Cloning Platform Research Articles

Novel specific TCRs targeting KRASG12V-related cancers.

e14528 Background: KRAS mutations act as oncogenic drivers in a variety of tumors, such as pancreatic, colorectal and lung cancer. Among these, the KRASG12V mutation, being one of the most common mutations, is associated with adverse outcomes in patients. KRAS has been regarded as an “undruggable” target, and no clinical trials targeting tumors carrying shared KRASG12V mutation have been initiated. Notably, KRASG12D specific TCR-T has shown high effectiveness, including the regression of metastases in patients with pancreatic cancer. Therefore, TCR-engineered T cells could be a promising strategy for the treatment of solid tumors harboring G12V mutation. Methods: We have developed an innovative approach to rapidly and sensitively identify natural TCRs from single T cell derived from patients using CorreGene’s Single T cell TCR Cloning platform, thus obviating the requirement for NGS sequencing and TCR gene synthesis. Additionally, natural TCRs can be refined with SMART-TCR system, utilizing T cell reporter cell lines to construct a high-throughput T-cell Display Platform for functional screening of TCRs. This system is meticulously designed to enrich TCRs with superior potency and specificity from a natural TCR mutation library. We performed a thorough assessment of each TCR identified, evaluating them across both in vitro and in vivo settings. Results: In the present study, we identified three natural TCRs from patients' TILs, designated as KVA11-N01, KVA11-N02 and KVA11-N04 respectively, that specifically recognized the HLA-A*11:01-restricted KRAS G12V epitope. KVA11-N01 exhibited lower affinity and potency, prompting us to develop an affinity-optimized variant, KVA11-M01-231, using the SMART-TCR system. For comparison, we used the murine TCR TRAV3-301/BV401, identified by NCI from HLA-A11:01 transgenic mice immunized with KRAS G12V7-16, as a benchmark. Three of our TCRs, including KVA11-N02, KVA11-N04 and the engineered KVA11-M01-231, outperformed TRAV3-301/BV401 in both in vitro and in vivo assays. These three TCRs exhibited excellent expression intensity and stability on T cells, and notably, their IFN-γ release potency surpassed that of TRAV3-3*01/BV4*01. Furthermore, in vivo experiments confirmed the significant tumor suppression efficacy of our TCRs in a tumor-bearing mouse model, showing enhanced tumor growth inhibition compared to TRAV3-301/BV401. TCRs from Corregene’s platform exhibited exceptional specificity, with no allo-reactivity, no reaction to KRASG12V-negative cell lines, and no off-target effects. Additionally, all our TCRs demonstrates favorable tolerance in mice during in vivo studies. Conclusions: TCRs via Corregene’s Single T cell TCR Cloning platform and SMART-TCR system showed significantly excellent anti-tumor activities with great specificity and offers a promising solution for the treatment of KRASG12V-related cancers.

Abstract 3194: Discovery of T cell receptor mimic antibody against MAGE-A4 with single B-cell cloning platform

Abstract Antibody therapeutics has been proven clinically against various cancer types and have achieved great success. Majority of the therapeutic antibodies target cell surface or extracellular proteins. Most of the tumor-specific antigens that control cell growth, proliferation, and death are intracellular, and traditional antibody therapies fail to recognize intracellular antigen targets. Such tumor specific intracellular targets consist of overexpressed self antigens, oncofetal protein, cancer testis antigens, viral protein and neo-antigens of mutant proteins. Recently, an emerging approach to target these neo-epitopes has been developed called T-cell receptor-like/TCR-mimic antibodies as they recognize similar epitopes to those of T cell receptors which target specific peptide-MHC complexes(pMHC). TCR mimic antibodies open a new avenue for targeting intracellular antigens yet there are lots of challenges for generating highly selective and potent TCR mimic antibodies. MAGE-A4, melanoma-associated antigen A4, is a member of the MAGE protein family of cancer-testis antigen (CTA). In healthy adult, MAGE-A4 expression is restricted to immune-privileged sites. But MAGE-A4 is widely expressed on many cancers such as lung cancer, head and neck squamous cell cancer, synovial sarcoma(SS), ovarian cancer, urothelial cancer and melanoma. The decapeptide GVYDGREHTV(amino acids 230-239) derived from MAGE-A4, can be presented by HLA-A*02:01 molecule, elicits specific cytotoxicity T cell response. Afami-cel, a genetically modified autologous T cell therapy against this pMHC complex, showed promising potency for patients with metastatic SS. So MAGE-A4/HLA-A*02:01 may be a good target for TCR mimic antibodies and cancer immunotherapy. In the present study, we utilized a newly established single cell cloning platform LyTARS to generate TCR mimic antibodies against HLA restricted MAGE-A4 peptide. Recombinant HLA-A*02:01 MAGE-A4 protein was used to immunize mice and plasma B cells from immunized mice were sorted and loaded onto LyTARS system. Clones that showed reactivity to recombinant HLA-A*02:01 MAGE-A4 but not to irrelevant pMHC (WT-1) were exported and sequenced. Purified antibodies were extensively characterized by the specificity, affinity, and potency by ADCC. Results demonstrated that the TCR mimic antibodies identified have sub-nano molar affinity by protein based ELISA, bind to peptide pulsed T2 cells that endogenously expressing HLA with nano-Molar apparent affinity. TCR mimic antibodies also demonstrated antibody dependent cell killing with the potency of sub-nanomolar. In summary, we have generated and extensively characterized a panel of high affinity and selective TCR mimic antibodies against HLA-A*02:01 MAGE-A4 using a newly established single cell cloning platform. Citation Format: Hao Cheng, You Wu, Tianfeng Shi, Yang Yu, Min Wang, Chenjun Jia, Wenfang Xin, Hu Liu, Teddy Yang, Danmei Yao. Discovery of T cell receptor mimic antibody against MAGE-A4 with single B-cell cloning platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3194.

Setup and Applications of Modular Protein Expression Toolboxes (MoPET) for Mammalian Systems.

The design and generation of an optimal protein expression construct is the first and essential step in the characterization of any protein of interest. However, the exchange and modification of the coding and/or noncoding elements to analyze their effect on protein function or generating the optimal result can be a tedious and time-consuming process using standard molecular biology cloning methods. To streamline the process to generate defined expression constructs or libraries of otherwise difficult to express proteins, the Modular Protein Expression Toolbox (MoPET) has been developed (Weber E, PloS One 12(5):e0176314, 2017). The system applies Golden Gate cloning as an assembly method and follows the standardized modular cloning (MoClo) principle (Weber E, PloS One 6(2):e16765, 2011). This cloning platform allows highly efficient DNA assembly of pre-defined, standardized functional DNA modules effecting protein expression with a focus on minimizing the cloning burden in coding regions. The original MoPET system consists of 53 defined DNA modules divided into eight functional main classes and can be flexibly expanded dependent on the need of the experimenter and expression host. However, already with a limited set of only 53 modules, 792,000 different constructs can be rationally designed or used to generate combinatorial expression optimization libraries. We provide here a detailed protocol for the (1) design and generation of level 0 basic parts, (2) generation of defined expressions constructs, and (3) generation of combinatorial expression libraries.

A Novel High-Throughput Method for Identifying T-Cell Receptor: Minor Histocompatibility Antigen Interactions in Mouse Models of Graft-Vs-Host Disease

Graft-vs-host disease is a complication of allogeneic stem cell transplant (alloSCT) in which donor T cells target alloantigens expressed by healthy recipient tissues. In major-histocompatibility-matched alloSCT, CD8-mediated GVHD is caused by T cell receptor (TCR) allorecognition of class-I presented minor histocompatibility antigens (miHAs). The vast majority of miHAs remain unknown between any given donor-recipient pairing. However, determining the identities of these miHAs and their cognate TCRs would prove useful towards the development of allografts that minimize GVHD yet preserve the therapeutic benefits of alloSCT. Here, we implement a high-throughput TCR cloning method, TCXpress, to screen alloreactive TCRs from a mouse model of MHC-matched alloSCT against putative miHA targets determined informatically. 129 (H-2 b) mice, which express the immunodominant miHA H60, were lethally irradiated and reconstituted with bone marrow and CD4 + and CD8 + T cells from B6 (H-2 b) donors. At day +10, recipient spleens were harvested and CD44 +PD-1 + donor CD8 + cells were single-cell sorted according to H-2Kb:H60 tetramer (Tet H60) staining into unknown miHA-reactive (Tet H60-) and control H60-reactive (Tet H60+) cohorts for TCR cloning using the TCXpress platform (BlueSphere Bio). Clonotyping was performed by sequencing the CDR3 region of TCRs. Putative miHAs were identified informatically by filtering non-synonymous variants between B6 and 129 reference exomes on predicted class I binding affinities. To interrogate TCR target specificity, Jurkat reporter cells, which express GFP and CD69 upon TCR activation, were transduced with selected alloreactive TCRs and reacted in a multiplexed fashion against a panel of B6WT3 antigen-presenting cells (H-2 b) transduced with tandem minigenes (TMG) of predicted miHAs. To test TCR reactivity against hematopoietically-expressed miHAs independent of our calling strategy, Jurkat reporters were also reacted against bone-marrow derived dendritic cells (BMDCs) from control B6 and 129 mice. From 3 recipient mice, 966 alloreactive TCRs were cloned and sequenced (735 Tet H60- and 231 Tet H60+) corresponding to 553 unique clonotypes (437 Tet H60- and 116 Tet H60+). Sixty-seven percent (N=668) of TCRs sequenced had clonotype occurrences of ≥ 2, indicating clonal expansion post-alloSCT, whereas there were no repeated clonotypes among donor B6 CD8 + cells pre-transplant (N=173 TCRs). A total of 47 Tet H60- TCR clones and 3 Tet H60+ control TCR clones were selected for transduction into Jurkat reporters and screened against a limited TMG library of 158 putative B6→129 miHAs, as well as H60. Expectedly, all TCR clonotypes isolated from the Tet H60+ sort gate reacted against H60-expressing B6WT3 cells and 129 BMDCs. From the Tet H60- TCRs, one clone was validated against another documented 129 miHA, H4, while an additional 4 clones were found to react against novel B6→129 miHAs (Serpinb8 and Cdt1). Interestingly, 2 highly over-represented clones were autoreactive against B6 tissues (B6WT3 cells and BMDCs), but not 129 BMDCs. In summary, we demonstrate the capacity of a novel TCR cloning platform to validate informatically-predicted miHAs and their cognate TCRs in a mouse model of GVHD. This approach may be readily adapted to develop new TCR:miHA therapeutics and gain a deeper understanding of GVH responses targeting miHAs.

PlayBack cloning: simple, reversible, cost-effective cloning for the combinatorial assembly of complex expression constructs.

With advancements in multicomponent molecular biological tools, the need for versatile, rapid and cost-effective cloning that enables successful combinatorial assembly of DNA plasmids of interest is becoming increasingly important. Unfortunately, current cloning platforms fall short regarding affordability, ease of combinatorial assembly and, above all, the ability to iteratively remove individual cassettes at will. Herein we construct, implement and make available a broad set of cloning vectors, called PlayBack vectors, that allow for the expression of several different constructs simultaneously under separate promoters. Overall, this system is substantially cheaper than other multicomponent cloning systems, has usability for a wide breadth of experimental paradigms and includes the novel feature of being able to selectively remove components of interest at will at any stage of the cloning platform.

FungalBraid 2.0: expanding the synthetic biology toolbox for the biotechnological exploitation of filamentous fungi.

Fungal synthetic biology is a rapidly expanding field that aims to optimize the biotechnological exploitation of fungi through the generation of standard, ready-to-use genetic elements, and universal syntax and rules for contributory use by the fungal research community. Recently, an increasing number of synthetic biology toolkits have been developed and applied to filamentous fungi, which highlights the relevance of these organisms in the biotechnology field. The FungalBraid (FB) modular cloning platform enables interchangeability of DNA parts with the GoldenBraid (GB) platform, which is designed for plants, and other systems that are compatible with the standard Golden Gate cloning and syntax, and uses binary pCAMBIA-derived vectors to allow Agrobacterium tumefaciens-mediated transformation of a wide range of fungal species. In this study, we have expanded the original FB catalog by adding 27 new DNA parts that were functionally validated in vivo. Among these are the resistance selection markers for the antibiotics phleomycin and terbinafine, as well as the uridine-auxotrophic marker pyr4. We also used a normalized luciferase reporter system to validate several promoters, such as PpkiA, P7760, Pef1α, and PafpB constitutive promoters, and PglaA, PamyB, and PxlnA inducible promoters. Additionally, the recently developed dCas9-regulated GB_SynP synthetic promoter collection for orthogonal CRISPR activation (CRISPRa) in plants has been adapted in fungi through the FB system. In general, the expansion of the FB catalog is of great interest to the scientific community since it increases the number of possible modular and interchangeable DNA assemblies, exponentially increasing the possibilities of studying, developing, and exploiting filamentous fungi.

Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense.

Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.

Synthetic Assembly DNA Cloning to Build Plasmids for Multiplexed Transgenic Selection, Counterselection or Any Other Genetic Strategies Using Drosophila melanogaster.

We recently described a drug-based selectable and counterselectable genetic platform for the animal model system Drosophila melanogaster, consisting of four resistance and two sensitivity markers that allow direct selection for, or counterselection against, a desired genotype. This platform eliminates the need to identify modified progeny by traditional laborious screening using the dominant eye and body color markers, white+ and yellow+ , respectively. The four resistance markers permit selection of animals using G418 sulfate, puromycin HCl, blasticidin S, or hygromycin B, while the two sensitivity markers allow counterselection of animals against ganciclovir or acyclovir and 5-fluorocytosine. The six markers can be used alone or in combination to perform co-selection, combination selection, and counterselection, as well as co-counterselection. To make this novel selection and counterselection genetics platform easily accessible to and rapidly implementable by the scientific community, we used a synthetic assembly DNA cloning platform, GoldenBraid 2.0 (GB2.0). GB2.0 relies on two Type IIs restriction enzymes that are alternatingly used during successive cloning steps to make increasingly complex genetic constructs. Here we describe, as an example, how to perform synthetic assembly DNA cloning using GB2.0 to build such complex plasmids via the assembly of both components of the binary LexA/LexA-Op overexpression system, a G418 sulfate-selectable LexA transactivator plasmid, and a blasticidin S-selectable LexA-Op responder plasmid. We demonstrate the functionality of these plasmids by including the expression pattern obtained after co-injection, followed by co-selection using G418 sulfate and blasticidin S, resulting in co-transgenesis of both plasmids. Protocols are provided on how to obtain, adapt, and clone DNA parts for synthetic assembly cloning after de novo DNA synthesis or PCR amplification of desired DNA parts and how to assemble those DNA parts into multipartite transcription units, followed by how to further assemble multiple transcription units into genetic constructs of increasing complexity to perform multiplexed transgenic selection and counterselection, or any other genetic strategies using Drosophila melanogaster. The protocols we present can be easily adapted to incorporate any of the six selectable and counterselectable markers, or any other, markers, to generate plasmids of unmatched complexity for various genetic applications. A protocol on how to generate transgenic animals using these synthetically assembled plasmids is described in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Obtaining and cloning a de novo-synthesized DNA part for synthetic assembly DNA cloning Basic Protocol 2: Obtaining and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Alternate Protocol: Obtaining, adapting, and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Basic Protocol 3: Synthetic assembly DNA cloning of individual DNA parts into a multipartite transcription unit Basic Protocol 4: Synthetic assembly DNA cloning of multiple transcription units into genetic constructs of increasing complexity.

FRAGLER: A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly.

Rapid and flexible plasmid construct generation at scale is one of the most limiting first steps in drug discovery projects. These hurdles can partly be overcome by adopting modular DNA design principles, automated sequence fragmentation, and plasmid assembly. To this end we have designed a robust, multimodule golden gate based cloning platform for construct generation with a wide range of applications. The assembly efficiency of the system was validated by splitting sfGFP and sfCherry3C cassettes and expressing them in E. coli followed by fluorometric assessment. To minimize timelines and cost for complex constructs, we developed a software tool named FRAGLER (FRAGment recycLER) that performs codon optimization, multiple sequence alignment, and automated generation of fragments for recycling. To highlight the flexibility and robustness of the platform, we (i) generated plasmids for SarsCoV2 protein reagents, (ii) automated and parallelized assemblies, and (iii) built modular libraries of chimeric antigen receptors (CARs) variants. Applying the new assembly framework, we have greatly streamlined plasmid construction and increased our capacity for rapid generation of complex plasmids.

A novel high-throughput single B-cell cloning platform for isolation and characterization of high-affinity and potent SARS-CoV-2 neutralizing antibodies

Monoclonal antibodies (mAbs) that are specific to SARS-CoV-2 can be useful in diagnosing, preventing, and treating the coronavirus (COVID-19) illness. Strategies for the high-throughput and rapid isolation of these potent neutralizing antibodies are critical toward the development of therapeutically targeting COVID-19 as well as other infectious diseases. In the present study, a single B-cell cloning method was used to screen the Wuhan-Hu-1 strain of SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing mAbs from patients’ blood samples. An RBD-specific antibody, SAR03, was discovered that showed high binding (ELISA and SPR) and neutralizing activity (competitive ELISA and pseudovirus-based reporter assay) against the Wuhan-Hu-1 strain of SARS-CoV-2. Mechanistic studies on human cells revealed that SAR03 competes with the ACE-2 receptor for binding with the RBD domain (S1 subunit) present in the spike protein of SARS-CoV-2. This study highlights the potential of the single B cell cloning method for the rapid and efficient screening of high-affinity and effective neutralizing antibodies for SARS-CoV-2 and other emerging infectious diseases.

Optimization of Vectors and Targeting Strategies Including GoldenBraid and Genome Editing Tools: GoldenBraid Assembly of Multiplex CRISPR /Cas12a Guide RNAs for Gene Editing in Nicotiana benthamiana.

New breeding techniques, especially CRISPR/Cas, could facilitate the expansion and diversification of molecular farming crops by speeding up the introduction of new traits that improve their value as biofactories. One of the main advantages of CRISPR/Cas is its ability to target multiple loci simultaneously, a key feature known as multiplexing. This characteristic is especially relevant for polyploid species, as it is the case of Nicotiana benthamiana and other species of the same genus widely used in molecular farming. Here, we describe in detail the making of a multiplex DNA construct for genome editing in N. benthamiana using the GoldenBraid modular cloning platform. In this case, the procedure is adapted for the requirements of LbCas12a (Lachnospiraceae bacterium Cas12a), a nuclease whose cloning strategy differs from that of the more often used SpCas9 (Streptococcus pyogenes Cas9) enzyme. LbCas12a-mediated edition has several advantages, as its high editing efficiency, described for different plant species, and its T/A-rich PAM sequence, which expands the range of genomic loci that can be targeted by site-specific nucleases. The protocol also includes recommendations for the selection of protospacer sequences and indications for the analysis of editing results.

Restriction-free cloning for molecular manipulation and augmented expression of banana bunchy top viral coat protein

The online version contains supplementary material available at 10.1007/s13205-021-03017-x.

The GB4.0 Platform, an All-In-One Tool for CRISPR/Cas-Based Multiplex Genome Engineering in Plants.

CRISPR/Cas ability to target several loci simultaneously (multiplexing) is a game-changer in plant breeding. Multiplexing not only accelerates trait pyramiding but also can unveil traits hidden by functional redundancy. Furthermore, multiplexing enhances dCas-based programmable gene expression and enables cascade-like gene regulation. However, the design and assembly of multiplex constructs comprising tandemly arrayed guide RNAs (gRNAs) requires scarless cloning and is still troublesome due to the presence of repetitive sequences, thus hampering a more widespread use. Here we present a comprehensive extension of the software-assisted cloning platform GoldenBraid (GB), in which, on top of its multigene cloning software, we integrate new tools for the Type IIS-based easy and rapid assembly of up to six tandemly-arrayed gRNAs with both Cas9 and Cas12a, using the gRNA-tRNA-spaced and the crRNA unspaced approaches, respectively. As stress tests for the new tools, we assembled and used for Agrobacterium-mediated stable transformation a 17 Cas9-gRNAs construct targeting a subset of the Squamosa-Promoter Binding Protein-Like (SPL) gene family in Nicotiana tabacum. The 14 selected genes are targets of miR156, thus potentially playing an important role in juvenile-to-adult and vegetative-to-reproductive phase transitions. With the 17 gRNAs construct we generated a collection of Cas9-free SPL edited T1 plants harboring up to 9 biallelic mutations and showing leaf juvenility and more branching. The functionality of GB-assembled dCas9 and dCas12a-based CRISPR/Cas activators and repressors using single and multiplexing gRNAs was validated using a Luciferase reporter with the Solanum lycopersicum Mtb promoter or the Agrobacterium tumefaciens nopaline synthase promoter in transient expression in Nicotiana benthamiana. With the incorporation of the new web-based tools and the accompanying collection of DNA parts, the GB4.0 genome edition turns an all-in-one open platform for plant genome engineering.

Lysinibacillus sphaericus III(3)7 and Plasmid Vector pMK4: New Challenges in Cloning Platforms

The acquisition and especially the maintenance of a plasmid usually brings a fitness cost that reduces the reproductive rate of the bacterial host; for strains like Lysinibacillus sphaericus III(3)7, which possesses important environmental properties, this alteration along with morphological changes and reduced sporulation rates may exert a negative effect on metabolic studies using plasmids as cloning platforms. The aim of this study is to approach the metabolic behavior of pMK4-bearing cells of L. sphaericus III(3)7 through the use of bioinformatic and in vitro analyses. An incompatibility model between the pMK4 vector and a predicted megaplasmid, pBsph, inside III(3)7 cells was constructed based on an incA region. Additionally, in vitro long-term plasmid stability was not found in plasmid-bearing cells. Alignments between replicons, mobile genetic elements and RNA-RNA interactions were assessed, pairwise alignment visualization, graphic models and morphological changes were evaluated by SEM. Metabolite analysis was done through HPLC coupled to a Q-TOF 6545, and electrospray ionization was used, finally, Aedes aegypti and Culex quinquefasciatus larvae were used for larvicidal activity assessment. Results found, a decreased growth rate, spore formation reduction and morphological changes, which supported the idea of metabolic cost exerted by pMK4. An incompatibility between pMK4 and pBsph appears to take place inside L. sphaericus III(3)7 cells, however, further in vitro studies are needed to confirm it.

A versatile plasmid architecture for mammalian synthetic biology (VAMSyB)

Current molecular cloning strategies generally lack inter-compatibility, are not strictly modular, or are not applicable to engineer multi-gene expression vectors for transient and stable integration. A standardized molecular cloning platform would advance research, for example, by promoting exchange of vectors between groups. Here, we present a versatile plasmid architecture for mammalian synthetic biology, which we designate VAMSyB, consisting of a three-tier vector family. Tier-1 is designed for easy engineering of fusion constructs, as well as easy swapping of genes and modules to tune the functionality of the vector. Tier-2 is designed for transient multi-gene expression, and is constructed by directly transferring the engineered expression cassettes from tier-1 vectors. Tier-3 enables stable integration into a mammalian host cell through viral transduction, transposons, or homology-directed recombination via CRISPR. This VAMSyB architecture is expected to have broad applicability in the field of mammalian synthetic biology. The VAMSyB collection of plasmids will be available through Addgene.

Fragment Exchange Plasmid Tools for CRISPR/Cas9-Mediated Gene Integration and Protease Production in Bacillus subtilis.

Since its discovery as part of the bacterial adaptative immune system, CRISPR/Cas has emerged as the most promising tool for targeted genome editing over the past few years. Various tools for genome editing in Bacillus subtilis have recently been developed, expanding and simplifying its potential development as an industrial species. A collection of vectors compatible with high-throughput (HTP) fragment exchange (FX) cloning for heterologous expression in Escherichia coli and Bacillus was previously developed. This vector catalogue was through this work supplemented with editing plasmids for genome engineering in Bacillus by adapting two CRISPR/Cas plasmids to the cloning technology. The customized tools allow versatile editing at any chosen genomic position (single-plasmid strategy) or at a fixed genomic locus (double-plasmid strategy). The single-plasmid strategy was validated by deleting the spoIIAC gene, which has an essential role in sporulation. Using the double-plasmid strategy, we demonstrate the quick transition from plasmid-based subtilisin expression to the stable integration of the gene into the amyE locus of a seven-protease-deficient KO7 strain. The newly engineered B. subtilis strain allowed the successful production of a functional enzyme. The customized tools provide improvements to the cloning procedure, should be useful for versatile genomic engineering, and contribute to a cloning platform for a quick transition from HTP enzyme expression to production through the fermentation of industrially relevant B. subtilis and related strains.IMPORTANCE We complemented a cloning platform with new editing plasmids that allow a quick transition from high-throughput cloning and the expression of new enzymes to the stable integration of genes for the production of enzymes through B. subtilis fermentation. We present two systems for the effective assembly cloning of any genome-editing cassette that shortens the engineering procedure to obtain the final editing constructs. The utility of the customized tools is demonstrated by disrupting Bacillus' capacity to sporulate and by introducing the stable expression of subtilisin. The tools should be useful to engineer B. subtilis strains by a variety of recombination events to ultimately improve the application range of this industry-relevant host.

Automating Cloning by Natural Transformation.

Affordable and automated cloning platforms are essential to many synthetic biology studies. However, the traditional E. coli-based cloning is a major bottleneck as it requires heat shock or electroporation implemented in the robotic workflows. To overcome this problem, we explored bacterial natural transformation for automatic DNA cloning and engineering. Recombinant plasmids are efficiently generated from Gibson or overlap extension PCR (OE-PCR) products by simply adding the DNA into Acinetobacter baylyi ADP1 cultures. No DNA purification, competence induction, or special equipment is required. Up to 10,000 colonies were obtained per microgram of DNA, while the number of false positive colonies was low. We cloned and engineered 21 biosynthetic gene clusters (BGCs) of various types, with length from 1.5 to 19 kb and GC content from 35% to 72%. One of them, a nucleoside BGC, showed antibacterial activity. Furthermore, the method was easily transferred to a low-cost benchtop robot with consistent cloning efficiency. Thus, this automatic natural transformation (ANT) cloning provides an easy, robust, and affordable platform for high throughput DNA engineering.

The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis.

Structural and biophysical characterization of molecular mechanisms of disease‐causing pathogens, such as Mycobacterium tuberculosis, often requires recombinant expression of large amounts highly pure protein. For the production of mycobacterial proteins, overexpression in the fast‐growing and non‐pathogenic species Mycobacterium smegmatis has several benefits over the standard Escherichia coli expression strains. However, unlike for E. coli, the range of expression vectors currently available is limited. Here we describe the development of the pMy vector series, a set of expression plasmids for recombinant production of single proteins and protein complexes in M. smegmatis. By incorporating an alternative selection marker, we show that these plasmids can also be used for co‐expression studies. All vectors in the pMy vector series are available in the Addgene repository (www.addgene.com).

Rapid Development of an Effective Newcastle Disease Virus Vaccine Candidate by Attenuation of a Genotype VII Velogenic Isolate Using a Simple Infectious Cloning System.

Genotype-matched vaccines provide ideal protection against infection caused by new Newcastle disease virus (NDV) genotypes or variants even in the vaccinated chickens. In this study, we report a protocol for attenuation and rapid development of a velogenic NDV isolate as an effective vaccine candidate, using a simple and reliable infectious cloning platform. Based on DHN3, a genotype VII velogenic NDV isolate, recombinant rDHN3 was rescued by co-transfection of plasmids expressing the genomic RNA, NDV proteins NP, P and L, and the T7 polymerase without using a helper virus. Subsequently, an attenuated strain rDHN3-mF was produced by substitution of residues from amino acids 112 to 117 in the DHN3 F protein with the corresponding sequence from the LaSota strain. Both rDHN3 and rDHN3-mF are genetically stable during propagation in cell culture and chicken embryos. Further characterization through determination of EID50, MDT and clinical assessments confirmed that rDHN3 is velogenic and rDHN3-mF lentogenic. Vaccination of one-week-old SPF chicks with inactivated rDHN3-mF produced much higher anti-DHN3 antibody response and better protection against live DHN3 challenge than did the commercial LaSota vaccine, providing 100% protection and much earlier viral clearance. This attenuated NDV isolate would merit further development into a vaccine product.

A unified multi-kingdom Golden Gate cloning platform

Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden Gate, one can efficiently assemble custom transcription units and piece units together to generate higher-order assemblies. Although Golden Gate cloning systems have been developed to assemble DNA plasmids required for experimental work in model species, they are not typically applicable to organisms from other kingdoms. Consequently, a typical molecular biology laboratory working across kingdoms must use multiple cloning strategies to assemble DNA constructs for experimental assays. To simplify the DNA assembly process, we developed a multi-kingdom (MK) Golden Gate assembly platform for experimental work in species from the kingdoms Fungi, Eubacteria, Protista, Plantae, and Animalia. Plasmid backbone and part overhangs are consistent across the platform, saving both time and resources in the laboratory. We demonstrate the functionality of the system by performing a variety of experiments across kingdoms including genome editing, fluorescence microscopy, and protein interaction assays. The versatile MK system therefore streamlines the assembly of modular DNA constructs for biological assays across a range of model organisms.