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additional information
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additional information
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the transposase encoded by Acidiphilium binds to the archaeal sliding clamp (PCNA) of Methanosarcina and to the beta sliding clamp of Acidiphilium, Leptospirillum, and Escherichia coli
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additional information
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for examination of the transposition activity of recombinant Tgf2 TPase, microinjection is performed in blunt snout bream embryos at 1-2 cell stage. When donor plasmid pTgf2-EF1alpha-EGFP is co-injected with recombinant Tgf2 TPase protein, 74% of the embryos show almost ubiquitous and uniform expression of EGFP, while 31% control embryos by injected donor plasmid show only mosaic expression of EGFP. Four EGFP-positive blunt snout bream are sampled from the group coinjected with donor plasmid with recombinant Tgf2 TPase. An 8-bp direct repeat of target DNA at the integration site, the signature of hAT family transposons, is created adjacent to both ends of Tgf2 at the integration sites in all fish, indicating the recombinant Tgf2 TPase insertions occur by transposition
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additional information
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for examination of the transposition activity of recombinant Tgf2 TPase, microinjection is performed in blunt snout bream embryos at 1-2 cell stage. When donor plasmid pTgf2-EF1alpha-EGFP is co-injected with recombinant Tgf2 TPase protein, 74% of the embryos show almost ubiquitous and uniform expression of EGFP, while 31% control embryos by injected donor plasmid show only mosaic expression of EGFP. Four EGFP-positive blunt snout bream are sampled from the group coinjected with donor plasmid with recombinant Tgf2 TPase. An 8-bp direct repeat of target DNA at the integration site, the signature of hAT family transposons, is created adjacent to both ends of Tgf2 at the integration sites in all fish, indicating the recombinant Tgf2 TPase insertions occur by transposition
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additional information
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Tgf2 is an autonomously active vertebrate transposon that is efficient at gene-transfer in teleost fish. The N-terminal zinc finger domain of Tgf2 transposase contributes to DNA binding and to transposition activity. Proposed model for Tgf2 transposition, overview
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additional information
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Tgf2 is an autonomously active vertebrate transposon that is efficient at gene-transfer in teleost fish. The N-terminal zinc finger domain of Tgf2 transposase contributes to DNA binding and to transposition activity. Proposed model for Tgf2 transposition, overview
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additional information
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identification of multiple DNA binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats, these TIRs and other Foldback-like elements may provide the transposase with its binding specificity
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additional information
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the TnpA transposase precisely cleaves leaft and right ends (LE and RE) of a gene without leaving behind a scar sequence. Development of a simple and precise method for genome manipulation in Escherichia coli that alters the gene sequence without leaving foreign DNA in the chromosome. This strategy involves PCR amplification of a DNA cassette containing ISHp608-LE (left end)-antibiotic resistance gene-counterselection marker-ISHp608-RE (right end) by using primers containing extensions homologous to the adjacent regions of the target gene on the chromosome. The lambda Red-mediated recombination of the PCR product and antibiotic resistance screening results in transformants with a modified gene target. The ISHp608-LE-antibiotic resistance gene-counterselection marker-ISHp608-RE cassette can then be excised using a temperature sensitive plasmid expressing the TnpA transposase, which precisely cleaves ISHp608-LE and ISHp608-RE without leaving a scar sequence. For introduction of IS608 LE and RE into the gene of interest, lambda-Red recombination is utilized, which does not require in vitro manipulations such as restriction digestion, ligation or construction of a suicide vector. Diagram of plasmids containing selectable and excisable IS608 cassettes, overview
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additional information
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the TnpA transposase precisely cleaves leaft and right ends (LE and RE) of a gene without leaving behind a scar sequence. Development of a simple and precise method for genome manipulation in Escherichia coli that alters the gene sequence without leaving foreign DNA in the chromosome. This strategy involves PCR amplification of a DNA cassette containing ISHp608-LE (left end)-antibiotic resistance gene-counterselection marker-ISHp608-RE (right end) by using primers containing extensions homologous to the adjacent regions of the target gene on the chromosome. The lambda Red-mediated recombination of the PCR product and antibiotic resistance screening results in transformants with a modified gene target. The ISHp608-LE-antibiotic resistance gene-counterselection marker-ISHp608-RE cassette can then be excised using a temperature sensitive plasmid expressing the TnpA transposase, which precisely cleaves ISHp608-LE and ISHp608-RE without leaving a scar sequence. For introduction of IS608 LE and RE into the gene of interest, lambda-Red recombination is utilized, which does not require in vitro manipulations such as restriction digestion, ligation or construction of a suicide vector. Diagram of plasmids containing selectable and excisable IS608 cassettes, overview
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additional information
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H2K A/J muscle cells properly express full-length human DYSF following SB-mediated gene transfer. A duplicate of Spc5-12 (2xSpc5-12) regulatory sequence proves to be the most efficient in driving transgene expression in H2K A/J myoblasts. Corrected H2K A/J myoblasts can efficiently be transplanted into Scid/BLA/J mouse muscle
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additional information
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the sleeping beauty transposon DNA contains the gene to be inserted into the target DNA flanked by inverted terminal repeats (IR-DRleft and IR-DRright). Each inverted terminal repeat contains two, inner and outer, direct repeats (DRs). The DRs represent binding sites for the transposase enzyme. Sleeping beauty, SB, appears to be the most random in preferences for integration sites, requiring only a TA dinucleotide basepair. Binding mechanism, detailed overview
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additional information
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interaction analysis of full-length enzyme and of PAI subdomain with transposon DNA, overview
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additional information
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Sleeping Beauty transposase excision activity is quantified using a fluorescence-activated cell sorting (FACS)-based excision assay in HeLa cells, overall SB transposition activity is also detected in HeLa cells
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additional information
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The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. 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. Only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. The PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C. DNA-binding of folded and unfolded conformations of the PAI subdomain, overview
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additional information
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incubation of Kat1 and a 197 bp duplex corresponding to TIR-R with 48 bp from the transposon and 149 bp flanking DNA. First Kat1 cleaves the transposon end, generating a free 3' hydroxyl. Joining of one 3'-OH to the target generates a nicked plasmid or single end-joining (SEJ) product. If two 3'-OHs join the target at complementary positions on opposite strands, the plasmid is linearized generating a double end-joining (DEJ) product. Kat1 displays target joining, generating both SEJ- and DEJ-products
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additional information
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incubation of Kat1 with a 40 bp duplex representing imperfect inverted repeat TIR-R and including 30 bp from the transposon end and 10 bp from the flanking DNA. Kat1 cleaves the upper strand primarily at GTATA*C and to less extent at GTAT*AC. In the reaction using 3' end-labeling of the upper strand a product of 23 nts is observed. The products formed from the lower strand are hairpin-capped. No substrate: a 40 bp duplex representing imperfect inverted repeat TIR-L
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additional information
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the transposase encoded by Methanosarcina IS1634 binds to the sliding clamp of Acidiphilium beta
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additional information
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the transposase encoded by Methanosarcina IS1634 binds to the sliding clamp of Acidiphilium beta
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additional information
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formation of a Hermes transposase-DNA complex. Bipartite DNA recognition at hAT transposon ends and Hermes-DNA interactions within the transpososome. No protein-DNA interactions involving bp 12-16 of the TIR. The avidity provided by multiple sites of interaction allows a transposase to locate its transposon ends amidst a sea of chromosomal DNA, mechanism, overview. The enzyme possesses a RNaseH-like catalytic domain interrupted by a large [.alpha]-helical insertion domain, and an N-terminal intertwined dimerization domain. Together, these domains catalyze the chemical steps of DNA nicking, hairpin formation, and DNA strand transfer that comprise hAT transposition
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additional information
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formation of a Hermes transposase-DNA complex. Bipartite DNA recognition at hAT transposon ends and Hermes-DNA interactions within the transpososome. No protein-DNA interactions involving bp 12-16 of the TIR. The avidity provided by multiple sites of interaction allows a transposase to locate its transposon ends amidst a sea of chromosomal DNA, mechanism, overview. The enzyme possesses a RNaseH-like catalytic domain interrupted by a large [.alpha]-helical insertion domain, and an N-terminal intertwined dimerization domain. Together, these domains catalyze the chemical steps of DNA nicking, hairpin formation, and DNA strand transfer that comprise hAT transposition
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evolution
enzyme Hermes is a member of the hAT transposon superfamily, which has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species
evolution
IS1634-1 or gene APM_2825 in the sequenced 2007 culture might be a recent insertion in the chromosome
evolution
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protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called sectors, which are useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. 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. Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate. Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. 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. Hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. Mutations in sector, conserved and core residues usually have a destabilizing effect on the structure, effects of mutations on folding energies, and effect of protein-protein and protein-DNA interactions on transposition rate, overview
evolution
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Sleeping Beauty is a member of the mariner family of DNA transposons
evolution
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Sleeping Beauty is a prominent Tc1/mariner superfamily DNA transposon, mobilized by a transposase enzyme that catalyses DNA cleavage and integration at short specific sequences at the transposon ends
evolution
Tgf2 belongs to the hAT superfamily of transposons, Carassius auratus Tgf2 transposon is another autonomously active vertebrate hAT transposon
evolution
the enzyme belongs to the family of hAT transposases
evolution
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the enzyme belongs to the IS711 transposases
evolution
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the enzyme Galileo is a members of the P-element superfamily. In contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. Different subfamilies of Galileo exist, known as DbuzGalileo-K and DbuzGalileo-N,while DbuzGalileo-G denotes the subfamily of the synthetic element. The various Galileo subfamilies have TIRs of different lengths, but share significant sequence homologies at the tips of the elements where one might expect the transposase to bind. Comparison of THAP domain protein sequences and cross-reactivity between the subfamilies, overview
evolution
the enzyme is a member of the IS1634 family
evolution
the enzyme is a member of the IS1634 family
evolution
the goldfish Tgf2 transposon belongs to the Hobo/Activator/Tam3 (hAT) family. hAT elements are an ancient family of transposons and are abundant throughout a variety of species
evolution
the goldfish Tgf2 transposon belongs to the Hobo/Activator/Tam3 (hAT) family. hAT elements are an ancient family of transposons and are abundant throughout a variety of species. The NLS of Tgf2 transposase is identical to that of the Tol2 transposase, indicating the evolutionary importance of these sequences for NLS function
evolution
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the IS1341-type transposase is part of the widespread IS200/605 family, the most ancient family in the archaeal domain of life. Presence in Halobacterium salinarum strain NRC-1 of a probable sotRNA in a nonfunctional IS1341-type transposase gene, a truncated small 120 bp long pseudogene identical to OE5220R, suggests that sotRNA presence may somehow be the reason why these defective elements have not been lost from the genomes
evolution
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the SB transposon is the most active DNA transposon in vertebrate animal cells
evolution
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the IS1341-type transposase is part of the widespread IS200/605 family, the most ancient family in the archaeal domain of life. Presence in Halobacterium salinarum strain NRC-1 of a probable sotRNA in a nonfunctional IS1341-type transposase gene, a truncated small 120 bp long pseudogene identical to OE5220R, suggests that sotRNA presence may somehow be the reason why these defective elements have not been lost from the genomes
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evolution
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the enzyme belongs to the IS711 transposases
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evolution
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the enzyme is a member of the IS1634 family
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malfunction
P13988; P13989
a TnsC mutant defective in interaction with TnsB is defective for Tn7 transposition both in vitro and in vivo
malfunction
loss of the nuclear localization signal (NLS) domain results in expression in the cytoplasm but not in the nucleus
malfunction
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mutation of the GI-2 int gene and the wbk IS transposase in Rev 1, resulting in strain Rev2, maintains the S phenotype and shows lower dissociation levels. Combining the two mutations results in a strain (Rev 2) displaying a 95% decrease in dissociation with respect to parental Rev 1 under conditions promoting dissociation. Rev 2 does not differ from Rev 1 in the characteristics used in Rev 1 typing, i.e. growth rate, colonial size, reactivity with O-polysaccharide antibodies, phage, dye and antibiotic susceptibility. Strains Rev 2 and Rev 1 show similar attenuation and afforded similar protection in the mouse model of brucellosis vaccines. Deletions involving GI-2 and wbkA are the major causes of S-R dissociation of Bacillus melitensis strain Rev 1
malfunction
two truncated recombinant Tgf2 transposases with deletions in the N-terminal zinc finger domain, S1- and S2-Tgf2TPase, from goldfish cDNAs both losing their DNA-binding ability in vitro, specifically at the ends of Tgf2 transposon. Mutant S1- and S2-Tgf2TPases mediate gene transfer in the zebrafish genome in vivo at a significantly lower efficiency (21%-25%), in comparison with L-Tgf2TPase (56% efficiency). Compared to L-Tgf2TPase, truncated Tgf2TPases catalyze imprecise excisions with partial deletion of TE ends and/or plasmid backbone insertion/deletion. The gene integration into the zebrafish genome mediated by truncated Tgf2TPases is imperfect, creating incomplete 8-bp target site duplications at the insertion sites. N-terminal truncated Tgf2 transposases lose their DNA-binding activity
malfunction
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mutation of the GI-2 int gene and the wbk IS transposase in Rev 1, resulting in strain Rev2, maintains the S phenotype and shows lower dissociation levels. Combining the two mutations results in a strain (Rev 2) displaying a 95% decrease in dissociation with respect to parental Rev 1 under conditions promoting dissociation. Rev 2 does not differ from Rev 1 in the characteristics used in Rev 1 typing, i.e. growth rate, colonial size, reactivity with O-polysaccharide antibodies, phage, dye and antibiotic susceptibility. Strains Rev 2 and Rev 1 show similar attenuation and afforded similar protection in the mouse model of brucellosis vaccines. Deletions involving GI-2 and wbkA are the major causes of S-R dissociation of Bacillus melitensis strain Rev 1
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metabolism
P13988; P13989
DNA cut-and-paste transposons are discrete DNA segments that move from place to place within genomes via excision from a donor site by double-strand DNA breaks and insertion into a target site. These events are mediated by nucleoprotein complexes whose assembly regulates and coordinates breakage and joining. Multiple protein-protein and protein-DNA interactions are involved in assembly of these nucleoprotein complexes
metabolism
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Hfq represses IS10/Tn10 transposase expression through both antisense RNA-dependent and independent mechanisms. Hfq binds directly to the ribosome-binding site of IS10 transposase mRNA to inhibit translation, regulatory role of Hfq in the absence of the IS10 antisense RNA. The interaction is critical for the in vivo association of Hfq and RNA-IN. Hfq is a critical component of post-transcriptional regulatory networks in most bacteria
physiological function
IS30-like transposase in the archaeal kingdom may have relevance for horizontal gene transfer
physiological function
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Galileo is a DNA transposon responsible for the generation of several chromosomal inversions in Drosophila
physiological function
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IS10R encodes a functional transposase protein that catalyzes the chemical steps in Tn10/IS10 transposition. In addition to transposase mRNA (RNA-IN), IS10 encodes an asRNA (RNA-OUT) that represses transposase translation by blocking ribosome binding
physiological function
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Sleeping Beauty (SB) transposon is a nonviral gene transfer vector, already used in clinical trials. Full-length dysferlin transfer by the hyperactive sleeping beauty transposase restores dysferlin-deficient muscle, which can be used for nonviral gene delivery of full-length human dysferlin into muscle cells, along with a successful and efficient transplantation into into skeletal muscle to cure dysferlin-deficient muscular dystrophy by gene therapy. Dysferlin-deficient muscular dystrophy is a progressive disease characterized by muscle weakness and wasting caused by mutations in DYSF, a large, multiexonic gene that forms a coding sequence of 6.2 kb. The hyperactive SB system consists of a transposon DNA sequence and a transposase protein, SB100X, that can integrate DNA over 10 kb into the target genome
physiological function
Tgf2 is an autonomously active vertebrate transposon that is efficient at gene-transfer in teleost fish
physiological function
Tgf2 transposase can mediate efficient gene transfer in teleost fish
physiological function
P13988; P13989
the excision of transposon Tn7 from a donor site and its insertion into its preferred target site, attachment site attTn7, is mediated by four Tn7-encoded transposition proteins: TnsA, TnsB, TnsC, and TnsD. Transposition requires the assembly of a nucleoprotein complex containing all four Tns proteins and the DNA substrates, the donor site containing Tn7, and the preferred target site attTn7. TnsA and TnsB together form the heteromeric Tn7 transposase, and TnsD is a target-selecting protein that binds specifically to attTn7. TnsC is the key regulator of transposition, interacting with both the TnsAB transposase and TnsD-attTn7. TnsC interacts directly with TnsB via its C-terminus, identification of the specific region of TnsC involved in the TnsB-TnsC interaction during transposition. TnsC amino acids L475 and L476 play important roles in the interaction of the peptide TnsB with TnsC. Tn7 displays cis-acting target immunity, which blocks Tn7 insertion into a target DNA that already contains Tn7, the direct TnsB-TnsC interaction also mediates cis-acting Tn7 target immunity. TnsC also interacts directly with the target selector protein TnsD, TnsC and TnsD together form a complex with the transposon attachment site attTn7. Interaction analysis, overview
physiological function
the maize activator (Ac) transposase recognizes and excises Ac and Dissociation (Ds) elements and mediates insertion elsewhere in the genome. Insertions of Ds can cause disruption in gene sequences, involvement of Ac transposase in Ds movement
physiological function
all the catalytic steps of transposition occur within the context of a dimeric transpososome. Transposition is carried out by a single transposase dimer and double strand cleavage at the transposon ends is carried out by the same active site. The DDE/D active site can hydrolyze DNA strands of opposite polarity
physiological function
Q9PTV0; Q9PTV1
following microinjection using a zebrafish embryo test system, purified Tol2-M transposase protein readily catalyzes gene transfer in both somatic and germline tissues in vivo. Purified Tol2-M transposase can promote both in vitro cutting and pasting in a defined system lacking other cellular factors. A primary sequence of the target site is likely to play a critical role in Tol2 integration site selection
physiological function
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hAT transposase Buster forms filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions. GFP-laced rodlets in human cells form quickly in a dynamic process involving fusion and fission. Transposition declines after transposase concentrations become high enough for visible transposase rodlets to appear
physiological function
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Kat1 promotes joining of the transposon end into a target DNA molecule in vitro. Kat1 can form hexamers when complexed with DNA. Kat1 binds DNA non-specifically and the DNA interaction is dependent on a Zn2+-finger motif in its N-terminus
physiological function
the C-terminal cysteine-rich domain is essential for DNA breakage, joining and transposition. The region of amino acids 530-594 binds to specific DNA sequences in the left and right transposon ends, and to an additional internal site at the left end. The C-terminal cysteine-rich domain adopts the specific fold of the cross-brace zinc finger protein family and interacts with the 5'-TGCGT-3'/3'-ACGCA-5' motif of the 19-bp repeats
physiological function
The IS30-like DDE transposase of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames on the element significantly affects the level of excision. ICE6013 conjugatively transfers to different Staphylococcus aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. Excision is required for conjugation, and not all Staphylococcus aureus backgrounds are successful recipients. Transconjugants acquire the ability to transfer ICE6013. A significant integration site preference is observed for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration
physiological function
the RING-finger domain present toward the C-terminus of the transposase is vital for dimerization of this enzyme. The deletion of the RING-finger domain or the last seven residues of the RING-finger domain results in a monomeric protein that binds the terminal end of the transposon with nearly the same affinity as wild type piggyBac transposase. The monomeric constructs exhibit more than 2fold enhancement in the excision activity of the enzyme
physiological function
Tn5 transposase is capable of direct tagmentation of RNA/DNA hybrids in vitro. This activity can be used to replace the traditional library construction procedure of RNA sequencing
physiological function
Tn5 transposase preferentially targets near the entry-exit DNA regions within the nucleosome. Tn5 transposase minimally cleaves the dinucleosome without a linker DNA. A linker DNA length of 10-15 base-pairs is important for the efficient Tn5 integration reaction. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry-exit sites of the nucleosome
physiological function
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transposase Pgm is essential for DNA cleavage at ends of internal eliminated sequences. The DDD triad and the cysteine-rich domain are essential for Pgm activity and mutations in either domain have a dominant-negative effect in wild-type cells. A mutant lacking the cysteine-rich domain is partially active in the presence of limiting Pgm amounts, but inactive when Pgm is completely absent
physiological function
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IS30-like transposase in the archaeal kingdom may have relevance for horizontal gene transfer
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additional information
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deletion of the GI-2 integrase and the wbkA flanking transposase improves the stability of Brucella melitensis , Rev 1 mutant strain Rev2 is more effectively used as a vaccine compared to strain Rev 1, overview
additional information
increasing the strength of the interaction between beta sliding clamp and transposase results in a higher transposition rate in vivo. The interaction might determine the potential of insertion sequences to be mobilized in bacterial populations and also their ability to proliferate within chromosomes. Insertion sequences are the simplest mobile genetic elements as they often contain just a single gene encoding the transposase required for transposition
additional information
increasing the strength of the interaction between beta sliding clamp and transposase results in a higher transposition rate in vivo. The interaction might determine the potential of insertion sequences to be mobilized in bacterial populations and also their ability to proliferate within chromosomes. Insertion sequences are the simplest mobile genetic elements as they often contain just a single gene encoding the transposase required for transposition. Ability of the Acidiphilium IS1634 family member to proliferate in Escherichia coli, an organism in which this IS family has never been detected
additional information
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modeling of the SB transposase/transposon end/target DNA complex, overview
additional information
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temperature dependence of the PAI self-diffusion coefficient at pH 5.0 and pH 7.0 over the temperature range 5-35°C, pH 5.0, detection by NMR spectroscopy and intrinsic tyrosine fluorescence and rayleigh light scattering
additional information
the Tgf2 element is 4,720 bp long, and the full length Tgf2 transposase is 686 aa long, structure modeling, overview
additional information
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the Tgf2 element is 4,720 bp long, and the full length Tgf2 transposase is 686 aa long, structure modeling, overview
additional information
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deletion of the GI-2 integrase and the wbkA flanking transposase improves the stability of Brucella melitensis , Rev 1 mutant strain Rev2 is more effectively used as a vaccine compared to strain Rev 1, overview
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additional information
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increasing the strength of the interaction between beta sliding clamp and transposase results in a higher transposition rate in vivo. The interaction might determine the potential of insertion sequences to be mobilized in bacterial populations and also their ability to proliferate within chromosomes. Insertion sequences are the simplest mobile genetic elements as they often contain just a single gene encoding the transposase required for transposition
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monomer
1 * 64000, mutant lacking the RING-finger domain, calculated from sequence
octamer
a tetramer of dimers, the dimer is the fundamental catalytic unit
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x * 80000, about, recombinant His6-tagged enzyme, SDS-PAGE
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x * 90000, about, recombinant full-length enzyme, SDS-PAGE
dimer
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tertiary structure of SB transposase and protein core, overview
dimer
2 * 68000, wild-type, calulated from sequence
homodimer
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homodimer
2 * 16379, calculated from sequence
additional information
amino acid sequence analysis based on Phyre2 prediction suggests that Tgf2 transposase contains an N-terminal zinc finger BED domain (65-120 aa), a helix-turn-helix (HTH) binding structure (163-201 aa) and an RNase-H domain (211-683 aa) with an insertion domain (362-493 aa). The cNLS mapper predicts the presence of a monopartite NLS (656-670 aa) of 15 amino acids (LLFSPKRARLDTNNF) within the RNase-H domain at the C-terminus of Tgf2 transposase. This predicted NLS is located downstream of the DDE residues (D228, D295 and E648). Construction of a 3D model of the NLS and DDE signature of Tgf2 transposase, molecular architecture of full-length Tgf2 transposase overview
additional information
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amino acid sequence analysis based on Phyre2 prediction suggests that Tgf2 transposase contains an N-terminal zinc finger BED domain (65-120 aa), a helix-turn-helix (HTH) binding structure (163-201 aa) and an RNase-H domain (211-683 aa) with an insertion domain (362-493 aa). The cNLS mapper predicts the presence of a monopartite NLS (656-670 aa) of 15 amino acids (LLFSPKRARLDTNNF) within the RNase-H domain at the C-terminus of Tgf2 transposase. This predicted NLS is located downstream of the DDE residues (D228, D295 and E648). Construction of a 3D model of the NLS and DDE signature of Tgf2 transposase, molecular architecture of full-length Tgf2 transposase overview
additional information
the full length Tgf2 transposase (L-Tgf2TPase) consisted of several functional domains: an N-terminal BED zinc finger domain (Cx2Cx19Hx4H, 65-120 aa) involved in DNA binding, dimerization domain defined by amino acids 153-213, presumably involved in the formation of oligomers, as well as in DNA binding, and a C-terminus RNase-H domain comprises amino acids 211-683 presumably the core catalytic domain for DNA excision and transposition. Three conserved amino acids residues (DDE) are identified in the RNase-H catalytic domain of Tgf2 transposase, residues of the DDE (D228, D295 and E648) are extremely close in their spatial distribution. A CX2H motif within the RNase-H catalytic domain of Tgf2 transposase is also identified, which which functions as insertion domain for the correct positioning of the final E648 residue of the catalytic triad in the active site. A monopartite nuclear localization signal (NLS, 656-670 aa) is found at the C-terminus. Domain organization, modeling, overview
additional information
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the full length Tgf2 transposase (L-Tgf2TPase) consisted of several functional domains: an N-terminal BED zinc finger domain (Cx2Cx19Hx4H, 65-120 aa) involved in DNA binding, dimerization domain defined by amino acids 153-213, presumably involved in the formation of oligomers, as well as in DNA binding, and a C-terminus RNase-H domain comprises amino acids 211-683 presumably the core catalytic domain for DNA excision and transposition. Three conserved amino acids residues (DDE) are identified in the RNase-H catalytic domain of Tgf2 transposase, residues of the DDE (D228, D295 and E648) are extremely close in their spatial distribution. A CX2H motif within the RNase-H catalytic domain of Tgf2 transposase is also identified, which which functions as insertion domain for the correct positioning of the final E648 residue of the catalytic triad in the active site. A monopartite nuclear localization signal (NLS, 656-670 aa) is found at the C-terminus. Domain organization, modeling, overview
additional information
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in contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. The synaptic complex between Galileo ends may be a complicated structure containing higher-order multimers of the transposase
additional information
P13988; P13989
trypsin peptide mapping of TnsC
additional information
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domain structure of SB transposase enzyme, and solution conformation of full-length DNA-binding domain of SB transposase, [15N,1H]-HSQC spectra, overview. The DNA-binding domain is predicted to have two subdomains, PAI and RED, containing three alpha-helices. Residues 97-123 represent a nuclear localization signal (NLS). The catalytic domain contains three conserved catalytic residues, the DDE motif. NMR solution structure of the PAI subdomain, overview
additional information
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the SB100X catalytic domain assumes an RNaseH-fold with all catalytic residues assembled in the active site, it contains conserved alpha-helices and beta-strands, structure modeling of the SB transposase/transposon end/target DNA complex using crystal structure, PDB ID 3HOS, overview
additional information
while isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple non-specific DNA binding surfaces for target capture, bipartite DNA recognition at hAT transposon ends. Overall architecture of the Hermes transpososome, the nucleoprotein assembly that carries out DNA transposition, overview
additional information
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while isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple non-specific DNA binding surfaces for target capture, bipartite DNA recognition at hAT transposon ends. Overall architecture of the Hermes transpososome, the nucleoprotein assembly that carries out DNA transposition, overview
additional information
the C-terminal 7 residues of the RING-finger domain are critical for dimer formation
additional information
AcTPase is an 807aa protein and consists of three N-terminal nuclear localization signals (residues 44-206), a bipartite DNA binding domain (159-206), a catalytic core domain, and a highly conserved C-terminal dimerization domain (674-754). The catalytic core domain of AcTPase is thought to form a retroviral integrase-like fold
additional information
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AcTPase is an 807aa protein and consists of three N-terminal nuclear localization signals (residues 44-206), a bipartite DNA binding domain (159-206), a catalytic core domain, and a highly conserved C-terminal dimerization domain (674-754). The catalytic core domain of AcTPase is thought to form a retroviral integrase-like fold
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A174V
substitution close to the putative N-terminal DNA-binding domain of TnpA, reduces immunity by approximately sixfold. Transposition activity is comparable to that of wild-type
E740G
C-terminal substitutions within the predicted RNaseH fold, reduces immunity up to about12fold. Transposition activity is comparable to that of wild-type
S911R
C-terminal substitution adjacent to the predicted RNaseH fold, reduces immunity up to about 25fold. Transposition activity is comparable to that of wild-type
W24R
substitution within the putative N-terminal DNA-binding domain of TnpA, reduces immunity by approximately twofold. Transposition activity is comparable to that of wild-type
W24R/A174V/E740G
triple mutant is hyperactive in vivo, giving elevated levels of transposition into both permissive and immune targets
D228N/E648Q
site-directed mutagenesis
E54K/L372P
mutations lead to a hyperactive Tn5 transposase
K212R/P214R/G251R/A338V
i.e. Tn5-059, mutant displays a lowered GC insertion bias. Tn5-059 reduces AT dropout and increases uniformity of genome coverage in both bacterial genomes and human genome
E279D
-
a catalytically inactive transposase mutant
K339
-
site-directed mutagenesis, the mutant shows 20% reduced activity compared to the wild-type enzyme
N280
-
site-directed mutagenesis, the mutant shows 50% reduced activity compared to the wild-type enzyme
N280/K339
-
site-directed mutagenesis, almost catalytically inactive mutant
D310A
-
mutation in the catalytic DDE-motif, catalytically inactive
D377A
-
mutation in the catalytic DDE-motif, catalytically inactive
E895A
-
mutation in the catalytic DDE-motif, catalytically inactive
W576A
-
mutation predicted to be impaired for hairpin formation, mutant is active for DNA cleavage and supports wild type levels of mating-type switching
K569A
mutant exhibits a sharp decrease in its apparent binding affinity to LE1-35 substrate
R567A
mutant exhibits a sharp decrease in its apparent binding affinity to LE1-35 substrate
Y558A
mutant exhibits a decrease in its apparent binding affinity to LE1-35 substrate
C130A/C133A
-
mutant losES detectable DNA binding
C130A/C133A
-
mutations in the BED zinc-finger domain, result in an unspecific nuclease activity
C402A/H405A
-
mutant binds DNA normally and is critical for hairpin formation
C402A/H405A
-
mutant completely blocks hairpinning and switching, but still generates nicks in the DNA
additional information
compared with wild-type TnpA, Tn4430 TnpA mutants that are proficient in transposition but impaired in target immunity exhibit deregulated activities. They spontaneously assemble a unique asymmetric synaptic complex in which one TnpA molecule simultaneously binds two transposon ends. In this complex, TnpA is in an activated state competent for DNA cleavage and strand transfer. Wild-type TnpA can form this complex only on precleaved ends mimicking the initial step of transposition
additional information
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generation of strain Rev2, by Rev 1 double in-frame deletion mutation in ISBm-1 transposase and GI-2 phage integrase giving mutant strain Rev2, improves the stability of Brucella melitensis Rev 1 vaccine. The parental Rev 1 strain, the Rev 2 double mutant DELTAISBm1DELTAint strain, and the virulent Bacillus melitensis strain H38 (as a control) are inoculated
additional information
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generation of strain Rev2, by Rev 1 double in-frame deletion mutation in ISBm-1 transposase and GI-2 phage integrase giving mutant strain Rev2, improves the stability of Brucella melitensis Rev 1 vaccine. The parental Rev 1 strain, the Rev 2 double mutant DELTAISBm1DELTAint strain, and the virulent Bacillus melitensis strain H38 (as a control) are inoculated
-
additional information
construction of C-terminal deletion mutants, i.e. pEGFP-C1-Tgf2TPDELTA31C containing a 31-aa C-terminal deletion of Tgf2 transposase that included the predicted 15-amino acid NLS, pEGFP-C1-Tgf2TPDELTA120N containing a 120-aa N-terminal deletion of Tgf2 transposase, and pEGFP-C1-Tgf2TPDELTA16C containing a 16-aa C-terminal deletion of Tgf2 transposase. Loss of the nuclear localization signal (NLS) domain results in expression in the cytoplasm but not in the nucleus
additional information
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construction of C-terminal deletion mutants, i.e. pEGFP-C1-Tgf2TPDELTA31C containing a 31-aa C-terminal deletion of Tgf2 transposase that included the predicted 15-amino acid NLS, pEGFP-C1-Tgf2TPDELTA120N containing a 120-aa N-terminal deletion of Tgf2 transposase, and pEGFP-C1-Tgf2TPDELTA16C containing a 16-aa C-terminal deletion of Tgf2 transposase. Loss of the nuclear localization signal (NLS) domain results in expression in the cytoplasm but not in the nucleus
additional information
contruction of two truncated recombinant Tgf2 transposases with deletions in the N-terminal zinc finger domain, S1- and S2-Tgf2TPase, from goldfish cDNAs. Both truncated Tgf2TPases lost their DNA-binding ability in vitro, specifically at the ends of Tgf2 transposon than native L-Tgf2TPase. Mutant S1- and S2-Tgf2TPases mediate gene transfer in the zebrafish genome in vivo at a significantly lower efficiency (21%-25%), in comparison with L-Tgf2TPase (56% efficiency). Compared to L-Tgf2TPase, truncated Tgf2TPases catalyze imprecise excisions with partial deletion of TE ends and/or plasmid backbone insertion/deletion. The gene integration into the zebrafish genome mediated by truncated Tgf2TPases is imperfect, creating incomplete 8-bp target site duplications at the insertion sites
additional information
-
contruction of two truncated recombinant Tgf2 transposases with deletions in the N-terminal zinc finger domain, S1- and S2-Tgf2TPase, from goldfish cDNAs. Both truncated Tgf2TPases lost their DNA-binding ability in vitro, specifically at the ends of Tgf2 transposon than native L-Tgf2TPase. Mutant S1- and S2-Tgf2TPases mediate gene transfer in the zebrafish genome in vivo at a significantly lower efficiency (21%-25%), in comparison with L-Tgf2TPase (56% efficiency). Compared to L-Tgf2TPase, truncated Tgf2TPases catalyze imprecise excisions with partial deletion of TE ends and/or plasmid backbone insertion/deletion. The gene integration into the zebrafish genome mediated by truncated Tgf2TPases is imperfect, creating incomplete 8-bp target site duplications at the insertion sites
additional information
P13988; P13989
construction of diverse truncation mutants of TnsB, TnsC, and TnsD, and of double-mutant MBP-TnsC361555 P468A/L470A
additional information
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development of a simple and precise method for genome manipulation in Escherichia coli that alters the gene sequence without leaving foreign DNA in the chromosome. This strategy involves PCR amplification of a DNA cassette containing ISHp608-LE (left end)-antibiotic resistance gene-counterselection marker-ISHp608-RE (right end) by using primers containing extensions homologous to the adjacent regions of the target gene on the chromosome. The lambda Red-mediated recombination of the PCR product and antibiotic resistance screening results in transformants with a modified gene target. The ISHp608-LE-antibiotic resistance gene-counterselection marker-ISHp608-RE cassette can then be excised using a temperature sensitive plasmid expressing the TnpA transposase, which precisely cleaves ISHp608-LE and ISHp608-RE without leaving a scar sequence. For introduction of IS608 LE and RE into the gene of interest, lambda-Red recombination is utilized, which does not require in vitro manipulations such as restriction digestion, ligation or construction of a suicide vector. Diagram of plasmids containing selectable and excisable IS608 cassettes, overview
additional information
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development of a simple and precise method for genome manipulation in Escherichia coli that alters the gene sequence without leaving foreign DNA in the chromosome. This strategy involves PCR amplification of a DNA cassette containing ISHp608-LE (left end)-antibiotic resistance gene-counterselection marker-ISHp608-RE (right end) by using primers containing extensions homologous to the adjacent regions of the target gene on the chromosome. The lambda Red-mediated recombination of the PCR product and antibiotic resistance screening results in transformants with a modified gene target. The ISHp608-LE-antibiotic resistance gene-counterselection marker-ISHp608-RE cassette can then be excised using a temperature sensitive plasmid expressing the TnpA transposase, which precisely cleaves ISHp608-LE and ISHp608-RE without leaving a scar sequence. For introduction of IS608 LE and RE into the gene of interest, lambda-Red recombination is utilized, which does not require in vitro manipulations such as restriction digestion, ligation or construction of a suicide vector. Diagram of plasmids containing selectable and excisable IS608 cassettes, overview
-
additional information
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design of two additional hyperactive transposase variants using the enzyme crystal structure, evaluation of structure-based engineering of tailored SB transposases, overview
additional information
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introduction of mutation I212S to variant SB100X increases solubility. Additional substitution C176S generates a remarkably high solubility. Mutations C197S, C304S and C316S compromise protein solubility
additional information
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mutations of predicted catalytic residues abolish both DNA cleavage and strand-transfer. Kat1 mutants defective for cleavage in vitro are also defective for mating-type switching
additional information
introduction of three point mutations into the interface disrupting the octamer shows that the resulting dimers are catalytically active in vitro. Generation of dimers by deleting the helix and surrounding residues, HermesDELTA497-516, also leads to active dimers in vitro, that can catalyze all of the catalytic steps. Although Hermes dimers are hyperactive in vitro at low ionic strength, their activities are severely reduced under more physiologically relevant conditions. Hermes dimers are inactive in vivo
additional information
-
introduction of three point mutations into the interface disrupting the octamer shows that the resulting dimers are catalytically active in vitro. Generation of dimers by deleting the helix and surrounding residues, HermesDELTA497-516, also leads to active dimers in vitro, that can catalyze all of the catalytic steps. Although Hermes dimers are hyperactive in vitro at low ionic strength, their activities are severely reduced under more physiologically relevant conditions. Hermes dimers are inactive in vivo
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