Structural features and evolutionary considerations of group IB introns in SSU rDNA of the lichen fungus Teloschistes

Fungal Genetics and Biology

Volumn 40, Issue 3, 2003, Pages 252-260

  Martín, María P ^a   Coucheron, Dag H ^b   Johansen, Steinar ^b  

^a CSIC   (Spain)

^b UNIVERSITY OF TROMSØ   (Norway)

Author keywords

Group I introns; Horizontal gene transfer; Intron evolution; Lichen; Ribosomal DNA; Teloschistes

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA;

ARTICLE; ASCOMYCETES; CATALYSIS; CLUSTER ANALYSIS; CONTROLLED STUDY; FUNGUS; FUNGUS ISOLATION; GENE SEQUENCE; INTRON; LICHEN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; RNA GENE; SPECIES DIFFERENTIATION; TELOSCHISTES VILLOSUS;

FUNGI; TELOSCHISTES; TELOSCHISTES VILLOSUS;

EID: 0242320928     PISSN: 10871845     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fgb.2003.07.001     Document Type: Article

References (45)

1. Belfort M., Roberts R.J. Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25:1997;3379-3388.
2. Bhattacharya D., Friedl T., Helms G. Vertical evolution and intragenic spread of lichen-fungal group I introns. J. Mol. Evol. 55:2002;74-84.
3. Bhattacharya D., Lutzoni F., Reeb V., Simon D., Nason J., Fernandez F. Widespread occurrence of spleisosomal introns in rDNA genes of ascomycetes. Mol. Biol. Evol. 17:2000;1971-1984.
4. Bhattacharya D., Surek B., Rüsing M., Damberger S., Melkonian M. Group-I introns are inherited through common ancestry in the nuclear-encoded rRNA of Zygnematales (Charophyceae). Proc. Natl. Acad. Sci. USA. 91:1994;9916-9920.
5. Cech T.R., Damberger S.H., Gutell R.R. Representation of the secondary and tertiary structure of group-I introns. Nat. Struct. Biol. 1:1994;273-280.
6. Cech T.R., Herschlag D. Group-I ribozymes: substrate recognition, catalytic strategies, and comparative mechanistic analysis. Nucleic Acids Mol. Biol. 10:1996;1-17.
7. Cho Y., Qiu Y.-L., Kuhlman P., Palmer J.D. Explosive invasion of plant mitochondria by a group-I intron. Proc. Natl. Acad. Sci. USA. 95:1998;14244-14249.
8. Cubero O.F., Bridge P.D., Crespo A. Terminal-sequence conservation identifies spliceosomal introns in ascomycete 18S RNA genes. Mol. Biol. Evol. 17:2000;751-756.
9. DePriest P.T., Been M.D. Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. J. Mol. Biol. 228:1992;315-321.
10. Einvik C., Elde M., Johansen S. Group I twintrons: genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs. J. Biotechnol. 64:1998;63-74.
11. Foley S., Bruttin A., Brüssow H. Widespread distribution of a group-I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. J. Virol. 74:2000;611-618.
12. Friedl T., Besendahl A., Pfeiffer P., Bhattacharya D. The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol. Phylogenet. Evol. 14:2000;343-353.
13. Gardes M., Bruns T. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol. Ecol. 2:1993;113-118.
14. Gargas A., De Priest P.T., Taylor J.W. Position of multiple insertions in the SSU rDNA of lichen-forming fungi. Mol. Biol. Evol. 12:1995;208-218.
15. Goddard M.R., Burt A. Recurrent invasion and extinction of a selfish gene. Proc. Natl. Acad. Sci. USA. 96:1999;13880-13885.
16. Golden B.L., Gooding A.R., Podell E.R., Cech T.R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science. 282:1998;259-264.
17. Grube M., Gutmann B., Arup U., de los Rios A., Mattsson J.-E., amd Wedin M. An exceptional group-I intron-like insertion in the SSU rDNA of lichen mycobionts. Curr. Genet. 35:1999;536-541.
18. Haugen P., Huss V.A.R., Nielsen H., Johansen S. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae. Curr. Genet. 36:1999;345-353.
19. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:2001;754-755.
20. Holst-Jensen A., Vaage M., Schumacher T., Johansen S. Structural characteristics and possible horizontal transfer of group-I introns between closely related plant pathogenic fungi. Mol. Biol. Evol. 16:1999;114-126.
21. Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R., Woodson S.A. Distribution of rRNA introns in the three-dimensional structure of the ribosome. J. Mol. Biol. 323:2002;35-52.
22. Jaeger L., Michel F., Westhof E. The structure of group I ribozymes. Nucleic Acids Mol. Biol. 10:1996;33-51.
23. Johansen S., Haugen P. A new nomenclature of group I introns in ribosomal DNA. RNA. 7:2001;935-936.
24. Johansen S., Muscarella D.E., Vogt V.M. Insertion elements in ribosomal DNA. Zimmermann A., Dahlberg A.E. Ribosomal RNA: Structure, Evolution, Processing, and Function in Biosynthesis. 1996;89-108 CRC Press, Boca Raton.
25. Kumar S., Tamura K., Jakobsen I.B., Nei M. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics. 17:2001;1244-1245.
26. Lambowitz A.M., Belfort M. Introns as mobile genetic elements. Annu. Rev. Biochem. 62:1993;587-622.
27. Lehnert V., Jaeger L., Michel F., Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup-IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3:1996;993-1009.
28. Martín M.P., Winka K. Alternative methods of extracting and amplifying DNA from lichens. Lichenology. 32:2000;189-196.
29. Martín M.P., Winka W., Llimona X., Lumbsch H.T. Evaluation of morphological variation in the lichen Diploschistes ocellatus (Ascomycota, Ostropales): evidence from nuclear rDNA ITS sequence data. Plant Biol. 2:2000;571-578.
30. Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
31. Müller K.M., Cannone J.J., Gutell R.R., Sheath R.G. A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta). Mol. Biol. Evol. 18:2001;1654-1667.
32. Nikoh N., Fukatsu T. Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps. Mol. Biol. Evol. 18:2001;1631-1642.
33. Nishida H., Tajiri Y., Sugiyama J. Multiple origins of fungal group-I introns located in the same position of nuclear SSU rRNA gene. J. Mol. Evol. 46:1998;442-448.
34. Noda H., Kodama K. Phylogenetic position of yeastlike endosymbionts of anobiid beetles. Appl. Environ. Microbiol. 62:1996;162-167.
35. Oliveira M.C., Ragan M.A. Variant forms of a group I intron in nuclear small subunit rRNA genes of the red alga Porphyra spiralis var. amplifolia. Mol. Biol. Evol. 11:1994;195-207.
36. Perotto S., Nepote-Fus P., Saletta L., Bandi C., Young J.P.W. 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. 17:2000;44-59.
37. Roman J., Rubin M.N., Woodson S.A. Sequence specificity of in vivo reverse splicing of the Tetrahymena group-I intron. RNA. 5:1999;1-13.
38. Roman J., Woodson S.A. Reverse splicing of the Tetrahymena IVS: evidence for multiple reaction sites in the 23S rRNA. RNA. 1:1995;478-490.
39. Shinohara M.L., LoBuglio K.F., Rogers S.O. Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates. Curr. Genet. 29:1996;377-387.
40. Shu S.O., Jones K.G., Blackwell M. A group I intron in the small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: evidence for a new major class of group I introns. J. Mol. Evol. 48:1999;493-500.
41. Shu S.O., Noda H., Blackwell M. Insect symbiosis: derivation of yeast-like endosymbionts with an entomopathogenic filamentous lineage. Mol. Biol. Evol. 18:2001;995-1000.
42. Stenroos S., De Priest P.T. Small insertion in a shared position in the SSU rDNA of Lecanorales lichen-forming Ascomycetes. Curr. Genet. 33:1998;124-130.
43. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony Version 4. 2002;Sinauer, Sunderland, MA.
44. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:1997;4876-4882.
45. White T.J., Bruns T., Lee S.B., Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Innis M.A., Gelfand D.H., Sninsky J.J., White T.J. PCR Protocols: A Guide to Methods and Applications. 1990;315-322 Academic Press, San Diego.