Invasion of a multitude of genetic niches by mobile endonuclease genes

FEMS Microbiology Letters

Volumn 185, Issue 2, 2000, Pages 99-107

  Gimble, Frederick S ^a  

^a TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; ENDONUCLEASE;

ALLELE; BACTERIOPHAGE; DNA REPAIR; DNA STRAND BREAKAGE; EVOLUTION; GENE CONVERSION; GENE INSERTION; GENETIC ANALYSIS; GENOME; INTRON; OPEN READING FRAME; PRIORITY JOURNAL; REVIEW; RNA SPLICING; TRANSPOSON;

EID: 0034656221     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(00)00069-0     Document Type: Article

References (58)

1. Kidwell M.G., Lisch D. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA. 94:1997;7704-7711.
2. Britten R.J. Cases of ancient mobile element DNA insertions that now affect gene regulation. Mol. Phylogenet. Evol. 5:1996;13-17.
3. Mueller, J.E., Bryk, M., Loizos, N. and Belfort, M. (1993) Homing endonucleases. In: Nucleases (Linn, S.M. et al., Eds.), pp. 111-143. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Belfort M., Roberts R.J. Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25:1997;3379-3388.
5. Dalgaard J.Z., Klar A.J., Moser M.J., Holley W.R., Chatterjee A., Mian I.S. 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. 25:1997;4626-4638.
6. Hensgens L.A.M., Bonen L., de Haan M., van der Horst G., Grivell L. Two intron sequences in yeast mitochondrial COX1 gene: Homology among URF-containing introns and strain-dependent variation in flanking exons. Cell. 32:1983;379-389.
7. Duan X., Gimble F.S., Quiocho F.A. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell. 89:1997;555-564.
8. Heath P.J., Stephens K.M., Monnat R.J. Jr., Stoddard B.L. The structure of I-CreI, a group I intron-encoded homing endonuclease. Nat. Struct. Biol. 4:1997;468-476.
9. Silva G.H., Dalgaard J.Z., Belfort M., Van Roey P. Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. J. Mol. Biol. 286:1999;1123-1136.
10. Johansen S., Embley T.M., Willassen N.P. A family of nuclear homing endonucleases. Nucleic Acids Res. 21:1993;4405.
11. Gorbalenya A.E. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci. 3:1994;1117-1120.
12. Shub D.A., Goodrich-Blair H., Eddy S.R. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19:1994;402-404.
13. Kühlmann U.C., Moore G.R., James R., Kleanthous C., Hemmings A.M. Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined? FEBS Lett. 463:1999;1-2.
14. Zimmerly S., Guo H., Eskes R., Yang J., Perlman P.S., Lambowitz A.M. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell. 83:1995;529-538.
15. Flick K.E., Jurica M.S., Monnat R.J. Jr., Stoddard B.L. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature. 394:1998;96-101.
16. Kleanthous C., Kuhlmann U.C., Pommer A.J., Ferguson N., Radford S.E., Moore G.R., James R., Hemmings A.M. Structural and mechanistic basis of immunity toward endonuclease colicins. Nat. Struct. Biol. 6:1999;243-252.
17. Miller M.D., Tanner J., Alpaugh M., Benedik M.J., Krause K.L. 2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. Nat. Struct. Biol. 1:1994;461-468.
18. Friedhoff P., Franke I., Meiss G., Wende W., Krause K.L., Pingoud A. A similar active site for non-specific and specific endonucleases. Nat. Struct. Biol. 6:1999;112-113.
19. Kowalski J.C., Belfort M., Stapleton M.A., Holpert M., Dansereau J.T., Pietrokovski S., Baxter S.M., Derbyshire V. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. Nucleic Acids Res. 27:1999;2115-2125.
20. Belfort M. Self-splicing introns in prokaryotes: migrant fossils? Cell. 64:1991;9-11.
21. Eddy S.R., Gold L. Artificial mobile DNA element constructed from the EcoRI endonuclease gene. Proc. Natl. Acad. Sci. USA. 89:1992;1544-1547.
22. Lambowitz A.M., Perlman P.S. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15:1990;440-444.
23. Dujardin G., Jacq C., Slonimski P.P. Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene. Nature. 298:1982;628-632.
24. Schafer B., Wilde B., Massardo D.R., Manna F., Del Giudice L., Wolf K. A mitochondrial group-I intron in fission yeast encodes a maturase and is mobile in crosses. Curr. Genet. 25:1994;336-341.
25. Ho Y., Kim S.-j., Waring R.B. A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease. Proc. Natl. Acad. Sci. USA. 94:1997;8994-8999.
26. Perler F.B., Olsen G.J., Adam E. Compilation and analysis of intein sequences. Nucleic Acids Res. 25:1997;1087-1094.
27. Gorbalenya A.E. Non-canonical inteins. Nucleic Acids Res. 26:1998;1741-1748.
28. Kidwell M.G. Lateral transfer in natural populations of eukaryotes. Annu. Rev. Genet. 27:1993;235-256.
29. Miller, W.J., Kruckenhauser, L. and Pinsker, W. (1996) In: Transgenic Organisms: Biological and Social Implications (Tomiuk, J. et al., Eds.), pp. 21-35. Birkhauser, Basel.
30. Moore J.K., Haber J.E. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature. 383:1996;644-646.
31. Ricchetti M., Fairhead C., Dujon B. Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature. 402:1999;96-100.
32. Yu X., Gabriel A. Patching broken chromosomes with extranuclear cellular DNA. Mol. Cell. 4:1999;873-881.
33. Loizos N., Tillier E.R.M., Belfort M. Evolution of mobile group I introns: Recognition of intron sequences by an intron-encoded endonuclease. Proc. Natl. Acad. Sci. USA. 91:1994;11983-11987.
34. Lambowitz A.M., Belfort M. Introns as mobile genetic elements. Annu. Rev. Biochem. 62:1993;587-622.
35. Turmel M., Cote V., Otis C., Mercier J.P., Gray M.W., Lonergan K.M., Lemieux C. Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol. 12:1995;533-545.
36. 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.
37. Gray M.W. Mass migration of a group I intron: promiscuity on a grand scale. Proc. Natl. Acad. Sci. USA. 95:1998;14003-14005.
38. Goddard M.R., Burt A. Recurrent invasion and extinction of a selfish gene. Proc. Natl. Acad. Sci. USA. 96:1999;13880-13885.
39. Gimble F.S., Thorner J. Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature. 357:1992;301-306.
40. Gu H.H., Xu J., Gallagher M., Dean G.E. Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis. J. Biol. Chem. 268:1993;7372-7381.
41. Derbyshire V., Wood D.W., Wu W., Dansereau J.T., Dalgaard J.Z., Belfort M. Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution. Proc. Natl. Acad. Sci. USA. 94:1997;11466-11471.
42. Dalgaard J.Z., Moser M.J., Hughey R., Mian I.S. Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. J. Comput. Biol. 4:1997;193-214.
43. Herskowitz, I., Rine, J. and Strathern, J.N. (1992) Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae. In: The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression (Jones, E.W. et al., Eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
44. Ban C., Yang W. Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J. 17:1998;1526-1534.
45. James R., Kleanthous C., Moore G.R. The biology of E colicins: paradigms and paradoxes. Microbiology. 142:1996;1569-1580.
46. - cells of Sulfolobus acidocaldarius. Proc. Natl. Acad. Sci. USA. 92:1995;12285-12289.
47. Goodrich-Blair H., Shub D.A. Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers. Cell. 84:1996;211-221.
48. Lykke-Andersen J., Garrett R.A., Kjems J. Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure. Nucleic Acids Res. 24:1996;3982-3989.
49. Aggarwal A.K. Homing in on intron-encoded endonucleases. Nat. Struct. Biol. 4:1997;423-424.
50. Gimble F.S., Hu D., Duan X., Quiocho F.A. Identification of Lys403 in the PI-SceI homing endonuclease as part of a symmetric catalytic center. J. Biol. Chem. 273:1998;30524-30529.
51. He Z., Crist M., Yen H.-C., Duan X., Quiocho F.A., Gimble F.S. Amino acid residues in both the protein splicing and endonuclease domains of the PI-SceI intein mediate DNA binding. J. Biol. Chem. 273:1998;4607-4615.
52. Perler F.B. Protein splicing of inteins and hedgehog autoproteolysis: structure, function, and evolution. Cell. 92:1998;1-4.
53. +-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J. Biol. Chem. 265:1990;6726-6733.
54. Gimble F.S., Wang J. Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing. J. Mol. Biol. 263:1996;163-180.
55. Pietrokovski S. Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci. 3:1994;2340-2350.
56. Nickoloff J.A., Chen E.Y., Heffron F. A 24-base-pair DNA sequence from the MAT locus stimulates intragenic recombination in yeast. Proc. Natl. Acad. Sci. USA. 83:1986;7831-7835.
57. Ho Y., Waring R.B. The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing. J. Mol. Biol. 292:1999;987-1001.
58. Jasin M. Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet. 12:1996;224-228.