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Skutel M, Yanovskaya D, Demkina A, Shenfeld A, Musharova O, Severinov K, Isaev A. RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation. Nucleic Acids Res 2024; 52:5195-5208. [PMID: 38567730 PMCID: PMC11109961 DOI: 10.1093/nar/gkae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 05/23/2024] Open
Abstract
Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria Yanovskaya
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Olga Musharova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Piscataway, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Keshav A, Murarka P, Srivastava P. Bending is required for activation of dsz operon by the TetR family protein (DszGR). Gene 2022; 810:146061. [PMID: 34774682 DOI: 10.1016/j.gene.2021.146061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022]
Abstract
The dsz operon responsible for the biodesulfurization of organosulfurs is under the control of a 385 bp long promoter. Recently, a TetR family protein was identified which served as an activator of operon. Here we report that the TetR family protein (WP_058249973.1), named DszGR can specifically activate the dsz operon. Direct binding of the DszGR to DNA was observed at single molecule level by AFM. It was found that the binding of DszGR to the promoter DNA induces a bend by about ∼40-50° degrees which may not be enough for the activation of the promoter. Thus, bendability in the promoter sequence was analyzed. The results show that the promoter has a curvature at around -235 and -200 bp with respect to dszA start codon. On mutating this region, a decrease in activity of the promoter was observed. Our results suggest that the DszGR protein binds to the upstream sequences and induces a bend, which is facilitated by further bending of the DNA which is required for dsz promoter activity. IHF binding site present in the promoter, and a significant reduction in desulphurization activity in the absence of either IHF subunits, suggested role of IHF in regulation of the dsz operon.
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Affiliation(s)
- Aditi Keshav
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pooja Murarka
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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3
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses - Part I. BIOCHEMISTRY (MOSCOW) 2021; 86:319-337. [PMID: 33838632 DOI: 10.1134/s0006297921030081] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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4
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Isaev A, Drobiazko A, Sierro N, Gordeeva J, Yosef I, Qimron U, Ivanov NV, Severinov K. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence. Nucleic Acids Res 2020; 48:5397-5406. [PMID: 32338761 PMCID: PMC7261183 DOI: 10.1093/nar/gkaa290] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 11/12/2022] Open
Abstract
BREX (for BacteRiophage EXclusion) is a superfamily of common bacterial and archaeal defence systems active against diverse bacteriophages. While the mechanism of BREX defence is currently unknown, self versus non-self differentiation requires methylation of specific asymmetric sites in host DNA by BrxX (PglX) methyltransferase. Here, we report that T7 bacteriophage Ocr, a DNA mimic protein that protects the phage from the defensive action of type I restriction-modification systems, is also active against BREX. In contrast to the wild-type phage, which is resistant to BREX defence, T7 lacking Ocr is strongly inhibited by BREX, and its ability to overcome the defence could be complemented by Ocr provided in trans. We further show that Ocr physically associates with BrxX methyltransferase. Although BREX+ cells overproducing Ocr have partially methylated BREX sites, their viability is unaffected. The result suggests that, similar to its action against type I R-M systems, Ocr associates with as yet unidentified BREX system complexes containing BrxX and neutralizes their ability to both methylate and exclude incoming phage DNA.
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Affiliation(s)
- Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
- Institute of Gene Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov str., 119334 Moscow, Russia
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5
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Gao Y, Cao D, Zhu J, Feng H, Luo X, Liu S, Yan XX, Zhang X, Gao P. Structural insights into assembly, operation and inhibition of a type I restriction-modification system. Nat Microbiol 2020; 5:1107-1118. [PMID: 32483229 DOI: 10.1038/s41564-020-0731-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/29/2020] [Indexed: 11/09/2022]
Abstract
Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (R2M2S1, R1M2S1 and M2S1) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems.
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Affiliation(s)
- Yina Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jingpeng Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Han Feng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiu Luo
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Songqing Liu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Pu Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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6
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Bower EKM, Cooper LP, Roberts GA, White JH, Luyten Y, Morgan RD, Dryden DTF. A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes. Nucleic Acids Res 2019; 46:9067-9080. [PMID: 30165537 PMCID: PMC6158711 DOI: 10.1093/nar/gky760] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/21/2018] [Indexed: 12/28/2022] Open
Abstract
Restriction Modification (RM) systems prevent the invasion of foreign genetic material into bacterial cells by restriction and protect the host's genetic material by methylation. They are therefore important in maintaining the integrity of the host genome. RM systems are currently classified into four types (I to IV) on the basis of differences in composition, target recognition, cofactors and the manner in which they cleave DNA. Comparing the structures of the different types, similarities can be observed suggesting an evolutionary link between these different types. This work describes the ‘deconstruction’ of a large Type I RM enzyme into forms structurally similar to smaller Type II RM enzymes in an effort to elucidate the pathway taken by Nature to form these different RM enzymes. Based upon the ability to engineer new enzymes from the Type I ‘scaffold’, an evolutionary pathway and the evolutionary pressures required to move along the pathway from Type I RM systems to Type II RM systems are proposed. Experiments to test the evolutionary model are discussed.
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Affiliation(s)
- Edward K M Bower
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Yvette Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - Richard D Morgan
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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7
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Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS NANO 2019; 13:4220-4229. [PMID: 30938988 DOI: 10.1021/acsnano.8b09234] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl2 and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl2-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl2. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Physics , University of Colorado , Boulder , Colorado 80309 , United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Molecular, Cellular, and Developmental Biology , University of Colorado , Boulder , Colorado 80309 , United States
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8
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Pisano S, Gilson E. Analysis of DNA-Protein Complexes by Atomic Force Microscopy Imaging: The Case of TRF2-Telomeric DNA Wrapping. Methods Mol Biol 2019; 1886:75-97. [PMID: 30374863 DOI: 10.1007/978-1-4939-8894-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) is a non-optical microscopy that enables the acquisition at the nanoscale level of a 3D topographical image of the sample. For 30 years, AFM has been a valuable tool in life sciences to study biological samples in the field of tissue, cellular and molecular imaging, of mechanical properties and of force spectroscopy. Since the early beginnings of the technique, AFM has been extensively exploited as an imaging tool for structural studies of nucleic acids and nucleoprotein complexes. The morphometric analysis performed on the images can unveil specific structural and functional aspects of the sample, such as the multimerization state of proteins bound to DNA, or DNA conformational changes led by the DNA-binding proteins. Herein, a method for analyzing a complex formed by a telomeric DNA sequence wrapped around the TRF2 binding protein is presented. The described procedure could be applied to the study of any type of DNA-protein complex.
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Affiliation(s)
- Sabrina Pisano
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France.
| | - Eric Gilson
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France
- International Laboratory in Hematology and Cancer, Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/INSERM/Nice University, Shanghai, China
- Department of Genetics, CHU Nice, Université Côte d'Azur, Nice, France
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9
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Youell J, Sikora AE, Vejsadová Š, Weiserova M, Smith JR, Firman K. Cofactor induced dissociation of the multifunctional multisubunit EcoR124I investigated using electromobility shift assays, AFM and SPR. RSC Adv 2017. [DOI: 10.1039/c7ra07505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have applied three techniques to the study of subunit assembly of the Type IC Restriction–Modification enzyme EcoR124I.
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Affiliation(s)
- James Youell
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Aneta E. Sikora
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Štěpánka Vejsadová
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Marie Weiserova
- Institute of Microbiology
- ASCR, v.v.i
- 142 20 Prague 4
- Czech Republic
| | - James R. Smith
- School of Pharmacy and Biomedical Sciences
- University of Portsmouth
- Portsmouth PO1 2DT
- UK
| | - Keith Firman
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
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10
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Park HS, Jang JH. Applications of Scanning Electrochemical Microscopy (SECM) Coupled to Atomic Force Microscopy with Sub-Micrometer Spatial Resolution to the Development and Discovery of Electrocatalysts. J ELECTROCHEM SCI TE 2016. [DOI: 10.5229/jecst.2016.7.4.316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Park HS, Jang JH. Applications of Scanning Electrochemical Microscopy (SECM) Coupled to Atomic Force Microscopy with Sub-Micrometer Spatial Resolution to the Development and Discovery of Electrocatalysts. J ELECTROCHEM SCI TE 2016. [DOI: 10.33961/jecst.2016.7.4.316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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13
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Rodriguez-Ramos J, Perrino AP, Garcia R. Dependence of the volume of an antibody on the force applied in a force microscopy experiment in liquid. Ultramicroscopy 2016; 171:153-157. [PMID: 27686276 DOI: 10.1016/j.ultramic.2016.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022]
Abstract
The volume of a protein can be estimated from its molecular weight. This approach has also been applied in force microscopy experiments. Two factors contribute to the determination of the volume from a force microscope image, the applied force and the tip radius. Those factors act in opposite directions. Here, we demonstrate that in the optimum conditions to image a protein, the apparent volume deduced from an AFM image overestimates the real protein volume. The lateral broadening due to the tip finite size, makes the simulated volume to exceed the real protein volume value, while the force applied by the tip tends to decrease the measured volume. The measured volume could coincide with the real volume for either a point-size tip at zero force or when the compression exerted by the tip compensates its dilation effects. The interplay between the above factors make unsuitable to apply the molecular weight method to determine the volume of a protein from AFM data.
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Affiliation(s)
- Jorge Rodriguez-Ramos
- Centro de Estudios Avanzados de Cuba, Carretera de San Antonio de los Baños, km 1 1/2, Valle Grande, La Habana, Cuba.
| | - Alma P Perrino
- Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
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14
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Structural model of FeoB, the iron transporter from Pseudomonas aeruginosa, predicts a cysteine lined, GTP-gated pore. Biosci Rep 2016; 36:BSR20160046. [PMID: 26934982 PMCID: PMC4847171 DOI: 10.1042/bsr20160046] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/29/2016] [Indexed: 01/23/2023] Open
Abstract
The bacterial ferrous iron acquisition protein FeoB assembles as a homotrimer that is predicted to form a central pore lined by conserved cysteine residues. Structure-function analysis of FeoB indicates a putative mechanism more akin to a GTP-gated channel than a transporter. Iron is essential for the survival and virulence of pathogenic bacteria. The FeoB transporter allows the bacterial cell to acquire ferrous iron from its environment, making it an excellent drug target in intractable pathogens. The protein consists of an N-terminal GTP-binding domain and a C-terminal membrane domain. Despite the availability of X-ray crystal structures of the N-terminal domain, many aspects of the structure and function of FeoB remain unclear, such as the structure of the membrane domain, the oligomeric state of the protein, the molecular mechanism of iron transport, and how this is coupled to GTP hydrolysis at the N-terminal domain. In the present study, we describe the first homology model of FeoB. Due to the lack of sequence homology between FeoB and other transporters, the structures of four different proteins were used as templates to generate the homology model of full-length FeoB, which predicts a trimeric structure. We confirmed this trimeric structure by both blue-native-PAGE (BN-PAGE) and AFM. According to our model, the membrane domain of the trimeric protein forms a central pore lined by highly conserved cysteine residues. This pore aligns with a central pore in the N-terminal GTPase domain (G-domain) lined by aspartate residues. Biochemical analysis of FeoB from Pseudomonas aeruginosa further reveals a putative iron sensor domain that could connect GTP binding/hydrolysis to the opening of the pore. These results indicate that FeoB might not act as a transporter, but rather as a GTP-gated channel.
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15
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Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI. Sci Rep 2014; 4:5897. [PMID: 25077775 PMCID: PMC4116625 DOI: 10.1038/srep05897] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 11/09/2022] Open
Abstract
DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic force microscopy (AFM) and magnetic tweezers (MT). With Ca(2+) substituted for the normal enzyme cofactor Mg(2+) and enzyme concentration below the critical concentration of 6 units/mL, AFM images of DNA-BspMI complex show that the number of binding and looping events increases with enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation concentration represents more than 8% of the total BspMI-DNA complexes directly observed in AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme concentration is higher than its saturation valueand the complex is incubated for a long time (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at less than saturation concentration has a peak at about 3 pN, which is lower than the force required to open additional loops due to enzyme aggregation at higher than saturation concentration (>6 pN).
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16
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Murugesapillai D, McCauley MJ, Huo R, Nelson Holte MH, Stepanyants A, Maher LJ, Israeloff NE, Williams MC. DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin. Nucleic Acids Res 2014; 42:8996-9004. [PMID: 25063301 PMCID: PMC4132745 DOI: 10.1093/nar/gku635] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The regulation of chromatin structure in eukaryotic cells involves abundant architectural factors such as high mobility group B (HMGB) proteins. It is not understood how these factors control the interplay between genome accessibility and compaction. In vivo, HMO1 binds the promoter and coding regions of most ribosomal RNA genes, facilitating transcription and possibly stabilizing chromatin in the absence of histones. To understand how HMO1 performs these functions, we combine single molecule stretching and atomic force microscopy (AFM). By stretching HMO1-bound DNA, we demonstrate a hierarchical organization of interactions, in which HMO1 initially compacts DNA on a timescale of seconds, followed by bridge formation and stabilization of DNA loops on a timescale of minutes. AFM experiments demonstrate DNA bridging between strands as well as looping by HMO1. Our results support a model in which HMO1 maintains the stability of nucleosome-free chromatin regions by forming complex and dynamic DNA structures mediated by protein–protein interactions.
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Affiliation(s)
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Molly H Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Armen Stepanyants
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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17
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Balasuriya D, Srivats S, Murrell-Lagnado RD, Edwardson JM. Atomic force microscopy (AFM) imaging suggests that stromal interaction molecule 1 (STIM1) binds to Orai1 with sixfold symmetry. FEBS Lett 2014; 588:2874-80. [PMID: 24996186 DOI: 10.1016/j.febslet.2014.06.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 01/29/2023]
Abstract
Depletion of Ca(2+) from the endoplasmic reticulum (ER) lumen triggers the opening of Ca(2+) release-activated Ca(2+) (CRAC) channels at the plasma membrane. CRAC channels are activated by stromal interaction molecule 1 (STIM1), an ER resident protein that senses Ca(2+) store depletion and interacts with Orai1, the pore-forming subunit of the channel. The subunit stoichiometry of the CRAC channel is controversial. Here we provide evidence, using atomic force microscopy (AFM) imaging, that Orai1 assembles as a hexamer, and that STIM1 binds to Orai1 with sixfold symmetry. STIM1 associates with Orai1 in the form of monomers, dimers, and multimeric string-like structures that form links between the Orai1 hexamers. Our results provide new insights into the nature of the interactions between STIM1 and Orai1.
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Affiliation(s)
- Dilshan Balasuriya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Shyam Srivats
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Ruth D Murrell-Lagnado
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom.
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18
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Fischer MJM, Balasuriya D, Jeggle P, Goetze TA, McNaughton PA, Reeh PW, Edwardson JM. Direct evidence for functional TRPV1/TRPA1 heteromers. Pflugers Arch 2014; 466:2229-41. [PMID: 24643480 DOI: 10.1007/s00424-014-1497-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 01/22/2023]
Abstract
Transient receptor potential cation channel, subfamily V, member 1 (TRPV1) plays a key role in sensing environmental hazards and in enhanced pain sensation following inflammation. A considerable proportion of TRPV1-expressing cells also express transient receptor potential cation channel, subfamily A, member 1 (TRPA1). There is evidence for a TRPV1-TRPA1 interaction that is predominantly calcium-dependent, and it has been suggested that the two proteins might form a heteromeric channel. Here, we constructed subunit concatemers to search for direct evidence for such an interaction. We found that a TRPV1::TRPV1 concatemer and TRPV1 formed channels with similar properties. A TRPV1::TRPA1 concatemer was responsive to TRPV1 agonists capsaicin, acidic pH and ethanol, but not to TRPA1 agonists. Isolated TRPV1 and TRPV1::TRPA1 imaged by atomic force microscopy (AFM) both had molecular volumes consistent with the formation of tetrameric channels. Antibodies decorated epitope tags on TRPV1 with a four-fold symmetry, as expected for a homotetramer. In contrast, pairs of antibodies decorated tags on TRPV1::TRPA1 predominantly at 180°, indicating the formation of a channel consisting of two TRPV1::TRPA1 concatemers arranged face to face. TRPV1::TRPA1 was sensitized by PKC activation and could be inhibited by a TRPV1 antagonist. TRPV1::TRPA1 was activated by heat and displayed a threshold and temperature coefficient similar to TRPV1. However, the channel formed by TRPV1::TRPA1 has only two binding sites for capsaicin and shows less total current and a smaller capsaicin-induced shift in voltage-dependent gating than TRPV1::TRPV1 or TRPV1. We conclude that the presence of TRPA1 exerts a functional inhibition on TRPV1.
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Affiliation(s)
- Michael J M Fischer
- Institute of Physiology and Pathophysiology, University of Erlangen-Nuremberg, Universitätsstrasse 17, 91052, Erlangen, Germany,
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19
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Namadurai S, Balasuriya D, Rajappa R, Wiemhöfer M, Stott K, Klingauf J, Edwardson JM, Chirgadze DY, Jackson AP. Crystal structure and molecular imaging of the Nav channel β3 subunit indicates a trimeric assembly. J Biol Chem 2014; 289:10797-10811. [PMID: 24567321 PMCID: PMC4036194 DOI: 10.1074/jbc.m113.527994] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The vertebrate sodium (Nav) channel is composed of an ion-conducting α subunit and associated β subunits. Here, we report the crystal structure of the human β3 subunit immunoglobulin (Ig) domain, a functionally important component of Nav channels in neurons and cardiomyocytes. Surprisingly, we found that the β3 subunit Ig domain assembles as a trimer in the crystal asymmetric unit. Analytical ultracentrifugation confirmed the presence of Ig domain monomers, dimers, and trimers in free solution, and atomic force microscopy imaging also detected full-length β3 subunit monomers, dimers, and trimers. Mutation of a cysteine residue critical for maintaining the trimer interface destabilized both dimers and trimers. Using fluorescence photoactivated localization microscopy, we detected full-length β3 subunit trimers on the plasma membrane of transfected HEK293 cells. We further show that β3 subunits can bind to more than one site on the Nav 1.5 α subunit and induce the formation of α subunit oligomers, including trimers. Our results suggest a new and unexpected role for the β3 subunits in Nav channel cross-linking and provide new structural insights into some pathological Nav channel mutations.
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Affiliation(s)
- Sivakumar Namadurai
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Dilshan Balasuriya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Rajit Rajappa
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - Martin Wiemhöfer
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom.
| | - Antony P Jackson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom.
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20
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Pallarés MC, Marcuello C, Botello-Morte L, González A, Fillat MF, Lostao A. Sequential binding of FurA from Anabaena sp. PCC 7120 to iron boxes: exploring regulation at the nanoscale. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:623-31. [PMID: 24440406 DOI: 10.1016/j.bbapap.2014.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/06/2014] [Accepted: 01/08/2014] [Indexed: 11/18/2022]
Abstract
Fur (ferric uptake regulator) proteins are involved in the control of a variety of processes in most prokaryotes. Although it is assumed that this regulator binds its DNA targets as a dimer, the way in which this interaction occurs remains unknown. We have focused on FurA from the cyanobacterium Anabaena sp. PCC 7120. To assess the molecular mechanism by which FurA specifically binds to "iron boxes" in PfurA, we examined the topology arrangement of FurA-DNA complexes by atomic force microscopy. Interestingly, FurA-PfurA complexes exhibit several populations, in which one is the predominant and depends clearly on the regulator/promoter ratio on the environment. Those results together with EMSA and other techniques suggest that FurA binds PfurA using a sequential mechanism: (i) a monomer specifically binds to an "iron box" and bends PfurA; (ii) two situations may occur, that a second FurA monomer covers the free "iron box" or that joins to the previously used forming a dimer which would maintain the DNA kinked; (iii) trimerization in which the DNA is unbent; and (iv) finally undergoes a tetramerization; the next coming molecules cover the DNA strands unspecifically. In summary, the bending appears when an "iron box" is bound to one or two molecules and decreases when both "iron boxes" are covered. These results suggest that DNA bending contributes at the first steps of FurA repression promoting the recruitment of new molecules resulting in a fine regulation in the Fur-dependent cluster associated genes.
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Affiliation(s)
- María Carmen Pallarés
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Carlos Marcuello
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Laura Botello-Morte
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Complex Systems Physics (BiFi), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Andrés González
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Complex Systems Physics (BiFi), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Francisca Fillat
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Complex Systems Physics (BiFi), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain; Fundación ARAID, Spain.
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21
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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22
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Oatley P, Talukder MMU, Stewart AP, Sandford R, Edwardson JM. Polycystin-2 induces a conformational change in polycystin-1. Biochemistry 2013; 52:5280-7. [PMID: 23848298 DOI: 10.1021/bi400233e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in the genes encoding either polycystin-1 (PC1) or polycystin-2 (PC2). PC2 acts as a nonselective cation channel and together with PC1 plays a role in intracellular Ca(2+) signaling. Using atomic force microscopy (AFM) imaging, we have shown previously that the N and C termini of PC1 appear as unequally sized particles connected by a "string" largely composed of tandem immunoglobulin-like, polycystic kidney disease (PKD) domains. Here, we show that coexpression of PC1 and PC2 causes an elongation of the PC1 string and a corresponding reduction in the size of the larger (C-terminal) particle. This change in the conformation of PC1 does not depend on its delivery to the plasma membrane. In addition, the use of the L3040H PC1 mutant showed that the conformational change does not require GPS cleavage. Coexpression of PC1 with PC2 mutants revealed that the conformational change in PC1 does not require either a stable interaction between PC1 and PC2 or PC2 channel function. Finally, we show that the tandem PKD repeats and to a lesser extent the receptor for egg jelly (REJ) domain both contribute to the extension of the PC1 string in the presence of PC2. We propose that the PKD repeats detach from the C-terminal fragment in response to PC2 activity. The resulting remodeling of PC1 may be responsible for enhancing GPS cleavage of PC1 and the separation of the PC1 N-terminal fragment from the C terminus during its maturation.
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Affiliation(s)
- Peter Oatley
- Department of Pharmacology, University of Cambridge , Tennis Court Road, Cambridge CB2 1PD, U.K
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23
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Creutz CE, Eaton JM, Harris TE. Assembly of high molecular weight complexes of lipin on a supported lipid bilayer observed by atomic force microscopy. Biochemistry 2013; 52:5092-102. [PMID: 23862673 DOI: 10.1021/bi4004765] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lipins are phosphatidic acid phosphatases involved in the biosynthesis of triacylglycerols and phospholipids. They are associated with the endoplasmic reticulum but can also travel into the nucleus and alter gene expression. Previous studies indicate lipins in solution form high molecular weight complexes, possibly tetramers. This study was undertaken to determine if lipins form complexes on membranes as well. Murine lipin 1b was applied to a supported bilayer of phosphatidylcholine, phosphatidylserine, and cholesterol and examined by atomic force microscopy (AFM) over time. Lipin on bare mica appeared as a symmetric particle with a volume consistent with the size of a monomer. On the bilayer, lipin initially bound as asymmetric, curved particles that sometimes assembled into circular structures with an open center. Subsequently, lipin assemblies grew into large, symmetric particles with an average volume 12 times that of the monomer. Over time, some of the lipin assemblies were removed from the bilayer by the AFM probe leaving behind "footprints" composed of complex patterns that may reflect the substructure of the lipin assemblies. The lipin complexes appeared very flat, with a diameter 20 times their height. The footprints had a similar diameter, providing confirmation of the extensive deformation of the protein under the AFM probe. The ability of lipin to form large complexes on membranes may have significant implications for the local concentrations of the product, diacylglycerol, formed during hydrolysis of phosphatidic acid and for cooperative hormonal regulation of lipin activity through phosphorylation of one or more monomers in the complexes.
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Affiliation(s)
- Carl E Creutz
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908, United States.
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24
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Balasuriya D, Goetze TA, Barrera NP, Stewart AP, Suzuki Y, Edwardson JM. α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors adopt different subunit arrangements. J Biol Chem 2013; 288:21987-98. [PMID: 23760273 PMCID: PMC3724652 DOI: 10.1074/jbc.m113.469205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ionotropic glutamate receptors are widely distributed in the central nervous system and play a major role in excitatory synaptic transmission. All three ionotropic glutamate subfamilies (i.e. AMPA-type, kainate-type, and NMDA-type) assemble as tetramers of four homologous subunits. There is good evidence that both heteromeric AMPA and kainate receptors have a 2:2 subunit stoichiometry and an alternating subunit arrangement. Recent studies based on presumed structural homology have indicated that NMDA receptors adopt the same arrangement. Here, we use atomic force microscopy imaging of receptor-antibody complexes to show that whereas the GluA1/GluA2 AMPA receptor assembles with an alternating (i.e. 1/2/1/2) subunit arrangement, the GluN1/GluN2A NMDA receptor adopts an adjacent (i.e. 1/1/2/2) arrangement. We conclude that the two types of ionotropic glutamate receptor are built in different ways from their constituent subunits. This surprising finding necessitates a reassessment of the assembly of these important receptors.
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Affiliation(s)
- Dilshan Balasuriya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
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25
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AFM volumetric methods for the characterization of proteins and nucleic acids. Methods 2013; 60:113-21. [DOI: 10.1016/j.ymeth.2013.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
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26
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Single-stranded DNA loops as fiducial markers for exploring DNA-protein interactions in single molecule imaging. Methods 2013; 60:122-30. [PMID: 23500656 DOI: 10.1016/j.ymeth.2013.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/20/2013] [Accepted: 03/01/2013] [Indexed: 11/21/2022] Open
Abstract
A polymerase chain reaction (PCR) based method of adding a single-stranded DNA (ssDNA) hairpin loop to one end of linear double-stranded (ds) DNA templates was developed. The loop structure serves as a fiducial marker in single molecule imaging by atomic force microscopy (AFM) and can be applied to study DNA-protein interactions. The nucleic acid end-labels allow discrimination of the polarity of the DNA template in the AFM while limiting non-specific interactions which might occur from non-nucleic acid labels. Homo-polynucleotide ssDNA loops made up of 20 base-pairs (bp) for each of the four bases (A, T, G, C) were investigated to determine the effects of sequence on template labelling. The products were produced with high efficiency and high yield with the loop readily distinguished from the dsDNA template by height and diameter in the AFM. The application of the method to study DNA transcription was investigated by firing Escherichia Coli RNA polymerase (RNAP) from a λPR promoter in the direction of the loop-labelled end. The ssDNA loops captured elongating complexes of RNAP, arresting transcription and preventing dissociation. The dual role of the loop as a polarity marker and retainer of previously active RNAP will allow mechanisms of gene expression to be studied with single molecule sensitivity by AFM. This will enable insight into molecular interactions of RNAP on single DNA templates in convergent or tandem transcription configurations.
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27
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Balasuriya D, Stewart AP, Crottès D, Borgese F, Soriani O, Edwardson JM. The sigma-1 receptor binds to the Nav1.5 voltage-gated Na+ channel with 4-fold symmetry. J Biol Chem 2012; 287:37021-9. [PMID: 22952230 PMCID: PMC3481303 DOI: 10.1074/jbc.m112.382077] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/20/2012] [Indexed: 12/19/2022] Open
Abstract
The sigma-1 receptor (Sig1R) is up-regulated in many human tumors and plays a role in the control of cancer cell proliferation and invasiveness. At the molecular level, the Sig1R modulates the activity of various ion channels, apparently through a direct interaction. We have previously shown using atomic force microscopy imaging that the Sig1R binds to the trimeric acid-sensing ion channel 1A with 3-fold symmetry. Here, we investigated the interaction between the Sig1R and the Nav1.5 voltage-gated Na(+) channel, which has also been implicated in promoting the invasiveness of cancer cells. We show that the Sig1R and Nav1.5 can be co-isolated from co-transfected cells, consistent with an intimate association between the two proteins. Atomic force microscopy imaging of the co-isolated proteins revealed complexes in which Nav1.5 was decorated by Sig1Rs. Frequency distributions of angles between pairs of bound Sig1Rs had two peaks, at ∼90° and ∼180°, and the 90° peak was about twice the size of the 180° peak. These results demonstrate that the Sig1R binds to Nav1.5 with 4-fold symmetry. Hence, each set of six transmembrane regions in Nav1.5 likely constitutes a Sig1R binding site, suggesting that the Sig1R interacts with the transmembrane regions of its partners. Interestingly, two known Sig1R ligands, haloperidol and (+)-pentazocine, disrupted the Nav1.5/Sig1R interaction both in vitro and in living cells. Finally, we show that endogenously expressed Sig1R and Nav1.5 also functionally interact.
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Affiliation(s)
- Dilshan Balasuriya
- From the Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom and
| | - Andrew P. Stewart
- From the Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom and
| | - David Crottès
- Institut de Biologie de Valrose, CNRS UMR 7277, INSERM U1091 UNS, Faculté des Sciences, Université de Nice Sophia Antipolis, 06108 Nice Cedex 2, France
| | - Franck Borgese
- Institut de Biologie de Valrose, CNRS UMR 7277, INSERM U1091 UNS, Faculté des Sciences, Université de Nice Sophia Antipolis, 06108 Nice Cedex 2, France
| | - Olivier Soriani
- Institut de Biologie de Valrose, CNRS UMR 7277, INSERM U1091 UNS, Faculté des Sciences, Université de Nice Sophia Antipolis, 06108 Nice Cedex 2, France
| | - J. Michael Edwardson
- From the Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom and
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28
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García J, Cordeiro TN, Prieto MJ, Pons M. Oligomerization and DNA binding of Ler, a master regulator of pathogenicity of enterohemorrhagic and enteropathogenic Escherichia coli. Nucleic Acids Res 2012; 40:10254-62. [PMID: 22965122 PMCID: PMC3488262 DOI: 10.1093/nar/gks846] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ler is a DNA-binding, oligomerizable protein that regulates pathogenicity islands in enterohemorrhagic and enteropathogenic Escherichia coli strains. Ler counteracts the transcriptional silencing effect of H-NS, another oligomerizable nucleoid-associated protein. We studied the oligomerization of Ler in the absence and presence of DNA by atomic force microscopy. Ler forms compact particles with a multimodal size distribution corresponding to multiples of 3–5 units of Ler. DNA wraps around Ler particles that contain more than 15–16 Ler monomers. The resulting shortening of the DNA contour length is in agreement with previous measurements of the length of DNA protected by Ler in footprinting assays. We propose that the repetition unit corresponds to the number of monomers per turn of a tight helical Ler oligomer. While the repressor (H-NS) and anti-repressor (Ler) have similar DNA-binding domains, their oligomerization domains are unrelated. We suggest that the different oligomerization behavior of the two proteins explains the opposite results of their interaction with the same or proximal regions of DNA.
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Affiliation(s)
- Jesús García
- Structural and Computational Biology, Institute for Research in Biomedicine, Department of Microbiology, University of Barcelona, Barcelona 08028, Spain.
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29
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Billingsley DJ, Crampton N, Kirkham J, Thomson NH, Bonass WA. Single-stranded loops as end-label polarity markers for double-stranded linear DNA templates in atomic force microscopy. Nucleic Acids Res 2012; 40:e99. [PMID: 22453274 PMCID: PMC3401461 DOI: 10.1093/nar/gks276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/13/2012] [Accepted: 03/13/2012] [Indexed: 11/24/2022] Open
Abstract
Visualization of DNA-protein interactions by atomic force microscopy (AFM) has deepened our understanding of molecular processes such as DNA transcription. Interpretation of systems where more than one protein acts on a single template, however, is complicated by protein molecules migrating along the DNA. Single-molecule AFM imaging experiments can reveal more information if the polarity of the template can be determined. A nucleic acid-based approach to end-labelling is desirable because it does not compromise the sample preparation procedures for biomolecular AFM. Here, we report a method involving oligonucleotide loop-primed synthesis for the end labelling of double-stranded DNA to discriminate the polarity of linear templates at the single-molecule level. Single-stranded oligonucleotide primers were designed to allow loop formation while retaining 3'-single-strand extensions to facilitate primer annealing to the template. Following a DNA polymerase extension, the labelled templates were shown to have the ability to form open promoter complexes on a model nested gene template using two Escherichia coli RNA polymerases in a convergent transcription arrangement. Analysis of the AFM images indicates that the added loops have no effect on the ability of the promoters to recruit RNA polymerase. This labelling strategy is proposed as a generic methodology for end-labelling linear DNA for studying DNA-protein interactions by AFM.
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Affiliation(s)
- Daniel J. Billingsley
- School of Physics and Astronomy and Department of Oral Biology, Leeds Dental Institute, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire, LS2 9JT, UK
| | - Neal Crampton
- School of Physics and Astronomy and Department of Oral Biology, Leeds Dental Institute, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire, LS2 9JT, UK
| | - Jennifer Kirkham
- School of Physics and Astronomy and Department of Oral Biology, Leeds Dental Institute, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire, LS2 9JT, UK
| | - Neil H. Thomson
- School of Physics and Astronomy and Department of Oral Biology, Leeds Dental Institute, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire, LS2 9JT, UK
| | - William A. Bonass
- School of Physics and Astronomy and Department of Oral Biology, Leeds Dental Institute, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire, LS2 9JT, UK
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30
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Tan HK, Li D, Gray RK, Yang Z, Ng MTT, Zhang H, Tan JMR, Hiew SH, Lee JY, Li T. Interference of intrinsic curvature of DNA by DNA-intercalating agents. Org Biomol Chem 2012; 10:2227-30. [PMID: 22331171 DOI: 10.1039/c2ob06811g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has been demonstrated in our studies that the intrinsic curvature of DNA can be easily interrupted by low concentrations of chloroquine and ethidium bromide. In addition, the changes of DNA curvature caused by varying the concentration of these two DNA intercalators can be readily verified through using an atomic force microscope.
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Affiliation(s)
- Hong Kee Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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31
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Oatley P, Stewart AP, Sandford R, Edwardson JM. Atomic force microscopy imaging reveals the domain structure of polycystin-1. Biochemistry 2012; 51:2879-88. [PMID: 22409330 DOI: 10.1021/bi300134b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mutation of polycystin-1 (PC1) is the major cause of autosomal dominant polycystic kidney disease. PC1 has a predicted molecular mass of ~460 kDa comprising a long multidomain extracellular N-terminal region, 11 transmembrane regions, and a short C-terminal region. Because of its size, PC1 has proven difficult to handle biochemically, and structural information is consequently sparse. Here we have isolated wild-type PC1, and several mutants, from transfected cells by immunoaffinity chromatography and visualized individual molecules using atomic force microscopy (AFM) imaging. Full-length PC1 appeared as two unequally sized blobs connected by a 35 nm string. The relative sizes of the two blobs suggested that the smaller one represents the N-terminus, including the leucine-rich repeats, the first polycystic kidney disease (PKD) domain, and the C-type lectin motif, while the larger one is the C-terminus, including the receptor for egg jelly (REJ) domain, all transmembrane domains, and the cytoplasmic tail. The intervening string would then consist of a series of tandem PKD domains. The structures of the various PC1 mutants were all consistent with this model. Our results represent the first direct visualization of the structure of PC1, and reveal the architecture of the protein, with intriguing implications for its function.
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Affiliation(s)
- Peter Oatley
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
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32
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Fuentes-Perez ME, Gwynn EJ, Dillingham MS, Moreno-Herrero F. Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope. Biophys J 2012; 102:839-48. [PMID: 22385855 DOI: 10.1016/j.bpj.2012.01.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/10/2012] [Accepted: 01/17/2012] [Indexed: 01/21/2023] Open
Abstract
Atomic force microscopy can potentially provide information on protein volumes, shapes, and interactions but is susceptible to variable tip-induced artifacts. In this study, we present an atomic force microscopy approach that can measure volumes of nonglobular polypeptides such as structural maintenance of chromosomes (SMC) proteins, and use it to study the interactions that occur within and between SMC complexes. Together with the protein of interest, we coadsorb a DNA molecule and use it as a fiducial marker to account for tip-induced artifacts that affect both protein and DNA, allowing normalization of protein volumes from images taken on different days and with different tips. This approach significantly reduced the error associated with volume analysis, and allowed determination of the oligomeric states and architecture of the Bacillus subtilis SMC complex, formed by the SMC protein, and by the smaller ScpA and ScpB subunits. This work reveals that SMC and ScpB are dimers and that ScpA is a stable monomer. Moreover, whereas ScpA binds directly to SMC, ScpB only binds to SMC in the presence of ScpA. Notably, the presence of both ScpA and ScpB favored the formation of higher-order structures of SMC complexes, suggesting a role for these subunits in the organization of SMC oligomers.
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Affiliation(s)
- M E Fuentes-Perez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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33
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Mela I, Kranaster R, Henderson RM, Balasubramanian S, Edwardson JM. Demonstration of Ligand Decoration, and Ligand-Induced Perturbation, of G-Quadruplexes in a Plasmid Using Atomic Force Microscopy. Biochemistry 2012; 51:578-85. [DOI: 10.1021/bi201600g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ioanna Mela
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge
CB2 1PD, U.K
| | - Ramon Kranaster
- Department
of Chemistry, University of Cambridge,
Lensfield Road, Cambridge
CB2 1EW, U.K
- Cancer Research
UK, Cambridge Research Institute, Li Ka
Shing Center, Cambridge
CB2 0RE, U.K
| | - Robert M. Henderson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge
CB2 1PD, U.K
| | - Shankar Balasubramanian
- Department
of Chemistry, University of Cambridge,
Lensfield Road, Cambridge
CB2 1EW, U.K
- Cancer Research
UK, Cambridge Research Institute, Li Ka
Shing Center, Cambridge
CB2 0RE, U.K
- School of
Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge
CB2 1PD, U.K
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34
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Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DT. Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes Dev 2012; 26:92-104. [PMID: 22215814 PMCID: PMC3258970 DOI: 10.1101/gad.179085.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/14/2011] [Indexed: 11/24/2022]
Abstract
Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.
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Affiliation(s)
- Christopher K. Kennaway
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James E. Taylor
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Chun Feng Song
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Wojciech Potrzebowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
| | - William Nicholson
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - John H. White
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Anna Swiderska
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Agnieszka Obarska-Kosinska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
| | - Philip Callow
- Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France
| | - Laurie P. Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Gareth A. Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Jean-Baptiste Artero
- Partnership for Structural Biology, Institut Laue-Langevin, Grenoble, Cedex 9, France
- EPSAM and ISTM, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, PL-02-109 Warsaw, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, PL-61-614 Poznan, Poland
| | - John Trinick
- Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - G. Geoff Kneale
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - David T.F. Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
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35
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Stewart AP, Haerteis S, Diakov A, Korbmacher C, Edwardson JM. Atomic force microscopy reveals the architecture of the epithelial sodium channel (ENaC). J Biol Chem 2011; 286:31944-52. [PMID: 21775436 DOI: 10.1074/jbc.m111.275289] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epithelial sodium channel (ENaC) is a member of the ENaC/degenerin superfamily. ENaC is a heteromultimer containing three homologous subunits (α, β, and γ); however, the subunit stoichiometry is still controversial. Here, we addressed this issue using atomic force microscopy imaging of complexes between isolated ENaC and antibodies/Fab fragments directed against specific epitope tags on the α-, β- and γ-subunits. We show that for α-, β- and γ-ENaC alone, pairs of antibodies decorate the channel at an angle of 120°, indicating that the individual subunits assemble as homotrimers. A similar approach demonstrates that αβγ-ENaC assembles as a heterotrimer containing one copy of each subunit. Intriguingly, all four subunit combinations also produce higher-order structures containing two or three individual trimers. The trimer-of-trimers organization would account for earlier reports that ENaC contains eight to nine subunits.
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Affiliation(s)
- Andrew P Stewart
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
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36
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Roberts GA, Cooper LP, White JH, Su TJ, Zipprich JT, Geary P, Kennedy C, Dryden DTF. An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme. Nucleic Acids Res 2011; 39:7667-76. [PMID: 21685455 PMCID: PMC3177214 DOI: 10.1093/nar/gkr480] [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: 12/03/2022] Open
Abstract
Type I DNA restriction/modification systems are oligomeric enzymes capable of switching between a methyltransferase function on hemimethylated host DNA and an endonuclease function on unmethylated foreign DNA. They have long been believed to not turnover as endonucleases with the enzyme becoming inactive after cleavage. Cleavage is preceded and followed by extensive ATP hydrolysis and DNA translocation. A role for dissociation of subunits to allow their reuse has been proposed for the EcoR124I enzyme. The EcoKI enzyme is a stable assembly in the absence of DNA, so recycling was thought impossible. Here, we demonstrate that EcoKI becomes unstable on long unmethylated DNA; reuse of the methyltransferase subunits is possible so that restriction proceeds until the restriction subunits have been depleted. We observed that RecBCD exonuclease halts restriction and does not assist recycling. We examined the DNA structure required to initiate ATP hydrolysis by EcoKI and find that a 21-bp duplex with single-stranded extensions of 12 bases on either side of the target sequence is sufficient to support hydrolysis. Lastly, we discuss whether turnover is an evolutionary requirement for restriction, show that the ATP hydrolysis is not deleterious to the host cell and discuss how foreign DNA occasionally becomes fully methylated by these systems.
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37
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Duzdevich D, Li J, Whang J, Takahashi H, Takeyasu K, Dryden DTF, Morton AJ, Edwardson JM. Unusual structures are present in DNA fragments containing super-long Huntingtin CAG repeats. PLoS One 2011; 6:e17119. [PMID: 21347256 PMCID: PMC3037965 DOI: 10.1371/journal.pone.0017119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/21/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the R6/2 mouse model of Huntington's disease (HD), expansion of the CAG trinucleotide repeat length beyond about 300 repeats induces a novel phenotype associated with a reduction in transcription of the transgene. METHODOLOGY/PRINCIPAL FINDINGS We analysed the structure of polymerase chain reaction (PCR)-generated DNA containing up to 585 CAG repeats using atomic force microscopy (AFM). As the number of CAG repeats increased, an increasing proportion of the DNA molecules exhibited unusual structural features, including convolutions and multiple protrusions. At least some of these features are hairpin loops, as judged by cross-sectional analysis and sensitivity to cleavage by mung bean nuclease. Single-molecule force measurements showed that the convoluted DNA was very resistant to untangling. In vitro replication by PCR was markedly reduced, and TseI restriction enzyme digestion was also hindered by the abnormal DNA structures. However, significantly, the DNA gained sensitivity to cleavage by the Type III restriction-modification enzyme, EcoP15I. CONCLUSIONS/SIGNIFICANCE "Super-long" CAG repeats are found in a number of neurological diseases and may also appear through CAG repeat instability. We suggest that unusual DNA structures associated with super-long CAG repeats decrease transcriptional efficiency in vitro. We also raise the possibility that if these structures occur in vivo, they may play a role in the aetiology of CAG repeat diseases such as HD.
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Affiliation(s)
- Daniel Duzdevich
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Jinliang Li
- Laragen, Inc., Culver City, California, United States of America
| | - Jhoon Whang
- Laragen, Inc., Culver City, California, United States of America
| | - Hirohide Takahashi
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - David T. F. Dryden
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
| | - A. Jennifer Morton
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AJM); (JME)
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AJM); (JME)
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38
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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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39
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Ghosh-Kumar M, Alam TI, Draper B, Stack JD, Rao VB. Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4. Nucleic Acids Res 2010; 39:2742-55. [PMID: 21109524 PMCID: PMC3074133 DOI: 10.1093/nar/gkq1191] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In genome packaging by tailed bacteriophages and herpesviruses, a concatemeric DNA is cut and inserted into an empty procapsid. A series of cuts follow the encapsidation of each unit-length 'headful' genome, but the mechanisms by which cutting is coupled to packaging are not understood. Here we report the first biochemical characterization of a headful nuclease from bacteriophage T4. Our results show that the T4 nuclease, which resides in the C-terminal domain of large 'terminase' gp17, is a weak endonuclease and regulated by a variety of factors; Mg, NaCl, ATP, small terminase gp16 and N-terminal ATPase domain. The small terminase, which stimulates gp17-ATPase, also stimulates nuclease in the presence of ATP but inhibits in the absence of ATP suggesting interdomain crosstalk. Comparison of the 'relaxed' and 'tensed' states of the motor show that a number of basic residues lining the nuclease groove are positioned to interact with DNA in the tensed state but change their positions in the relaxed state. These results suggest that conformational changes in the ATPase center remodel the nuclease center via an interdomain 'communication track'. This might be a common regulatory mechanism for coupling DNA cutting to DNA packaging among the headful packaging nucleases from dsDNA viruses.
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Affiliation(s)
- Manjira Ghosh-Kumar
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
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40
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Suresh S, Edwardson JM. The Endophilin N-BAR Domain Perturbs the Structure of Lipid Bilayers. Biochemistry 2010; 49:5766-71. [DOI: 10.1021/bi100760e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Swetha Suresh
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
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41
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Carnally SM, Johannessen M, Henderson RM, Jackson MB, Edwardson JM. Demonstration of a direct interaction between sigma-1 receptors and acid-sensing ion channels. Biophys J 2010; 98:1182-91. [PMID: 20371317 PMCID: PMC2849097 DOI: 10.1016/j.bpj.2009.12.4293] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 12/08/2009] [Accepted: 12/15/2009] [Indexed: 10/19/2022] Open
Abstract
The sigma-1 receptor is a widely expressed protein that interacts with a variety of ion channels, including the acid-sensing ion channel (ASIC) 1a. Here we used atomic force microscopy to determine the architecture of the ASIC1a/sigma-1 receptor complex. When isolated His(8)-tagged ASIC1a was imaged in complex with anti-His(6) antibodies, the angle between pairs of bound antibodies was 135 degrees , consistent with the known trimeric structure of the channel. When ASIC1a was coexpressed with FLAG/His(6)-tagged sigma-1 receptor, ASIC1a became decorated with small particles, and pairs of these particles bound at an angle of 131 degrees . When these complexes were incubated with anti-FLAG antibodies, pairs of antibodies bound at an angle of 134 degrees , confirming that the small particles were sigma-1 receptors. Of interest, we found that the sigma-1 receptor ligand haloperidol caused an approximately 50% reduction in ASIC1a/sigma-receptor binding, suggesting a way in which sigma-1 ligands might modulate channel properties. For the first time, to our knowledge, we have resolved the structure of a complex between the sigma-1 receptor and a target ion channel, and demonstrated that the stoichiometry of the interaction is 1 sigma-1 receptor/1 ASIC1a subunit.
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Affiliation(s)
- Stewart M. Carnally
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Molly Johannessen
- Department of Physiology, University of Wisconsin, Madison, Wisconsin
| | - Robert M. Henderson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Meyer B. Jackson
- Department of Physiology, University of Wisconsin, Madison, Wisconsin
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42
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Smith RM, Josephsen J, Szczelkun MD. The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops. Nucleic Acids Res 2010; 37:7219-30. [PMID: 19783815 PMCID: PMC2790907 DOI: 10.1093/nar/gkp794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To cleave DNA, the single polypeptide restriction–modification enzyme LlaGI must communicate between a pair of indirectly repeated recognition sites. We demonstrate that this communication occurs by a 1-dimensional route, namely unidirectional dsDNA loop translocation rightward of the specific recognition sequence 5′-CTnGAyG-3′ as written (where n is either A, G, C or T and y is either C or T). Motion across thousands of base pairs is catalysed by the helicase domain and requires the hydrolysis of 1.5-2 ATP per base pair. DNA loop extrusion is accompanied by changes in DNA twist consistent with the motor following the helical pitch of the polynucleotide track. LlaGI is therefore an example of a polypeptide that is a completely self-contained, multi-functional molecular machine.
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Affiliation(s)
- Rachel M Smith
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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43
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Lenhert S, Mirkin CA, Fuchs H. In situ lipid dip-pen nanolithography under water. SCANNING 2010; 32:15-23. [PMID: 20213823 DOI: 10.1002/sca.20166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Lipids form the structural and functional basis of biological membranes, and methods for studying their self-organization in well-defined nano- and micro-scale model systems can provide insights into biology. Using lipids as an ink for dip-pen nanolithography (lipid DPN) permits the rapid nanostructuring of multicomponent model lipid membrane systems, but this technique has so far been limited to air. Here we demonstrate that lipid DPN can be carried out under water with single tips or parallel arrays. Using the same tip for deposition and imaging in aqueous solution permits imaging of self-spreading lipid bilayer spots in situ and quantification of the nanoscale spreading kinetics in real time by means of lateral-force microscopy. Furthermore, using fluorophore-labeled phospholipids, we directly observed, by confocal laser scanning microscopy, a two-phase (oil in water) meniscus formed around the contact point between the DPN tip and surface, gaining insights into the mechanisms of the ink transport. The methods described here provide a new tool and environment for high-resolution studies of lipid nanodynamics and molecular printing processes in general.
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Affiliation(s)
- Steven Lenhert
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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44
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Wang H, Finzi L, Lewis DEA, Dunlap D. AFM studies of lambda repressor oligomers securing DNA loops. Curr Pharm Biotechnol 2009; 10:494-501. [PMID: 19689317 DOI: 10.2174/138920109788922155] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Large, cooperative assemblies of proteins that wrap and/or loop genomic DNA may "epigenetically" shift configurational equilibria that determine developmental pathways. Such is the case of the lambda bacteriophage which may exhibit virulent (lytic) or quiescent (lysogenic) growth. The lysogenic state of lambda prophages is maintained by the lambda repressor (CI), which binds to tripartite operator sites in each of the O(L) and O(R) control regions located about 2.3 kbp apart on the phage genome and represses lytic promoters. Dodd and collaborators have suggested that an initial loop formed by interaction between CI bound at O(R) and O(L) provides the proper scaffold for additional CI binding to attenuate the P(RM) promoter and avoid over production of CI. Recently, the looping equilibrium as a function of CI concentration was measured using tethered particle motion analysis, but the oligomerization of CI in looped states could not be determined. Scanning force microscopy has now been used to probe these details directly. An equilibrium distribution of looped and unlooped molecules confined to a plane was found to be commensurate to that for tethered molecules in solution, and the occupancies of specific operator sites for several looped and unlooped conformations were determined. Some loops appeared to be sealed by oligomers of 6-8, most by oligomers of 10-12, and a few by oligomers of 14-16.
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Affiliation(s)
- Haowei Wang
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
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Neaves KJ, Huppert JL, Henderson RM, Edwardson JM. Direct visualization of G-quadruplexes in DNA using atomic force microscopy. Nucleic Acids Res 2009; 37:6269-75. [PMID: 19696072 PMCID: PMC2764456 DOI: 10.1093/nar/gkp679] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/14/2009] [Accepted: 08/01/2009] [Indexed: 12/11/2022] Open
Abstract
The formation of G-quadruplexes in G-rich regions of DNA is believed to affect DNA transcription and replication. However, it is currently unclear how this formation occurs in the presence of a complementary strand. We have used atomic force microscopy (AFM) to image stable RNA/DNA hybrid loops generated by transcription of the plasmid pPH600, which contains a 604-bp fragment of the murine immunoglobulin Sgamma3 switch region. We show that the non-RNA-containing portion folds into G-quadruplexes, consistent with computational predictions. We also show that hybrid formation prevents further transcription from occurring, implying a regulatory role. After in vitro transcription, almost all (93%) of the plasmids had an asymmetric loop, a large asymmetric blob or a spur-like projection at the appropriate position on the DNA contour. The loops disappeared following treatment of the transcribed plasmid with RNase H, which removes mRNA hybridized with the template strand. Replacement of K+ in the transcription buffer with either Na+ or Li+ caused a reduction in the percentage of plasmids containing loops, blobs or spurs, consistent with the known effects of monovalent cations on G-quadruplex stability. The minimal sample preparation required for AFM imaging has permitted direct observation of the structural changes resulting from G-quadruplex formation.
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Affiliation(s)
- Kelly J. Neaves
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Julian L. Huppert
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Robert M. Henderson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - J. Michael Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD and Physics of Medicine, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
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