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Manakova E, Mikutenaite M, Golovenko D, Gražulis S, Tamulaitiene G. Crystal structure of restriction endonuclease Kpn2I of CCGG-family. Biochim Biophys Acta Gen Subj 2021; 1865:129926. [PMID: 33965438 DOI: 10.1016/j.bbagen.2021.129926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Restriction endonucleases belong to prokaryotic restriction-modification systems, that protect host cells from invading DNA. Type II restriction endonucleases recognize short 4-8 bp sequences in the target DNA and cut both DNA strands producing double strand breaks. Type II restriction endonuclease Kpn2I cleaves 5'-T/CCGGA DNA sequence ("/" marks the cleavage position). Analysis of protein sequences suggested that Kpn2I belongs to the CCGG-family, which contains ten enzymes that recognize diverse nucleotides outside the conserved 5'-CCGG core and share similar motifs for the 5'-CCGG recognition and cleavage. METHODS We solved a crystal structure of Kpn2I in a DNA-free form at 2.88 Å resolution. From the crystal structure we predicted active center and DNA recognition residues and tested them by mutational analysis. We estimated oligomeric state of Kpn2I by SEC-MALS and performed plasmid DNA cleavage assay to elucidate DNA cleavage mechanism. RESULTS Structure comparison confirmed that Kpn2I shares a conserved active site and structural determinants for the 5'-CCGG tetranucleotide recognition with other restriction endonucleases of the CCGG-family. Guided by structural similarity between Kpn2I and the CCGG-family restriction endonucleases PfoI and AgeI, Kpn2I residues involved in the outer base pair recognition were proposed. CONCLUSIONS Kpn2I is an orthodox Type IIP restriction endonuclease, which acts as a dimer. Kpn2I shares structural similarity to the CCGG-family restriction endonucleases PfoI, AgeI and PspGI. GENERAL SIGNIFICANCE The Kpn2I structure concluded the studies of the CCGG-family, covering detailed structural and biochemical characterization of eleven restriction enzymes and their complexes with DNA.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Migle Mikutenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Dmitrij Golovenko
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Gražulis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
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2
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Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V. Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. Nucleic Acids Res 2019; 47:997-1010. [PMID: 30445642 PMCID: PMC6344858 DOI: 10.1093/nar/gky1137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/26/2018] [Indexed: 01/23/2023] Open
Abstract
Restriction endonucleases (REs) of the CCGG-family recognize a set of 4–8 bp target sequences that share a common CCGG or CCNGG core and possess PD…D/ExK nuclease fold. REs that interact with 5 bp sequence 5′-CCNGG flip the central N nucleotides and ‘compress’ the bound DNA to stack the inner base pairs to mimic the CCGG sequence. PfoI belongs to the CCGG-family and cleaves the 7 bp sequence 5′-T|CCNGGA ("|" designates cleavage position). We present here crystal structures of PfoI in free and DNA-bound forms that show unique active site arrangement and mechanism of sequence recognition. Structures and mutagenesis indicate that PfoI features a permuted E…ExD…K active site that differs from the consensus motif characteristic to other family members. Although PfoI also flips the central N nucleotides of the target sequence it does not ‘compress’ the bound DNA. Instead, PfoI induces a drastic change in DNA backbone conformation that shortens the distance between scissile phosphates to match that in the unperturbed CCGG sequence. Our data demonstrate the diversity and versatility of structural mechanisms employed by restriction enzymes for recognition of related DNA sequences.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Virginija Jovaisaite
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Grazulis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Matthias Bochtler
- Laboratory of Structural Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Dept. of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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3
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Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Nucleic Acids Res 2019; 47:450-467. [PMID: 30395313 PMCID: PMC6326814 DOI: 10.1093/nar/gky1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5'-CCTCAGC-3', generating 3-base, 5'-overhangs. BbvCI is composed of two protein subunits, each containing one catalytic site. Either site can be inactivated by mutation resulting in enzyme variants that nick DNA in a strand-specific manner. Here we demonstrate that the holoenzyme is labile, with the R1 subunit dissociating at low pH. Crystallization of the R2 subunit under such conditions revealed an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH revealed a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage. This domain organization was further validated with single-chain protein constructs in which the two enzyme subunits were tethered via peptide linkers of variable length. We were unable to crystallize a DNA-bound complex; however, structural similarity to previously crystallized restriction endonucleases facilitated creation of an energy-minimized model bound to DNA, and identification of candidate residues responsible for target recognition. Mutation of residues predicted to recognize the central C:G base pair resulted in an altered enzyme that recognizes and cleaves CCTNAGC (N = any base).
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Phil Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Daniel F Heiter
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Keith D Lunnen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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A-ZIP53, a dominant negative reveals the molecular mechanism of heterodimerization between bZIP53, bZIP10 and bZIP25 involved in Arabidopsis seed maturation. Sci Rep 2017; 7:14343. [PMID: 29084982 PMCID: PMC5662769 DOI: 10.1038/s41598-017-14167-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022] Open
Abstract
In Arabidopsis, maturation phase, an intricate process in seed formation is tightly regulated by the DNA binding activity of protagonist basic leucine zipper 53 (bZIP53) transcription factor and its heterodimerizing partners, bZIP10 and bZIP25. Structural determinants responsible for heterodimerization specificity of bZIP53 are poorly understood. Analysis of amino acid sequences of three bZIPs does not identify interactions that may favor heterodimerization. Here, we describe a designed dominant negative termed A-ZIP53 that has a glutamic acid-rich amphipathic peptide sequence attached to N-terminal of bZIP53 leucine zipper. Circular dichroism (CD) and mass spectrometry studies with equimolar mixture of three bZIP proteins in pairs showed no heterodimer formation whereas A-ZIP53 interacted and formed stable heterodimers with bZIP53, bZIP10, and bZIP25. A-ZIP53 electrostatically mimics DNA and can overcome repulsion between basic DNA binding regions of three bZIP proteins. Gel shift experiments showed that A-ZIP53 can inhibit the DNA binding of three proteins. CD studies demonstrated the specificity of A-ZIP53 as it did not interact with bZIP39 and bZIP72. Transient co-transfections in Arabidopsis protoplasts showed that A-ZIP53 inhibited three bZIPs and their putative heterodimers-mediated transactivation of GUS reporter gene. Furthermore, four newly designed acidic extensions were evaluated for their ability to interact with three bZIPs.
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Tutkus M, Sasnauskas G, Rutkauskas D. Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET. Biopolymers 2017; 107. [DOI: 10.1002/bip.23075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/22/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Marijonas Tutkus
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231; Vilnius 02300 Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7; Vilnius 10257 Lithuania
| | - Danielis Rutkauskas
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231; Vilnius 02300 Lithuania
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Toliusis P, Zaremba M, Silanskas A, Szczelkun MD, Siksnys V. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases. Nucleic Acids Res 2017; 45:8435-8447. [PMID: 28854738 PMCID: PMC5737866 DOI: 10.1093/nar/gkx580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/28/2017] [Indexed: 01/10/2023] Open
Abstract
The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric 5′-GCCGC-3′ site and cleaves the DNA 7 and 6/7 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent reaction. CglI is composed of two different proteins: an endonuclease (R.CglI) and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a heterotetrameric complex with R2H2 stoichiometry. However, the R2H2·CglI complex has only one nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to introduce a double strand break. Here, we report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and two-site circular DNA substrates we show that CglI does not require two sites on the same DNA for optimal catalytic activity. However, one-site linear DNA is a poor substrate, supporting a mechanism where CglI complexes must communicate along the one-dimensional DNA contour before cleavage is activated. Based on experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by CglI produces translocation on DNA preferentially in a downstream direction from the target, although upstream translocation is also possible. Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes.
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Affiliation(s)
- Paulius Toliusis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257, Vilnius, Lithuania
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Sasnauskas G, Tamulaitienė G, Tamulaitis G, Čalyševa J, Laime M, Rimšelienė R, Lubys A, Siksnys V. UbaLAI is a monomeric Type IIE restriction enzyme. Nucleic Acids Res 2017; 45:9583-9594. [PMID: 28934493 PMCID: PMC5766183 DOI: 10.1093/nar/gkx634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 01/11/2023] Open
Abstract
Type II restriction endonucleases (REases) form a large and highly diverse group of enzymes. Even REases specific for a common recognition site often vary in their oligomeric structure, domain organization and DNA cleavage mechanisms. Here we report biochemical and structural characterization of the monomeric restriction endonuclease UbaLAI, specific for the pseudosymmetric DNA sequence 5'-CC/WGG-3' (where W = A/T, and '/' marks the cleavage position). We present a 1.6 Å co-crystal structure of UbaLAI N-terminal domain (UbaLAI-N) and show that it resembles the B3-family domain of EcoRII specific for the 5'-CCWGG-3' sequence. We also find that UbaLAI C-terminal domain (UbaLAI-C) is closely related to the monomeric REase MvaI, another enzyme specific for the 5'-CCWGG-3' sequence. Kinetic studies of UbaLAI revealed that it requires two recognition sites for optimal activity, and, like other type IIE enzymes, uses one copy of a recognition site to stimulate cleavage of a second copy. We propose that during the reaction UbaLAI-N acts as a handle that tethers the monomeric UbaLAI-C domain to the DNA, thereby helping UbaLAI-C to perform two sequential DNA nicking reactions on the second recognition site during a single DNA-binding event. A similar reaction mechanism may be characteristic to other monomeric two-domain REases.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrė Tamulaitienė
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jelena Čalyševa
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Miglė Laime
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Renata Rimšelienė
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, V. A. Graiciuno str. 8, LT-02241, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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Tutkus M, Marciulionis T, Sasnauskas G, Rutkauskas D. DNA-Endonuclease Complex Dynamics by Simultaneous FRET and Fluorophore Intensity in Evanescent Field. Biophys J 2017; 112:850-858. [PMID: 28297644 DOI: 10.1016/j.bpj.2017.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/06/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
The single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study interactions and conformational changes of biological molecules in the distance range from a few to 10 nm. In this study, we demonstrate a method to augment this range with longer distances. The method is based on the intensity changes of a tethered fluorophore, diffusing in the exponentially decaying evanescent excitation field. In combination with FRET it allowed us to reveal and characterize the dynamics of what had been inaccessible conformations of the DNA-protein complex. Our model system, restriction enzyme Ecl18kI, interacts with a FRET pair-labeled DNA fragment to form two different DNA loop conformations. The DNA-protein interaction geometry is such that the efficient FRET is expected for one of these conformations-"antiparallel" loop. In the alternative "parallel" loop, the expected distance between the dyes is outside the range accessible by FRET. Therefore, "antiparallel" looping is observed in a single-molecule time trajectory as discrete transitions to a state of high FRET efficiency. At the same time, transitions to a high-intensity state of the directly excited acceptor fluorophore on a DNA tether are due to a change of its average position in the evanescent field of excitation and can be associated with a loop of either "parallel" or "antiparallel" configuration. Simultaneous analysis of FRET and acceptor intensity trajectories then allows us to discriminate different DNA loop conformations and access the average lifetimes of different states.
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Affiliation(s)
- Marijonas Tutkus
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Tomas Marciulionis
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | | | - Danielis Rutkauskas
- Institute of Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania.
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Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 2017; 45:3547-3558. [PMID: 28039325 PMCID: PMC5389614 DOI: 10.1093/nar/gkw1310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023] Open
Abstract
Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5΄-A/CCGGT-3΄ and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Virginija Jovaisaite
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Inga Songailiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Grazulis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Shuang-yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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Rusinov I, Ershova A, Karyagina A, Spirin S, Alexeevski A. Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. BMC Genomics 2015; 16:1084. [PMID: 26689194 PMCID: PMC4687349 DOI: 10.1186/s12864-015-2288-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/11/2015] [Indexed: 01/10/2023] Open
Abstract
Background Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. Results Only Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called ‘orthodox’ here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of 1774 studied cases. It is known that prokaryotes can acquire and lose R-M systems. Thus it is possible to talk about the lifespan of an R-M system in a genome. We have shown that the recognition site avoidance correlates with the lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. We also found cases of site avoidance in absence of the corresponding R-M systems in the genome. An analysis of closely related bacteria shows that such avoidance can be a trace of lost R-M systems. Sites of Type I, IIС/G, IIM, III, and IV R-M systems are not avoided in vast majority of cases. Conclusions The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. Presence of an R-M system without an underrepresentation of its site may indicate that the R-M system was acquired recently. At the same time, a significant underrepresentation of a site may be a sign of presence of the corresponding R-M system in this organism or in its ancestors for a long time. The drastic difference between site avoidance for orthodox Type II R-M systems and R-M systems of other types can be explained by a higher rate of specificity changes or a less self-toxicity of the latter. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2288-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Rusinov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Anna Ershova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Anna Karyagina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Sergey Spirin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
| | - Andrei Alexeevski
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
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11
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Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Nucleic Acids Res 2015; 43:8100-10. [PMID: 26240380 PMCID: PMC4652773 DOI: 10.1093/nar/gkv768] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/17/2015] [Indexed: 02/03/2023] Open
Abstract
Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5′-W/CCGGW-3′ (W stands for A or T, ‘/’ denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an ‘open’ configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes.
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Affiliation(s)
- Gintautas Tamulaitis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Marius Rutkauskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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12
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Rutkauskas D, Petkelyte M, Naujalis P, Sasnauskas G, Tamulaitis G, Zaremba M, Siksnys V. Restriction Enzyme Ecl18kI-Induced DNA Looping Dynamics by Single-Molecule FRET. J Phys Chem B 2014; 118:8575-82. [DOI: 10.1021/jp504546v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Danielis Rutkauskas
- Institute
of Physics, Center for Physical Sciences and Technology, Savanoriu
231, LT-02300, Vilnius, Lithuania
| | - Milda Petkelyte
- Institute
of Physics, Center for Physical Sciences and Technology, Savanoriu
231, LT-02300, Vilnius, Lithuania
| | - Paulius Naujalis
- Institute
of Physics, Center for Physical Sciences and Technology, Savanoriu
231, LT-02300, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
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13
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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14
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Mendes MA, Guerra RF, Berns MC, Manzo C, Masiero S, Finzi L, Kater MM, Colombo L. MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis. THE PLANT CELL 2013; 25:2560-72. [PMID: 23847151 PMCID: PMC3753383 DOI: 10.1105/tpc.112.108688] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
MADS domain transcription factors are key regulators of eukaryotic development. In plants, the homeotic MIKC MADS factors that regulate floral organ identity have been studied in great detail. Based on genetic and protein-protein interaction studies, a floral quartet model was proposed that describes how these MADS domain proteins assemble into higher order complexes to regulate their target genes. However, despite the attractiveness of this model and its general acceptance in the literature, solid in vivo proof has never been provided. To gain deeper insight into the mechanisms of transcriptional regulation by MADS domain factors, we studied how SEEDSTICK (STK) and SEPALLATA3 (SEP3) directly regulate the expression of the reproductive meristem gene family transcription factor-encoding gene VERDANDI (VDD). Our data show that STK-SEP3 dimers can induce loop formation in the VDD promoter by binding to two nearby CC(A/T)6GG (CArG) boxes and that this is essential for promoter activity. Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model.
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Affiliation(s)
- Marta Adelina Mendes
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | | | | | - Carlo Manzo
- Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Simona Masiero
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Martin M. Kater
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
- Consiglio Nazionale delle Richerche, Istituto di Biofisica, Università di Milano, 20133 Milan, Italy
- Address correspondence to
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15
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Ma L, Chen K, Clarke DJ, Nortcliffe CP, Wilson GG, Edwardson JM, Morton AJ, Jones AC, Dryden DTF. Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats. Nucleic Acids Res 2013; 41:4999-5009. [PMID: 23525471 PMCID: PMC3643589 DOI: 10.1093/nar/gkt176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The type II restriction endonuclease TseI recognizes the DNA target sequence 5′-G^CWGC-3′ (where W = A or T) and cleaves after the first G to produce fragments with three-base 5′-overhangs. We have determined that it is a dimeric protein capable of cleaving not only its target sequence but also one containing A:A or T:T mismatches at the central base pair in the target sequence. The cleavage of targets containing these mismatches is as efficient as cleavage of the correct target sequence containing a central A:T base pair. The cleavage mechanism does not apparently use a base flipping mechanism as found for some other type II restriction endonuclease recognizing similarly degenerate target sequences. The ability of TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated with Huntington’s disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).
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Affiliation(s)
- Long Ma
- EaStChem School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JJ, UK
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16
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Smith RM, Marshall JJT, Jacklin AJ, Retter SE, Halford SE, Sobott F. Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA. Nucleic Acids Res 2012; 41:391-404. [PMID: 23147005 PMCID: PMC3592470 DOI: 10.1093/nar/gks1023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Type IIB restriction-modification systems, such as BcgI, feature a single protein with
both endonuclease and methyltransferase activities. Type IIB nucleases require two
recognition sites and cut both strands on both sides of their unmodified sites. BcgI cuts
all eight target phosphodiester bonds before dissociation. The BcgI protein contains A and
B polypeptides in a 2:1 ratio: A has one catalytic centre for each activity; B recognizes
the DNA. We show here that BcgI is organized as A2B protomers, with B at its
centre, but that these protomers self-associate to assemblies containing several
A2B units. Moreover, like the well known FokI nuclease, BcgI bound to its
site has to recruit additional protomers before it can cut DNA. DNA-bound BcgI can
alternatively be activated by excess A subunits, much like the activation of FokI by its
catalytic domain. Eight A subunits, each with one centre for nuclease activity, are
presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction may thus
involve two A2B units, each bound to a recognition site, with two more
A2B units bridging the complexes by protein–protein interactions
between the nuclease domains.
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Affiliation(s)
- Rachel M Smith
- The DNA-proteins Interaction Unit, School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
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17
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Horton JR, Mabuchi MY, Cohen-Karni D, Zhang X, Griggs RM, Samaranayake M, Roberts RJ, Zheng Y, Cheng X. Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease. Nucleic Acids Res 2012; 40:9763-73. [PMID: 22848107 PMCID: PMC3479186 DOI: 10.1093/nar/gks719] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The MspJI modification-dependent restriction endonuclease recognizes 5-methylcytosine or 5-hydroxymethylcytosine in the context of CNN(G/A) and cleaves both strands at fixed distances (N12/N16) away from the modified cytosine at the 3′-side. We determined the crystal structure of MspJI of Mycobacterium sp. JLS at 2.05-Å resolution. Each protein monomer harbors two domains: an N-terminal DNA-binding domain and a C-terminal endonuclease. The N-terminal domain is structurally similar to that of the eukaryotic SET and RING-associated domain, which is known to bind to a hemi-methylated CpG dinucleotide. Four protein monomers are found in the crystallographic asymmetric unit. Analytical gel-filtration and ultracentrifugation measurements confirm that the protein exists as a tetramer in solution. Two monomers form a back-to-back dimer mediated by their C-terminal endonuclease domains. Two back-to-back dimers interact to generate a tetramer with two double-stranded DNA cleavage modules. Each cleavage module contains two active sites facing each other, enabling double-strand DNA cuts. Biochemical, mutagenesis and structural characterization suggest three different monomers of the tetramer may be involved respectively in binding the modified cytosine, making the first proximal N12 cleavage in the same strand and then the second distal N16 cleavage in the opposite strand. Both cleavage events require binding of at least a second recognition site either in cis or in trans.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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18
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Zaremba M, Sasnauskas G, Siksnys V. The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I. FEBS Lett 2012; 586:3324-9. [PMID: 22828280 DOI: 10.1016/j.febslet.2012.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 11/18/2022]
Abstract
Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety-catch to prevent host DNA cleavage if a single unmodified site becomes available.
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19
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Plénat T, Tardin C, Rousseau P, Salomé L. High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion. Nucleic Acids Res 2012; 40:e89. [PMID: 22422843 PMCID: PMC3384352 DOI: 10.1093/nar/gks250] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/21/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
Tethered particle motion (TPM) monitors the variations in the effective length of a single DNA molecule by tracking the Brownian motion of a bead tethered to a support by the DNA molecule. Providing information about DNA conformations in real time, this technique enables a refined characterization of DNA-protein interactions. To increase the output of this powerful but time-consuming single-molecule assay, we have developed a biochip for the simultaneous acquisition of data from more than 500 single DNA molecules. The controlled positioning of individual DNA molecules is achieved by self-assembly on nanoscale arrays fabricated through a standard microcontact printing method. We demonstrate the capacity of our biochip to study biological processes by applying our method to explore the enzymatic activity of the T7 bacteriophage exonuclease. Our single molecule observations shed new light on its behaviour that had only been examined in bulk assays previously and, more specifically, on its processivity.
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Affiliation(s)
- Thomas Plénat
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Catherine Tardin
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Philippe Rousseau
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Laurence Salomé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
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20
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Laurens N, Rusling DA, Pernstich C, Brouwer I, Halford SE, Wuite GJL. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Res 2012; 40:4988-97. [PMID: 22373924 PMCID: PMC3367208 DOI: 10.1093/nar/gks184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond.
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Affiliation(s)
- Niels Laurens
- Department of Physics and Astronomy, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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21
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Rusling DA, Laurens N, Pernstich C, Wuite GJL, Halford SE. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. Nucleic Acids Res 2012; 40:4977-87. [PMID: 22362745 PMCID: PMC3367207 DOI: 10.1093/nar/gks183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology.
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Affiliation(s)
- David A Rusling
- The DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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22
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Marshall JJT, Smith RM, Ganguly S, Halford SE. Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease. Nucleic Acids Res 2011; 39:7630-40. [PMID: 21653548 PMCID: PMC3177199 DOI: 10.1093/nar/gkr453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The BcgI endonuclease exemplifies a subset of restriction enzymes, the Type IIB class, which make two double-strand breaks (DSBs) at each copy of their recognition sequence, one either side of the site, to excise the sequence from the remainder of the DNA. In this study, we show that BcgI is essentially inactive when bound to a single site and that to cleave a DNA with one copy of its recognition sequence, it has to act in trans, bridging two separate DNA molecules. We also show that BcgI makes the two DSBs at an individual site in a highly concerted manner. Intermediates cut on one side of the site do not accumulate during the course of the reaction: instead, the DNA is converted straight to the final products cut on both sides. On DNA with two sites, BcgI bridges the sites in cis and then generally proceeds to cut both strands on both sides of both sites without leaving the DNA. The BcgI restriction enzyme can thus excise two DNA segments together, by cleaving eight phosphodiester bonds within a single-DNA binding event.
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23
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Dryden DTF, Edwardson JM, Henderson RM. DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements. Nucleic Acids Res 2011; 39:4525-31. [PMID: 21310716 PMCID: PMC3113558 DOI: 10.1093/nar/gkq1285] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.
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Affiliation(s)
- David T F Dryden
- School of Chemistry, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK.
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