria. Clarendon Press, Oxford.
15. Doolittle, R. F., Feng, D. F., Anderson, K. L. & Alberro, M. R. 1990. A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J. Mol. Evol., 31:383-388.
16. Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G. & Little, E. 1996 Determining divergence times of the major kingdoms of living organisms with a protein clock. Science, 271:470-477
17. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool., 27:401-410.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39:783-791.
19. Felsenstein, J. 1996. PHYLIP (Phytogeny Inference Package), Vers. 3.57c. Department of Genetics, University of Washington, Seattle.
20. Fenchel, T. & Patterson, D. J. 1986. Percolomonas cosmopolitus (Ruinen) n. gen., a new type of filter feeding flagellate from marine plankton. J. Mar. Biol. Ass. U. K., 66:465-482.
21. Fothergill-Gilmore, L. A. & Michels, P. A. 1993. Evolution of glycolysis. Prog. Biophys. Mol. Biol., 59:105-235.
22. Galtier, N. & Gouy, M. 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proc. Nat. Acad. Sci. USA, 92:11317-11321.
23. Hasegawa, M. & Hashimoto, T. 1993. Ribosomal RNA trees misleading? Nature, 361:23.
24. Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N. & Miyata, T. 1993. Early branchings in the evolution of eukaryotes: ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. J. Mol. Evol., 36:380-388.
25. Hashimoto, T., Nakamura, Y., Nakamura, F., Shirakura, T., Adachi, J., Goto, N., Okamoto, K. & Hasegawa, M. 1994. Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia. Mol. Biol. Evol., 11:65-71.
26. Hensel, R., Zwickl, P., Fabry, S., Lang, J. & Palm, P. 1989. Sequence comparison of glyceraldehyde-3-phosphate dehydrogenases from the three kingdoms: evolutionary implication. Can. J. Microbiol., 35:81-85.
27. 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. Nat. Acad. Sci. USA, 92: 9122-9126.
28. Hinkle, G. & Sogin, M. L. 1993. The evolution of the Vahlkampfiidae as deduced from 16S-like ribosomal RNA analysis. J. Euk. Microbiol., 40:599-603.
29. Kersanach, R., Brinkmann, H., Liaud, M. F., Zhang, D. X., Martin, W. & Cerff, R. 1994. Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature, 367:387-389.
30. Klenk, H.-P., Zillig, W., Lanzendorfer, M., Grampp, M. & Palm, P. 1995. Location of protist lineages in a phylogenetic tree inferred from sequences of DNA-dependent RNA polymerases. Arch. Protistenkd., 145:221-230.
31. Kuma, K., Nikoh, N., Iwabe, N. & Miyata, T. 1995. Phylogenetic position of Dictyostelium inferred from multiple protein data sets. J. Mol. Evol., 41:238-246.
32. Levine, N. D., Corliss, J. O., Cox, F. E. G., Deroux. G., Grain, J., Honigberg, B. M., Leedale, G. F., Loeblich, A. R., III, Lorn, J., Lynn, D., Merinfeld, F. G., Page, F. C , Poljansky, G., Sprague, V., Vavra, J. & Wallace, F. G. 1980. A newly revised classification of the Protozoa. J. Protozool., 27:37-58.
33. Logsdon, J., Jr., Tyshenko, M. G., Dixon, C., D., Jafari, J., Walker, V. K. & Palmer, J. D. 1995. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. Proc. Nat. Acad. Sci. USA, 92:8507-8511.
34. Logsdon, J. M., Jr. & Palmer, J D. 1994. Origin of introns - early or late? Nature, 369:526
35. Loomis, W. F. & Smith, D. W. 1990. Molecular phytogeny of Dictyostelium discoideum by protein sequence comparison. Proc. Nat. Acad. Sci USA, 87:9093-9097.
36. Loomis, W. F. & Smith, D. W. 1995. Consensus phylogeny of Dictyostelium. Experientia, 51:1110-1115.
37. Margulis, L. & Schwartz, K. V. 1988. Five kingdoms: an illustrated guide to the phyla of life on earth W. H. Freeman, New York.
38. Markós, A., Miretsky, A. & Müller, M. 1993. A glyceraldehyde-3-phosphate dehydrogenase with eubacterial features in the amitochondriate eukaryote, Trichomonas vaginalis. J. Mol. Evol., 37:631-643.
39. Martin, W., Brinkmann, H., Savonna, C. & Cerff, R. 1993. Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc. Nat. Acad. Sci. USA, 90:8692-8696.
40. O'Kelly, C. J. 1993. The jakobid flagellates: structural features of Jakoba, Reclinomonas and Histiona and implications for the early diversification of eukaryotes. J. Euk. Microbiol., 40:627-636.
41. Olive, E. W. 1902. Monograph of the Acrasieae. Proc. Boston Soc. Nat. Hist., 30:451-513.
42. Olive, L. S. 1970. The Mycetozoa: a revised classification. Bot. Rev., 36:59-87.
43. Olive, L. S. 1975. The Mycetozoa. Academic Press, New York.
44. Olive, L. S., Stoianovitch, C. & Bennet, W. E. 1983. Descriptions of acrasid cellular slime molds: Pocheina rosea and a new species, Pocheina flagellata. Mycologia, 75.1019-1029.
45. Page, F. C. & Blanton, R. L. 1985. The Heterolobosea (Sarcodina: Rhizopoda), a new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica, 21:121-132.
46. Palmer, J. D. & Logsdon, J M., Jr. 1991. The recent origins of introns. Curr. Opin. Genet. Dev , 1:470-477.
47. Patterson, D. J. 1994. Protozoa: evolution and systematics. In: Hausmann, K. & Hülsmann, N. (ed.), Progress in Protozoology. Gustav Fischer, Stuttgart, Germany. Pp. 1-14
48. Philippe, H , Chenuil, A. & Adoutte, A. 1994. Can the Cambrian explosion be interred through molecular phylogeny? Development 1994(suppl.): 15-25.
49. Remillard, S. P., Lai, E. Y., Levy, Y. Y. & Fulton, C. 1995. A calcineurin-B-encoding gene expressed during differentiation of the amoeboflagellate Naegleria gruben contains two introns. Gene, 154: 39-45.
50. Roger, A. J., Keeling, P. J. & Doolittle, W. F. 1994. Introns, the broken transposons. Soc. Gen. Physiol. Ser., 49:27-37.
51. Rozario, C., Morin, L., Roger, A. J., Smith, M. W. & Müller, M. 1996. Primary structure and phylogenetic relationships of glyceraldehyde-3-phosphate dehydrogenase genes of free-living and parasitic diplomonad flagellates. J. Euk. Microbiol., 43:330-340.
52. Schlegel, M. 1994. Molecular phylogeny of eukaryotes. Trends Ecol. Evol., 9:330-335.
53. Skarzynski, T., Moody, P. C. & Wonacott, A. J. 1987. Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 ° resolution. J. Mol. Biol., 193:171-187.
54. Smith, M. W., Feng, D. F. & Doolittle, R. F. 1992. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci., 17:489-493.
55. Smith, T. L. 1989. Disparate evolution of yeasts and filamentous fungi indicated by phylogenetic analysis of glyceraldehyde-3-phosphate dehydrogenase genes. Proc. Nat. Acad. Sci. USA, 86:7063-7066.
56. Sogin, M. L. 1991. Early evolution and the origin of eukaryotes. Curr. Opin. Gen. Devel., 1:457-463.
57. Sogin, M. L. & Gunderson, J. H. 1987. Structural diversity of eukaryotic small subunit ribosomal RNAs. Evolutionary implications. Ann. N. Y. Acad. Sci., 503:125-139.
58. Soltys, B. J. & Gupta, R. S. 1994. Presence and cellular distribution of a 60-kDa protein related to mitochondrial hsp60 in Giardia lamblia. J. Parasitol., 80:580-590.
59. Spiegel, F. W., Lee, S. B. & Rusk, S. A. 1995. Eumycetozoans and molecular systematics. Can. J. Bot., 73(suppl. 1):S738-S746.
60. Swofford, D. L. 1993. PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1. Illinois Natural History Survey, Champaign, Illinois.
61. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994. CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res., 22:4673-4680.
62. van Tieghern, M. P. 1880. Sur quelques myxomycètes à plasmode agrégé. Bull. Soc. Bot. Fr., 27:317-322.
63. Wainright, P. O., Hinkle, G., Sogin, M. L. & Stickel, S. K. 1993. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science , 260:340-342.
64. Whittaker, R. H. 1969. New concepts of kingdoms of organisms. Science, 163:150-160.
65. Wiemer, E. A., Hannaert, V , van den Ijssel, P. R., Van Roy, J., Opperdoes, F. R. & Michels, P. A. 1995. Molecular analysis of glyceraldehyde-3-phosphate dehydrogenase in Trypanoplasma borelli: an evolutionary scenario of subcellular compartmentation in kinetoplastida. J. Mol. Evol., 40:443-454.
66. Wolters, J. 1991. The troublesome parasites - molecular and morphological evidence that Apicomplexa belong to the dinoflagellateciliate clade. Biosystems, 25:75-83.
67. Zhou, Y. & Ragan, M. A. 1995. The nuclear gene and cDNAs encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from the marine red alga Gracilaria verrucosa: cloning, characterization and phylogenetic analysis. Curr. Genet., 28:324-332.