1
|
Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCRJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
Collapse
Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| |
Collapse
|
2
|
Gajdos L, Forsyth VT, Blakeley MP, Haertlein M, Imberty A, Samain E, Devos JM. Production of perdeuterated fucose from glyco-engineered bacteria. Glycobiology 2020; 31:151-158. [PMID: 32601663 PMCID: PMC7874385 DOI: 10.1093/glycob/cwaa059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/31/2022] Open
Abstract
l-Fucose and l-fucose-containing polysaccharides, glycoproteins or glycolipids play an important role in a variety of biological processes. l-Fucose-containing glycoconjugates have been implicated in many diseases including cancer and rheumatoid arthritis. Interest in fucose and its derivatives is growing in cancer research, glyco-immunology, and the study of host–pathogen interactions. l-Fucose can be extracted from bacterial and algal polysaccharides or produced (bio)synthetically. While deuterated glucose and galactose are available, and are of high interest for metabolic studies and biophysical studies, deuterated fucose is not easily available. Here, we describe the production of perdeuterated l-fucose, using glyco-engineered Escherichia coli in a bioreactor with the use of a deuterium oxide-based growth medium and a deuterated carbon source. The final yield was 0.2 g L−1 of deuterated sugar, which was fully characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. We anticipate that the perdeuterated fucose produced in this way will have numerous applications in structural biology where techniques such as NMR, solution neutron scattering and neutron crystallography are widely used. In the case of neutron macromolecular crystallography, the availability of perdeuterated fucose can be exploited in identifying the details of its interaction with protein receptors and notably the hydrogen bonding network around the carbohydrate binding site.
Collapse
Affiliation(s)
- Lukas Gajdos
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France.,Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France.,Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Eric Samain
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France
| |
Collapse
|
3
|
Moulin M, Strohmeier GA, Hirz M, Thompson KC, Rennie AR, Campbell RA, Pichler H, Maric S, Forsyth VT, Haertlein M. Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris. Chem Phys Lipids 2018; 212:80-87. [PMID: 29357283 DOI: 10.1016/j.chemphyslip.2018.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/20/2017] [Accepted: 01/15/2018] [Indexed: 02/08/2023]
Abstract
Deuteration of biomolecules has a major impact on both quality and scope of neutron scattering experiments. Cholesterol is a major component of mammalian cells, where it plays a critical role in membrane permeability, rigidity and dynamics, and contributes to specific membrane structures such as lipid rafts. Cholesterol is the main cargo in low and high-density lipoprotein complexes (i.e. LDL, HDL) and is directly implicated in several pathogenic conditions such as coronary artery disease which leads to 17 million deaths annually. Neutron scattering studies on membranes or lipid-protein complexes exploiting contrast variation have been limited by the lack of availability of fully deuterated biomolecules and especially perdeuterated cholesterol. The availability of perdeuterated cholesterol provides a unique way of probing the structural and dynamical properties of the lipoprotein complexes that underly many of these disease conditions. Here we describe a procedure for in vivo production of perdeuterated recombinant cholesterol in lipid-engineered Pichia pastoris using flask and fed-batch fermenter cultures in deuterated minimal medium. Perdeuteration of the purified cholesterol was verified by mass spectrometry and its use in a neutron scattering study was demonstrated by neutron reflectometry measurements using the FIGARO instrument at the ILL.
Collapse
Affiliation(s)
- Martine Moulin
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gernot A Strohmeier
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Organic Chemistry, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Melanie Hirz
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Adrian R Rennie
- Centre for Neutron Scattering, Uppsala University, 751 20 Uppsala, Sweden
| | | | - Harald Pichler
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Selma Maric
- Biofilms - Research Centre for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö 20506, Sweden
| | - V Trevor Forsyth
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Michael Haertlein
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France.
| |
Collapse
|
4
|
Zhou MB, Hu H, Miskey C, Lazarow K, Ivics Z, Kunze R, Yang G, Izsvák Z, Tang DQ. Transposition of the bamboo Mariner-like element Ppmar1 in yeast. Mol Phylogenet Evol 2017; 109:367-374. [PMID: 28189615 DOI: 10.1016/j.ympev.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expression cassette and a non-autonomous transposon on two separate plasmids. We demonstrate that the Ppmar1 transposase Pptpase1 catalyses excision of the non-autonomous Ppmar1NA element from the plasmid and reintegration at TA dinucleotide sequences in the yeast chromosomes. In addition, we generated 14 hyperactive Ppmar1 transposase variants by systematic single amino acid substitutions. The most active transposase variant, S171A, induces 10-fold more frequent Ppmar1NA excisions in yeast than the wild type transposase. The Ppmar1 transposon is a promising tool for insertion mutagenesis in moso bamboo and may be used in other plants as an alternative to the established transposon tagging systems.
Collapse
Affiliation(s)
- Ming-Bing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Hui Hu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Csaba Miskey
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Katina Lazarow
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Guojun Yang
- Department of Biology, University of Toronto, Mississauga, ON, Canada
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany.
| | - Ding-Qin Tang
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China.
| |
Collapse
|
5
|
Wang Y, Pryputniewicz-Dobrinska D, Nagy EÉ, Kaufman CD, Singh M, Yant S, Wang J, Dalda A, Kay MA, Ivics Z, Izsvák Z. Regulated complex assembly safeguards the fidelity of Sleeping Beauty transposition. Nucleic Acids Res 2016; 45:311-326. [PMID: 27913727 PMCID: PMC5224488 DOI: 10.1093/nar/gkw1164] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/03/2016] [Accepted: 11/16/2016] [Indexed: 01/21/2023] Open
Abstract
The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end. This extra layer of regulation suppresses aberrant, potentially genotoxic recombination activities, and the mobilization of internally deleted copies in the IR/DR subgroup, including Sleeping Beauty (SB). In contrast, internally deleted sequences (MITEs) are preferred substrates of mariner transposition, and this process is associated with the emergence of Hsmar1-derived miRNA genes in the human genome. Translating IR/DR regulation to in vitro evolution yielded an SB transposon version with optimized substrate recognition (pT4). The ends of SB transposons excised by a K248A excision+/integration- transposase variant are processed by hairpin resolution, representing a link between phylogenetically, and mechanistically different recombination reactions, such as V(D)J recombination and transposition. Such variants generated by random mutation might stabilize transposon-host interactions or prepare the transposon for a horizontal transfer.
Collapse
Affiliation(s)
- Yongming Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | | | - Enikö Éva Nagy
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | - Christopher D Kaufman
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | - Manvendra Singh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | - Steve Yant
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305-5164, USA
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | - Anna Dalda
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305-5164, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin 13125, Germany
| |
Collapse
|
6
|
Dunne O, Weidenhaupt M, Callow P, Martel A, Moulin M, Perkins SJ, Haertlein M, Forsyth VT. Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:425-432. [PMID: 27844110 PMCID: PMC5486828 DOI: 10.1007/s00249-016-1186-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 10/19/2016] [Accepted: 10/28/2016] [Indexed: 12/17/2022]
Abstract
Small-angle neutron scattering (SANS) is a powerful technique for the characterisation of macromolecular structures and interactions. Its main advantage over other solution state approaches is the ability to use D2O/H2O solvent contrast variation to selectively match out specific parts of a multi-component system. While proteins, nucleic acids, and lipids are readily distinguished in this way, it is not possible to locate different parts of a protein–protein system without the introduction of additional contrast by selective deuteration. Here, we describe new methods by which ‘matchout labelled’ proteins can be produced using Escherichia coli and Pichia pastoris expression systems in high cell-density cultures. The method is designed to produce protein that has a scattering length density that is very close to that of 100% D2O, providing clear contrast when used with hydrogenated partner proteins in a complex. This allows the production of a single sample system for which SANS measurements at different solvent contrasts can be used to distinguish and model the hydrogenated component, the deuterated component, and the whole complex. The approach, which has significant cost advantages, has been extensively tested for both types of expression system.
Collapse
Affiliation(s)
- O Dunne
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - M Weidenhaupt
- University Grenoble Alpes, CNRS, LMGP, F-38000, Grenoble, France
| | - P Callow
- Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - A Martel
- Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - M Moulin
- Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - S J Perkins
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - M Haertlein
- Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - V T Forsyth
- Institut Laue Langevin, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France. .,Macromolecular Structure Group, Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
| |
Collapse
|
7
|
Abrusán G, Yant SR, Szilágyi A, Marsh JA, Mátés L, Izsvák Z, Barabás O, Ivics Z. Structural Determinants of Sleeping Beauty Transposase Activity. Mol Ther 2016; 24:1369-77. [PMID: 27401040 DOI: 10.1038/mt.2016.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.
Collapse
Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Stephen R Yant
- Department of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California, USA.,Present address: Gilead Sciences Inc., Foster City, California, USA
| | - András Szilágyi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Lajos Mátés
- Instistute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Orsolya Barabás
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| |
Collapse
|
8
|
Morris ER, Grey H, McKenzie G, Jones AC, Richardson JM. A bend, flip and trap mechanism for transposon integration. eLife 2016; 5. [PMID: 27223327 PMCID: PMC5481204 DOI: 10.7554/elife.15537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
Cut-and-paste DNA transposons of the mariner/Tc1 family are useful tools for genome engineering and are inserted specifically at TA target sites. A crystal structure of the mariner transposase Mos1 (derived from Drosophila mauritiana), in complex with transposon ends covalently joined to target DNA, portrays the transposition machinery after DNA integration. It reveals severe distortion of target DNA and flipping of the target adenines into extra-helical positions. Fluorescence experiments confirm dynamic base flipping in solution. Transposase residues W159, R186, F187 and K190 stabilise the target DNA distortions and are required for efficient transposon integration and transposition in vitro. Transposase recognises the flipped target adenines via base-specific interactions with backbone atoms, offering a molecular basis for TA target sequence selection. Our results will provide a template for re-designing mariner/Tc1 transposases with modified target specificities. DOI:http://dx.doi.org/10.7554/eLife.15537.001 The complete set of DNA in a cell is referred to as its genome. Most genomes contain short fragments of DNA called transposons that can jump from one place to another. Transposons carry sections of DNA with them when they move, which creates diversity and can influence the evolution of a species. Transposons are also being exploited to develop tools for biotechnology and medical applications. One family of transposons – the Mariner/Tc1 family – has proved particularly useful in these endeavours because it is widespread in nature and can jump around the genomes of a broad range of species, including mammals. DNA transposons are cut out of their position and then pasted at a new site by an enzyme called transposase, which is encoded by some of the DNA within the transposon. DNA is made up of strings of molecules called bases and Mariner/Tc1-family transposons can only insert into a new position in the genome at sites that have a specific sequence of two bases. However, it was not known how this target sequence is chosen and how the transposon inserts into it. Morris et al. have now used a technique called X-ray crystallography to build a three-dimensional model of a Mariner/Tc1-family transposon as it inserts into a new position. The model shows that, as the transposon is pasted into its new site, the surrounding DNA bends. This causes two DNA bases in the surrounding DNA to flip out from their normal position in the DNA molecule, which enables them to be recognised by the transposase. Further experiments showed that this base-flipping is dynamic, that is, the two bases continuously flip in and out of position. Furthermore, Morris et al. identified which parts of the transposase enzyme are required for the transposon to be efficiently pasted into the genome. Together these findings may help researchers to alter the transposase so that it can insert the transposon into different locations in a genome. This will hopefully lead to new tools for biotechnology and medical applications. DOI:http://dx.doi.org/10.7554/eLife.15537.002
Collapse
Affiliation(s)
- Elizabeth R Morris
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Grey
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Anita C Jones
- EaStCHEM School of Chemistry, Edinburgh, United Kingdom
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
9
|
Voigt F, Wiedemann L, Zuliani C, Querques I, Sebe A, Mátés L, Izsvák Z, Ivics Z, Barabas O. Sleeping Beauty transposase structure allows rational design of hyperactive variants for genetic engineering. Nat Commun 2016; 7:11126. [PMID: 27025571 PMCID: PMC4820933 DOI: 10.1038/ncomms11126] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 02/22/2016] [Indexed: 01/11/2023] Open
Abstract
Sleeping Beauty (SB) is a prominent Tc1/mariner superfamily DNA transposon that provides a popular genome engineering tool in a broad range of organisms. It is mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends. To facilitate SB's applications, here we determine the crystal structure of the transposase catalytic domain and use it to model the SB transposase/transposon end/target DNA complex. Together with biochemical and cell-based transposition assays, our structure reveals mechanistic insights into SB transposition and rationalizes previous hyperactive transposase mutations. Moreover, our data enables us to design two additional hyperactive transposase variants. Our work provides a useful resource and proof-of-concept for structure-based engineering of tailored SB transposases. Sleeping Beauty is used as a genome engineering tool in a range of organisms. Here, the authors solve an atomic structure of Sleeping Beauty (SB) transposase and model the target DNA into the active site, elucidating details that may enable the rational design of novel transposases.
Collapse
Affiliation(s)
- Franka Voigt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Lisa Wiedemann
- Paul Ehrlich Institute, Division of Medical Biotechnology, Paul Ehrlich Strasse 51-59, Langen 63225, Germany
| | - Cecilia Zuliani
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Irma Querques
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Attila Sebe
- Paul Ehrlich Institute, Division of Medical Biotechnology, Paul Ehrlich Strasse 51-59, Langen 63225, Germany
| | - Lajos Mátés
- Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, Berlin 13092, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, Berlin 13092, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Division of Medical Biotechnology, Paul Ehrlich Strasse 51-59, Langen 63225, Germany
| | - Orsolya Barabas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| |
Collapse
|
10
|
Abstract
The IS630-Tc1-mariner (ITm) family of transposons is one of the most widespread in nature. The phylogenetic distribution of its members shows that they do not persist for long in a given lineage, but rely on frequent horizontal transfer to new hosts. Although they are primarily selfish genomic-parasites, ITm transposons contribute to the evolution of their hosts because they generate variation and contribute protein domains and regulatory regions. Here we review the molecular mechanism of ITm transposition and its regulation. We focus mostly on the mariner elements, which are understood in the greatest detail owing to in vitro reconstitution and structural analysis. Nevertheless, the most important characteristics are probably shared across the grouping. Members of the ITm family are mobilized by a cut-and-paste mechanism and integrate at 5'-TA dinucleotide target sites. The elements encode a single transposase protein with an N-terminal DNA-binding domain and a C-terminal catalytic domain. The phosphoryl-transferase reactions during the DNA-strand breaking and joining reactions are performed by the two metal-ion mechanism. The metal ions are coordinated by three or four acidic amino acid residues located within an RNase H-like structural fold. Although all of the strand breaking and joining events at a given transposon end are performed by a single molecule of transposase, the reaction is coordinated by close communication between transpososome components. During transpososome assembly, transposase dimers compete for free transposon ends. This helps to protect the host by dampening an otherwise exponential increase in the rate of transposition as the copy number increases.
Collapse
|
11
|
Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
12
|
Palomeque T, Sanllorente O, Maside X, Vela J, Mora P, Torres MI, Periquet G, Lorite P. Evolutionary history of the Azteca-like mariner transposons and their host ants. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2015. [PMID: 26195134 DOI: 10.1007/s00114-015-1294-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three different complete mariner elements were found in the genome of the ant Tapinoma nigerrimum. One (Tnigmar-Mr) was interrupted by a 900-bp insertion that corresponded to an incomplete member of a fourth mariner element, called Azteca. In this work, we isolate and characterize full-length Tnigmar-Az elements in T. nigerrimum. The purpose of this study is to clarify the evolutionary history of Azteca elements and their hosts as well as the possible existence of horizontal transfer processes. For this, Azteca-like elements were also retrieved from the available sequences of various ant genomes, representing four different ant subfamilies: Dolichoderinae, Formicinae, Myrmicinae, and Ponerinae. The tree topology resulting for the Azteca-like elements bore very little resemblance to that of their respective hosts. The pervasive presence of Azteca-like elements in all ant genomes, together with the observation that extant copies are usually younger than the genomes that host them, could be explained either by lineage sorting or by recent horizontal transfer of active elements. However, the finding of closer genetic relationships between elements than between the ants that host them is consistent with the latter scenario. This is clearly observed in Sinvmar-Az, Tnigmar-Az, Acepmar-Az, and Cflomar-Az elements, suggesting the existence of horizontal transfer processes. On the contrary, some elements displayed more divergence than did the hosts harboring them. This may reflect either further horizontal transfer events or random lineage sorting.
Collapse
Affiliation(s)
- Teresa Palomeque
- Departamento de Biología Experimental, Universidad de Jaén, 23071, Jaén, Spain
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Edlich-Muth C, Artero JB, Callow P, Przewloka MR, Watson AA, Zhang W, Glover DM, Debski J, Dadlez M, Round AR, Forsyth VT, Laue ED. The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. J Mol Biol 2015; 427:1949-63. [PMID: 25813344 PMCID: PMC4414354 DOI: 10.1016/j.jmb.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/17/2015] [Accepted: 03/17/2015] [Indexed: 11/28/2022]
Abstract
Nucleoplasmin is a histone chaperone that consists of a pentameric N-terminal domain and an unstructured C-terminal tail. The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family. Here, we report the first structure of a nucleoplasmin-like domain (NPL) from the unrelated Drosophila protein, FKBP39, and we present evidence that this protein associates with chromatin. Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2. Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.
Collapse
Affiliation(s)
- Christian Edlich-Muth
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Jean-Baptiste Artero
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Phil Callow
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Marcin R Przewloka
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Aleksandra A Watson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - David M Glover
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Janusz Debski
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Dadlez
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Adam R Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-European Molecular Biology Laboratory-CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.
| |
Collapse
|
14
|
Trubitsyna M, Grey H, Houston DR, Finnegan DJ, Richardson JM. Structural Basis for the Inverted Repeat Preferences of mariner Transposases. J Biol Chem 2015; 290:13531-40. [PMID: 25869132 PMCID: PMC4505599 DOI: 10.1074/jbc.m115.636704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
The inverted repeat (IR) sequences delimiting the left and right ends of many naturally active mariner DNA transposons are non-identical and have different affinities for their transposase. We have compared the preferences of two active mariner transposases, Mos1 and Mboumar-9, for their imperfect transposon IRs in each step of transposition: DNA binding, DNA cleavage, and DNA strand transfer. A 3.1 Å resolution crystal structure of the Mos1 paired-end complex containing the pre-cleaved left IR sequences reveals the molecular basis for the reduced affinity of the Mos1 transposase DNA-binding domain for the left IR as compared with the right IR. For both Mos1 and Mboumar-9, in vitro DNA transposition is most efficient when the preferred IR sequence is present at both transposon ends. We find that this is due to the higher efficiency of cleavage and strand transfer of the preferred transposon end. We show that the efficiency of Mboumar-9 transposition is improved almost 4-fold by changing the 3′ base of the preferred Mboumar-9 IR from guanine to adenine. This preference for adenine at the reactive 3′ end for both Mos1 and Mboumar-9 may be a general feature of mariner transposition.
Collapse
Affiliation(s)
| | - Heather Grey
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, United Kingdom
| | - Douglas R Houston
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, United Kingdom
| | | | - Julia M Richardson
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, United Kingdom
| |
Collapse
|
15
|
Abstract
DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.
Collapse
Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Center Dr., Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Center Dr., Bethesda, MD 20892, USA
| |
Collapse
|
16
|
Esnault C, Jaillet J, Delorme N, Bouchet N, Renault S, Douziech-Eyrolles L, Pilard JF, Augé-Gouillou C. Kinetic analysis of the interaction of Mos1 transposase with its inverted terminal repeats reveals new insight into the protein-DNA complex assembly. Chembiochem 2015; 16:140-8. [PMID: 25487538 DOI: 10.1002/cbic.201402466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 11/08/2022]
Abstract
Transposases are specific DNA-binding proteins that promote the mobility of discrete DNA segments. We used a combination of physicochemical approaches to describe the association of MOS1 (an eukaryotic transposase) with its specific target DNA, an event corresponding to the first steps of the transposition cycle. Because the kinetic constants of the reaction are still unknown, we aimed to determine them by using quartz crystal microbalance on two sources of recombinant MOS1: one produced in insect cells and the other produced in bacteria. The prokaryotic-expressed MOS1 showed no cooperativity and displayed a Kd of about 300 nM. In contrast, the eukaryotic-expressed MOS1 generated a cooperative system, with a lower Kd (∼ 2 nm). The origins of these differences were investigated by IR spectroscopy and AFM imaging. Both support the conclusion that prokaryotic- and eukaryotic-expressed MOS1 are not similarly folded, thereby resulting in differences in the early steps of transposition.
Collapse
Affiliation(s)
- Charles Esnault
- Groupe Instabilité Génétique et Transposases, EA 6306, Fédération GICC, UFR Sciences Pharmaceutiques, Université François Rabelais, 31 Avenue Monge, 37200 Tours (France)
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Maric S, Thygesen MB, Schiller J, Marek M, Moulin M, Haertlein M, Forsyth VT, Bogdanov M, Dowhan W, Arleth L, Pomorski TG. Biosynthetic preparation of selectively deuterated phosphatidylcholine in genetically modified Escherichia coli. Appl Microbiol Biotechnol 2015; 99:241-54. [PMID: 25301578 PMCID: PMC4289089 DOI: 10.1007/s00253-014-6082-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 01/07/2023]
Abstract
Phosphatidylcholine (PC) is a major component of eukaryotic cell membranes and one of the most commonly used phospholipids for reconstitution of membrane proteins into carrier systems such as lipid vesicles, micelles and nanodiscs. Selectively deuterated versions of this lipid have many applications, especially in structural studies using techniques such as NMR, neutron reflectivity and small-angle neutron scattering. Here we present a comprehensive study of selective deuteration of phosphatidylcholine through biosynthesis in a genetically modified strain of Escherichia coli. By carefully tuning the deuteration level in E. coli growth media and varying the deuteration of supplemented carbon sources, we show that it is possible to achieve a controlled deuteration for three distinct parts of the PC lipid molecule, namely the (a) lipid head group, (b) glycerol backbone and (c) fatty acyl tail. This biosynthetic approach paves the way for the synthesis of specifically deuterated, physiologically relevant phospholipid species which remain difficult to obtain through standard chemical synthesis.
Collapse
Affiliation(s)
- Selma Maric
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Mikkel B. Thygesen
- CARB Centre, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jürgen Schiller
- Institut für Medizinische Physik und Biophysik, Medizinische Fakultät, Universität Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Magdalena Marek
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Lise Arleth
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Thomas Günther Pomorski
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| |
Collapse
|
18
|
Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCRJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
Collapse
Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| |
Collapse
|
19
|
Bouuaert CC, Tellier M, Chalmers R. One to rule them all: A highly conserved motif in mariner transposase controls multiple steps of transposition. Mob Genet Elements 2014; 4:e28807. [PMID: 24812590 PMCID: PMC4013102 DOI: 10.4161/mge.28807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 01/16/2023] Open
Abstract
The development of transposon-based genome manipulation tools can benefit greatly from understanding transposons’ inherent regulatory mechanisms. The Tc1-mariner transposons, which are being widely used in biotechnological applications, are subject to a self-inhibitory mechanism whereby increasing transposase expression beyond a certain point decreases the rate of transposition. In a recent paper, Liu and Chalmers performed saturating mutagenesis on the highly conserved WVPHEL motif in the mariner-family transposase from the Hsmar1 element. Curiously, they found that the majority of all possible single mutations were hyperactive. Biochemical characterizations of the mutants revealed that the hyperactivity is due to a defect in communication between transposase subunits, which normally regulates transposition by reducing the rate of synapsis. This provides important clues for improving transposon-based tools. However, some WVPHEL mutants also showed features that would be undesirable for most biotechnological applications: they showed uncontrolled DNA cleavage activities and defects in the coordination of cleavage between the two transposon ends. The study illustrates how the knowledge of inhibitory mechanisms can help improve transposon tools but also highlights an important challenge, which is to specifically target a regulatory mechanism without affecting other important functions of the transposase.
Collapse
Affiliation(s)
- Corentin Claeys Bouuaert
- Molecular Biology Program; Howard Hughes Medical Institute; Memorial Sloan Kettering Cancer Center; New York, NY USA
| | - Michael Tellier
- School of Life Sciences; University of Nottingham; Queen's Medical Centre; Nottingham, UK
| | - Ronald Chalmers
- School of Life Sciences; University of Nottingham; Queen's Medical Centre; Nottingham, UK
| |
Collapse
|
20
|
Backfisch B, Kozin VV, Kirchmaier S, Tessmar-Raible K, Raible F. Tools for gene-regulatory analyses in the marine annelid Platynereis dumerilii. PLoS One 2014; 9:e93076. [PMID: 24714200 PMCID: PMC3979674 DOI: 10.1371/journal.pone.0093076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/03/2014] [Indexed: 01/22/2023] Open
Abstract
The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species.
Collapse
Affiliation(s)
- Benjamin Backfisch
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Vitaly V. Kozin
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Stephan Kirchmaier
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Florian Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
- * E-mail:
| |
Collapse
|
21
|
Trubitsyna M, Morris ER, Finnegan DJ, Richardson JM. Biochemical characterization and comparison of two closely related active mariner transposases. Biochemistry 2014; 53:682-9. [PMID: 24404958 PMCID: PMC3922039 DOI: 10.1021/bi401193w] [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] [Indexed: 11/22/2022]
Abstract
![]()
Most DNA transposons move from one
genomic location to another
by a cut-and-paste mechanism and are useful tools for genomic manipulations.
Short inverted repeat (IR) DNA sequences marking each end of the transposon
are recognized by a DNA transposase (encoded by the transposon itself).
This enzyme cleaves the transposon ends and integrates them at a new
genomic location. We report here a comparison of the biophysical and
biochemical properties of two closely related and active mariner/Tc1 family DNA transposases: Mboumar-9 and Mos1. We compared the in vitro cleavage activities of the enzymes on their own
IR sequences, as well as cross-recognition of their inverted repeat
sequences. We found that, like Mos1, untagged recombinant Mboumar-9
transposase is a dimer and forms a stable complex with inverted repeat
DNA in the presence of Mg2+ ions. Mboumar-9 transposase
cleaves its inverted repeat DNA in the manner observed for Mos1 transposase.
There was minimal cross-recognition of IR sequences between Mos1 and
Mboumar-9 transposases, despite these enzymes having 68% identical
amino acid sequences. Transposases sharing common biophysical and
biochemical properties, but retaining recognition specificity toward
their own IR, are a promising platform for the design of chimeric
transposases with predicted and improved sequence recognition.
Collapse
Affiliation(s)
- Maryia Trubitsyna
- School of Biological Sciences, University of Edinburgh , The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
| | | | | | | |
Collapse
|
22
|
Bouchet N, Jaillet J, Gabant G, Brillet B, Briseño-Roa L, Cadene M, Augé-Gouillou C. cAMP protein kinase phosphorylates the Mos1 transposase and regulates its activity: evidences from mass spectrometry and biochemical analyses. Nucleic Acids Res 2014; 42:1117-28. [PMID: 24081583 PMCID: PMC3902898 DOI: 10.1093/nar/gkt874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 12/19/2022] Open
Abstract
Genomic plasticity mediated by transposable elements can have a dramatic impact on genome integrity. To minimize its genotoxic effects, it is tightly regulated either by intrinsic mechanisms (linked to the element itself) or by host-mediated mechanisms. Using mass spectrometry, we show here for the first time that MOS1, the transposase driving the mobility of the mariner Mos1 element, is phosphorylated. We also show that the transposition activity of MOS1 is downregulated by protein kinase AMP cyclic-dependent phosphorylation at S170, which renders the transposase unable to promote Mos1 transposition. One step in the transposition cycle, the assembly of the paired-end complex, is specifically inhibited. At the cellular level, we provide evidence that phosphorylation at S170 prevents the active transport of the transposase into the nucleus. Our data suggest that protein kinase AMP cyclic-dependent phosphorylation may play a double role in the early stages of genome invasion by mariner elements.
Collapse
Affiliation(s)
- Nicolas Bouchet
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Jérôme Jaillet
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Guillaume Gabant
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Benjamin Brillet
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Luis Briseño-Roa
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Martine Cadene
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Corinne Augé-Gouillou
- Innovation Moléculaire Thérapeutique, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Université François Rabelais, 37200 Tours, France, Centre de Biophysique Moléculaire, UPR 4301 CNRS, Rue Charles Sadron, 45071 Orléans, France, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IUT de Quimper, Université de Bretagne Occidentale, 6 rue de l’Université, 29000 Quimper, France and Biologie Cellulaire de la Synapse, INSERM U789, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| |
Collapse
|
23
|
Liu D, Chalmers R. Hyperactive mariner transposons are created by mutations that disrupt allosterism and increase the rate of transposon end synapsis. Nucleic Acids Res 2013; 42:2637-45. [PMID: 24319144 PMCID: PMC3936726 DOI: 10.1093/nar/gkt1218] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
New applications for transposons in vertebrate genetics have spurred efforts to develop hyperactive variants. Typically, a genetic screen is used to identify several hyperactive point mutations, which are then incorporated in a single transposase gene. However, the mechanisms responsible for the increased activity are unknown. Here we show that several point mutations in the mariner transposase increase their activities by disrupting the allostery that normally serves to downregulate transposition by slowing synapsis of the transposon ends. We focused on the conserved WVPHEL amino acid motif, which forms part of the mariner transposase dimer interface. We generated almost all possible single substitutions of the W, V, E and L residues and found that the majority are hyperactive. Biochemical analysis of the mutations revealed that they disrupt signals that pass between opposite sides of the developing transpososome in response to transposon end binding. In addition to their role in allostery, the signals control the initiation of catalysis, thereby preventing non-productive double-strand breaks. Finally, we note that such breaks may explain the puzzling ‘self-inflicted wounds’ at the ends of the Mos1 transposon in Drosophila.
Collapse
Affiliation(s)
- Danxu Liu
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | |
Collapse
|
24
|
Pflieger A, Jaillet J, Petit A, Augé-Gouillou C, Renault S. Target capture during Mos1 transposition. J Biol Chem 2013; 289:100-11. [PMID: 24269942 DOI: 10.1074/jbc.m113.523894] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA transposition contributes to genomic plasticity. Target capture is a key step in the transposition process, because it contributes to the selection of new insertion sites. Nothing or little is known about how eukaryotic mariner DNA transposons trigger this step. In the case of Mos1, biochemistry and crystallography have deciphered several inverted terminal repeat-transposase complexes that are intermediates during transposition. However, the target capture complex is still unknown. Here, we show that the preintegration complex (i.e., the excised transposon) is the only complex able to capture a target DNA. Mos1 transposase does not support target commitment, which has been proposed to explain Mos1 random genomic integrations within host genomes. We demonstrate that the TA dinucleotide used as the target is crucial both to target recognition and in the chemistry of the strand transfer reaction. Bent DNA molecules are better targets for the capture when the target DNA is nicked two nucleotides apart from the TA. They improve strand transfer when the target DNA contains a mismatch near the TA dinucleotide.
Collapse
Affiliation(s)
- Aude Pflieger
- From the EA 6306 Innovation Moléculaire et Thérapeutique, Université François Rabelais, UFR des Sciences et Techniques, UFR de Pharmacie, 37200 Tours, France
| | | | | | | | | |
Collapse
|
25
|
Mos1 transposon-based transformation of fish cell lines using baculoviral vectors. Biochem Biophys Res Commun 2013; 439:18-22. [PMID: 23958306 DOI: 10.1016/j.bbrc.2013.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 08/10/2013] [Indexed: 11/24/2022]
Abstract
Drosophila Mos1 belongs to the mariner family of transposons, which are one of the most ubiquitous transposons among eukaryotes. We first determined nuclear transportation of the Drosophila Mos1-EGFP fusion protein in fish cell lines because it is required for a function of transposons. We next constructed recombinant baculoviral vectors harboring the Drosophila Mos1 transposon or marker genes located between Mos1 inverted repeats. The infectivity of the recombinant virus to fish cells was assessed by monitoring the expression of a fluorescent protein encoded in the viral genome. We detected transgene expression in CHSE-214, HINAE, and EPC cells, but not in GF or RTG-2 cells. In the co-infection assay of the Mos1-expressing virus and reporter gene-expressing virus, we successfully transformed CHSE-214 and HINAE cells. These results suggest that the combination of a baculovirus and Mos1 transposable element may be a tool for transgenesis in fish cells.
Collapse
|