The spread of LAGLIDADG homing endonuclease genes in rDNA

Nucleic Acids Research

Volumn 32, Issue 6, 2004, Pages 2049-2057

  Haugen, Peik ^a   Bhattacharya, Debashish ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; HOMING ENDONUCLEASE; RIBOSOME DNA; RIBOZYME; UNCLASSIFIED DRUG;

ARTICLE; CLUSTER ANALYSIS; GENE DUPLICATION; GENE FUSION; GENE INSERTION; GENETIC CODE; INTRON; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN MOTIF;

AMINO ACID MOTIFS; DNA, RIBOSOMAL; ENDONUCLEASES; GENES, RRNA; INTERSPERSED REPETITIVE SEQUENCES; INTRONS; PROTEINS;

EID: 3042568753     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh520     Document Type: Article

References (37)

1. Jurica,M.S. and Stoddard,B.L. (1999) Homing endonucleases: structure, function and evolution. Cell. Mol. Life Sci., 55, 1304-1326.
2. Turmel,M., Cote,V., Otis,C., Mercier,J.P., Gray,M.W., Lonergan,K.M. and Lemieux,C. (1995) Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol., 12, 533-545.
3. Turmel,M., Otis,C., Cote,V. and Lemieux,C. (1997) Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease. Nucleic Acids Res., 25, 2610-2619.
4. Dalgaard,J.Z., Klar,A.J., Moser,M.J., Holley,W.R., Chatterjee,A. and Mian,I.S. (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res., 25, 4626-4638.
5. Goddard,M.R and Burt,A. (1999) Recurrent invasion and extinction of a selfish gene. Proc. Natl Acad. Sci. USA, 96, 13880-13885.
6. Nesbø,C.L. and Doolittle,W.F. (2003) Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles. Proc. Natl Acad. Sci. USA, 100, 10806-10811.
7. Busse,I. and Preisfeld,A. (2003) Discovery of a group I intron in the SSU rDNA of Ploeotia costata (Euglenozoa). Protist, 154, 57-69.
8. Haugen,P., Reeb,V., Lutzoni,F. and Bhattacharya,D. (2004) The evolution of homing endonuclease genes and group I introns in nuclear rDNA. Mol. Biol. Evol., 21, 129-140.
9. Belfort,M. and Perlman,P.S. (1995) Mechanisms of intron mobility. J. Biol. Chem., 270, 30237-30240.
10. Woodson,S.A. and Cech,T.R. (1989) Reverse self-splicing of the Tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell, 57, 335-345.
11. Roman,J. and Woodson,S.A. (1998) Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl Acad. Sci. USA, 95, 2134-2139.
12. Friedl,T., Besendahl,A., Pfeiffer,P. and Bhattacharya,D. (2002) The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol. Phylogenet. Evol., 14, 342-352.
13. Chevalier,B.S. and Stoddard,B.L. (2001) Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res., 29, 3757-3774.
14. Chevalier,B., Turmel,M., Lemieux,C., Monnat,R.J.,Jr and Stoddard,B.L. (2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol., 329, 253-269.
15. Moure,C.M., Gimble,F.S. and Quiocho,F.A. (2003) The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol., 334, 685-695.
16. Flick,K.E., Jurica,M.S., Monnat,R.J.,Jr and Stoddard,B.L. (1998) DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature, 394, 96-101.
17. Loizos,N., Tillier,E.R. and Belfort,M. (1994) Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease. Proc. Natl Acad. Sci. USA, 91, 11983-11987.
18. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2003) GenBank. Nucleic Acids Res., 31, 23-27.
19. Lucas,P., Otis,C., Mercier,J.P., Turmel,M. and Lemieux,C. (2001) Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases. Nucleic Acids Res., 29, 960-969.
20. Thompson,J.D., Higgins,D.G. and 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. Nucleic Acids Res., 22, 4673-4680.
21. Schmidt,H.A., Strimmer,K., Vingron,M. and von Haeseler,A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502-504.
22. Whelan,S. and Goldman,N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
23. Felsenstein,J. (2002) PHYLIP, V3.6a3. Department of Genome Sciences, University of Washington, Seattle, WA.
24. Page,R.D.M. (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci., 12, 357-358.
25. Kumar,S., Tamura,K., Jakobsen,I.B. and Nei,M. (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics, 17, 1244-1245.
26. Ronquist,F. and Huelsenbeck,J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
27. Swofford,D.L. (2002) PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) 4.0b8. Sinauer, Sunderland, MA.
28. Hibbett,D.S. (1996) Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi. Mol. Biol. Evol., 13, 903-917.
29. Bhattacharya,D. (1998) The origin and evolution of protist group I introns. Protist, 149, 113-122.
30. Perotto,S., Nepote-Fus,P., Saletta,L., Bandi,C. and Young,J.P. (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.
31. Müller,K.M., Cannone,J.J., Gutell,R.R. and Sheath,R.G. (2001) A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta). Mol. Biol. Evol., 18, 1654-1667.
32. Nikoh,N. and Fukatsu,T. (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.
33. Bhattacharya,D., Simon,D., Huang,J., Cannone,J.J. and Gutell,R.R. (2003) The exon context and distribution of Euascomycetes rRNA spliceosomal introns. BMC Evol. Biol., 3, 7.
34. Jackson,S.A., Cannone,J.J., Lee,J.C., Gutell,R.R and Woodson,S.A. (2002) Distribution of rRNA introns in the three-dimesional structure of the ribosome. J. Mol. Biol., 323, 35-52.
35. Lykke-Andersen,J., Garrett,R.A. and Kjems,J. (1996) Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure. Nucleic Acids Res., 24, 3982-3989.
36. Belfort,M. and Roberts,R.J. (1997) Homing endonucleases: keeping the house in order. Nucleic Acids Res., 25, 3379-3388.
37. Silva,G.H., Dalgaard,J.Z., Belfort,M. and Van Roey,P. (1999) Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. J. Mol. Biol., 286, 1123-1136.