Mitochondrial Group II Introns in the Raphidophycean Flagellate Chattonella spp. Suggest a Diatom-to-Chattonella Lateral Group II Intron Transfer

Protist

Volumn 160, Issue 3, 2009, Pages 364-375

  Kamikawa, Ryoma ^a   Masuda, Isao ^a   Demura, Mikihide ^b   Oyama, Kenichi ^c   Yoshimatsu, Sadaaki ^c   Kawachi, Masanobu ^b   Sako, Yoshihiko ^a  

^a KYOTO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE FOR ENVIRONMENTAL STUDIES   (Japan)

^c Akashio Research Institute of Kagawa Prefecture   (Japan)

Author keywords

Chattonella; cytochrome c oxidase subunit 1 (cox1); diatoms; group II intron; lateral transfer; Raphidophyceae

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; PROTOZOAL DNA; PROTOZOAL PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; CONFORMATION; DIATOM; DNA SEQUENCE; FLAGELLATE; GENETICS; HORIZONTAL GENE TRANSFER; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

ANIMALS; DIATOMS; DNA, MITOCHONDRIAL; DNA, PROTOZOAN; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; INTRONS; MASTIGOPHORA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

BACILLARIOPHYTA; CHATTONELLA; CHATTONELLA ANTIQUA; CHATTONELLA MARINA; CHATTONELLA OVATA; CHATTONELLA SUBSALSA; EUKARYOTA; MASTIGOPHORA (FLAGELLATES); RAPHIDOPHYCEAE;

EID: 67649418038     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2009.02.003     Document Type: Article

References (51)

1. Asakura Y., and Barkan A. Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Physiol 142 (2006) 1656-1663
2. Bonen L., and Vogel J. The ins and outs of group II introns. Trends Genet 17 (2001) 322-331
3. Bowers H.A., Tomas C., Tengs T., Kempton J.W., Lewitus A.J., and Oldach D.W. Raphidophyceae (Chadefaud ex Silva) systematics and rapid identification: sequence analyses and real-time PCR assays. J Phycol 42 (2006) 1333-1348
4. Burger G., Saint-Louis D., Gray M.W., and Lang B.F. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11 (1999) 1675-1694
5. Carignani G., Groudinsky O., Frezza D., Schiavon E., Bergantino E., and Slonimski P.P. An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35 (1983) 733-742
6. Dai L., Toor N., Olson R., Keeping A., and Zimmerly S. Database for mobile group II introns. Nucleic Acids Res 31 (2003) 424-426
7. Ehara M., Watanabe K.I., and Ohama T. Distribution of cognates of group II introns detected in mitochondrial cox1 genes of a diatom and a haptophyte. Gene 256 (2000) 157-167
8. Eskes R., Liu L., Ma H., Chao M.Y., Dickson L., Lambowitz A.M., and Perlman P.S. Multiple homing pathways used by yeast mitochondrial group II introns. Mol Cell Biol 20 (2000) 8432-8446
9. Ferat J.L., and Michel F. Group II self-splicing introns in bacteria. Nature 364 (1993) 358-361
10. Fontaine J.M., Goux D., Kloareg B., and Loiseaux-de Goer S. The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribosyme lineages. J Mol Evol 44 (1997) 33-42
11. Fontaine J.M., Rousvoal S., LeBlanc C., Kloareg B., and Loiseaux-de Goer S. The mitochondrial LSU rDNA of the brown alga Pylaiella littoralis reveals α-proteobacterial features and is split by four group IIB introns with an atypical phylogeny. J Mol Biol 151 (1995) 378-389
12. Goddard M.R., and Burt A. Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA 96 (1999) 13880-13885
13. Gogarten J.P., and Hilario E. Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol Biol 6 (2006) 94
14. Guillard R.R.L. Culture of Phytoplankton for Feeding Marine Invertabrates. In: Smith W.L., and Chanley M.H. (Eds). Culture of Marine Invertabrates Animals (1975), Plenum Press, New York 26-60
15. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 (2003) 696-704
16. Hara Y., Doi K., and Chihara M. Four new species of Chattonella (Raphidophyceae, Chromophyta) from Japan. Jpn J Phycol (Sorui) 42 (1994) 407-420
17. Hauth A.M., Maier U.G., Lang B.F., and Burger G. The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region. Nucleic Acids Res 33 (2005) 4433-4442
18. Hosaka M., Takayama N., Hirai S., Gonda M., and Hara Y. The occurrence of raphidophycean alga Chattonella sp. (globular type) in Tokyo Bay, Japan. Bull Plank Soc Jpn 38 (1991) 1-8
19. Ikuta K., Kawai H., Muller D.G., and Ohama T. Recurrent invasion of mitochondrial group II introns in specimens of Pylaiella littoralis (brown alga), collected worldwide. Curr Genet 53 (2008) 207-216
20. Jacquier A., and Michel F. Base-pairing interactions involving the 5′ and 3′ terminal nucleotides of group II self-splicing introns. J Mol Biol 213 (1990) 437-447
21. Kamikawa R., Inagaki Y., and Sako Y. Fragmentation of mitochondrial large subunit ribosomal RNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria. Protist 158 (2007) 239-245
22. Kamikawa R., Hosoi-Tanabe S., Nagai S., Itakura S., and Sako Y. Development of a quantification assay for the cysts of the toxic dinoflagellate Alexandrium tamarense using real-time polymerase chain reaction assay. Fish Sci 71 (2005) 987-991
23. Kamikawa R., Masuda I., Oyama K., Yoshimatsu S., and Sako Y. Genetic variation of mitochondrial genes and intergenic spacer region in harmful algae Chattonella species. Fish Sci 73 (2007) 871-880
24. Kamikawa R., Hosoi-Tanabe S., Yoshimatsu S., Oyama K., Masuda I., and Sako Y. Development of a novel molecular marker on the mitochondrial genome of a toxic dinoflagellates Alexandrium spp., and its application in single-cell PCR. J Appl Phycol 20 (2008) 153-159
25. Kamikawa R., Asai J., Miyahara T., Murata K., Oyama K., Yoshimatsu S., Yoshida T., and Sako Y. Application of a real-time PCR assay to a comprehensive method for monitoring harmful algae. Microbes Environ 21 (2006) 163-173
26. Lambowitz A.M., and Zimmerly S. Mobile group II introns. Annu Rev Genet 38 (2004) 1-35
27. Le S.Q., and Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 25 (2008) 1307-1320
28. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288 (1999) 911-940
29. Michel F., and Lang B.F. Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses. Nature 316 (1985) 641-643
30. Michel F., Jacquier A., and Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie 64 (1982) 867-881
31. Michel F., Umesono K., and Ozeki H. Comparative and functional anatomy of group II catalytic introns - a review. Gene 82 (1989) 5-30
32. Mohr G., Perlman P.S., and Lambowitz A.M. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res 21 (1993) 4991-4997
33. Moran J.V., Mecklenburg K.L., Sass P., Belcher S.M., Mahnke D., Lewin A., and Perlman P.S. Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2. Nucleic Acids Res 22 (1994) 2057-2064
34. Mueller M.W., Allmaier M., Eskes R., and Schweyen R.J. Transposition of group II intron aI1 in yeast and invasion of mitochondrial genes at new locations. Nature 366 (1993) 174-176
35. Pramateftaki P.V., Kouvelis V.N., Lanaridis P., and Typas M.A. Complete mitochondrial genome sequence of the wine yeast Candida zemplinia: intraspecies distribution of a novel group-IIB1 intron with eubacterial affiliations. FEMS Yeast Res 8 (2008) 311-327
36. Peebles C.L., Perlman P.S., Mecklenburg K.L., Petrillo M.L., Tabor J.H., Jarrell K.A., and Cheng H.L. A self-splicing RNA excises an intron lariat. Cell 44 (1986) 213-223
37. Pombert J.F., Beauchamp P., Otis C., Lemieux C., and Turmel M. The complete mitochondrial DNA sequences of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae. Curr Genet 50 (2006) 137-147
38. Saldanha R., Chen B., Wank H., Matsuura M., Edwards J., and Lambowitz A.M. RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry 38 (1999) 9069-9083
39. San Filippo J., and Lambowitz A.M. Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J Mol Biol 324 (2002) 933-951
40. Schmelzer C., and Schweyen R.J. Self-splicing of group II introns in vitro: mapping of the branching point and mutation inhibition of lariat formation. Cell 46 (1986) 557-565
41. Sellem C.H., Lecellier G., and Belcour L. Transposition of a group II intron. Nature 366 (1993) 176-178
42. Toor N., and Zimmerly S. Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns. RNA 8 (2002) 1373-1377
43. Toor N., Hausner G., and Zimmerly S. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7 (2001) 1142-1152
44. Toro N. Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment. Environ Microbiol 5 (2003) 143-151
45. Turmel M., Otis C., and Lemieux C. An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus. BMC Genomics 8 (2007) 137
46. Vallès Y., Halanych K.M., and Boore J.L. Group II introns break new boundaries: presence in a bilaterian's genome. PLoS ONE 3 (2008) e1488
47. van der Veen R., Arnberg A.C., van der Horst G., Bonen L., Tabak H.F., and Grivell L.A. Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell 44 (1986) 225-234
48. Vrieling E., Koeman R., Nagasaki K., Ishida Y., Peperzak L., Gieskes W., and Veenhuis M. Chattonella and Fibrocapsa (Raphidophyceae) novel, potentially harmful red tide organisms in Dutch coastal waters. Neth J Sea Res 33 (1995) 183-191
49. Yamaguchi H., Hoppenrath M., Takishita K., and Horiguchi T. Haramonas pauciplastida sp. nov. (Raphidophyceae, Heterokontophyta) and phylogenetic analyses of Haramonas species using SSU rDNA sequences. Phycol Res 56 (2008) 127-138
50. Zimmerly S., Hausner G., and Wu X. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res 25 (2001) 1238-1250
51. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 (2003) 3406-3415