Environmental PCR survey to determine the distribution of a non-canonical genetic code in uncultivable oxymonads

Environmental Microbiology

Volumn 10, Issue 1, 2008, Pages 65-74

  De Koning, Audrey P ^a   Noble, Geoffrey P ^a   Heiss, Aaron A ^a   Wong, Jensen ^a   Keeling, Patrick J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PROTOZOAL DNA; TUBULIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; COCKROACH; ENVIRONMENT; ENVIRONMENTAL MONITORING; FLAGELLATE; GENE; GENETIC CODE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PARASITOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; START CODON; STOP CODON;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; COCKROACHES; CODON, INITIATOR; CODON, TERMINATOR; DNA, PROTOZOAN; ENVIRONMENT; ENVIRONMENTAL MONITORING; GENES, PROTOZOAN; GENETIC CODE; MASTIGOPHORA; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; POLYMERASE CHAIN REACTION; TUBULIN;

BLATTARIA; CRYPTOCERCUS PUNCTULATUS; EUKARYOTA; OXYMONADIDA; POLYMASTIGIDAE; PROTISTA; STREBLOMASTIX;

EID: 38149066642     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01430.x     Document Type: Article

References (34)

1. Andersson, S.G. Kurland, C.G. (1995) Genomic evolution drives the evolution of the translation system. Biochem Cell Biol 73 : 775 787.
2. Brugerolle, G. Lee, J.J. (2000) Order Oxymonadida. In The Illustrated Guide to the Protozoa. Lee, J., Leedale, G.F. Bradbury, P. (eds). Lawrence, KS, USA : J. Allen Press, pp. 1186 1195.
3. Cleveland, L.R. (1966) Nuclear division without cytokinesis followed by fusion of pronuclei in Paranotila lata General et sp. nov. J Protozool 13 : 132 136.
4. Cleveland, L.R., Hall, S.R., Sanders, E.P. Collier, J. (1934) The wood-feeding roach Cryptocercus, its protozoa and the symbiosis between protozoa and roach. Mem Am Acad Arts Sci 17 : 185 342.
5. Dacks, J.B., Silberman, J.D., Simpson, A.G., Moriya, S., Kudo, T., Ohkuma, M. Redfield, R.J. (2001) Oxymonads are closely related to the excavate taxon Trimastix. Mol Biol Evol 18 : 1034 1044.
6. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package). Seattle, WA, USA : University of Washington.
7. Guindon, S. Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 : 696 704.
8. Hampl, V., Horner, D.S., Dyal, P., Kulda, J., Flegr, J., Foster, P.G. Embley, T.M. (2005) Inference of the phylogenetic position of oxymonads based on nine genes: support for metamonada and excavata. Mol Biol Evol 22 : 2508 2518.
9. Heiss, A.A. Keeling, P.J. (2006) The phylogenetic position of the oxymonad Saccinobaculus based on SSU rRNA. Protist 157 : 335 344.
10. Hollande, A. Carruette-Valentin, J. (1970) La lignée des Pyrsonymphines et les caractères infrastructuraux communs aux genres Opisthomitus, Oxymonas, Saccinobacculus, Pyrsonympha et Streblomastix. C R Acad Sci Paris 270 : 1587 1590.
11. Keeling, P.J. Doolittle, W.F. (1996) A non-canonical genetic code in an early diverging eukaryotic lineage. EMBO J 15 : 2285 2290.
12. Keeling, P.J. Doolittle, W.F. (1997) Widespread and ancient distribution of a noncanonical genetic code in diplomonads. Mol Biol Evol 14 : 895 901.
13. Keeling, P.J. Leander, B.S. (2003) Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix. J Mol Biol 326 : 1337 1349.
14. Knight, R.D., Freeland, S.J. Landweber, L.F. (2001) Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2 : 49 58.
15. Kulda, J. Nohynkova, E. (1978) Flagellates of human intestine and of intestines of other species. In Parasitic Protozoa. Kreier, J.P. (ed.). New York, NY, USA : Academic Press, pp. 2 138.
16. Leander, B.S. Keeling, P.J. (2004) Symbiotic innovation in the oxymonad Streblomastix strix. J Eukaryot Microbiol 51 : 291 300.
17. Lozupone, C.A., Knight, R.D. Landweber, L.F. (2001) The molecular basis of nuclear genetic code change in ciliates. Curr Biol 11 : 65 74.
18. McIntosh, J.R. (1973) The Axostyle of Saccinobacculus II. Motion of the microtubule bundle and a structural comparison of straight and bent axostyles. J Cell Biol 56 : 324 339.
19. Moriya, S., Ohkuma, M. Kudo, T. (1998) Phylogenetic position of symbiotic protist Dinenympha[correction of Dinemympha] exilis in the hindgut of the termite Reticulitermes speratus inferred from the protein phylogeny of elongation factor 1 alpha. Gene 210 : 221 227.
20. Moriya, S., Tanaka, K., Ohkuma, M., Sugano, S. Kudo, T. (2001) Diversification of the microtubule system in the early stage of eukaryote evolution: elongation factor 1 alpha and alpha-tubulin protein phylogeny of termite symbiotic oxymonad and hypermastigote protists. J Mol Evol 52 : 6 16.
21. Moriya, S., Dacks, J.B., Takagi, A., Noda, S., Ohkuma, M., Doolittle, W.F. Kudo, T. (2003) Molecular phylogeny of three oxymonad genera: Pyrsonympha, Dinenympha and Oxymonas. J Eukaryot Microbiol 50 : 190 197.
22. Nie, D. (1950) Morphology and taxonomy of the intestinal protozoa of the guinea-pig Cavia porcella. J Morphol 86 : 391 493.
23. Osawa, S., Jukes, T.H., Watanabe, K. Muto, A. (1992) Recent evidence for evolution of the genetic code. Microbiol Rev 56 : 229 264.
24. Schneider, S.U. de Groot, E.J. (1991) Sequences of two rbcS cDNA clones of Batophora oerstedii: structural and evolutionary considerations. Curr Genet 20 : 173 175.
25. Shimodaira, H. (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51 : 492 508.
26. Shimodaira, H. Hasegawa, M. (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 : 1246 1247.
27. Slamovits, C.H. Keeling, P.J. (2006a) Pyruvate-phosphate dikinase of oxymonads and parabasalia and the evolution of pyrophosphate-dependent glycolysis in anaerobic eukaryotes. Eukaryot Cell 5 : 148 154.
28. Slamovits, C.H. Keeling, P.J. (2006b) A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol Biol 6 : 34.
29. Swofford, D.L. (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA, USA : Sinauer Associates.
30. Trager, W. (1934) The cultivation of a cellulose- digesting flagellate. Trichomonas termopsidis, and of certain other termite protozoa. Biol Bull 66 : 182 190.
31. Yamao, F., Muto, A., Kawauchi, Y., Iwami, M., Iwagami, S., Azumi, Y. Osawa, S. (1985) UGA is read as tryptophan in Mycoplasma capricolum. Proc Natl Acad Sci USA 82 : 2306 2309.
32. Yamin, M.A. (1979) Flagellates of the orders Trichomonadida Kirby, Oxymonadida Grassé, and Hypermastigida Grassi & Foà reported from lower termites (Isoptera Falilies Mastotermitidae, Kalotermitidae, Hodotermitidae, Termopsidae, Rhinotermitidae, and Serritermididae) and from the wood-feeding roach Cryptocercus (Dictyoptera: Ceyptocercidae). Sociobiology 4 : 1 120.
33. Yarus, M., Caporaso, J.G. Knight, R. (2005) Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 74 : 179 198.
34. Yokobori, S., Suzuki, T. Watanabe, K. (2001) Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol 53 : 314 326.