Group I introns in small subunit ribosomal DNA (SSUrDNA) of cereal Phaeosphaeria speciess

Botanical Studies

Volumn 50, Issue 2, 2009, Pages 137-147

  Wang, Chih Li ^a   Chang, Pi Fang Linda ^b   Lin, Ying Hong ^b   Malkus, Arkadiusz ^c   Gao, Ling Yan ^d   Ueng, Peter P ^e  

^a Department of Plant Protection   (Taiwan)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^c PLANT BREEDING AND ACCLIMATIZATION INSTITUTE NATIONAL RESEARCH INSTITUTE   (Poland)

^d Inner Mongolia Agricultural University   (Mongolia)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Introns; Phaeosphaeria; Phylogenetic relationships; Ribosomal RNA gene; Small subunit; Wheat

Indexed keywords

AVENA SATIVA; ESCHERICHIA COLI; HORDEUM; HORDEUM JUBATUM; PAA; PASPALUM; PASPALUM DILATATUM; PHAEOSPHAERIA; PHAEOSPHAERIA AVENARIA F. SP. AVENARIA; PHAEOSPHAERIA NODORUM; SECALE CEREALE; TRITICUM AESTIVUM;

EID: 66749174086     PISSN: 1817406X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (65)

1. Adams, P.L., M.R. Stahley, A.B. Kosek, J. Wang, and S.A. Strobel. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50.
2. Beagley, C.T., R. Okimoto, and D.R. Wolstenholme. 1998. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a nearstandard genetic code. Genetics 148: 1091-1108.
3. Been, M.D. and T.R. Cech. 1986. One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing and RNA enzyme activity. Cell 47: 207-216.
4. Belfort, M. and P.S. Perlman. 1995. Mechanisms of intron mobility. J. Biol. Chem. 270: 30237-30240.
5. Burke, J.M., M. Belfort, T.R. Cech, R.W. Davies, R.J. Schweyen, D.A. Shub, J.W. Szostak, and H.F. Tabak. 1987. Structural conventions for group I introns. Nucleic Acids Res. 15 : 7217-7221.
6. Cannone, J.J., S. Subramanian, M.N. Schnare, J.R. Collett, L.M. D'Souza, Y. Du, B. Feng, N. Lin, L.V. Madabusi, K.M. Müller, N. Pande, Z. Shang, N. Yu, and R.R. Gutell. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
7. Cech, T.R. 1988. Conserved sequences and structures of group I introns: building an active site for RNA catalysis-a review. Gene 73: 259-271.
8. Chen, W., L.E. Gray, and C.R. Grau. 1998. Characterization of a group I intron in the nuclear rDNA differentiating Phialophora gregata f.sp. adzukicola from P. gregata f.sp. sojae. Mycoscience 39: 279-283.
9. Chen, W., C.A. Shearer, and J.L. Crane. 1996. Identification of a group I intron in the nuclear small subunit rDNA of Pseudohalonectria lignicola. Curr. Microbiol. 33: 84-88.
10. CĈté, M.J., M. Prud'homme, A.J. Meldrum, and M.C. Tardif. 2004. Variation in sequence and occurrence of SSU rDNA group introns in Monilinia fructicola isolates. Mycologia 96: 240-248.
11. De Rijk, P., J. Wuyts, and R. De Wachter. 2003. RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics 19: 299-300.
12. De Wachter, R., J.M. Neefs, A. Goris, and Y. Van de Peer. 1992. The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron. Nucleic Acids Res. 20: 1251-1257.
13. Egger, K.N., G. Osmond, and J.L. Goodier. 1995. Sequence and putative secondary structure of group I introns in the nuclear-encoded ribosomal RNA genes of the fungus Hymenoscyphus ericae. Biochimica et Biophysica Acta 1261: 275-278.
14. Feau, N., R.C. Hamelin, and L. Bernier. 2007. Variability of nuclear SSU-rDNA group introns within Septoria species: incongruence with host sequence phylogenies. J. Mol. Evol. 64: 489-499.
15. Fukami, H., C.A. Chen, C.Y. Chiou, and N. Knowlton. 2007. Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of scleractinian corals. J. Mol. Evol. 64: 591-600.
16. Gibb, E.A. and G. Hausner. 2003. A group I intron-like sequence in the nuclear small ribosomal subunit gene of the ophiostomatoid fungus Gondwanamyces proteae. Mycol. Res. 107: 1442-1450.
17. Goddard, M.R. and A. Burt. 1999. Recurrent invasion and extinction of a selfish gene. Proc. Natl. Acad. Sci. USA 96: 13880-13885.
18. Golden, B.L., A.R. Gooding, E.R. Podell, and T.R. Cech. 1998. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282: 259-264.
19. Gutell, R.R. 1993. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 21: 3051-3054.
20. Haugen, P., H.J. Runge, and D. Bhattacharya. 2004. Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns. RNA 10: 1084-1096.
21. Haugen, P., D.M. Simon, and D. Bhattacharya. 2005. The natural history of group I introns. Trends Genet. 21: 111-119.
22. Holst-Jensen, A., M. Vaage, T. Schumacher, and S. Johansen. 1999. Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi. Mol. Biol. Evol. 16: 114-126.
23. Ito, Y. and T. Hirano. 1999. A group I intron in the 18S ribosomal DNA from the parasitic fungus Isaria japonica. J. Mol. Evol. 48: 337-340.
24. Johansen, S. and P. Haugen. 2001. A new nomenclature of group I introns in ribosomal DNA. RNA 7: 935-936.
25. Lambowitz, A.M. and M. Belfort. 1993. Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
26. Li, Z. and Y. Zhang. 2005. Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup. Nucleic Acids Res. 33: 2118-2128.
27. Lickey, E.B., K.W. Hughes, and R.H. Petersen. 2003. Variability and phylogenetic incongruence of an SSU nrDNA group I intron in Artomyces, Auriscalpium, and Lentinellus (Auriscalpiaceae: Homobasidiomycetes). Mol. Biol. Evol. 20: 1909-1916.
28. Lin, H., M.T. Niu, T. Yoganathan, and G.A. Buck. 1992. Characterization of the rRNA-encoding genes and transcripts, and a group-1 self-splicing intron in Pneumocystis carinii. Gene 119: 163-173.
29. Liu, Y. and M.J. Leibowitz. 1993. Variation and in vitro splicing of group I introns in rRNA genes of Pneumocystic aarinii. Nucleic Acids Res. 21: 2415-2421.
30. Lonergan, K.M. and M.W. Gray. 1994. The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA. A case of evolutionary transfer of introns between mitochondria and plastids? J. Mol. Biol. 239: 476-499.
31. Martín, M.P., D.H. Coucheron, and S. Johansen. 2003. Structural features and evolutionary considerations of group IB introns 146 Botanical Studies, Vol. 50, 2009 in SSU rDNA of the lichen fungus Teloschistes. Fungal Genet. Biol. 40: 252-260.
32. Malkus, A., P.F.L. Chang, S.M. Zuzga, K.R. Chung, J. Shao, B.M. Cunfer, E. Arseniuk, and P.P. Ueng. 2006. RNA polymerase II gene (RPB2) encoding the second largest protein subunit in Phaeosphaeria nodorum and P. avenaria. Mycol. Res. 110: 1152-1164.
33. Malkus, A., E. Reszka, C.J. Chang, E. Arseniuk, P.F.L. Chang, and P.P. Ueng. 2005. Sequence diversity of β-tubulin (tubA) gene in Phaeosphaeria nodorum and P. avenaria. FEMS Microbiol. Lett. 249: 49-56.
34. Mathews, D.H., J. Sabina, M. Zuker, and D.H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
35. Mathews, D.H., M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, and D.H. Turner. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101: 7287-7292.
36. Mavridou, A., J. Cannone, and M.A. Typas. 2000. Identification of group-I introns at three different positions within the 28S rDNA gene of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae. Fungal Genet. Biol. 31: 79-90.
37. Mercure, S., S. Montplaisir, and G. Lemay. 1993. Correlation between the presence of a self-splicing intron in the 25S rDNA of C. albicans and strains susceptibility to 5-fluorocytosine. Nucleic Acids Res. 21: 6020-6027.
38. Michel, F. and E. Westhof. 1990. Modelling of the threedimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216: 585-610.
39. Myllys, L., M. Källersjö, and A. Tehler. 1999. Variable sizes of introns in the SSU rDNA in three species of Roccella (Arthoniales, Euascomycetes). Curr. Genet. 36: 79-85.
40. Neuvèglise, C., Y. Brygoo, and G. Riba. 1997. 28S rDNA group-I introns: a powerful tool for identifying strains of Beauveria brongniartii. Mol. Ecol. 6: 373-381.
41. Nikoh, N., and T. Fukatsu. 2001. Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps. Mol. Biol. Evol. 18 : 1631-1642.
42. Nishida, K., S. Suzuki, Y. Kimura, N. Nomura, M. Fujie, and T. Yamada. 1998. Group I introns found in Chlorella viruses: biological implications. Virology 242: 319-326.
43. Perotto, S., P. Nepote-Fus, L. Saletta, C. Bandi, and J.P.W. Young. 2000. A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes. Mol. Biol. Evol. 17: 44-59.
44. Pyle, A.M. and T.R. Cech. 1991. Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups. Nature 350: 628-631.
45. Reszka, E., E. Arseniuk, A. Malkus, K.R. Chung, N.R. O'Neill, Q.J. Song, and P.P. Ueng. 2006. A new biotype of Phaeosphaeria sp. of uncertain affinity causing Stagonospora leaf blotch disease in cereals in Poland. Plant Dis. 90: 113.
46. Reszka, E., K.R. Chung, A. Tekauz, A. Malkus, E. Arseniuk, J.M. Krupinsky, H. Tsang, and P.P. Ueng. 2005. Presence of β-glucosidase (bgl1) gene in Phaeosphaeria nodorum and Phaeosphaeria avenaria f.sp. triticea. Can. J. Bot. 83: 1001-1014.
47. Riipinen, K.A. and T Alatossava. 2004. Two self-splicing group I introns interrupt two late transcribed genes of prolateheaded Lactobacillus delbrueckii phage JCL1032. Arch. Virol. 149: 2013-2024.
48. Roman, J. and S. A. Woodson. 1998. Integration of the Tetrahymena Group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl. Acad. Sci. USA 95: 2134-2139.
49. Saldanha, R., G. Mohr, M. Belfort, and A.M. Lambowitz. 1993. Group I and group II introns. The FASEB J. 7: 15-24.
50. Sandegren, L. and B.M. Sjöberg. 2004. Distribution, sequence homology, and homing of group I introns among T-evenlike bacteriophages. J. Biol. Chem. 279: 22218-22227.
51. Shinohara, M.L., K.F. LoBuglio, and S.O. Rogers. 1996. Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates. Current Genetics 29: 377-387.
52. Simon, D., J. Moline, G. Helms, T. Friedl, and D. Bhattacharya. 2005. Divergent histories of rDNA group I introns in the lichen family Physciaceae. J. Mol. Evol. 60: 434-446.
53. Stankovic, S., B. Soldo, T. Beric-Bjedov, J. Knezevic-Vukcevic, D. Simic, and V. Lazarevic. 2007. Subspecies-specific distribution of intervening sequences in the Bacillus subtilis prophage ribonucleotide reductase genes. Syst. Appl. Microbiol. 30: 8-15.
54. Suga, H., K. Oyabu, M. Ito, K. Kageyama, and M. Hyakumachi. 2000. Detection of intron-like sequences in the small subunit rDNA 3' region of Fusarium solani. Mycol. Res. 104: 782-787.
55. Suh, S-O., K.G. Jones, and M. Blackwell. 1999. A group I intron in nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: Evidence for a new major class of group I introns. J. Mol. Evol. 48: 493-500.
56. Takashima, M. and T. Nakase. 1997. A phylogenetic analysis of three group I introns found in the nuclear small subunit ribosomal RNA gene of the ballistoconidiogenous anamorphic yeast-like fungus Tilletiopsis flava. Genes Genet. Syst. 72: 205-214.
57. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
58. Tan, M.K. 1997. Origin and inheritance of group I introns in 26S rRNA genes of Gaeumannomyces graminis. J. Mol. Evol. 44: 637-645.
59. Turmel, M., J. Boulanger, M.N. Schnare, M.W. Gray, and C. Lemieux. 1991. Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos. J. Mol. Biol. 218: 293-311.
60. Ueng, P.P., G.C. Bergstrom, R.M. Slay, E.A. Geiger, G. Shaner, and A.L. Scharen. 1992. Restriction fragment length polymorphisms in the wheat glume blotch fungus, Phaeosphaeria nodorum. Phytopathology 82: 1302-1305.
61. Ueng, P.P., E. Reszka, K.R. Chung, E. Arseniuk, and J.M. Krupinsky. 2003. Comparison of glyceraldehyde-3- phosphate dehydrogenase genes in Phaeosphaeria nodorum and P. avenaria species. Plant Pathol. Bull. 12: 255-268.
62. Wang, C., Z. Li, M.A. Typas, and T.M. Butt. 2003. Nuclear large subunit rDNA group I intron distribution in a population of Beauveria bassiana strains: phylogenetic implications. Mycol. Res. 107: 1189-1200.
63. Wang, C.L., A. Malkus, S.M. Zuzga, P.F.L. Chang, B.M. Cunfer, E. Arseniuk, and P.P. Ueng. 2007. Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species. Genome 50: 595-609.
64. Wetzel, H.C., S.H. Hulbert, and N.A. Tisserat. 1999. Molecular evidence for the presence of Ophiosphaerella narmari n. comb., a cause of spring dead spot of Bermuda grass, in North America. Mycol. Res. 103: 981-989.
65. Xiao, M., T. Li, X. Yuan, Y. Shang, F. Wang, S. Chen, and Y. Zhang. 2005. A peripheral element assembles the compact core structure essential for group I intron self-splicing. Nucleic Acids Res. 33: 4602-4611.