T-DNA binary vectors and systems

Boosting genome editing in plants with single transcript unit surrogate reporter systems

CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of editing events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are used to restore functional reporter genes after genome editing, including efficient single-strand annealing (SSA) for homologous recombination in STU-SR-SSA systems. STU-SR-base editor systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are shown to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.

Accelerated Long-Fragment Circular PCR for Genetic Manipulation of Plant Viruses in Unveiling Functional Genomics

Molecular cloning, a crucial prerequisite for engineering plasmid constructs intended for functional genomic studies, relies on successful restriction and ligation processes. However, the lack of unique restriction sites often hinders construct preparation, necessitating multiple modifications. Moreover, achieving the successful ligation of large plasmid constructs is frequently challenging. To address these limitations, we present a novel PCR strategy in this study, termed 'long-fragment circular-efficient PCR' (LC-PCR). This technique involves one or two rounds of PCR with an additional third-long primer that complements both ends of the newly synthesized strand of a plasmid construct. This results in self-circularization with a nick-gap in each newly formed strand. The LC-PCR technique was successfully employed to insert a partial sequence (210 nucleotides) of the phytoene desaturase gene from Nicotiana benthamiana and a full capsid protein gene (770 nucleotides) of a begomovirus (tomato leaf curl New Delhi virus) into a 16.4 kb infectious construct of a tobamovirus, cucumber green mottle mosaic virus (CGMMV), cloned in pCambia. This was done to develop the virus-induced gene silencing vector (VIGS) and an expression vector for a foreign protein in plants, respectively. Furthermore, the LC-PCR could be applied for the deletion of a large region (replicase enzyme) and the substitution of a single amino acid in the CGMMV genome. Various in planta assays of these constructs validate their biological functionality, highlighting the utility of the LC-PCR technique in deciphering plant-virus functional genomics. The LC-PCR is not only suitable for modifying plant viral genomes but also applicable to a wide range of plant, animal, and human gene engineering under in-vitro conditions. Additionally, the LC-PCR technique provides an alternative to expensive kits, enabling quick introduction of modifications in any part of the nucleotide within a couple of days. Thus, the LC-PCR proves to be a suitable 'all in one' technique for modifying large plasmid constructs through site-directed gene insertion, deletion, and mutation, eliminating the need for restriction and ligation.

Rice transformation treatments leave specific epigenome changes beyond tissue culture

During transgenic plant production, tissue culture often carries epigenetic, and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes toward transcriptional variations remain unknown. Here, the impact of individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were colocalized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is, way beyond the tissue culture effect.

Breakthrough in CRISPR/Cas system: Current and future directions and challenges

Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.

Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology

Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.

Development of constitutive and IPTG-inducible integron promoter-based expression systems for Escherichia coli and Agrobacterium tumefaciens

Broad host range (BHR) expression vector is a vital tool in molecular biology research and application. Currently, most of the plasmid vectors used in Agrobacterium spp. are binary vectors that are designed for plant transformation, and very few are designed for expressing transgenes in Agrobacterium spp. Class 1 integrons are common genetic elements that allow for the efficient capture and expression of antibiotic resistance genes, especially in Gram-negative bacteria. One of its compound promoters, PcS + P2, was used in this study and has been reported to be the strongest class 1 integron constitutive promoter; it is referred to as "integron promoter" (P int) henceforth. Herein, we created two versions of isopropyl-d-thiogalactopyranoside (IPTG)-inducible promoters by substituting and/or inserting lacO sequence(s) into P int. These inducible promoters, which possess different degrees of stringency and inducibility, were used to construct two broad host range expression vectors (pWK102 and pWK103) based on the versatile pGREEN system. This allows them to be stably maintained and replicated in both Escherichia coli and Agrobacterium tumefaciens. Functional validation of these vectors was performed by the expression of the reporter gene, superfolder green fluorescent protein (sfGFP), which was cloned downstream of these promoters. Due to the strong induction and tunable expression of a transgene located downstream to the inducible integron promoter, these vectors may be useful for heterologous gene expression in both E. coli and A. tumefaciens, thus facilitating recombinant protein production and genetic studies in Gram-negative bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03507-0.

Genetic analysis of DNA-damage tolerance pathways in Arabidopsis

Genetic analysis revealed a two-branch DNA-damage tolerance mechanism in Arabidopsis, namely translesion DNA synthesis and error-free lesion bypass, represented by Rev3 and Rad5a-Uev1C/D, respectively. DNA-damage tolerance (DDT) is a mechanism by which cells complete replication in the presence of replication-blocking lesions. In budding yeast, DDT is achieved through Rad6-Rad18-mediated monoubiquitination of proliferating cell nuclear antigen (PCNA), which promotes translesion DNA synthesis (TLS) and is followed by Ubc13-Mms2-Rad5 mediated K63-linked PCNA polyubiquitination that promotes error-free lesion bypass. Arabidopsis and other known plant genomes contain all of the above homologous genes except RAD18, and whether plants possess an intact DDT mechanism is unclear. In this study, we created Arabidopsis UEV1 (homologous to yeast MMS2) gene mutations and obtained two sets of double mutant lines Atuev1ab and Atuev1cd. It turned out that the Atuev1cd, but not the Atuev1ab mutant, was sensitive to DNA damage. Genetic analyses revealed that AtUEV1C/D and AtRAD5a function in the same pathway, while TLS represented by AtREV3 functions in a separate pathway in response to replication-blocking lesions. Furthermore, unlike budding yeast RAD5 that also functions in the TLS pathway, AtRAD5a is not required for TLS. Observations in this study collectively establish a two-branch DDT model in plants with similarity to and difference from the yeast DDT.

Production and Purification of Virus-Like Particles by Transient Expression in Plants

Transient expression in plants has become a useful production system for virus-like particle (VLP) expression. High yields and flexible approaches to assembling complex VLPs, combine with ease of scale-up and inexpensive reagents to provide an attractive method for recombinant protein expression in general. Plants have demonstrated excellent capacity for the assembly and production of protein cages for use in vaccine design and nanotechnology. Furthermore, numerous virus structures have now been determined using plant-expressed VLPs, showing the utility of this approach in structural virology. Transient protein expression in plants uses common microbiology techniques, leading to a straightforward transformation procedure that does not result in stable transgenesis. In this chapter, we aim to provide a generic protocol for transient expression of VLPs in Nicotiana benthamiana using soil-free plant cultivation and a simple vacuum infiltration procedure, along with methodology for purifying VLPs from plant leaves.

Multiplex CRISPR/Cas9-mediated genome editing to address drought tolerance in wheat

Genome editing tools have rapidly been adopted by plant scientists for crop improvement. Genome editing using a multiplex sgRNA-CRISPR/Cas9 genome editing system is a useful technique for crop improvement in monocot species. In this study, we utilized precise gene editing techniques to generate wheat 3'(2'), 5'-bisphosphate nucleotidase (TaSal1) mutants using a multiplex sgRNA-CRISPR/Cas9 genome editing system. Five active TaSal1 homologous genes were found in the genome of Giza168 in addition to another apparently inactive gene on chromosome 4A. Three gRNAs were designed and used to target exons 4, 5 and 7 of the five wheat TaSal1 genes. Among the 120 Giza168 transgenic plants, 41 lines exhibited mutations and produced heritable TaSal1 mutations in the M1 progeny and 5 lines were full 5 gene knock-outs. These mutant plants exhibit a rolled-leaf phenotype in young leaves and bended stems, but there were no significant changes in the internode length and width, leaf morphology, and stem shape. Anatomical and scanning electron microscope studies of the young leaves of mutated TaSal1 lines showed closed stomata, increased stomata width and increase in the size of the bulliform cells. Sal1 mutant seedlings germinated and grew better on media containing polyethylene glycol than wildtype seedlings. Our results indicate that the application of the multiplex sgRNA-CRISPR/Cas9 genome editing is efficient tool for mutating more multiple TaSal1 loci in hexaploid wheat.

Engineering the plastid and mitochondrial genomes of flowering plants

Engineering the plastid genome based on homologous recombination is well developed in a few model species. Homologous recombination is also the rule in mitochondria, but transformation of the mitochondrial genome has not been realized in the absence of selective markers. The application of transcription activator-like (TAL) effector-based tools brought about a dramatic change because they can be deployed from nuclear genes and targeted to plastids or mitochondria by an N-terminal targeting sequence. Recognition of the target site in the organellar genomes is ensured by the modular assembly of TALE repeats. In this paper, I review the applications of TAL effector nucleases and TAL effector cytidine deaminases for gene deletion, base editing and mutagenesis in plastids and mitochondria. I also review emerging technologies such as post-transcriptional RNA modification to regulate gene expression, Agrobacterium- and nanoparticle-mediated organellar genome transformation, and self-replicating organellar vectors as production platforms.

Co-silencing of ABA receptors (SlRCAR) reveals interactions between ABA and ethylene signaling during tomato fruit ripening

The ripening of fleshy fruits is highly dependent on the regulation of endogenous hormones, including ethylene, abscisic acid (ABA) and other phytohormones. However, the regulatory mechanism of ABA signaling and its interaction with ethylene signaling in fruit ripening are still unclear. In this study, multi-gene interference (RNAi) was applied to silence the ABA receptor genes in tomato for screening the specific receptors that mediate ABA signaling during fruit ripening. The results indicated that the ABA receptors, including SlRCAR9, SlRCAR12, SlRCAR11, and SlRCAR13, participate in the regulation of tomato fruit ripening. Comparative analysis showed that SlRCAR11 and SlRCAR13 play more important roles in mediating ABA signaling during tomato fruit ripening. Co-silencing of the four genes encoding these receptors could weaken the ethylene biosynthesis and signaling pathway at the early stage of tomato fruit ripening, leading to delayed fruit ripening. Meanwhile, co-silencing enhanced fruit firmness, and altered the shelf-life and susceptibility to Botrytis cinerea of the transgenic fruits. Furthermore, blocking ABA signaling did not affect the ability of ethylene to induce fruit ripening, whereas the block may inhibit the effectiveness of ABA in promoting fruit ripening. These results suggested that ABA signaling may be located upstream of ethylene signaling in regulating fruit ripening. Our findings provide a new insight into the complex regulatory network of phytohormones in regulating fruit ripening in tomato.

The effect of opine on matrix metalloproteinase expression in mice with breast cancer

Regarding the anti-inflammatory and anti-tumour effects of arginine and its derivatives, this study evaluates matrix metalloproteinase (MMPs) expression in an animal model of breast cancer following administration of octopine. In this study, 40 animals of Balb/C mice were divided into 5 groups: the healthy control, the cancer control, the cancer group receiving 50 mg of octopine, the cancer group receiving 100 mg of octopine and the cancer group receiving 150 mg of octopine for 3 weeks. 4T1 cell line was used to induce cancer. Biopsy specimens were enrolled from mice and MMP-1, MMP-3 and MMP-9 gene expression evaluated using real-time PCR, while these protein amounts were measured using immunohistochemistry and ELISA methods. Data were analysed using one-way ANOVA, Kruskal-Wallis and Mann-Whitney U tests (p < .05). The results showed that 100 mg octopine consumption had significant decreasing effect on MMP-9 expression (p = .02) in the treatment group compared with cancerous non-treated mice. Furthermore, results from immunohistochemistry and ELISA confirmed this effect, the protein amount of MMP-9 was significantly decreased in group treating with 100 mg octopine (.005). The use of octopine has a beneficial effect on reducing MMP-9 in mice breast cancer.

Development of a new recombineering system for Agrobacterium species

Discovery of new and efficient genetic engineering technologies for Agrobacterium will broaden the capacity for fundamental research on this genus and for its utilization as a transgenic vehicle. In this study, we aim to develop an efficient recombineering system for Agrobacterium species. We examined isolates of Agrobacterium and the closely related genus Rhizobium to identify pairs of ET-like recombinases that would aid in the recombineering of Agrobacterium species. Four pairs of ET-like recombinases, named RecETh1h2h3h4_AGROB6, RecETh1h2P3_RHI597, RecET_RHI145, and RecETh_RHI483, were identified in Agrobacterium tumefaciens str. B6, Rhizobium leguminosarum bv. trifolii WSM597, Rhizobium sp. LC145, and Rhizobium sp. Root483D2, respectively. Eight more candidate recombineering systems were generated by combining the new ET-like recombinases with Redγ or Pluγ. The PluγET_RHI145 system, RecETh1h2h3h4_AGROB6 system, and PluγETh_RHI483 system were determined to be the most efficient recombineering system for the type strains A. tumefaciens C58, A. tumefaciens EHA105, and R. rhizogenes NBCR13257, respectively. The utility of these systems was demonstrated by knocking out the istB and istA fusion gene in C58, the celI gene in EHA105, and the 3'-5' exonuclease gene and endoglucanase gene in NBCR13257. Our work provides an effective genetic manipulation strategy for Agrobacterium species. IMPORTANCE Agrobacterium is a powerful transgenic vehicle for the genetic manipulation of numerous plant and fungal species and even animal cells. In addition to improving the utility of Agrobacterium as a transgenic vehicle, genetic engineering tools are important for revealing crucial components that are functionally involved in T-DNA translocation events. This work developed an efficient and versatile recombineering system for Agrobacterium. Successful genome modification of Agrobacterium strains revealed that this new recombineering system could be used for the genetic engineering of Agrobacterium.

Modular evolution of secretion systems and virulence plasmids in a bacterial species complex

BACKGROUND

Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes.

RESULTS

We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins.

CONCLUSIONS

We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.

Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions

Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.

An Efficient Root Transformation System for Recalcitrant Vicia sativa

Common vetch (Vicia sativa) is a multi-purpose legume widely used in pasture and crop rotation systems. Vetch seeds have desirable nutritional characteristics and are often used to feed ruminant animals. Although transcriptomes are available for vetch, problems with genetic transformation and plant regeneration hinder functional gene studies in this legume species. Therefore, the aim of this study was to develop a simple, efficient and rapid hairy root transformation system for common vetch to facilitate functional gene analysis. At first, we infected the hypocotyls of 5-day-old in vitro or in vivo, soil-grown seedlings with Rhizobium rhizogenes K599 using a stabbing method and produced transgenic hairy roots after 24 days at 19 and 50% efficiency, respectively. We later improved the hairy root transformation in vitro by infecting different explants (seedling, hypocotyl-epicotyl, and shoot) with R. rhizogenes. We observed hairy root formation at the highest efficiency in shoot and hypocotyl-epicotyl explants with 100 and 93% efficiency, respectively. In both cases, an average of four hairy roots per explant were obtained, and about 73 and 91% of hairy roots from shoot and hypocotyl-epicotyl, respectively, showed stable expression of a co-transformed marker β-glucuronidase (GUS). In summary, we developed a rapid, highly efficient, hairy root transformation method by using R. rhizogenes on vetch explants, which could facilitate functional gene analysis in common vetch.

Production of Recombinant Proteins in Transgenic Tobacco Plants

Nicotiana tabacum (the tobacco plant ) has numerous advantages for molecular farming, including rapid growth, large biomass and the possibility of both cross- and self-fertilization. In addition, genetic transformation and tissue culture protocols for regeneration of transgenic plants are well-established. Here, we describe the production of transgenic tobacco using Agrobacterium tumefaciens and the analysis of recombinant proteins, either in crude plant extracts or after purification, by enzyme-linked immunosorbent assays, sodium dodecyl sulfate polyacrylamide gel electrophoresis with western blotting and surface plasmon resonance.

Production of Recombinant Proteins by Agrobacterium-Mediated Transient Expression

The agroinfiltration of plant tissue is a robust method that allows the rapid and transient expression of recombinant proteins. Using wild-type plants as biomass, agroinfiltration exploits the ability of plants to synthesize even complex multimeric proteins that require oxidative folding and/or post-translational modifications, while avoiding the expensive and time-consuming creation of stably transformed plant lines. Here we describe a generic method for the transient expression of recombinant proteins in Nicotiana benthamiana at the small to medium laboratory scale, including appropriate binary vectors, the design and cloning of expression constructs, the transformation, selection, and cultivation of recombinant Agrobacterium tumefaciens, the infiltration of plants using a syringe or vacuum device, and finally the extraction of recombinant proteins from plant tissues.

Generation of Stable Catharanthus roseus Hairy Root Lines with Agrobacterium rhizogenes

Agrobacterium rhizogenes is the bacterial agent that causes hairy root disease in dicots and is purposefully engineered for the development of transgenic hairy root cultures. Due to their genetic and metabolic stability, hairy root cultures offer advantages as a tissue culture system for investigating the function of transgenes and as a production platform for specialized metabolites or proteins. The process for generating hairy root cultures involves first infecting the explant with A. rhizogenes, excising and eliminating A. rhizogenes from the emerging hairy roots, selecting for transgenic hairy roots on plates containing the selective agent, confirming genomic integration of transgenes by PCR, and finally adapting the hairy roots in liquid media. Here we provide a detailed protocol for developing and maintaining transgenic hairy root cultures of our medicinal plant of interest, Catharanthus roseus.

Near-Complete Genome Assembly of the Grapevine Crown Gall Pathogen Allorhizobium vitis Strain K377

Here, we report the annotated, near-complete genome sequence of Allorhizobium vitis K377, a phytopathogenic Rhizobiales strain isolated from a grapevine in South Australia. The assembled genome sequence is 6.40 Mb long, with 5,855 predicted protein-coding sequences, 56 tRNAs, and 12 rRNAs, and contains ttuC (tartrate metabolism; chromosomal) and nopaline synthesis, uptake, and catabolic genes (tumor-inducing plasmid-encoded).

Biotechnological Insights on the Expression and Production of Antimicrobial Peptides in Plants

The emergence of drug-resistant pathogens poses a serious critical threat to global public health and requires immediate action. Antimicrobial peptides (AMPs) are a class of short peptides ubiquitously found in all living forms, including plants, insects, mammals, microorganisms and play a significant role in host innate immune system. These peptides are considered as promising candidates to treat microbial infections due to its distinct advantages over conventional antibiotics. Given their potent broad spectrum of antimicrobial action, several AMPs are currently being evaluated in preclinical/clinical trials. However, large quantities of highly purified AMPs are vital for basic research and clinical settings which is still a major bottleneck hindering its application. This can be overcome by genetic engineering approaches to produce sufficient amount of diverse peptides in heterologous host systems. Recently plants are considered as potential alternatives to conventional protein production systems such as microbial and mammalian platforms due to their unique advantages such as rapidity, scalability and safety. In addition, AMPs can also be utilized for development of novel approaches for plant protection thereby increasing the crop yield. Hence, in order to provide a spotlight for the expression of AMP in plants for both clinical or agricultural use, the present review presents the importance of AMPs and efforts aimed at producing recombinant AMPs in plants for molecular farming and plant protection so far.

Transient expression of recombinant proteins in plants using potato virus X based vectors

Plants become a promising biofactory for the large-scale production of recombinant proteins due to low cost, scalability, and safety. Agroinfiltration of plant leaves with a plant viral vector carrying a gene of interest is a rapid and efficient method for protein production in plants. Currently this method is in use for producing a wide range of proteins for multiple applications, including vaccine antigens, antibodies, and protein nanoparticles such as virus-like particles. A number of pharmaceutical proteins produced by transient expression are currently in clinical development. Here, we describe potato virus X based vector pEff-GFP enabling fast and high-level expression of recombinant proteins in Nicotiana benthamiana plants. The pEff vector provides green fluorescent protein expression levels of up to 30% of total soluble protein (about 1mg per g of fresh leaf tissue) and was successfully applied for the production of the immunogens of potential clinical interest.

Maize transformation: history, progress, and perspectives

Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.

Current progress and challenges in crop genetic transformation

Plant transformation remains the most sought-after technology for functional genomics and crop genetic improvement, especially for introducing specific new traits and to modify or recombine already existing traits. Along with many other agricultural technologies, the global production of genetically engineered crops has steadily grown since they were first introduced 25 years ago. Since the first transfer of DNA into plant cells using Agrobacterium tumefaciens, different transformation methods have enabled rapid advances in molecular breeding approaches to bring crop varieties with novel traits to the market that would be difficult or not possible to achieve with conventional breeding methods. Today, transformation to produce genetically engineered crops is the fastest and most widely adopted technology in agriculture. The rapidly increasing number of sequenced plant genomes and information from functional genomics data to understand gene function, together with novel gene cloning and tissue culture methods, is further accelerating crop improvement and trait development. These advances are welcome and needed to make crops more resilient to climate change and to secure their yield for feeding the increasing human population. Despite the success, transformation remains a bottleneck because many plant species and crop genotypes are recalcitrant to established tissue culture and regeneration conditions, or they show poor transformability. Improvements are possible using morphogenetic transcriptional regulators, but their broader applicability remains to be tested. Advances in genome editing techniques and direct, non-tissue culture-based transformation methods offer alternative approaches to enhance varietal development in other recalcitrant crops. Here, we review recent developments in plant transformation and regeneration, and discuss opportunities for new breeding technologies in agriculture.

Efficient CRISPR-mediated base editing in Agrobacterium spp

Agrobacterium spp. are important plant pathogens that are the causative agents of crown gall or hairy root disease. Their unique infection strategy depends on the delivery of part of their DNA to plant cells. Thanks to this capacity, these phytopathogens became a powerful and indispensable tool for plant genetic engineering and agricultural biotechnology. Although Agrobacterium spp. are standard tools for plant molecular biologists, current laboratory strains have remained unchanged for decades and functional gene analysis of Agrobacterium has been hampered by time-consuming mutation strategies. Here, we developed clustered regularly interspaced short palindromic repeats (CRISPR)-mediated base editing to enable the efficient introduction of targeted point mutations into the genomes of both Agrobacterium tumefaciens and Agrobacterium rhizogenes As an example, we generated EHA105 strains with loss-of-function mutations in recA, which were fully functional for maize (Zea mays) transformation and confirmed the importance of RolB and RolC for hairy root development by A. rhizogenes K599. Our method is highly effective in 9 of 10 colonies after transformation, with edits in at least 80% of the cells. The genomes of EHA105 and K599 were resequenced, and genome-wide off-target analysis was applied to investigate the edited strains after curing of the base editor plasmid. The off-targets present were characteristic of Cas9-independent off-targeting and point to TC motifs as activity hotspots of the cytidine deaminase used. We anticipate that CRISPR-mediated base editing is the start of "engineering the engineer," leading to improved Agrobacterium strains for more efficient plant transformation and gene editing.

Agrobacterium strains and strain improvement: Present and outlook

Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.

A Highly Efficient Agrobacterium-Mediated Method for Transient Gene Expression and Functional Studies in Multiple Plant Species

Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.

Unexpected conservation and global transmission of agrobacterial virulence plasmids

The accelerated evolution and spread of pathogens are threats to host species. Agrobacteria require an oncogenic Ti or Ri plasmid to transfer genes into plants and cause disease. We developed a strategy to characterize virulence plasmids and applied it to analyze hundreds of strains collected between 1927 and 2017, on six continents and from more than 50 host species. In consideration of prior evidence for prolific recombination, it was surprising that oncogenic plasmids are descended from a few conserved lineages. Characterization of a hierarchy of features that promote or constrain plasticity allowed inference of the evolutionary history across the plasmid lineages. We uncovered epidemiological patterns that highlight the importance of plasmid transmission in pathogen diversification as well as in long-term persistence and the global spread of disease.

Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology

Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.

Agrobacterium-mediated delivery of CRISPR/Cas reagents for genome editing in plants enters an era of ternary vector systems

Lack of appropriate methods for delivery of genome-editing reagents is a major barrier to CRISPR/Cas-mediated genome editing in plants. Agrobacterium-mediated genetic transformation (AMGT) is the preferred method of CRISPR/Cas reagent delivery, and researchers have recently made great improvements to this process. In this article, we review the development of AMGT and AMGT-based delivery of CRISPR/Cas reagents. We give an overview of the development of AMGT vectors including binary vector, superbinary vector, dual binary vector, and ternary vector systems. We also review the progress in Agrobacterium genomics and Agrobacterium genetic engineering for optimal strains. We focus in particular on the ternary vector system and the resources we developed. In summary, it is our opinion that Agrobacterium-mediated CRISPR/Cas genome editing in plants is entering an era of ternary vector systems, which are often integrated with morphogenic regulators. The new vectors described in this article are available from Addgene and/or MolecularCloud for sharing with academic investigators for noncommercial research.

Differentiations in Gene Content and Expression Response to Virulence Induction Between Two Agrobacterium Strains

Agrobacterium tumefaciens is important in biotechnology due to its ability to transform eukaryotic cells. Although the molecular mechanisms have been studied extensively, previous studies were focused on the model strain C58. Consequently, nearly all of the commonly used strains for biotechnology application were derived from C58 and share similar host ranges. To overcome this limitation, better understanding of the natural genetic variation could provide valuable insights. In this study, we conducted comparative analysis between C58 and 1D1609. These two strains belong to different genomospecies within the species complex and have distinct infectivity profiles. Genome comparisons revealed that each strain has >1,000 unique genes in addition to the 4,115 shared genes. Furthermore, the divergence in gene content and sequences vary among replicons. The circular chromosome is much more conserved compared to the linear chromosome. To identify the genes that may contribute to their differentiation in virulence, we compared the transcriptomes to screen for genes differentially expressed in response to the inducer acetosyringone. Based on the RNA-Seq results with three biological replicates, ∼100 differentially expressed genes were identified in each strain. Intriguingly, homologous genes with the same expression pattern account for <50% of these differentially expressed genes. This finding indicated that phenotypic variation may be partially explained by divergence in expression regulation. In summary, this study characterized the genomic and transcriptomic differences between two representative Agrobacterium strains. Moreover, the short list of differentially expressed genes are promising candidates for future characterization, which could improve our understanding of the genetic mechanisms for phenotypic divergence.

Differential efficiency of wild type rhizogenic strains for rol gene transformation of plants

Rhizogenic agrobacteria induce extensive root proliferation, in several economically valuable, dicotyledonous plant species, a phenomenon referred to as "hairy roots." Besides their pathogenic nature, agrobacteria have proven to be a valuable asset in biotechnology and molecular plant breeding. To assess the potential of frequently used rhizogenic strains, growth in yeast extract glucose broth and antibiotic resistance was analyzed. Growth curves were established for Arqua1, NCPPB2659, LMG150, LMG152, and ATCC15834; and regression analysis of the exponential growth phase resulted in a reliable and standardized method for preparation of a bacterial suspension for inoculation. Cell density did not correlate with the timing of hairy root emergence. The highest number of hairy roots was obtained with an inoculum of 1 × 10⁸ CFU ml^-1 for Arqua1, NCPPB2659, and LMG152. Cell density of ATCC15834 did not affect the number of hairy roots formed. The identity of the rhizogenic strains for plant transformation was verified in phylogenetic analysis using average nucleotide identity (ANI), which also provided insight in their genetic diversity within the Rhizobium taxon.

Genome Editing in Agriculture: Technical and Practical Considerations

The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.

Agrobacterium-mediated vacuum infiltration and floral dip transformation of rapid-cycling Brassica rapa

BACKGROUND

Rapid-cycling Brassica rapa (RCBr), also known as Wisconsin Fast Plants, are small robust plants with a short lifecycle that are widely used in biology teaching. RCBr have been used for decades but there are no published reports of RCBr genetic transformation. Agrobacterium-mediated vacuum infiltration has been used to transform pakchoi (Brassica rapa ssp. chinensis) and may be suitable for RCBr transformation. The floral dip transformation method, an improved version of vacuum infiltration, could make the procedure easier.

RESULTS

Based on previous findings from Arabidopsis and pakchoi, plants of three different ages were inoculated with Agrobacterium. Kanamycin selection was suboptimal with RCBr; a GFP screen was used to identify candidate transformants. RCBr floral bud dissection showed that only buds with a diameter less than 1 mm carried unsealed carpels, a key point of successful floral dip transformation. Plants across a wide range of inflorescence maturities but containing these immature buds were successfully transformed, at an overall rate of 0.1% (one per 1000 T₁ seeds). Transformation was successful using either vacuum infiltration or the floral dip method, as confirmed by PCR and Southern blot.

CONCLUSION

A genetic transformation system for RCBr was established in this study. This will promote development of new biology teaching tools as well as basic biology research on Brassica rapa.

Rapid and user-friendly open-source CRISPR/Cas9 system for single- or multi-site editing of tomato genome

CRISPR/Cas9-induced genome editing is a powerful tool for studying gene function in a variety of organisms, including plants. Using multi-sgRNAs to target one or more genes is helpful to improve the efficacy of gene editing and facilitate multi-gene editing. Here, we describe a CRISPR/Cas9 system which can be conveniently developed as a CRISPR kit. SgRNA expression cassettes can be rapidly generated by one-step PCR using our CRISPR kit. In our kit, there are two binary vectors pHNCas9 and pHNCas9HT. The binary vector pHNCas9 was constructed to allow to assemble up to eight sgRNA expression cassettes by one-step Golden Gate cloning. Another binary vector pHNCas9HT can be used to generate a large number of single target constructs by directly transforming ligation reactions products into A. tumefaciens without several procedures, such as PCR and plasmid extraction. The two binary vectors are designed according to the principles of standard BioBrick assembly to be used as an open-source tool. For example, we used BioBrick as a visual T-DNA tag. We also developed a primer design aid to complement the system. With this primer design aid, researchers can rapidly obtain primers and GC content, and sgRNA sequence of target site. Our CRISPR/Cas9 system can perform single- and multi-site editing and multiple gene editing to produce various types of mutations in tomato. This rapid and user-friendly CRISPR/Cas9 system for tomato can be potentially used for mutagenesis of important crop species for genetic improvement and is suitable for research into the function of genes.

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

BACKGROUND

Despite wheat being a worldwide staple, it is still considered the most difficult to transform out of the main cereal crops. Therefore, for the wheat research community, a freely available and effective wheat transformation system is still greatly needed.

RESULTS

We have developed and optimised a reproducible Agrobacterium-mediated transformation system for the spring wheat cv 'Fielder' that yields transformation efficiencies of up to 25%. We report on some of the important factors that influence transformation efficiencies. In particular, these include donor plant health, stage of the donor material, pre-treatment by centrifugation, vector type and selection cassette. Transgene copy number data for independent plants regenerated from the same original immature embryo suggests that multiple transgenic events arise from single immature embryos, therefore, actual efficiencies might be even higher than those reported.

CONCLUSION

We reported here a high-throughput, highly efficient and repeatable transformation system for wheat and this system has been used successfully to introduce genes of interest, for RNAi, over-expression and for CRISPR-Cas9 based genome editing.

Agrobacterium-mediated horizontal gene transfer: Mechanism, biotechnological application, potential risk and forestalling strategy

The extraordinary capacity of Agrobacterium to transfer its genetic material to host cell makes it evolve from phytopathogen to a powerful transgenic vector. Agrobacterium-mediated stable transformation is widely used as the preferred method to create transgenic plants for molecular plant biology research and crop breeding. Recent years, both mechanism and application of Agrobacterium-mediated horizontal gene transfer have made significant progresses, especially Agrobacterium-mediated transient transformation was developed for plant biotechnology industry to produce recombinant proteins. Agrobacterium strains are almost used and saved not only by each of microbiology and molecular plant labs, but also by many of plant biotechnology manufacturers. Agrobacterium is able to transfer its genetic material to a broad range of hosts, including plant and non-plant hosts. As a consequence, the concern of environmental risk associated with the accidental release of genetically modified Agrobacterium arises. In this article, we outline the recent progress in the molecular mechanism of Agrobacterium-meditated gene transfer, focus on the application of Agrobacterium-mediated horizontal gene transfer, and review the potential risk associated with Agrobacterium-meditated gene transfer. Based on the comparison between the infecting process of Agrobacterium as a pathogen and the transgenic process of Agrobacterium as a transgenic vector, we realize that chemotaxis is the distinct difference between these two biological processes and thus discuss the possible role of chemotaxis in forestalling the potential risk of Agrobacterium-meditated horizontal gene transfer to non-target plant species.

Presence of an Agrobacterium-Type Tumor-Inducing Plasmid in Neorhizobium sp. NCHU2750 and the Link to Phytopathogenicity

The genus Agrobacterium contains a group of plant-pathogenic bacteria that have been developed into an important tool for genetic transformation of eukaryotes. To further improve this biotechnology application, a better understanding of the natural genetic variation is critical. During the process of isolation and characterization of wild-type strains, we found a novel strain (i.e., NCHU2750) that resembles Agrobacterium phenotypically but exhibits high sequence divergence in several marker genes. For more comprehensive characterization of this strain, we determined its complete genome sequence for comparative analysis and performed pathogenicity assays on plants. The results demonstrated that this strain is closely related to Neorhizobium in chromosomal organization, gene content, and molecular phylogeny. However, unlike the characterized species within Neorhizobium, which all form root nodules with legume hosts and are potentially nitrogen-fixing mutualists, NCHU2750 is a gall-forming pathogen capable of infecting plant hosts across multiple families. Intriguingly, this pathogenicity phenotype could be attributed to the presence of an Agrobacterium-type tumor-inducing plasmid in the genome of NCHU2750. These findings suggest that these different lineages within the family Rhizobiaceae are capable of transitioning between ecological niches by having novel combinations of replicons. In summary, this work expanded the genomic resources available within Rhizobiaceae and provided a strong foundation for future studies of this novel lineage. With an infectivity profile that is different from several representative Agrobacterium strains, this strain may be useful for comparative analysis to better investigate the genetic determinants of host range among these bacteria.

Transient Expression of Human Cytochrome P450s 2D6 and 3A4 in Nicotiana benthamiana Provides a Possibility for Rapid Substrate Testing and Production of Novel Compounds

Employment of transient expression of foreign genes for bioconversion of pharmaceutically valuable low-molecular-weight compounds, including plant secondary metabolites, is an enticing trend still scantily explored in plant biotechnology. In the present work, an efficient protocol for rapid assessment of synthetic and plant-derived metabolites as potential substrates for human P450s (CYP2D6 and CYP3A4) via Agrobacterium-mediated transient expression in Nicotiana benthamiana is put forth. Animal P450s with broad substrate specificity are promising candidates for transformation of diverse metabolites. The efficiency of P450s in heterologous surroundings is not always satisfactory and depends on the availability of an associated electron-transfer enzyme. Plants represent an attractive assortment of prospective hosts for foreign P450s expression. The optimal composition of genetic blocks providing the highest transient expression efficiency is designed, an effective substrate administration scheme is validated, and biological activity of the investigated P450s against loratadine and several indole alkaloids with different molecular scaffold structures is tested. A novel indole alkaloid, 11-hydroxycorynanthine, is isolated from N. benthamiana plants transiently expressing CYP2D6 and supplemented with corynanthine, and its structure was elucidated. The proposed technique might be of value in realization of combinatorial biosynthesis concept comprising the junction of heterologous enzymes and substrates in different metabolic surroundings.

Plant synthetic biology could drive a revolution in biofuels and medicine

Population growth, climate change, and dwindling finite resources are amongst the major challenges which are facing the planet. Requirements for food, materials, water, and energy will soon exceed capacity. Green biotechnology, fueled by recent plant synthetic biology breakthroughs, may offer solutions. This review summarizes current progress towards robust and predictable engineering of plants. I then discuss applications from the lab and field, with a focus on bioenergy, biomaterials, and medicine.

Acetosyringone treatment duration affects large T-DNA molecule transfer to rice callus

Background

Large T-DNA fragment transfer has long been a problem for Agrobacterium-mediated transformation. Although vector systems, such as the BIBAC series, were successfully developed for the purpose, low transformation efficiencies were consistently observed.

Results

To gain insights of this problem in monocot transformation, we investigated the T-strand accumulation of various size of T-DNA in two kinds of binary vectors (one copy vs. multi-copy) upon acetosyringone (AS) induction and explored ways to improve the efficiency of the large T-DNA fragment transfer in Agrobacterium-mediated rice transformation. By performing immuno-precipitation of VirD2-T-strands and quantitative real-time PCR assays, we monitored the accumulation of the T-strands in Agrobacterium tumeficiens after AS induction. We further demonstrated that extension of AS induction time highly significantly improved large-size T-DNA transfer to rice cells.

Conclusions

Our data provide valuable information of the T-strand dynamics and its impact on large T-DNA transfer in monocots, and likely dicots as well.

Genetic Analysis of Chloroplast Biogenesis, and Function and Mutant Collections

Since the time DNA was discovered as the code of life, genetic analysis has greatly advanced our understanding of the relation between genotype and phenotype and associated molecular mechanisms in various organisms including plants and algae. Forward genetics from phenotype to genotype has identified causal genes of interesting phenotypes induced by chemical, ionizing-radiation, or DNA insertional mutagenesis. Meanwhile, reverse genetics from genotype to phenotype has revealed physiological and molecular roles of known gene sequences. During the past dozen years, many molecular genetic tools have been developed to investigate gene functions quickly and efficiently. In this chapter, we introduce several approaches of forward and reverse genetics, including random chemical and DNA insertional mutagenesis, activation tagging, RNA interference, and gene overexpression and induction systems, with some examples of genetic studies of chloroplast biology mainly in Arabidopsis thaliana. We also briefly describe methods for chemical and DNA insertion mutagenesis and how to obtain sequence-tagged mutants from public collections. With greatly improved DNA sequencing and genome-editing technologies, model organisms as well as diverse species can be used for molecular biology. Genetic analysis can play an increasingly important role in elucidating chloroplast biogenesis and functions.

Genetic Transformation of Pentalinon andrieuxii Tissue Cultures

Pentalinon andrieuxii is a species used in Mayan traditional medicine due to its biological properties. Recent studies indicate that it produces a pentacyclic triterpene-denominated betulinic acid, which presents various biological activities: antibacterial, antifungal, antiplasmodial, anti-inflammatory, antimalarial, anticancer, leishmanicidal, and antiviral, as well as steroids and sterols with leishmanicidal properties. A recent study also reported the presence of urechitol A and B in the roots; these are secondary metabolites whose biochemical function is as yet unknown. This plant therefore represents a natural source of metabolites with potential application in the pharmaceutical industry. In this chapter, a protocol is described for obtaining transgenic plants, at the reporter gene of the β-glucuronidase (GUS) via Agrobacterium tumefaciens from hypocotyl and root explants. The protocol established herein could be employed for the manipulation of the genes involved in the biosynthesis of isoprenoids or secondary metabolites of interest. To our knowledge, this is the first report of stable transformation of Pentalinon andrieuxii via Agrobacterium tumefaciens.

A simplified and efficient Agrobacterium tumefaciens electroporation method

Agrobacterium tumefaciens is a widely used microbial tool in plant molecular biology to transfer DNA into plant cells and produce, e.g., stable or transient transformants or induce gene silencing. In our study, we present a simplified version of electrocompetent cell preparation that is not only time and cost efficient, but it requires minimal handling of bacterial cells. Liquid cultures are normally used to prepare competent Agrobacterium cells. To overcome the difficulties of working with liquid cultures, we propose suspending bacterial cells directly from overnight agar plate cultures. In addition, we optimized several parameters to simplify the procedure and maximize the number of transformants (e.g., Agrobacterium strains, number of washing steps, amount of required plasmid DNA, electroporation parameters, type of incubation media, or incubation time). This optimized, simple, and fast protocol has proved to be efficient enough to obtain transformed colonies with low amounts (as little as 1 ng) of plasmid DNA. In addition, it also enabled us to introduce ligated plasmids directly into Agrobacterium omitting the E. coli transformation step and accelerating the cloning procedure further.

Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis

Background

Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. Currently, information on the key metabolic pathways and their molecular basis of regulation remains scarce, severely limiting efforts to engineer it as an industrial host.

Results

We have adapted Agrobacterium tumefaciens-mediated transformation (ATMT) as a gene-tagging tool for the identification of novel genes in R. toruloides. Multiple factors affecting transformation efficiency in several species in the Pucciniomycotina subphylum were optimized. The Agrobacterium transfer DNA (T-DNA) showed predominantly single-copy chromosomal integrations in R. toruloides, which were trackable by high efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). To demonstrate the application of random T-DNA insertions for strain improvement and gene hunting, 3 T-DNA insertional libraries were screened against cerulenin, nile red and tetrazolium violet respectively, resulting in the identification of 22 mutants with obvious phenotypes in fatty acid or lipid metabolism. Similarly, 5 carotenoid biosynthetic mutants were obtained through visual screening of the transformants. To further validate the gene tagging strategy, one of the carotenoid production mutants, RAM5, was analyzed in detail. The mutant had a T-DNA inserted at the putative phytoene desaturase gene CAR1. Deletion of CAR1 by homologous recombination led to a phenotype similar to RAM5 and it could be genetically complemented by re-introduction of the wild-type CAR1 genome sequence.

Conclusions

T-DNA insertional mutagenesis is an efficient forward genetic tool for gene discovery in R. toruloides and related oleaginous yeast species. It is also valuable for metabolic engineering in these hosts. Further analysis of the 27 mutants identified in this study should augment our knowledge of the lipid and carotenoid biosynthesis, which may be exploited for oil and isoprenoid metabolic engineering.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1151-6) contains supplementary material, which is available to authorized users.

Visualization of RMRs (Receptor Membrane RING-H2) Dimerization in Nicotiana benthamiana Leaves Using a Bimolecular Fluorescence Complementation (BiFC) Assay

The bimolecular fluorescent complementation (BiFC) is a fluorescent complementation method largely used to investigate protein-protein interaction in living cells. This method is based on the ability of two nonfluorescent fragments to assemble forming a native fluorescent reporter with the same spectral properties of the native reporter. Such fragments are fused to putative protein partners that in case of interaction will bring the two halves in close proximity, allowing for the reconstitution of an active fluorescent reporter. The BiFC has been used to investigate protein-protein interaction in a number of different organisms, including plants. In plant cells, many essential pathways of protein trafficking and subcellular localization necessitate the intervention of several protein units organized in multisubunit complexes. It is well known that vacuolar sorting of many secretory soluble proteins require the intervention of specific transmembrane cargo receptors able to interact forming dimers. In this chapter we describe a BiFC method for the efficient visualization of RMR (Receptor Membrane RING-H2) type 2 dimerization in agro-infiltrated Nicotiana benthamiana leaves. Furthermore, this relatively simple method represents an optimal strategy to test protein-protein interaction using any other putative protein partners of interest in plant cells.