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Freeman ADJ, Liu Y, Déclais AC, Gartner A, Lilley DMJ. GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes. J Mol Biol 2014; 426:3946-3959. [PMID: 25315822 PMCID: PMC4270448 DOI: 10.1016/j.jmb.2014.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/28/2022]
Abstract
Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3' to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1.
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Affiliation(s)
- Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Sukackaite R, Lagunavicius A, Stankevicius K, Urbanke C, Venclovas Č, Siksnys V. Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family. Nucleic Acids Res 2007; 35:2377-89. [PMID: 17392342 PMCID: PMC1874659 DOI: 10.1093/nar/gkm164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type IIS restriction endonucleases (REases) recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. REase BpuJI recognizes the asymmetric sequence 5′-CCCGT, however it cuts at multiple sites in the vicinity of the target sequence. We show that BpuJI is a dimer, which has two DNA binding surfaces and displays optimal catalytic activity when bound to two recognition sites. BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which lacks catalytic activity but binds specifically to the recognition sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer with non-specific nuclease activity. Fold recognition approach reveals that the CTD of BpuJI is structurally related to archaeal Holliday junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD of BpuJI possesses end-directed nuclease activity and preferentially cuts 3 nt from the 3′-terminus of blunt-ended DNA. The nuclease activity of the CTD is repressed in the apo-enzyme and becomes activated upon specific DNA binding by the NTDs. This leads to a complicated pattern of specific DNA cleavage in the vicinity of the target site. Bioinformatics analysis identifies the AHJR-like domain in the putative Type III enzymes and functionally uncharacterized proteins.
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Affiliation(s)
- Rasa Sukackaite
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
| | - Arunas Lagunavicius
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
| | - Kornelijus Stankevicius
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
| | - Claus Urbanke
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
| | - Česlovas Venclovas
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Graičiūno 8, LT-02241 Vilnius, Lithuania and Strukturanalyse, Medizinische Hochschule Hannover, Carl Neuberg Strasse 1, D-30632 Hannover, Germany
- *To whom correspondence should be addressed.
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