piggyBac-like elements in the tobacco budworm, Heliothis virescens (Fabricius)

Functional characterization of piggyBac-like elements from Nilaparvata lugens (Stål) (Hemiptera: Delphacidae)

PiggyBac is a transposable DNA element originally discovered in the cabbage looper moth (Trichoplusia ni). The T. ni piggyBac transposon can introduce exogenous fragments into a genome, constructing a transgenic organism. Nevertheless, the comprehensive analysis of endogenous piggyBac-like elements (PLEs) is important before using piggyBac, because they may influence the genetic stability of transgenic lines. Herein, we conducted a genome-wide analysis of PLEs in the brown planthopper (BPH) Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), and identified a total of 28 PLE sequences. All N. lugens piggyBac-like elements (NlPLEs) were present as multiple copies in the genome of BPH. Among the identified NlPLEs, NlPLE25 had the highest copy number and it was distributed on five chromosomes. The full length of NlPLE25 consisted of terminal inverted repeats and sub-terminal inverted repeats at both terminals, as well as a single open reading frame transposase encoding 546 amino acids. Furthermore, NlPLE25 transposase caused precise excision and transposition in cultured insect cells and also restored the original TTAA target sequence after excision. A cross-recognition between the NlPLE25 transposon and the piggyBac transposon was also revealed in this study. These findings provide useful information for the construction of transgenic insect lines.

Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase

The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.

Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication

The piggyBac transposable element was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and specificity compared to the other Class II elements, the diversity and evolution of this superfamily have been only partially analyzed. Two main types of elements can be distinguished: the piggyBac-like elements (PBLE) with terminal inverted repeats, untranslated region, and an open reading frame encoding a transposase, and the piggyBac-derived sequences (PGBD), containing a sequence derived from a piggyBac transposase, and which correspond to domesticated elements. To define the distribution, their structural diversity and phylogenetic relationships, analyses were conducted using known PBLE and PGBD sequences to scan databases. From this data mining, numerous new sequences were characterized (50 for PBLE and 396 for PGBD). Structural analyses suggest that four groups of PBLE can be defined according to the presence/absence of sub-terminal repeats. The transposase is characterized by highly variable catalytic domain and C-terminal region. There is no relationship between the structural groups and the phylogeny of these PBLE elements. The PGBD are clearly structured into nine main groups. A new group of domesticated elements is suspected in Neopterygii and the remaining eight previously described elements have been investigated in more detail. In all cases, these sequences are no longer transposable elements, the catalytic domain of the ancestral transposase is not always conserved, but they are under strong purifying selection. The phylogeny of both PBLE and PGBD suggests multiple and independent domestication events of PGBD from different PBLE ancestors.

Molecular characterization of the piggyBac-like element, a candidate marker for phylogenetic research of Chilo suppressalis (Walker) in China

Background

Transposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. Therefore, TEs have been crucial in the shaping of hosts’ current genomes. TEs can be utilized as genetic markers to study population genetic diversity. The rice stem borer Chilo suppressalis Walker is one of the most important insect pests of many subtropical and tropical paddy fields. This insect occurs in all the rice-growing areas in China. This research was carried out in order to find diversity between C. suppressalis field populations and detect the original settlement of C. suppressalis populations based on the piggyBac-like element (PLE). We also aim to provide insights into the evolution of PLEs in C. suppressalis and the phylogeography of C. suppressalis.

Results

Here we identify a new piggyBac-like element (PLE) in the rice stem borer Chilo suppressalis Walker, which is called CsuPLE1.1 (GenBank accession no. JX294476). CsuPLE1.1 is transcriptionally active. Additionally, the CsuPLE1.1 sequence varied slightly between field populations, with polymorphic indels (insertion/deletion) and hyper-variable regions including the identification of the 3′ region outside the open reading frame (ORF). CsuPLE1.1 insertion frequency varied between field populations. Sequences variation was found between CsuPLE1 copies and varied within and among field populations. Twenty-one different insertion sites for CsuPLE1 copies were identified with at least two insertion loci found in all populations.

Conclusions

Our results indicate that the initial invasion of CsuPLE1 into C. suppressalis occurred before C. suppressalis populations spread throughout China, and suggest that C. suppressalis populations have a common ancestor in China. Additionally, the lower reaches of the Yangtze River are probably the original settlement of C. suppressalis in China. Finally, the CsuPLE1 insertion site appears to be a candidate marker for phylogenetic research of C. suppressalis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12867-014-0028-y) contains supplementary material, which is available to authorized users.

Cloning and characterization of piggyBac-like elements in lepidopteran insects

PiggyBac-like elements (PLE) are widespread in variety of organisms, however, few of them are active or have an intact transposon structure. To further define the distribution PLEs in Lepidoptera, where the original active piggyBac IFP2 was discovered, and potentially isolate new functional elements, a survey for PLEs by PCR amplification and Southern dot blots was performed. Two new PLEs, AyPLE and AaPLE, were successfully isolated from the noctuid species, Agrotis ypsilon and Argyrogramma agnate, respectively. These elements were found to be closely related to each other by sequence similarity, and by sharing the same 16 bp inverted terminal repeat sequences. The AyPLE1.1 and AaPLE1.1 elements are structurally intact having characteristic TTAA target site duplications, inverted terminal repeats and intact open reading frames encoding putative transposases with the presumed piggyBac DDD domains, which are features consistent with autonomous functional transposons. Phylogenetic analysis revealed that AyPLE1.1 and AaPLE1.1 cluster with another noctuid species element, HaPLE1.1, suggesting a common ancestor for the three types of PLEs. This contributes to our understanding of the distribution and evolution of piggyBac in Lepidoptera.

piggyBac-like elements in the pink bollworm, Pectinophora gossypiella

A transgenic line of the pink bollworm, Pectinophora gossypiella, a key lepidopteran cotton pest, was generated previously using the piggyBac transposon IFP2 from Trichoplusia ni. Here we identified an endogenous piggyBac-like element (PLE), designated as PgPLE1, in the pink bollworm. A putatively intact copy of PgPLE1 (PgPLE1.1) presents the canonical features of PLE: inverted terminal repeats with three C/G residues at the extreme ends, inverted subterminal repeats, TTAA target site and an open reading frame encoding transposase with 68% similarity to IFP2. Vectorette PCR revealed large variation in the insertion sites of PgPLE1 amongst worldwide populations, indicating the potential mobility of PgPLE1. The PgPLE1 was undetectable in the genome of Pectinophora endema, implying the recent invasion of PgPLE1 after the divergence of these two closely related species.

Perspectives on the state of insect transgenics

Genetic transformation is a critical component to the fundamental genetic analysis of insect species and holds great promise for establishing strains that improve population control and behavior for practical application. This is especially so for insects that are disease vectors, many of which are currently subject to genomic sequence analysis, and intensive population control measures that must be improved for better efficacy and cost-effectiveness. Transposon-mediated germ-line transformation has been the ultimate goal for most fundamental and practical studies, and impressive strides have been made in recent development of transgene vector and marker systems for several mosquito species. This has resulted in rapid advances in functional genomic sequence analysis and new strategies for biological control based on conditional lethality. Importantly, advances have also been made in our ability to use these systems more effectively in terms of enhanced stability and targeting to specific genomic loci. Nevertheless, not all insects are currently amenable to germ-line transformation techniques, and thus advances in transient somatic expression and paratransgenesis have also been critical, if not preferable for some applications. Of particular importance is how this technology will be used for practical application. Early ideas for population replacement of indigenous pests with innocuous transgenic siblings by transposon-vector spread, may require reevaluation in terms of our current knowledge of the behavior of transposons currently available for transformation. The effective implementation of any control program using released transgenics, will also benefit from broadening the perspective of these control measures as being more mainstream than exotic.

Highly similar piggyBac elements in Bactrocera that share a common lineage with elements in noctuid moths

The piggyBac IFP2 transposable element, originally discovered in a Trichoplusia ni cell line, also exists as nearly identical elements in other noctuid lepidopterans, and in several species of the tephritid genus Bactrocera. To further define the distribution of piggyBacs in Bactrocera, and compare their relationship to sequences found in Lepidoptera, a survey by PCR amplification was performed in a range of Bactrocera species. Highly similar piggyBac sequences were found in all B. dorsalis complex species tested, as well as in species in the B. zonata and B. frauenfeldi complexes. All nucleotide sequences had > 94% identity to corresponding sequences in the T. ni IFP2 element, and > 88% identity among the sequences. Conserved primers did not amplify any distantly related sequences that have been found by computational searches in a wider range of insect and non-insect species. Notably, 55 nucleotide substitutions relative to IFP2 were common to all the Bactrocera sequences, 44 of which exist in piggyBacs previously sequenced from moths, with 17 resulting in amino acid substitutions. These piggyBac elements, that apparently traversed orders by horizontal transfer, probably arose from a lineage separate from IFP2 and the other known elements in T. ni. Implications for the presence of nearly identical piggyBacs, in widely distributed insects, to the applied use of piggyBac vectors are discussed.

Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum

The piggyBac transposable element (TE), originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of T. castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats (ITRs) or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16bp ITRs flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies.

piggyBac-like elements in cotton bollworm, Helicoverpa armigera (Hübner)

Two piggyBac-like elements (PLEs) were identified in the cotton bollworm, Helicoverpa armigera, and were designated as HaPLE1 and HaPLE2. HaPLE1 is flanked by 16 bp inverted terminal repeats (ITRs) and the duplicated TTAA tetranucleotide, and contains an open reading frame (ORF) of 1794 bp with the presumed DDD domain, indicating that this element may be an active autonomously mobile element. HaPLE2 was found with the same ITRs, but lacks the majority of an ORF-encoding transposase. Thus, this element was thought to be a non-autonomous element. Transposable element displays and distribution of the two PLEs in individuals from three different H. armigera populations suggest that transmobilization of HaPLE2 by the transposase of HaPLE1 may be likely, and mobilization of HaPLE1 might occur not only within the same individual, but also among different individuals. In addition, horizontal transfer was probably involved in the evolution of PLEs between H. armigera and Trichoplusia ni.

Excision and transposition of piggyBac transposable element in tobacco budworm embryos

The TTAA-specific lepidopteran transposon piggyBac has already proved useful as a gene-transfer vector for efficient transformation of a wide variety of insects. Transposable element excision and transposition assays are useful indicators of an element's ability to be mobilized in vivo and, thus, potentially serve as a transforming vector. Here, we report that this transposon is capable of excision and transposition in tobacco budworm embryos with relatively low frequency.