From Monomeric to Homodimeric Endonucleases and Back: Engineering Novel Specificity of LAGLIDADG Enzymes

Journal of Molecular Biology

Volumn 361, Issue 4, 2006, Pages 744-754

  Silva, George H ^a   Belfort, Marlene ^b   Wende, Wolfgang ^a   Pingoud, Alfred ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b WADSWORTH CENTER   (United States)

Author keywords

homing; intron endonuclease; LAGLIDADG; protein engineering; specificity

Indexed keywords

DEOXYRIBONUCLEASE; ENDONUCLEASE; HOMODIMER; HYBRID PROTEIN; MAGNESIUM; MANGANESE; MONOMER; PALINDROMIC DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; BINDING AFFINITY; DIMERIZATION; DNA BINDING; DNA CLEAVAGE; DNA SEQUENCE; ENZYME ENGINEERING; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN EXPRESSION; THERMOSTABILITY; WILD TYPE;

EID: 33746820661     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.06.063     Document Type: Article

References (34)

1. Pingoud A., Noël A.J., Pingoud V., Steuer S., and Wende W. Homing endonucleases-tools and targets for protein engineering. In: Svendesen A. (Ed). Enzyme Functionality: Design, Engineering and Screening (2003), Marcel Dekker, Inc., New York 325-351
2. Chevalier B., Turmel M., Lemieux C., Monnat Jr. R.J., and Stoddard B.L. Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol. 329 (2003) 253-269
3. Moure C.M., Gimble F.S., and Quiocho F.A. The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol. 334 (2003) 685-695
4. Stoddard B.L. Homing endonuclease structure and function. Quart. Rev. Biophys. 38 (2006) 49-95
5. Chevalier B.S., Kortemme T., Chadsey M.S., Baker D., Monnat R.J., and Stoddard B.L. Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell 10 (2002) 895-905
6. Moure C.M., Gimble F.S., and Quiocho F.A. Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Nature Struct. Biol. 9 (2002) 764-770
7. Bolduc J.M., Spiegel P.C., Chatterjee P., Brady K.L., Downing M.E., Caprara M.G., et al. Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev. 17 (2003) 2875-2888
8. Silva G.H., Dalgaard J.Z., Belfort M., and Van Roey P. Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. J. Mol. Biol. 286 (1999) 1123-1136
9. Lanio T., Jeltsch A., and Pingoud A. On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target. Protein Eng. 13 (2000) 275-281
10. Galburt E.A., and Stoddard B.L. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41 (2002) 13851-13860
11. Epinat J.C., Arnould S., Chames P., Rochaix P., Desfontaines D., Puzin C., et al. A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucl. Acids Res. 31 (2003) 2952-2962
12. Seligman L.M., Chisholm K.M., Chevalier B.S., Chadsey M.S., Edwards S.T., Savage J.H., and Veillet A.L. Mutations altering the cleavage specificity of a homing endonuclease. Nucl. Acids Res. 30 (2002) 3870-3879
13. Arnould S., Chames P., Perez C., Lacroix E., Duclert A., Epinat J.C., et al. Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol. 355 (2006) 443-458
14. Kortemme T., Kim D.E., and Baker D. Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004 (2004) pl2
15. Silva G.H., and Belfort M. Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI. Nucl. Acids Res. 32 (2004) 3156-3168
16. Dalgaard J.Z., Garrett R.A., and Belfort M. Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron. J. Biol. Chem. 269 (1994) 28885-28892
17. Wang J., Kim H.H., Yuan X., and Herrin D.L. Purification, biochemical characterization and protein-DNA interactions of the I-CreI endonuclease produced in Escherichia coli. Nucl. Acids Res. 25 (1997) 3767-3776
18. Aagaard C., Awayez M.J., and Garrett R.A. Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI. Nucl. Acids Res. 25 (1997) 1523-1530
19. Downing M.E., Brady K.L., and Caprara M.G. A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing. RNA 11 (2005) 437-446
20. Longo A., Leonard C.W., Bassi G.S., Berndt D., Krahn J.M., Hall T.M., and Weeks K.M. Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nature Struct. Mol. Biol. 12 (2005) 779-787
21. Steuer S., Pingoud V., Pingoud A., and Wende W. Chimeras of the homing endonuclease PI-SceI and the homologous Candida tropicalis intein: a study to explore the possibility of exchanging DNA-binding modules to obtain highly specific endonucleases with altered specificity. ChemBiochem. 5 (2004) 206-213
22. Chevalier B., Sussman D., Otis C., Noel A.J., Turmel M., Lemieux C., et al. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 43 (2004) 14015-14026
23. Perrin A., Buckle M., and Dujon B. Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions. EMBO J. 12 (1993) 2939-2947
24. Monteilhet C., Dziadkowiec D., Szczepanek T., and Lazowska J. Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli. Nucl. Acids Res. 28 (2000) 1245-1251
25. Nakayama H., Morinaga Y., Nomura N., Nunoura T., Sako Y., and Uchida A. An archaeal homing endonuclease I-PogI cleaves at the insertion site of the neighboring intron, which has no nested open reading frame. FEBS Letters 544 (2003) 165-170
26. Nomura N., Morinaga Y., Shirai N., and Sako Y. I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1. Nucl. Acids Res. 33 (2005) e116
27. Duan X., Gimble F.S., and Quiocho F.A. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell 89 (1997) 555-564
28. Heath P.J., Stephens K.M., Monnat Jr. R.J., and Stoddard B.L. The structure of I-Crel, a group I intron-encoded homing endonuclease. Nature Struct. Biol. 4 (1997) 468-476
29. Gruen M., Chang K., Serbanescu I., and Liu D.R. An in vivo selection system for homing endonuclease activity. Nucl. Acids Res. 30 (2002) e29
30. Chen Z., and Zhao H. A highly sensitive selection method for directed evolution of homing endonucleases. Nucl. Acids Res. 33 (2005) e154
31. Doyon J.B., Pattanayak V., Meyer C.B., and Liu D.R. Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J. Am. Chem. Soc. 128 (2006) 2477-2484
32. Collaborative Computing Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
33. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
34. Horton R.M., Cai Z.L., Ho S.N., and Pease L.R. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. BioTechniques 8 (1990) 528-535