Intein-mediated Trans-splicing Research Articles

Strategies for all-at-once and stepwise selection of cells with multiple genetic manipulations

The genetic manipulation of cells followed by their selection is indispensable for cell biological research. Although antibiotics-resistant genes are commonly used as selection markers, optimization of the condition for each selective agent is required. Here we utilized split-inteins and the drug-selectable marker puromycin N-acetyltransferase (PAC) to develop a system that enables the selection of cells simultaneously or sequentially transfected with multiple genetic constructs, using only puromycin. The active PAC enzyme was reconstituted by intein-mediated trans-splicing at several inherent or engineered serine/cysteine residues. Multiple splitting and reconstitution of active PAC was readily achieved by selecting optimum division sites based on the cellular tolerance to various puromycin concentrations. To achieve the stepwise selection method, PAC-intein fragments were transduced into cells using a virus-like particle (VLP) composed of HIV-1 gag-pol and VSV-G. The PAC-intein-VLP successfully conferred sufficient PAC activity for puromycin selection, which was quickly diminished in the absence of the VLP. Our findings demonstrate a versatile strategy for establishing markers for all-at-once or stepwise selection of multiple genetic manipulations, which will be useful in many fields of biology.

Development of HBc virus-like particles as modular nanocarrier by intein-mediated trans-splicing

Hepatitis B virus core protein (HBc) spontaneously assembles as Virus-like particles (VLPs) in Escherichia coli (E. coli) which is extensively used as a nanocarrier to boost antigen immunogenicity. Genetic fusion of cargo protein with HBc occasionally forms inclusion bodies instead of properly assembled VLPs. To this end, we devised HBc VLPs as a modular nanocarrier for antigen delivery by intein-mediated trans-splicing (TS). We introduced split inteinC (intC) to the C-terminus of split HBc N-core to employ intein-mediated TS technology to HBc VLPs. Split HBc with the insertion of intC at N-core C-terminus (designated as HBc N-intC-C) existed in inclusion bodies. Interestingly, introduction of a soluble tag, gb1, to intC C-terminus remarkably improved the solubility of recombinant protein (named HBc N-intC-gb1-C). Moreover, newly designed recombinant spontaneously assembled as VLPs and endowed efficiently coupling two different model antigens onto HBc N-intC-gb1-C VLPs. Furthermore, model antigens delivered by HBc VLPs induced a dramatically enhanced antigen-specific immune responses. Antigen proteins mainly elicited Th2 IgG responses while antigens delivered by HBc VLPs steered Th1/Th2 balanced IgG responses. Taken together, intein-mediated TS was amenable to decorate HBc VLPs with antigens and showed good potential for antigen delivery.

Facile and Modular Pipeline for Protein-Specific Antibody Customization.

Antibodies are fundamental tools for basic science; however, high-quality antibodies suitable for multiple experimental applications are often inaccessible to research laboratories. To this end, a modular and low-cost pipeline for small-scale antibody customization is developed. First, soluble antigens are designed according to the secondary structure of a desired protein. Then, the antigens are efficiently displayed on a modular nanoplatform by intein-mediated trans-splicing (TS) that enables elicitation of high titers of protein-specific antibodies. After that, target antibodies are obtained by a modular HaloLink resin platform with antigens as the ligand that is devised by intein-mediated TS. Finally, purified antibodies show excellent properties in immunofluorescence, immunoprecipitation, and western blotting assays. Overall, these results suggest that the proposed pipeline is amenable to the generation of high-quality, research-grade antibodies and to aid in protein functional studies.

The application of gene splitting technique for controlling transgene flow in rice.

Controlling transgene flow in China is important, as this country is part of the center of origin of rice. A gene-splitting technique based on intein-mediated trans-splicing represents a new strategy for controlling transgene flow via biological measures. In this study, the G2-aroA gene which provides glyphosate tolerance was split into an N-terminal and a C-terminal region, which were then fused to intein N and intein C of the Ssp DnaE intein, ultimately forming EPSPSn:In and Ic:EPSPSc fusion genes, respectively. These fusion genes were subsequently transformed into the rice cultivar Zhonghua 11 via the Agrobacterium-mediated method. The two split gene fragments were then introduced into the same rice genome by genetic crossings. Glyphosate tolerance analysis revealed that the functional target protein was reconstituted by Ssp DnaE intein-mediated trans-splicing and that the resultant hybrid rice was glyphosate tolerant. The reassembly efficiency of the split gene fragments ranged from 67 to 91% at the molecular level, and 100% of the hybrid F1 progeny were glyphosate tolerant. Transgene flow experiments showed that when the split gene fragments are inserted into homologous chromosomes, the gene-splitting technique can completely avoid the escape of the target trait to the environment. This report is the first on the reassembly efficiency and effectiveness of transgene flow containment via gene splitting in rice. This study provides not only a new biological strategy for controlling rice transgene flow but also a new method for cultivating hybrid transgenic rice.

Versatile Functionalization of Ferritin Nanoparticles by Intein-Mediated Trans-Splicing for Antigen/Adjuvant Co-delivery.

Self-assembling protein nanoparticles are extensively and increasingly engineered to integrate adjuvants with antigens to elicit potent and long-term immunity due to uniform architecture, inherent biocompatibility, and excellent plasticity. However, functionalization of nanoparticles by surface tailoring has two common problems: (1) disassembly caused by loaded cargoes; and (2) an adjuvant that is inconvenient to co-deliver with an antigen by genetic fusion. Here, we report an intein-mediated trans-splicing approach that overcomes the detrimental effects of loaded proteins on ferritin nanoparticle stability and allows concurrent display of antigen and adjuvant in a facile, efficient, and site-specific manner. An immunization study with an epitope-based model antigen reveals that antigen and adjuvant co-delivery nanoparticles induce a more potent protective immunity than other formulations do. Our results demonstrate that protein engineering represents an intriguing approach for antigen/adjuvant co-delivery to potentiate antigen-associated immune responses.

Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity.

Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.

Development of an intein-mediated split-Cas9 system for gene therapy.

Using CRISPR/Cas9, it is possible to target virtually any gene in any organism. A major limitation to its application in gene therapy is the size of Cas9 (>4 kb), impeding its efficient delivery via recombinant adeno-associated virus (rAAV). Therefore, we developed a split–Cas9 system, bypassing the packaging limit using split-inteins. Each Cas9 half was fused to the corresponding split-intein moiety and, only upon co-expression, the intein-mediated trans-splicing occurs and the full Cas9 protein is reconstituted. We demonstrated that the nuclease activity of our split-intein system is comparable to wild-type Cas9, shown by a genome-integrated surrogate reporter and by targeting three different endogenous genes. An analogously designed split-Cas9D10A nickase version showed similar activity as Cas9D10A. Moreover, we showed that the double nick strategy increased the homologous directed recombination (HDR). In addition, we explored the possibility of delivering the repair template accommodated on the same dual-plasmid system, by transient transfection, showing an efficient HDR. Most importantly, we revealed for the first time that intein-mediated split–Cas9 can be packaged, delivered and its nuclease activity reconstituted efficiently, in cells via rAAV.

Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum.

The potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. This work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. Two fusion genes, EPSPSn-In and Ic-EPSPSc, were constructed and integrated into N. tabacum, using Agrobacterium tumefaciens-mediated transformation. EPSPSn-In encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) fused with the first 123 aa of the Ssp DnaE intein (In), whereas Ic-EPSPSc encodes the 36 C-terminal aa of the Ssp DnaE intein (Ic) fused to the rest of EPSPS C terminus peptide sequences. Both EPSPSn-In and Ic-EPSPSc constructs were introduced into the same N. tabacum genome by genetic crossing. Hybrids displayed resistance to the herbicide N-(phosphonomethyl)-glycine (glyphosate). Western blot analysis of protein extracts from hybrid plants identified full-length EPSPS. Furthermore, all hybrid seeds germinated and grew normally on glyphosate selective medium. The 6-8 leaf hybrid plants showed tolerance of 2000 ppm glyphosate in field spraying. These results indicated that functional EPSPS protein was reassembled in vivo by intein-mediated trans-splicing in 100% of plants. In order to evaluate the effect of the gene splitting technique for containment of transgene flow, backcrossing experiments were carried out between hybrids, in which the foreign genes EPSPSn-In and Ic-EPSPSc were inserted into different chromosomes, and non-transgenic plants NC89. Among the 2812 backcrossing progeny, about 25% (664 plantlets) displayed glyphosate resistance. These data indicated that transgene flow could be reduced by 75%. Overall, our findings provide a new and highly effective approach for biological containment of transgene flow.

The production of male-sterile wheat plants through split barnase expression is promoted by the insertion of introns and flexible peptide linkers

The successful use of transgenic plants depends on the strong and stable expression of the heterologous genes. In this study, three introns (PSK7-i1 and PSK7-i3 from Petunia and UBQ10-i1 from Arabidopsis) were tested for their ability to enhance the tapetum-specific expression of a split barnase transgene. We also analyzed the effects of introducing multiple copies of flexible peptide linkers that bridged the fusion domains of the assembled protein. The barnase fragments were assembled into a functional cytotoxin via intein-mediated trans-splicing, thus leading to male sterility through pollen ablation. A total of 14 constructs carrying different combinations of introns and peptide linkers were transformed into wheat plants. The resulting populations (between 41 and 301 independent plants for each construct) were assayed for trait formation. Depending on which construct was used, there was an increase of up to fivefold in the proportion of plants exhibiting male sterility compared to the populations harboring unmodified constructs. Furthermore, the average barnase copy number in the plants displaying male sterility could be reduced. The metabolic profiles of male-sterile transgenic plants and non-transgenic plants were compared using gas chromatography-mass spectrometry. The profiles generated from leaf tissues displayed no differences, thus corroborating the anther specificity of barnase expression. The technical advances achieved in this study may be a valuable contribution for future improvement of transgenic crop systems.

Native-sized spider silk proteins synthesized in planta via intein-based multimerization

The synthesis of native-sized proteins is a pre-requisite for exploiting the potential of spider silk as a bio-based material. The unique properties of spider silk, such as extraordinary tensile strength and elasticity, result from the highly repetitive nature of spider silk protein motifs. The present report describes the combination of spider silk flagelliform protein (FLAG) production in the endoplasmic reticulum of tobacco plant leaf cells with an intein-based posttranslational protein fusion technology. The repeated ligation of FLAG monomers resulted in the formation of large multimers. This method avoids the need for highly repetitive transgenes, which may result in a higher genetic and transcriptional stability. Here we show, for the first time, the production of synthetic, high molecular weight spider silk proteins larger than 250kDa based on the assembly of protein monomers via intein-mediated trans-splicing in planta. The resulting multimeric structures form microfibers, thereby demonstrating their great potential as a biomaterial.

Functional characterization of a naturally occurring trans-splicing intein from Synechococcus elongatus in a mammalian cell system

We have cloned and characterized a naturally occurring split mini-DnaE intein capable of protein trans-splicing in the cyanobacterium Synechococcus elongatus ( Sel DnaE intein). Sel DnaE intein is homologous to Synechocystis sp. PCC6803 ( Ssp) DnaE intein and Nostoc punctiforme ( Npu) DnaE intein, with a protein sequence identity of 60% for the N-terminal part of intein and 61% for the C-terminal part of intein. Our results demonstrate that the split reporters, split Renilla luciferase (Rluc) and enhanced green fluorescent protein (EGFP), can be reconstituted via Sel DnaE intein-mediated trans-splicing in mammalian cells. Based on Sel DnaE intein-mediated reconstitution of split Rluc, a human immunodeficiency virus (HIV) entry-mimicking cell–cell fusion assay was developed and validated as a useful assay for screening and pharmacologically characterizing potential HIV entry-targeting inhibitors.

Carbohydrate transporters of the bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS)

The glucose transporter of Escherichia coli couples translocation with phosphorylation of glucose. The IICB Glc subunit spans the membrane eight times. Split, circularly permuted and cyclized forms of IICB Glc are described. The split variant was 30 times more active when the two proteins were encoded by a dicistronic mRNA than by two genes. The stability and activity of circularly permuted forms was improved when they were expressed as fusion proteins with alkaline phosphatase. Cyclized IICB Glc and IIA Glc were produced in vivo by RecA intein-mediated trans-splicing. Purified, cyclized IIA Glc and IICB Glc had 100% and 30% of wild-type glucose phosphotransferase activity, respectively. Cyclized IIA Glc displayed increased stability against temperature and GuHCl-induced unfolding.