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4  structures 527  species 0  interactions 9660  sequences 383  architectures

Family: DDE_Tnp_1_7 (PF13843)

Summary: Transposase IS4

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This is the Wikipedia entry entitled "PiggyBac transposon system". More...

PiggyBac transposon system Edit Wikipedia article

PiggyBac Transposon System
Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
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PiggyBac transposable element-derived / Transposase IS4
Identifiers
SymbolDDE_Tnp_1_7, PGBD
PfamPF13843
InterProIPR029526

The PiggyBac (PB) transposon is a mobile genetic element that efficiently transposes between vectors and chromosomes via a "cut and paste" mechanism. During transposition, the PB transposase recognizes transposon-specific inverted terminal repeat sequences (ITRs) located on both ends of the transposon vector and efficiently moves the contents from the original sites and integrates them into TTAA chromosomal sites. The powerful activity of the PiggyBac transposon system enables genes of interest between the two ITRs in the PB vector to be easily mobilized into target genomes. The TTAA-specific transposon piggyBac is rapidly becoming a highly useful transposon for genetic engineering of a wide variety of species, particularly insects.[1] They were discovered in 1989 by Malcolm Fraser at the University of Notre Dame.[2][3]

Origin

The TTAA-specific, short repeat elements are a group of transposons that share similarity of structure and properties of movement. These elements were originally defined in the Cabbage Looper,[4] but appear to be common among other animals as well. They might prove to be useful tools for the transformation of insects. The original identification of these unusual TTAA-specific elements came through a somewhat unconventional route relative to most other Class II mobile elements. Spontaneous plaque morphology mutants of baculoviruses were observed to arise during propagation of these viruses in the TN-368 cell line. Genetic characterization of these mutations often revealed an associated insertion of host-derived DNAs, some of which appeared to be transposons.

Several different mobile host DNA insertions have been identified within the few-polyhedra (FP) locus of the baculoviruses AcMNPV and GmMNPV. The insertions most extensively studied are those now designated as tagalong (formerly TFP3) and piggyBac (formerly IFP2). These insertions exhibit a unique preference for TTAA target sites, whether inserting within the viral FP-locus or at other regions of the viral genome. Both of these elements are part of a larger family of TTAA-target site specific insertion elements that includes the T. ni derived piggyBac and tagalong elements, the Spodoptera frugiperda derived elements IFP1.6 and 290 bp insertion of Carstens, and the transposon-like insertion within the EcoRI-J,N region of Autographa californica nuclear polyhedrosis virus, whose origin is undefined.

More recently, analysis of sequences obtained from the human genome has revealed what appear to be 100 to 500 copies of a fossil element called LOOPER, which has sequence homology to piggyBac, terminates in 5' CCY....GGG 3', and apparently targets TTAA insertion sites. The LOOPER consensus sequence is on average 77% similar to individual sequences identified in the human genome, indicating it is at least 60 million years old. There are two other TTAA-specific fossil repeat elements, MER75 and MER85 (estimated at 2000 copies per genome) which appear to target TTAA insertion sites and terminate in 5' CCC....GGG 3'. Evidence is accumulating that suggests a superfamily of TTAA-specific mobile elements exists in a diversity of organisms, and that piggyBac-related sequences may be present in a diversity of species.[5]

Structure

The transposon consists of the transposase gene flanked by inverted terminal repeats.

The PB superfamily transposase consists of three domains, a variable N-terminal domain, a catalytic DDE triad domain and a C-terminal region with the nuclear localization signal.[6]

It has apparently been domesticated in a wide range of animals, losing the repeats and thus its mobility. The new functions these copies gain are sometimes significant enough to show signs of positive or purifying selection. In humans, these genes are:[7]

As a tool

Hyperactive versions of PiggyBac transposase are suited for genetic engineering purposes.[8] A version called mPB was created by optimizing codon usage for mammalian (mouse) with a 20x increase in activity,[9] and further mutation screening generated hyPB with 10x the activity of mPB.[10]

Nomenclature

These elements were first identified as insertions in Baculovirus mutants by Dr. Malcolm Fraser,[5] professor at the University of Notre Dame, and were originally named as IFP for Insertions in FP mutants. The name was then changed to TFP for Transposon in FP. Finally the name PiggyBac was adopted to keep the interest of the audience and to bear some resemblance to Drosophila gene nomenclature.

References

  1. ^ "Piggybac Transposon System".
  2. ^ Cary, L. C.; Goebel, M.; Corsaro, B. G.; Wang, H. G.; Rosen, E.; Fraser, M. J. (September 1989). "Transposon mutagenesis of baculoviruses: analysis of Trichoplusia ni transposon IFP2 insertions within the FP-locus of nuclear polyhedrosis viruses". Virology. 172 (1): 156–169. doi:10.1016/0042-6822(89)90117-7. ISSN 0042-6822. PMID 2549707.
  3. ^ Chen, Qiujia; Luo, Wentian; Veach, Ruth Ann; Hickman, Alison B.; Wilson, Matthew H.; Dyda, Fred (2020-07-10). "Structural basis of seamless excision and specific targeting by piggyBac transposase". Nature Communications. 11 (1): 3446. Bibcode:2020NatCo..11.3446C. doi:10.1038/s41467-020-17128-1. ISSN 2041-1723. PMC 7351741. PMID 32651359.
  4. ^ Fraser MJ, Smith GE, Summers MD (August 1983). "Acquisition of Host Cell DNA Sequences by Baculoviruses: Relationship Between Host DNA Insertions and FP Mutants of Autographa californica and Galleria mellonella Nuclear Polyhedrosis Viruses". Journal of Virology. 47 (2): 287–300. doi:10.1128/JVI.47.2.287-300.1983. PMC 255260. PMID 16789244.
  5. ^ a b Fraser, Mac. "PiggyBac". Mac Fraser. Archived from the original on 2012-01-20.
  6. ^ Sarkar A, Sim C, Hong YS, Hogan JR, Fraser MJ, Robertson HM, Collins FH (November 2003). "Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences". Molecular Genetics and Genomics. 270 (2): 173–80. doi:10.1007/s00438-003-0909-0. PMID 12955498. S2CID 16272611.
  7. ^ Bouallègue M, Rouault JD, Hua-Van A, Makni M, Capy P (February 2017). "Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication". Genome Biology and Evolution. 9 (2): 323–339. doi:10.1093/gbe/evw292. PMC 5381638. PMID 28082605.
  8. ^ Grabundzija I, Irgang M, Mátés L, Belay E, Matrai J, Gogol-Döring A, et al. (June 2010). "Comparative analysis of transposable element vector systems in human cells". Molecular Therapy. 18 (6): 1200–9. doi:10.1038/mt.2010.47. PMC 2889740. PMID 20372108.
  9. ^ Cadiñanos J, Bradley A (2007). "Generation of an inducible and optimized piggyBac transposon system". Nucleic Acids Research. 35 (12): e87. doi:10.1093/nar/gkm446. PMC 1919496. PMID 17576687.
  10. ^ Yusa K, Zhou L, Li MA, Bradley A, Craig NL (January 2011). "A hyperactive piggyBac transposase for mammalian applications". Proceedings of the National Academy of Sciences of the United States of America. 108 (4): 1531–6. Bibcode:2011PNAS..108.1531Y. doi:10.1073/pnas.1008322108. PMC 3029773. PMID 21205896.

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Transposase IS4 Provide feedback

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This tab holds annotation information from the InterPro database.

InterPro entry IPR029526

This entry represents a domain found in the human PiggyBac transposable element-derived proteins (PGBDs) and some uncharacterised proteins. Its function is not clear.

Domain organisation

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(26)
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(9660)
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(3413)
RP35
(6514)
RP55
(9380)
RP75
(11037)
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  Seed
(26)
Full
(9660)
Representative proteomes UniProt
(15532)
RP15
(3413)
RP35
(6514)
RP55
(9380)
RP75
(11037)
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  Seed
(26)
Full
(9660)
Representative proteomes UniProt
(15532)
RP15
(3413)
RP35
(6514)
RP55
(9380)
RP75
(11037)
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Curation and family details

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Seed source: Jackhmmer:Q96DM1
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 26
Number in full: 9660
Average length of the domain: 212.20 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 52.21 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 350
Family (HMM) version: 9
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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DDE_Tnp_1_7 domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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