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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 230] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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Taylor JEN, Callow P, Swiderska A, Kneale GG. Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124I NT. J Mol Biol 2010; 398:391-9. [PMID: 20302878 PMCID: PMC2877798 DOI: 10.1016/j.jmb.2010.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/02/2010] [Accepted: 03/04/2010] [Indexed: 11/17/2022]
Abstract
The Type I R-M system EcoR124I is encoded by three genes. HsdM is responsible for modification (DNA methylation), HsdS for DNA sequence specificity and HsdR for restriction endonuclease activity. The trimeric methyltransferase (M2S) recognises the asymmetric sequence (GAAN6RTCG). An engineered R-M system, denoted EcoR124INT, has two copies of the N-terminal domain of the HsdS subunit of EcoR124I, instead of a single S subunit with two domains, and recognises the symmetrical sequence GAAN7TTC. We investigate the methyltransferase activity of EcoR124INT, characterise the enzyme and its subunits by analytical ultracentrifugation and obtain low-resolution structural models from small-angle neutron scattering experiments using contrast variation and selective deuteration of subunits.
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Affiliation(s)
- James E N Taylor
- Biophysics Laboratories, Institute of Biomedical and Biomolecular
Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Phil Callow
- Partnership for Structural Biology, Institut Laue Langevin, 38042
Grenoble Cedex 9, Grenoble, France
| | - Anna Swiderska
- Biophysics Laboratories, Institute of Biomedical and Biomolecular
Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - G. Geoff Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular
Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
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Bogdanova E, Djordjevic M, Papapanagiotou I, Heyduk T, Kneale G, Severinov K. Transcription regulation of the type II restriction-modification system AhdI. Nucleic Acids Res 2008; 36:1429-42. [PMID: 18203750 PMCID: PMC2275141 DOI: 10.1093/nar/gkm1116] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 11/28/2007] [Accepted: 11/28/2007] [Indexed: 11/15/2022] Open
Abstract
The Restriction-modification system AhdI contains two convergent transcription units, one with genes encoding methyltransferase subunits M and S and another with genes encoding the controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription is controlled by two independent regulatory loops that are well-optimized to ensure successful establishment in a naïve bacterial host. Transcription from the strong MS promoter is attenuated by methylation of an AhdI site overlapping the -10 element of the promoter. Transcription from the weak CR promoter is regulated by the C protein interaction with two DNA-binding sites. The interaction with the promoter-distal high-affinity site activates transcription, while interaction with the weaker promoter-proximal site represses it. Because of high levels of cooperativity, both C protein-binding sites are always occupied in the absence of RNA polymerase, raising a question how activated transcription is achieved. We develop a mathematical model that is in quantitative agreement with the experiment and indicates that RNA polymerase outcompetes C protein from the promoter-proximal-binding site. Such an unusual mechanism leads to a very inefficient activation of the R gene transcription, which presumably helps control the level of the endonuclease in the cell.
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Affiliation(s)
- Ekaterina Bogdanova
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
| | - Marko Djordjevic
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
| | - Ioanna Papapanagiotou
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
| | - Tomasz Heyduk
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
| | - Geoff Kneale
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
| | - Konstantin Severinov
- Waksman Institute, Piscataway, NJ 08854, USA, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142292 Russia, Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA, Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, UK, E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117312 and Institute of Molecular Genetics, Moscow 123182, Russia
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Callow P, Sukhodub A, Taylor JEN, Kneale GG. Shape and subunit organisation of the DNA methyltransferase M.AhdI by small-angle neutron scattering. J Mol Biol 2007; 369:177-185. [PMID: 17418232 PMCID: PMC2878638 DOI: 10.1016/j.jmb.2007.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/07/2007] [Accepted: 03/08/2007] [Indexed: 11/28/2022]
Abstract
Type I restriction-modification (R-M) systems encode multisubunit/multidomain enzymes. Two genes (M and S) are required to form the methyltransferase (MTase) that methylates a specific base within the recognition sequence and protects DNA from cleavage by the endonuclease. The DNA methyltransferase M.AhdI is a 170 kDa tetramer with the stoichiometry M2S2 and has properties typical of a type I MTase. The M.AhdI enzyme has been prepared with deuterated S subunits, to allow contrast variation using small-angle neutron scattering (SANS) methods. The SANS data were collected in a number of 1H:2H solvent contrasts to allow matching of one or other of the subunits in the multisubunit enzyme. The radius of gyration (Rg) and maximum dimensions (Dmax) of the M subunits in situ in the multisubunit enzyme (50 A and 190 A, respectively) are close of those of the entire MTase (51 A and 190 A). In contrast, the S subunits in situ have experimentally determined values of Rg=35 A and Dmax=110 A, indicating their more central location in the enzyme. Ab initio reconstruction methods yield a low-resolution structural model of the shape and subunit organization of M.AhdI, in which the Z-shaped structure of the S subunit dimer can be discerned. In contrast, the M subunits form a much more elongated and extended structure. The core of the MTase comprises the two S subunits and the globular regions of the two M subunits, with the extended portion of the M subunits most probably forming highly mobile regions at the outer extremities, which collapse around the DNA when the MTase binds.
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Affiliation(s)
- P Callow
- EPSAM and ISTM Research Institutes, Keele University, Staffordshire ST5 5BG, UK; ILL-EMBL Deuteration Laboratory, Partnership for Structural Biology, Institut Laue Langevin, 38042 Grenoble Cedex 9, Grenoble, France
| | - A Sukhodub
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, UK
| | - James E N Taylor
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, UK
| | - G G Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, UK.
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