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Chandrasegaran S, Carroll D. Origins of Programmable Nucleases for Genome Engineering. J Mol Biol 2015; 428:963-89. [PMID: 26506267 DOI: 10.1016/j.jmb.2015.10.014] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 02/06/2023]
Abstract
Genome engineering with programmable nucleases depends on cellular responses to a targeted double-strand break (DSB). The first truly targetable reagents were the zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences could be addressed for cleavage by protein engineering, ushering in the breakthrough in genome manipulation. ZFNs resulted from basic research on zinc finger proteins and the FokI restriction enzyme (which revealed a bipartite structure with a separable DNA-binding domain and a non-specific cleavage domain). Studies on the mechanism of cleavage by 3-finger ZFNs established that the preferred substrates were paired binding sites, which doubled the size of the target sequence recognition from 9 to 18bp, long enough to specify a unique genomic locus in plant and mammalian cells. Soon afterwards, a ZFN-induced DSB was shown to stimulate homologous recombination in cells. Transcription activator-like effector nucleases (TALENs) that are based on bacterial TALEs fused to the FokI cleavage domain expanded this capability. The fact that ZFNs and TALENs have been used for genome modification of more than 40 different organisms and cell types attests to the success of protein engineering. The most recent technology platform for delivering a targeted DSB to cellular genomes is that of the RNA-guided nucleases, which are based on the naturally occurring Type II prokaryotic CRISPR-Cas9 system. Unlike ZFNs and TALENs that use protein motifs for DNA sequence recognition, CRISPR-Cas9 depends on RNA-DNA recognition. The advantages of the CRISPR-Cas9 system-the ease of RNA design for new targets and the dependence on a single, constant Cas9 protein-have led to its wide adoption by research laboratories around the world. These technology platforms have equipped scientists with an unprecedented ability to modify cells and organisms almost at will, with wide-ranging implications across biology and medicine. However, these nucleases have also been shown to cut at off-target sites with mutagenic consequences. Therefore, issues such as efficacy, specificity and delivery are likely to drive selection of reagents for particular purposes. Human therapeutic applications of these technologies will ultimately depend on risk versus benefit analysis and informed consent.
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Affiliation(s)
- Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Salt Lake City, UT 84112, USA.
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Pernstich C, Halford SE. Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer. Nucleic Acids Res 2011; 40:1203-13. [PMID: 21993298 PMCID: PMC3273807 DOI: 10.1093/nar/gkr809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The FokI restriction endonuclease is a monomeric protein that recognizes an asymmetric sequence and cleaves both DNA strands at fixed loci downstream of the site. Its single active site is positioned initially near the recognition sequence, distant from its downstream target 13 nucleotides away. Moreover, to cut both strands, it has to recruit a second monomer to give an assembly with two active sites. Here, the individual steps in the FokI reaction pathway were examined by fluorescence resonance energy transfer (FRET). To monitor DNA binding and domain motion, a fluorescence donor was attached to the DNA, either downstream or upstream of the recognition site, and an acceptor placed on the catalytic domain of the protein. A FokI variant incapable of dimerization was also employed, to disentangle the signal due to domain motion from that due to protein association. Dimerization was monitored separately by using two samples of FokI labelled with donor and acceptor, respectively. The stopped-flow studies revealed a complete reaction pathway for FokI, both the sequence of events and the kinetics of each individual step.
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Affiliation(s)
- Christian Pernstich
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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Lippow SM, Aha PM, Parker MH, Blake WJ, Baynes BM, Lipovsek D. Creation of a type IIS restriction endonuclease with a long recognition sequence. Nucleic Acids Res 2009; 37:3061-73. [PMID: 19304757 PMCID: PMC2685105 DOI: 10.1093/nar/gkp182] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 02/27/2009] [Accepted: 03/05/2009] [Indexed: 12/19/2022] Open
Abstract
Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are therefore particularly useful in the assembly of DNA from smaller fragments. A limitation of type IIS restriction endonucleases in assembly of long DNA sequences is the relative abundance of their target sites. To facilitate ligation-based assembly of extremely long pieces of DNA, we have engineered a new type IIS restriction endonuclease that combines the specificity of the homing endonuclease I-SceI with the type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined site outside the target site. Whereas previously described chimeric endonucleases do not produce type IIS-like precise DNA overhangs suitable for ligation, our chimeric endonuclease cleaves double-stranded DNA exactly 2 and 6 nt from the target site to generate homogeneous, 5', four-base overhangs, which can be ligated with 90% fidelity. We anticipate that these enzymes will be particularly useful in manipulation of DNA fragments larger than a thousand bases, which are very likely to contain target sites for all natural type IIS restriction endonucleases.
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Jurėnaitė-Urbanavičienė S, Šerkšnaitė J, Kriukienė E, Giedrienė J, Venclovas Č, Lubys A. Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proc Natl Acad Sci U S A 2007; 104:10358-63. [PMID: 17553965 PMCID: PMC1965518 DOI: 10.1073/pnas.0610365104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within or close to their recognition sequences. Shortly after their discovery in 1970, REases have become one of the primary tools in molecular biology. However, the list of available specificities of type II REases is relatively short despite the extensive search for them in natural sources and multiple attempts to artificially change their specificity. In this study, we examined the possibility of generating cleavage specificities of REases by swapping putative target recognition domains (TRDs) between the type IIB enzymes AloI, PpiI, and TstI. Our results demonstrate that individual TRDs recognize distinct parts of the bipartite DNA targets of these enzymes and are interchangeable. Based on these properties, we engineered a functional type IIB REase having previously undescribed DNA specificity. Our study suggests that the TRD-swapping approach may be used as a general technique for the generation of type II enzymes with predetermined specificities.
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Affiliation(s)
| | | | - Edita Kriukienė
- Institute of Biotechnology, V. Graičiūno 8, LT-02241, Vilnius, Lithuania; and
| | - Jolanta Giedrienė
- Institute of Biotechnology, V. Graičiūno 8, LT-02241, Vilnius, Lithuania; and
| | - Česlovas Venclovas
- Institute of Biotechnology, V. Graičiūno 8, LT-02241, Vilnius, Lithuania; and
| | - Arvydas Lubys
- Fermentas UAB, V. Graičiūno 8, LT-02241, Vilnius, Lithuania
- To whom correspondence should be addressed. E-mail:
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Xu Y, Lunnen KD, Kong H. Engineering a nicking endonuclease N.AlwI by domain swapping. Proc Natl Acad Sci U S A 2001; 98:12990-5. [PMID: 11687651 PMCID: PMC60812 DOI: 10.1073/pnas.241215698] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changing enzymatic function through genetic engineering still presents a challenge to molecular biologists. Here we present an example in which changing the oligomerization state of an enzyme changes its function. Type IIs restriction endonucleases such as AlwI usually fold into two separate domains: a DNA-binding domain and a catalytic/dimerization domain. We have swapped the putative dimerization domain of AlwI with a nonfunctional dimerization domain from a nicking enzyme, N.BstNBI. The resulting chimeric enzyme, N.AlwI, no longer forms a dimer. Interestingly, the monomeric N.AlwI still recognizes the same sequence as AlwI but only cleaves the DNA strand containing the sequence 5'-GGATC-3' (top strand). In contrast, the wild-type AlwI exists as a dimer in solution and cleaves two DNA strands; the top strand is cleaved by an enzyme binding to that sequence, and its complementary bottom strand is cleaved by the second enzyme dimerized with the first enzyme. N.AlwI is unable to form a dimer and therefore nicks DNA as a monomer. In addition, the engineered nicking enzyme is at least as active as the wild-type AlwI and is thus a useful enzyme. To our knowledge, this is the first report of creating a nicking enzyme by domain swapping.
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Affiliation(s)
- Y Xu
- New England Biolabs, 32 Tozertypeoad, Beverly, MA 01915, USA
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7
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Abstract
Chimeric restriction enzymes are a novel class of engineered nucleases in which the non-specific DNA cleavage domain of Fokl (a type IIS restriction endonuclease) is fused to other DNA-binding motifs. The latter include the three common eukaryotic DNA-binding motifs, namely the helix-turn-helix motif, the zinc finger motif and the basic helix-loop-helix protein containing a leucine zipper motif. Such chimeric nucleases have been shown to make specific cuts in vitro very close to the expected recognition sequences. The most important chimeric nucleases are those based on zinc finger DNA-binding proteins because of their modular structure. Recently, one such chimeric nuclease, Zif-QQR-F(N) was shown to find and cleave its target in vivo. This was tested by microinjection of DNA substrates and the enzyme into frog oocytes (Carroll et al., 1999). The injected enzyme made site-specific double-strand breaks in the targets even after assembly of the DNA into chromatin. In addition, this cleavage activated the target molecules for efficient homologous recombination. Since the recognition specificity of zinc fingers can be manipulated experimentally, chimeric nucleases could be engineered so as to target a specific site within a genome. The availability of such engineered chimeric restriction enzymes should make it feasible to do genome engineering, also commonly referred to as gene therapy.
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Affiliation(s)
- S Chandrasegaran
- Department of Environmental Health Sciences, School of Public Health, The Johns Hopkins University, Baltimore, MD 21205, USA
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Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK. Structure of FokI has implications for DNA cleavage. Proc Natl Acad Sci U S A 1998; 95:10564-9. [PMID: 9724743 PMCID: PMC27934 DOI: 10.1073/pnas.95.18.10564] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FokI is a member an unusual class of restriction enzymes that recognize a specific DNA sequence and cleave nonspecifically a short distance away from that sequence. FokI consists of an N-terminal DNA recognition domain and a C-terminal cleavage domain. The bipartite nature of FokI has led to the development of artificial enzymes with novel specificities. We have solved the structure of FokI to 2.3 A resolution. The structure reveals a dimer, in which the dimerization interface is mediated by the cleavage domain. Each monomer has an overall conformation similar to that found in the FokI-DNA complex, with the cleavage domain packing alongside the DNA recognition domain. In corroboration with the cleavage data presented in the accompanying paper in this issue of Proceedings, we propose a model for FokI DNA cleavage that requires the dimerization of FokI on DNA to cleave both DNA strands.
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Affiliation(s)
- D A Wah
- Structural Biology Program, Department of Physiology and Biophysics, Box 1677, 1425 Madison Avenue, Mount Sinai School of Medicine, New York, NY 10029, USA
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Kim YG, Smith J, Durgesha M, Chandrasegaran S. Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain. Biol Chem 1998; 379:489-95. [PMID: 9628342 DOI: 10.1515/bchm.1998.379.4-5.489] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gal4, a yeast protein, activates transcription of genes required for metabolism of galactose and melibiose. It binds as a dimer to a consensus palindromic 17-base pair DNA sequence. It is a member of the third family of proteins that contain zinc-mediated peptide loops that interact specifically with nucleic acids. Gal4 has a very distinctive zinc coordination profile and mode of DNA-binding. Here, we report the creation of a novel site-specific endonuclease by linking the N-terminal 147 amino acids of Gal4 to the cleavage domain of FokI endonuclease. The fusion protein is active and under optimal conditions, binds to a 17 bp consensus DNA site and cleaves near this site. As expected, the cleavage occurs on either side of the consensus binding site(s).
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Affiliation(s)
- Y G Kim
- Department of Environmental Health Sciences, The Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205-2179, USA
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Colandene JD, Topal MD. The domain organization of NaeI endonuclease: separation of binding and catalysis. Proc Natl Acad Sci U S A 1998; 95:3531-6. [PMID: 9520400 PMCID: PMC19870 DOI: 10.1073/pnas.95.7.3531] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
NaeI is a remarkable type II restriction endonuclease. It must bind two recognition sequences to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from topoisomerase and recombinase activity. The latter activities apparently derive from reactivation of a cryptic DNA ligase active site. Here, we demonstrate that NaeI has two protease-resistant domains, involving approximately the N-terminal and C-terminal halves of the protein, linked by a protease-accessible region of 30 aa. The domains were purified by cloning. The C-terminal domain was shown by gel mobility-shift assay to have approximately 8-fold lower DNA-binding ability than intact NaeI. Analytical ultracentrifugation showed this domain to be a monomer in solution. The N-terminal domain, which contains the catalytic region defined by random mutagenesis, did not bind DNA and was a mixture of different-sized complexes in solution implying that it mediates self-association. DNA greatly inhibited proteolysis of the linker region. The results identify the DNA-binding domain, imply that DNA cleavage and recognition are independent and separable, and lead us to speculate about a cleft-like structure for NaeI.
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Affiliation(s)
- J D Colandene
- Lineberger Comprehensive Cancer Center and Department of Pathology, University of North Carolina Medical School, Chapel Hill, NC 27599-7295, USA
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Abstract
Site-specific hydrolysis of DNA is common to many biological processes. Three new structures, FokI, I-CreI and PI-SceI, were reported in the past year, providing the first view of type IIs endonucleases and homing endonucleases. Together, they reveal an extraordinary set of new mechanisms by which endonucleases target the hydrolysis of specific DNA sequences.
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Affiliation(s)
- A K Aggarwal
- Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA.
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12
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Coombs GS, Corey DR. Site-Directed Mutagenesis and Protein Engineering. Proteins 1998. [DOI: 10.1016/b978-012058785-8/50006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK. Structure of the multimodular endonuclease FokI bound to DNA. Nature 1997; 388:97-100. [PMID: 9214510 DOI: 10.1038/40446] [Citation(s) in RCA: 196] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
FokI is a member of an unusual class of bipartite restriction enzymes that recognize a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence. Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with new specificities. We have determined the crystal structure at 2.8A resolution of the complete FokI enzyme bound to DNA. As anticipated, the enzyme contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. The CAP core has been extensively embellished in the first two subdomains, whereas in the third subdomain it has been co-opted for protein-protein interactions. Surprisingly, the cleavage domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. Unexpectedly, the cleavage domain is sequestered in a 'piggyback' fashion by the recognition domain. The structure suggests a new mechanism for nuclease activation and provides a framework for the design of chimaeric enzymes with altered specificities.
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Affiliation(s)
- D A Wah
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, USA
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Kita K, Suisha M, Shintoh M, Yanase H, Kato N. Overproduction and characterization of the StsI restriction endonuclease. Gene 1996; 169:69-73. [PMID: 8635752 DOI: 10.1016/0378-1119(95)00797-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The StsI restriction endonuclease (R-StsI), a class-IIS restriction endonuclease, found in Streptococcus sanguis 54, is a heteroschizomer of R-FokI, which recognizes 5'-GGATG-3'. To overproduce R-StsI in Escherichia coli, the coding region of R-StsI was joined to the tac promoter of an expression vector, pKK223-3. By introduction of the plasmid into E. coli UT481 cells expressing the fokIM gene, R-StsI activity was overproduced, from which R-StsI was purified homogeneously. We compared the properties of R-StsI with those of R-FokI. The optimum reaction conditions for R-StsI were quite different fron those for R-FokI. R-StsI is an acidic protein (pI 6.3). Anti-R-StsI serum did not cross-react with R-FokI, indicating three-dimensional structural dissimilarity. The domain structure of R-StsI was elucidated by digestion with trypsin. In the presence of substrate DNA, R-StsI was digested to yield 45-kDa N-terminal and 23-kDa C-terminal fragments. The amino-acid sequences around the trypsin cleavage sites of R-StsI and R-FokI were quite homologous.
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Affiliation(s)
- K Kita
- Department of Biotechnology, Tottori University, Japan.
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Kim YG, Li L, Chandrasegaran S. Insertion and deletion mutants of FokI restriction endonuclease. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)31791-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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