Novel site-specific DNA endonucleases

Current Opinion in Structural Biology

Volumn 8, Issue 1, 1998, Pages 19-25

  Aggarwal, Aneel K ^a   Wah, David A ^a  

^a NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE;

DNA CLEAVAGE; ENZYME MECHANISM; ENZYME STRUCTURE; HYDROLYSIS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW;

EID: 0032005037     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80005-5     Document Type: Article

References (40)

1. Roberts RJ, Halford SE. Type II restriction endonucleases. Linn SM, Lloyd RS, Roberts RJ. Nucleases. 1993;35-88 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
2. Aggarwal AK. Structure and function of restriction endonucleases. Curr Opin Struct Biol. 5:1995;11-19.
3. Skowron P, Kaczorowski T, Tucholski J, Podhajska AJ. Atypical DNA-binding properties of class-IIS restriction endonucleases: evidence for recognition of the cognate sequence by a Fokl monomer. Gene. 125:1993;1-10.
4. Li L, Wu LP, Chandrasegaran S. Functional domains in Fokl restriction endonuclease. Proc Natl Acad Sci USA. 89:1992;4275-4279.
5. Kim Y-G, Chandrasegaran S. Chimeric restriction endonuclease. Proc Natl Acad Sci USA. 91:1994;883-887.
6. of special interest Kim Y-G, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fokl cleavage domain. Proc Natl Acad Sci USA. 93:1996;1156-1160 The authors report the creation of novel site-specific endonucleases by linking two different zinc-finger proteins to the Fokl cleavage domain. Both fusion proteins are active and cleave DNA in a sequence-specific manner. Because each zinc finger binds DNA as an independent module, artificial enzymes with novel specificities can be generated by fusing multiple zinc fingers in tandem with a Fokl cleavage domain; a promising modular approach to endonuclease design.
7. of special interest Huang B, Schaeffer CJ, Li Q, Tsai M-D. Splase: a new class lls zinc-finger restriction endonuclease with specificity for Sp1 binding sites. J Prot Chem. 15:1996;481-489 A new restriction endonuclease, named Splase. was constructed by fusing the zinc-finger domain from the transcription factor Sp1 to the Fokl cleavage domain. Splase recognizes a 10 base pair sequence, making it a 'rare cutter'.
8. Podhajska AJ, Szybalski W. Conversion of the Fokl endonuclease to a universal restriction enzyme: cleavage of phage M13mp7 DNA at predetermined sites. Gene. 40:1985;175-182.
9. of special interest Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK. Structure of the multimodular endonuclease Fokl bound to DNA. of outstanding interest Nature. 388:1997;97-100 The first structure of a type lls restriction endonuclease is presented. The structure reveals an unexpected configuration in which the cleavage domain is sequestered in a 'piggy-back" fashion by the recognition domain. Surprisingly, the catalytic domain contains a single catalytic center, raising questions as to how the enzyme manages to cleave both DNA strands. The structure provides a framework for the design of chimaeric enzymes with novel specificities [5,6,7].
10. Waugh DS, Sauer RT. Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fokl endonuclease. Proc Natl Acad Sci USA. 90:1993;9596-9600.
11. Yonezawa A, Sugiura Y. DNA binding mode of class-lls restriction endonuclease Fokl revealed by DNA footprinting analysis. Biochim Biophys Acta. 1219:1994;369-379.
12. Li L, Wu LP, Clarke R, Chandrasegaran S. C-terminal deletion mutants of the Fokl restriction endonuclease. Gene. 133:1993;79-84.
13. Waugh DS, Sauer RT. A novel class of Fokl restriction endonuclease mutants that cleave hemi-methylated substrates. J Biol Chem. 269:1994;12298-12303.
14. Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 253:1991;1001-1007.
15. Churchill ME, Tullius TD, Klug A. Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. Proc Natl Acad Sci USA. 87:1990;5528-5532.
16. Clemens KR, Liao X, Wolf V, Wright PE, Gottesfeld JM. Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5S RNA gene complex. Proc Natl Acad Sci USA. 89:1992;10822-10826.
17. Pavletich NP, Pabo CO. Crystal structure of a five-finger GLI-DNA complex: new perspectives on Zn fingers. Science. 261:1993;1701-1707.
18. Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 368:1994;660-664.
19. Mueller JE, Bryk M, Loizos N, Belfort M. Homing endonucleases. Linn SM, Lloyd RS, Roberts RJ. Nucleases. 1993;111-143 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
20. Cooper AA, Stevens TH. Protein splicing: self-splicing of genetically mobile elements at the protein level. Trends Biochem Sci. 20:1995;351-356.
21. of special interest Belfort M, Roberts RJ. Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25:1997;3379-3388 This is a recent review of homing endonucleases, with suggestions for their nomenclature based on restriction enzymes. An excellent comparison of the biological and biochemical properties of restriction endonucleases and homing endonucleases.
22. of outstanding interest Heath PJ, Stephens KM, Monnat RJ Jr, Stoddard BL. The structure of I-Crel, a group I intron-encoded homing endonuclease. Nat Struct Biol. 4:1997;468-476 The authors report the first structure determination of an intron-encoded homing endonuclease. The enzyme crystallizes as a dimer, forming an elongated saddle-shaped molecule that is ideally suited for mounting a long DNA sequence. The LAGLIDADG motif, common amongst homing endonucleases, helps to form the dimer interface and position the catalytic residues in the vicinity of the scissile phosphodiesters.
23. Kim Y, Geiger JH, Hahn S, Sigler PB. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520.
24. Kim JL, Nikolov DB, Burley SK. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 365:1993;520-527.
25. Endrizzi JA, Cronk JD, Wang W, Crabtree GR, Alber T. Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science. 268:1995;556-559.
26. Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystal structure of a zif268-DNA complex at 2.1 Å Science. 252:1991;809-817.
27. Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell. 77:1994;21-32.
28. Jacobson EM, Li P, Leon-del-Rio A, Rosenfeld MG, Aggarwal AK. Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility. Genes Dev. 11:1997;198-212.
29. Gimble FS, Stephens BW. Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-Scel endonuclease. J Biol Chem. 270:1995;5849-5856.
30. Anderson JE. Restriction endonucleases and modification methylases. Curr Opin Struct Biol. 3:1993;24-30.
31. of special interest Gimble FS, Wang J. Substrate recognition and induced DNA distortion by the PI-Scel endonuclease, an enzyme generated by protein splicing. J Mol Biol. 263:1996;163-180 The study defines the PI-Scel recognition sequence as a minimal 31 base pair site, containing a high-affinity region (region II) and a low-affinity region (region I). The enzyme binds the site, yielding two species, one that is due to binding to region II only and the other due to binding to both regions. The enzyme distorts the DNA to varying extents, from a bend of ~40° on binding to region II, to a cumulative bend of ~60° on binding to both regions.
32. of special interest Wende W, Grindl W, Christ F, Pingoud A, Pingoud V. Binding, bending and cleavage of DNA substrates by the homing endonuclease PI-Scel. Nucleic Acids Res. 24:1996;4123-4132 An independent study with analogous results to [31]. The authors come to similar conclusions regarding the high and low affinity regions within the PI-Scel site and the formation of two complexes. The minimal site was found to vary from 30 to greater than 50 base pairs, however, depending upon the degree of torsional stress. Also the DNA bends calculated are larger than in [31]: 45° and 75° for the two complexes, respectively.
33. of special interest Duan X, Gimble FS, Quiocho FA. Crystal structure of PI-Scel, a homing endonuclease with protein splicing activity. of outstanding interest Cell. 89:1997;555-564 The first structure determination of an intein, revealing the basis of the protein splicing and endonuclease activities of PI-Scel. The endonuclease domain adopts a compact, pseudo-twofold symmetric structure with similarities to the I-Crel dimer [22]. Recognization of a long homing sequence [31,32], however, appears to require the participation of the protein splicing domain. The authors also consider how inteins may have evolved by an invasion of an endonuclease ORF into a pre-existing protein-splicing gene.
34. Li L, Chandrasegaran S. Alteration of the cleavage distance of Fokl restriction endonuclease by insertion mutagenesis. Proc Natl Acad Sci USA. 90:1993;2764-2768.
35. Henke RM, Butow RA, Perlman PS. Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron al4 α of yeast mitochondrial DNA. EMBO J. 14:1995;5094-5099.
36. of special interest Szczepanek T, Lazowska J. Replacement of two non-adjacent amino acids in the S. cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity. EMBO J. 15:1996;3758-3767 Intriguingly, the proteins encoded within the group I introns of the cyt b gene from S. capensis and S. cerevisiae differ by only four amino acids, but one functions as a homing endonuclease and the other as an RNA maturase. The authors take advantage of this remarkable similarity to show that the replacement of only two amino acids in the maturase by the corresponding residues in the endonuclease (Thr212 to alanine and Thr239 to histidine) is sufficient to confer homing endonuclease activity on the maturase.
37. of special interest Ho Y, Kim SJ, Waring RB. 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 The authors show that a protein encoded within an intron of Aspergillus nidulans mitochondria has both maturase and endonuclease activities. The maturase activity is tested directly in vitro. Together with [35], the results reinforce an association between RNA splicing and endonuclease activities, implied by the common occurrence of LAGLIDADG motifs.
38. Bryk M, Belisle M, Mueller JE, Belfort M. Selection of remote cleavage site by I-Tevl, the td intron-encoded endonuclease. J Mol Biol. 247:1995;197-210.
39. Loizos N, Silva GH, Belfort M. Intron-encoded endonuclease I-Tevll binds across the minor groove and induces two distinct conformational changes in its DNA substrate. J Mol Biol. 255:1996;412-424.
40. of special interest Derbyshire V, Kowalski JC, Dansereau JT, Hauer CR, Belfort M. Two-domain structure of the td intron-encoded endonuclease I-Tevl correlates with the two-domain configuration of the homing site. J Mol Biol. 265:1997;494-506 Partial proteolysis experiments demonstrate that I-Tevl is a bipartite enzyme consisting of a C-terminal DNA-recognition domain tethered to an N-terminal catalytic domain. The GlY-YlG motif coincides with the catalytic domain. The recognition domain binds DNA with the same affinity as the full-length protein. The bipartite structure of the enzyme matches the bipartite nature of the homing site as determined by biochemical methods [38].