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Ramakrishnan M, Zhou M, Pan C, Hänninen H, Yrjälä K, Vinod KK, Tang D. Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element. Int J Mol Sci 2019; 20:ijms20153692. [PMID: 31357686 PMCID: PMC6696609 DOI: 10.3390/ijms20153692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR's affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5-2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
| | - Chunfang Pan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Heikki Hänninen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, Tamil Nadu 612101, India
| | - Dingqin Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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2
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Trubitsyna M, Michlewski G, Finnegan DJ, Elfick A, Rosser SJ, Richardson JM, French CE. Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection. Nucleic Acids Res 2017; 45:e89. [PMID: 28204586 PMCID: PMC5449632 DOI: 10.1093/nar/gkx113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
Delivery of DNA to cells and its subsequent integration into the host genome is a fundamental task in molecular biology, biotechnology and gene therapy. Here we describe an IP-free one-step method that enables stable genome integration into either prokaryotic or eukaryotic cells. A synthetic mariner transposon is generated by flanking a DNA sequence with short inverted repeats. When purified recombinant Mos1 or Mboumar-9 transposase is co-transfected with transposon-containing plasmid DNA, it penetrates prokaryotic or eukaryotic cells and integrates the target DNA into the genome. In vivo integrations by purified transposase can be achieved by electroporation, chemical transfection or Lipofection of the transposase:DNA mixture, in contrast to other published transposon-based protocols which require electroporation or microinjection. As in other transposome systems, no helper plasmids are required since transposases are not expressed inside the host cells, thus leading to generation of stable cell lines. Since it does not require electroporation or microinjection, this tool has the potential to be applied for automated high-throughput creation of libraries of random integrants for purposes including gene knock-out libraries, screening for optimal integration positions or safe genome locations in different organisms, selection of the highest production of valuable compounds for biotechnology, and sequencing.
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Affiliation(s)
- Maryia Trubitsyna
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Gracjan Michlewski
- Institute of Cell Biology, School of Biological Sciences, Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David J Finnegan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Alistair Elfick
- Institute of BioEngineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK
| | - Susan J Rosser
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Christopher E French
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
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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.
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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
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Bire S, Casteret S, Piégu B, Beauclair L, Moiré N, Arensbuger P, Bigot Y. Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2. PLoS Genet 2016; 12:e1005902. [PMID: 26939020 PMCID: PMC4777549 DOI: 10.1371/journal.pgen.1005902] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/05/2016] [Indexed: 12/31/2022] Open
Abstract
Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes. Here, we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame (ORF) which functions in vertebrate and arthropod cells. Functional silencers are also found at similar locations within three other animal mariner elements, i.e. IS630-Tc1-mariner (ITm) DD34D elements, Himar1, Hsmar1 and Mcmar1. These silencers are able to impact eukaryotic promoters monitoring strong, moderate or low expression as well as those of mariner elements located upstream of the transposase ORF. We report that the silencing involves at least two transcription factors (TFs) that are conserved within animal species, NFAT-5 and Alx1. These cooperatively act with YY1 to trigger the silencing activity. Four other housekeeping transcription factors (TFs), neuron restrictive silencer factor (NRSF), GAGA factor (GAF) and GTGT factor (GTF), were also found to have binding sites within mariner silencers but their impact in modulating the silencer activity remains to be further specified. Interestingly, an NRSF binding site was found to overlap a 30 bp motif coding a highly conserved PHxxYSPDLAPxD peptide in mariner transposases. We also present experimental evidence that silencing is mainly achieved by co-opting the host Polycomb Repressive Complex 2 pathway. However, we observe that when PRC2 is impaired another host silencing pathway potentially takes over to maintain weak silencer activity. Mariner silencers harbour features of Polycomb Response Elements, which are probably a way for mariner elements to self-repress their transcription and mobility in somatic and germinal cells when the required TFs are expressed. At the evolutionary scale, mariner elements, through their exaptation, might have been a source of silencers playing a role in the chromatin configuration in eukaryotic genomes. Transposons are mobile DNA sequences that have long co-evolved with the genome of their hosts. Consequently, they are involved in the generation of mutations, as well as the creation of genes and regulatory networks. Controlling the transposon activity, and consequently its negative effects on both the host soma and germ line, is a challenge for the survival of both the host and the transposon. To silence transposons, hosts often use defence mechanisms involving DNA methylation and RNA interference pathways. Here we show that mariner transposons can self-regulate their activity by using a silencer element located in their DNA sequence. The silencer element interferes with host housekeeping protein transcription factors involved in the polycomb silencing pathways. As the regulation of chromatin configuration by polycomb is an important regulator of animal development, our findings open the possibility that mariner silencers might have been exapted during animal evolution to participate in certain regulation pathways of their hosts. Since some of the TFs involved in mariner silencer activity play a role at different stages of nervous system development and neuron differentiation, it might be possible that mariner transposons can be active during some steps of cell differentiation. Interestingly, mariner transposons (i.e. IS630-Tc1-mariner (ITm) DD34D transposons) have so far only been found in genomes of animals having a nervous system.
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Affiliation(s)
- Solenne Bire
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | | | | | | | | | - Peter Arensbuger
- Biological Sciences Department, California State Polytechnic University, Pomona, California, United States of America
| | - Yves Bigot
- PRC, UMR INRA-CNRS 7247, PRC, Nouzilly, France
- * E-mail:
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5
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Olson KE, Franz AWE. Advances in genetically modified Aedes aegypti to control transmission of dengue viruses. Future Virol 2015. [DOI: 10.2217/fvl.15.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Dengue viruses (DENV) are mosquito-borne viruses that infect millions of humans each year. DENVs are endemic in tropical regions of the world and maintained in a transmission cycle between mosquito vectors (Aedes aegypti) and humans. DEN disease control relies on vector control approaches that have had limited success and are difficult to sustain. Genetically modified mosquitoes (GMM) may be an alternative control strategy to limit DENV transmission. GMM-based control strategies include: conditional expression of a dominant lethal gene (RIDL) to reduce vector populations; and introgression of antipathogen (AP) genes into wild-type vectors for population replacement. In this review, we describe novel GMM-based strategies to limit DENV transmission and discuss potential hurdles to their successful implementation in the field.
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Affiliation(s)
- Ken E Olson
- Arthropod-borne & Infectious Diseases Laboratory, Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alexander WE Franz
- Department of Veterinary Pathobiology, 303 Connaway Hall, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
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Leighton GO, Konnova TA, Idiyatullin B, Hurr SH, Zuev YF, Nesmelova IV. The folding of the specific DNA recognition subdomain of the sleeping beauty transposase is temperature-dependent and is required for its binding to the transposon DNA. PLoS One 2014; 9:e112114. [PMID: 25375127 PMCID: PMC4222973 DOI: 10.1371/journal.pone.0112114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 12/26/2022] Open
Abstract
The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase.
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Affiliation(s)
- Gage O. Leighton
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Tatiana A. Konnova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Bulat Idiyatullin
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Sophia H. Hurr
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russian Federation
| | - Irina V. Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, United States of America
- Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina, United States of America
- * E-mail:
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7
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Wallau GL, Capy P, Loreto E, Hua-Van A. Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus. BMC Genomics 2014; 15:727. [PMID: 25163909 PMCID: PMC4161770 DOI: 10.1186/1471-2164-15-727] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes. RESULTS We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies. CONCLUSIONS This analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all "life cycle" stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.
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Affiliation(s)
- Gabriel Luz Wallau
- Pós-Graduaíão em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Brasil.
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Abstract
A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal is commonly interpreted to relate to the helical pitch of negatively supercoiled DNA. Functions in supercoiling-dependent RNA transcription or as a 'structural code' for DNA packaging have been suggested. Cyanobacterial genomes showed especially strong periodic signals and, on the other hand, DNA supercoiling and supercoiling-dependent transcription are highly dynamic and underlie circadian rhythms of these phototrophic bacteria. Focusing on this phylum and dinucleotides, we find that a minimal motif of AT-tracts (AT2) yields the strongest signal. Strong genome-wide periodicity is ancestral to a clade of unicellular and polyploid species but lost upon morphological transitions into two baeocyte-forming and a symbiotic species. The signal is intermediate in heterocystous species and weak in monoploid picocyanobacteria. A pronounced 'structural code' may support efficient nucleoid condensation and segregation in polyploid cells. The major source of the AT2 signal are protein-coding regions, where it is encoded preferentially in the first and third codon positions. The signal shows only few relations to supercoiling-dependent and diurnal RNA transcription in Synechocystis sp. PCC 6803. Strong and specific signals in two distinct transposons suggest roles in transposase transcription and transpososome formation.
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Affiliation(s)
- Robert Lehmann
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany
| | - Rainer Machné
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090, Vienna, Austria
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany
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Piégu B, Guizard S, Yeping T, Cruaud C, Asgari S, Bideshi DK, Federici BA, Bigot Y. Genome sequence of a crustacean iridovirus, IIV31, isolated from the pill bug, Armadillidium vulgare. J Gen Virol 2014; 95:1585-1590. [PMID: 24722681 DOI: 10.1099/vir.0.066076-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. The invertebrate iridovirus 31 (IIV31) was originally isolated from adult pill bugs, Armadillidium vulgare (class Crustacea, order Isopoda, suborder Oniscidea), found in southern California on the campus of the University of California, Riverside, USA. IIV31 virions are icosahedral, have a diameter of about 135 nm, and contain a dsDNA genome 220.222 kbp in length, with 35.09 mol % G+C content and 203 ORFs. Here, we describe the complete genome sequence of this virus and its annotation. This is the eighth genome sequence of an IIV reported.
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Affiliation(s)
- Benoît Piégu
- UMR INRA-CNRS 7247, PRC, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Sébastien Guizard
- UMR INRA-CNRS 7247, PRC, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Tan Yeping
- Interdepartmental Graduate Programs in Cell, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA.,Department of Entomology, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA
| | - Corinne Cruaud
- CEA/Institut de Génomique GENOSCOPE, 2 Rue Gaston Crémieux, CP 5706, 91057 Evry CEDEX, France
| | - Sassan Asgari
- School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Dennis K Bideshi
- California Baptist University, Department of Natural and Mathematical Sciences, 8432 Magnolia Avenue, Riverside, CA 92504, USA.,Department of Entomology, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA
| | - Brian A Federici
- Interdepartmental Graduate Programs in Cell, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA.,Department of Entomology, Molecular and Developmental Biology, University of California, Riverside, CA 92521, USA
| | - Yves Bigot
- UMR INRA-CNRS 7247, PRC, Centre INRA Val de Loire, 37380 Nouzilly, France
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10
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Suicidal autointegration of sleeping beauty and piggyBac transposons in eukaryotic cells. PLoS Genet 2014; 10:e1004103. [PMID: 24625543 PMCID: PMC3952818 DOI: 10.1371/journal.pgen.1004103] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 11/23/2013] [Indexed: 01/04/2023] Open
Abstract
Transposons are discrete segments of DNA that have the distinctive ability to move and replicate within genomes across the tree of life. 'Cut and paste' DNA transposition involves excision from a donor locus and reintegration into a new locus in the genome. We studied molecular events following the excision steps of two eukaryotic DNA transposons, Sleeping Beauty (SB) and piggyBac (PB) that are widely used for genome manipulation in vertebrate species. SB originates from fish and PB from insects; thus, by introducing these transposons to human cells we aimed to monitor the process of establishing a transposon-host relationship in a naïve cellular environment. Similarly to retroviruses, neither SB nor PB is capable of self-avoidance because a significant portion of the excised transposons integrated back into its own genome in a suicidal process called autointegration. Barrier-to-autointegration factor (BANF1), a cellular co-factor of certain retroviruses, inhibited transposon autointegration, and was detected in higher-order protein complexes containing the SB transposase. Increasing size sensitized transposition for autointegration, consistent with elevated vulnerability of larger transposons. Both SB and PB were affected similarly by the size of the transposon in three different assays: excision, autointegration and productive transposition. Prior to reintegration, SB is completely separated from the donor molecule and followed an unbiased autointegration pattern, not associated with local hopping. Self-disruptive autointegration occurred at similar frequency for both transposons, while aberrant, pseudo-transposition events were more frequently observed for PB.
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11
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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.
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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
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Jaillet J, Genty M, Cambefort J, Rouault JD, Augé-Gouillou C. Regulation of mariner transposition: the peculiar case of Mos1. PLoS One 2012; 7:e43365. [PMID: 22905263 PMCID: PMC3419177 DOI: 10.1371/journal.pone.0043365] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/20/2012] [Indexed: 01/18/2023] Open
Abstract
Background Mariner elements represent the most successful family of autonomous DNA transposons, being present in various plant and animal genomes, including humans. The introduction and co-evolution of mariners within host genomes imply a strict regulation of the transposon activity. Biochemical data accumulated during the past decade have led to a convergent picture of the transposition cycle of mariner elements, suggesting that mariner transposition does not rely on host-specific factors. This model does not account for differences of transposition efficiency in human cells between mariners. We thus wondered whether apparent similarities in transposition cycle could hide differences in the intrinsic parameters that control mariner transposition. Principal Findings We find that Mos1 transposase concentrations in excess to the Mos1 ends prevent the paired-end complex assembly. However, we observe that Mos1 transposition is not impaired by transposase high concentration, dismissing the idea that transposase over production plays an obligatory role in the down-regulation of mariner transposition. Our main finding is that the paired-end complex is formed in a cooperative way, regardless of the transposase concentration. We also show that an element framed by two identical ITRs (Inverted Terminal Repeats) is more efficient in driving transposition than an element framed by two different ITRs (i.e. the natural Mos1 copy), the latter being more sensitive to transposase concentration variations. Finally, we show that the current Mos1 ITRs correspond to the ancestral ones. Conclusions We provide new insights on intrinsic properties supporting the self-regulation of the Mos1 element. These properties (transposase specific activity, aggregation, ITR sequences, transposase concentration/transposon copy number ratio…) could have played a role in the dynamics of host-genomes invasion by Mos1, accounting (at least in part) for the current low copy number of Mos1 within host genomes.
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Affiliation(s)
- Jérôme Jaillet
- Innovation Moléculaire Thérapeutique, EA 6306 – Université François Rabelais, Parc Grandmont, Tours, France
| | - Murielle Genty
- Innovation Moléculaire Thérapeutique, EA 6306 – Université François Rabelais, Parc Grandmont, Tours, France
| | - Jeanne Cambefort
- Innovation Moléculaire Thérapeutique, EA 6306 – Université François Rabelais, Parc Grandmont, Tours, France
| | - Jacques-Deric Rouault
- Laboratoire Evolution, Génomes et Spéciation – CNRS UPR9034, Gif-sur-Yvette, France
- Université Paris-Sud 11, Orsay, France
| | - Corinne Augé-Gouillou
- Innovation Moléculaire Thérapeutique, EA 6306 – Université François Rabelais, Parc Grandmont, Tours, France
- * E-mail:
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13
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Carpentier G, Jaillet J, Pflieger A, Adet J, Renault S, Augé-Gouillou C. Transposase-transposase interactions in MOS1 complexes: a biochemical approach. J Mol Biol 2010; 405:892-908. [PMID: 21110982 DOI: 10.1016/j.jmb.2010.11.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/03/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022]
Abstract
Transposases are proteins that have assumed the mobility of class II transposable elements. In order to map the interfaces involved in transposase-transposase interactions, we have taken advantage of 12 transposase mutants that impair mariner transposase-transposase interactions taking place during transposition. Our data indicate that transposase-transposase interactions regulating Mos1 transposition are sophisticated and result from (i) active MOS1 dimerization through the first HTH of the N-terminal domain, which leads to inverted terminal repeat (ITR) binding; (ii) inactive dimerization carried by part of the C-terminal domain, which prevents ITR binding; and (iii) oligomerization. Inactive dimers are nonpermissive in organizing complexes that produce ITR binding, but the interfaces (or interactions) supplied in this state could play a role in the various rearrangements needed during transposition. Oligomerization is probably not due to a specific MOS1 domain, but rather the result of nonspecific interactions resulting from incorrect folding of the protein. Our data also suggest that the MOS1 catalytic domain is a main actor in the overall organization of MOS1, thus playing a role in MOS1 oligomerization. Finally, we propose that MOS1 behaves as predicted by the pre-equilibrium existing model, whereby proteins are found to exist simultaneously in populations with diverse conformations, monomers and active and inactive dimers for MOS1. We were able to identify several MOS1 mutants that modify this pre-existing equilibrium. According to their properties, some of these mutants will be useful tools to break down the remaining gaps in our understanding of mariner transposition.
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Affiliation(s)
- Guillaume Carpentier
- Université François Rabelais de Tours, GICC, CNRS, UMR 6239, UFR Sciences & Techniques, Parc Grandmont, 37200 Tours, France
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14
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Thomas X, Hedhili S, Beuf L, Demattéi MV, Laparra H, Khong GN, Breitler JC, Montandon F, Carnus E, Norre F, Burtin D, Gantet P, Bigot Y, Renault S. The mariner Mos1 transposase produced in tobacco is active in vitro. Genetica 2010; 138:519-30. [PMID: 19847655 DOI: 10.1007/s10709-009-9414-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 10/05/2009] [Indexed: 11/25/2022]
Abstract
The mariner-like transposon Mos1 is used for insertional mutagenesis and transgenesis in different animals (insects, nematodes), but has never been used in plants. In this paper, the transposition activity of Mos1 was tested in Nicotiana tabacum, but no transposition event was detected. In an attempt to understand the absence of in planta transposition, Mos1 transposase (MOS1) was produced and purified from transgenic tobacco (HMNtMOS1). HMNtMOS1 was able to perform all transposition reaction steps in vitro: binding to ITR, excision and integration of the same pseudo-transposon used in in planta transposition assays. The in vitro transposition reaction was not inhibited by tobacco nuclear proteins, and did not depend on the temperature used for plant growth. Several hypotheses are proposed that could explain the inhibition of HMNtMOS1 activity in planta.
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Affiliation(s)
- Xavier Thomas
- Université François Rabelais de Tours, GICC, Parc de Grandmont, 37200 Tours, France
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15
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Atkinson H, Chalmers R. Delivering the goods: viral and non-viral gene therapy systems and the inherent limits on cargo DNA and internal sequences. Genetica 2010; 138:485-98. [PMID: 20084428 DOI: 10.1007/s10709-009-9434-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 12/20/2009] [Indexed: 11/25/2022]
Abstract
Viruses have long been considered to be the most promising tools for human gene therapy. However, the initial enthusiasm for the use of viruses has been tarnished in the light of potentially fatal side effects. Transposons have a long history of use with bacteria in the laboratory and are now routinely applied to eukaryotic model organisms. Transposons show promise for applications in human genetic modification and should prove a useful addition to the gene therapy tool kit. Here we review the use of viruses and the limitations of current approaches to gene therapy, followed by a more detailed analysis of transposon length and the physical properties of internal sequences, which both affect transposition efficiency. As transposon length increases, transposition decreases: this phenomenon is known as length-dependence, and has implications for vector cargo capacity. Disruption of internal sequences, either via deletion of native DNA or insertion of exogenous DNA, may reduce or enhance genetic mobility. These effects may be related to host factor binding, essential spacer requirements or other influences yet to be elucidated. Length-dependence is a complex phenomenon driven not simply by the distance between the transposon ends, but by host proteins, the transposase and the properties of the DNA sequences encoded within the transposon.
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Affiliation(s)
- Helen Atkinson
- School of Biomedical Sciences, University of Nottingham, Queen's Medical Center, Nottingham NG7 2UH, UK
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16
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Claeys Bouuaert C, Chalmers R. Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage. Nucleic Acids Res 2009; 38:190-202. [PMID: 19858101 PMCID: PMC2800235 DOI: 10.1093/nar/gkp891] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Hsmar1 is a member of the mariner family of DNA transposons. Although widespread in nature, their molecular mechanism remains obscure. Many other cut-and-paste elements use a hairpin intermediate to cleave the two strands of DNA at each transposon end. However, this intermediate is absent in mariner, suggesting that these elements use a fundamentally different mechanism for second-strand cleavage. We have taken advantage of the faithful and efficient in vitro reaction provided by Hsmar1 to characterize the products and intermediates of transposition. We report different factors that particularly affect the reaction, which are the reaction pH and the transposase concentration. Kinetic analysis revealed that first-strand nicking and integration are rapid. The rate of the reaction is limited in part by the divalent metal ion-dependent assembly of a complex between transposase and the transposon end(s) prior to the first catalytic step. Second-strand cleavage is the rate-limiting catalytic step of the reaction. We discuss our data in light of a model for the two metal ion catalytic mechanism and propose that mariner excision involves a significant conformational change between first- and second-strand cleavage at each transposon end. Furthermore, this conformational change requires specific contacts between transposase and the flanking TA dinucleotide.
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Physical properties of DNA components affecting the transposition efficiency of the mariner Mos1 element. Mol Genet Genomics 2009; 282:531-46. [PMID: 19774400 DOI: 10.1007/s00438-009-0484-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
Abstract
Previous studies have shown that the transposase and the inverted terminal repeat (ITR) of the Mos1 mariner elements are suboptimal for transposition; and that hyperactive transposases and transposon with more efficient ITR configurations can be obtained by rational molecular engineering. In an attempt to determine the extent to which this element is suboptimal for transposition, we investigate here the impact of the three main DNA components on its transposition efficiency in bacteria and in vitro. We found that combinations of natural and synthetic ITRs obtained by systematic evolution of ligands by exponential enrichment did increase the transposition rate. We observed that when untranslated terminal regions were associated with their respective natural ITRs, they acted as transposition enhancers, probably via the early transposition steps. Finally, we demonstrated that the integrity of the Mos1 inner region was essential for transposition. These findings allowed us to propose prototypes of optimized Mos1 vectors, and to define the best sequence features of their associated marker cassettes. These vector prototypes were assayed in HeLa cells, in which Mos1 vectors had so far been found to be inactive. The results obtained revealed that using these prototypes does not circumvent this problem. However, such vectors can be expected to provide new tools for the use in genome engineering in systems such as Caenorhabditis elegans in which Mos1 is very active.
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18
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Germon S, Bouchet N, Casteret S, Carpentier G, Adet J, Bigot Y, Augé-Gouillou C. Mariner Mos1 transposase optimization by rational mutagenesis. Genetica 2009; 137:265-76. [PMID: 19533383 DOI: 10.1007/s10709-009-9375-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 05/25/2009] [Indexed: 11/28/2022]
Abstract
Mariner transposons are probably the most widespread transposable element family in animal genomes. To date, they are believed not to require species-specific host factors for transposition. Despite this, Mos1, one of the most-studied mariner elements (with Himar1), has been shown to be active in insects, but inactive in mammalian genomes. To circumvent this problem, one strategy consists of both enhancing the activity of the Mos1 transposase (MOS1), and making it insensitive to activity-altering post-translational modifications. Here, we report rational mutagenesis studies performed to obtain hyperactive and non-phosphorylable MOS1 variants. Transposition assays in bacteria have made it possible to isolate numerous hyperactive MOS1 variants. The best mutant combinations, named FETY and FET, are 60- and 800-fold more active than the wild-type MOS1 version, respectively. However, there are serious difficulties in using them, notably because they display severe cytotoxicity. On the other hand, three positions lying within the HTH motif, T88, S99, and S104 were found to be sensitive to phosphorylation. Our efforts to obtain active non-phosphorylable mutants at S99 and S104 positions were unsuccessful, as these residues, like the co-linear amino acids in their close vicinity, are critical for MOS1 activity. Even if host factors are not essential for transposition, our data demonstrate that the host machinery is essential in regulating MOS1 activity.
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Affiliation(s)
- Stéphanie Germon
- GICC, Université François Rabelais de Tours, 37200, Tours, France
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