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Optimization of Transposon Mutagenesis Methods in Pseudomonas antarctica. Microorganisms 2023; 11:microorganisms11010118. [PMID: 36677410 PMCID: PMC9864612 DOI: 10.3390/microorganisms11010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/14/2022] [Indexed: 01/04/2023] Open
Abstract
Pseudomonas is a widespread genus in various host and environmental niches. Pseudomonas exists even in extremely cold environments such as Antarctica. Pseudomonas antarctica is a psychrophilic bacterium isolated from Antarctica. P. antarctica is also known to produce antimicrobial substances. Although P. antarctica can provide insight into how bacteria have adapted to low temperatures and has significant potential for developing novel antimicrobial substances, progress in genetic and molecular studies has not been achieved. Transposon mutagenesis is a useful tool to screen genes of interest in bacteria. Therefore, we attempted for the first time in P. antarctica to generate transposon insertion mutants using the transfer of a conjugational plasmid encoding a transposon. To increase the yield of transposon insertion mutants, we optimized the methods, in terms of temperature for conjugation, the ratio of donor and recipient during conjugation, and the concentration of antibiotics. Here, we describe the optimized methods to successfully generate transposon insertion mutants in P. antarctica.
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2
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Jedlicka P, Lexa M, Vanat I, Hobza R, Kejnovsky E. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. Mob DNA 2019; 10:50. [PMID: 31871489 PMCID: PMC6911290 DOI: 10.1186/s13100-019-0186-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/31/2019] [Indexed: 01/08/2023] Open
Abstract
Background Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements. Results We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family ("autoinsertions"). Nested LTR retrotransposons were preferentially located in the 3'UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons. Conclusions We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
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Affiliation(s)
- Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Matej Lexa
- 2Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Ivan Vanat
- 2Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
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Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont PY, Berry D, Ram A, Scott B, Cox MP. Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genet 2018; 14:e1007467. [PMID: 30356280 PMCID: PMC6218096 DOI: 10.1371/journal.pgen.1007467] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/05/2018] [Accepted: 08/27/2018] [Indexed: 11/18/2022] Open
Abstract
Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.
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Affiliation(s)
- David J. Winter
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Austen R. D. Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Carolyn A. Young
- Noble Research Institute, LLC, Ardmore, Oklahoma, United States of America
| | - Ivan Liachko
- Phase Genomics Inc, Seattle, Washington, United States of America
| | - Christopher L. Schardl
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Pierre-Yves Dupont
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Daniel Berry
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Arvina Ram
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Murray P. Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- * E-mail:
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4
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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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5
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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.
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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.
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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.
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7
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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.
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Affiliation(s)
- Maryia Trubitsyna
- School of Biological Sciences, University of Edinburgh , The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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8
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Pflieger A, Waffo Teguo P, Papastamoulis Y, Chaignepain S, Subra F, Munir S, Delelis O, Lesbats P, Calmels C, Andreola ML, Merillon JM, Auge-Gouillou C, Parissi V. Natural stilbenoids isolated from grapevine exhibiting inhibitory effects against HIV-1 integrase and eukaryote MOS1 transposase in vitro activities. PLoS One 2013; 8:e81184. [PMID: 24312275 PMCID: PMC3842960 DOI: 10.1371/journal.pone.0081184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 10/18/2013] [Indexed: 01/07/2023] Open
Abstract
Polynucleotidyl transferases are enzymes involved in several DNA mobility mechanisms in prokaryotes and eukaryotes. Some of them such as retroviral integrases are crucial for pathogenous processes and are therefore good candidates for therapeutic approaches. To identify new therapeutic compounds and new tools for investigating the common functional features of these proteins, we addressed the inhibition properties of natural stilbenoids deriving from resveratrol on two models: the HIV-1 integrase and the eukaryote MOS-1 transposase. Two resveratrol dimers, leachianol F and G, were isolated for the first time in Vitis along with fourteen known stilbenoids: E-resveratrol, E-piceid, E-pterostilbene, E-piceatannol, (+)-E-ε-viniferin, E-ε-viniferinglucoside, E-scirpusin A, quadragularin A, ampelopsin A, pallidol, E-miyabenol C, E-vitisin B, hopeaphenol, and isohopeaphenol and were purified from stalks of Vitis vinifera (Vitaceae), and moracin M from stem bark of Milliciaexelsa (Moraceae). These compounds were tested in in vitro and in vivo assays reproducing the activity of both enzymes. Several molecules presented significant inhibition on both systems. Some of the molecules were found to be active against both proteins while others were specific for one of the two models. Comparison of the differential effects of the molecules suggested that the compounds could target specific intermediate nucleocomplexes of the reactions. Additionally E-pterostilbene was found active on the early lentiviral replication steps in lentiviruses transduced cells. Consequently, in addition to representing new original lead compounds for further modelling of new active agents against HIV-1 integrase, these molecules could be good tools for identifying such reaction intermediates in DNA mobility processes.
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Affiliation(s)
- Aude Pflieger
- Université François Rabelais de Tours, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Tours, France
| | - Pierre Waffo Teguo
- Groupe d'Etude des Substances Végétales à Activité Biologique, EA 3675 - UFR Pharmacie, Université Bordeaux Segalen, Institut des Sciences de la Vigne et du Vin (ISVV), Bordeaux, France
| | - Yorgos Papastamoulis
- Groupe d'Etude des Substances Végétales à Activité Biologique, EA 3675 - UFR Pharmacie, Université Bordeaux Segalen, Institut des Sciences de la Vigne et du Vin (ISVV), Bordeaux, France
| | - Stéphane Chaignepain
- Plateforme Protéome - Centre Génomique Fonctionnelle, UMR 5248 CBMN, Université Bordeaux Segalen, Bordeaux France
| | | | | | | | - Paul Lesbats
- Université François Rabelais de Tours, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Tours, France
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, Potters Bar, United Kingdom
| | - Christina Calmels
- Laboratoire MFP, UMR 5234-CNRS, Université Bordeaux Segalen, Bordeaux, France
| | - Marie-Line Andreola
- Laboratoire MFP, UMR 5234-CNRS, Université Bordeaux Segalen, Bordeaux, France
| | - Jean-Michel Merillon
- Groupe d'Etude des Substances Végétales à Activité Biologique, EA 3675 - UFR Pharmacie, Université Bordeaux Segalen, Institut des Sciences de la Vigne et du Vin (ISVV), Bordeaux, France
| | - Corinne Auge-Gouillou
- Université François Rabelais de Tours, EA 6306, UFR Sciences Pharmaceutiques, Parc Grandmont, Tours, France
| | - Vincent Parissi
- Laboratoire MFP, UMR 5234-CNRS, Université Bordeaux Segalen, Bordeaux, France
- * E-mail:
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9
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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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Wei L, Xiao M, An Z, Ma B, Mason AS, Qian W, Li J, Fu D. New insights into nested long terminal repeat retrotransposons in Brassica species. MOLECULAR PLANT 2013; 6:470-482. [PMID: 22930733 DOI: 10.1093/mp/sss081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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11
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Claeys Bouuaert C, Chalmers R. Hsmar1 transposition is sensitive to the topology of the transposon donor and the target. PLoS One 2013; 8:e53690. [PMID: 23341977 PMCID: PMC3544897 DOI: 10.1371/journal.pone.0053690] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/04/2012] [Indexed: 01/08/2023] Open
Abstract
Hsmar1 is a member of the Tc1-mariner superfamily of DNA transposons. These elements mobilize within the genome of their host by a cut-and-paste mechanism. We have exploited the in vitro reaction provided by Hsmar1 to investigate the effect of DNA supercoiling on transposon integration. We found that the topology of both the transposon and the target affect integration. Relaxed transposons have an integration defect that can be partially restored in the presence of elevated levels of negatively supercoiled target DNA. Negatively supercoiled DNA is a better target than nicked or positively supercoiled DNA, suggesting that underwinding of the DNA helix promotes target interactions. Like other Tc1-mariner elements, Hsmar1 integrates into 5′-TA dinucleotides. The direct vicinity of the target TA provides little sequence specificity for target interactions. However, transposition within a plasmid substrate was not random and some TA dinucleotides were targeted preferentially. The distribution of intramolecular target sites was not affected by DNA topology.
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12
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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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Lundin KE, Simonson OE, Moreno PMD, Zaghloul EM, Oprea II, Svahn MG, Smith CIE. Nanotechnology approaches for gene transfer. Genetica 2009; 137:47-56. [PMID: 19488829 DOI: 10.1007/s10709-009-9372-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/14/2009] [Indexed: 01/07/2023]
Abstract
In both basic research as well as experimental gene therapy the need to transfer genetic material into a cell is of vital importance. The cellular compartment, which is the target for the genetic material, depends upon application. An siRNA that mediates silencing is preferably delivered to the cytosol while a transgene would need to end up in the nucleus for successful transcription to occur. Furthermore the ability to regulate gene expression has grown substantially since the discovery of RNA interference. In such diverse fields as medical research and agricultural pest control, the capability to alter the genetic output has been a useful tool for pushing the scientific frontiers. This review is focused on nanotechnological approaches to assemble optimised structures of nucleic acid derivatives to facilitate gene delivery as well as promoting down regulation of endogenous genes.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden.
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