Glycine betaine allows enhanced induction of the Agrobacterium tumefaciens vir genes by acetosyringone at low pH

Towards a seamless product and process development workflow for recombinant proteins produced by plant molecular farming

Plant molecular farming (PMF) has been promoted as a fast, efficient and cost-effective alternative to bacteria and animal cells for the production of biopharmaceutical proteins. Numerous plant species have been tested to produce a wide range of drug candidates. However, PMF generally lacks a systematic, streamlined and seamless workflow to continuously fill the product pipeline. Therefore, it is currently unable to compete with established platforms in terms of routine, throughput and horizontal integration (the rapid translation of product candidates to preclinical and clinical development). Individual management decisions, limited funding and a lack of qualified production capacity can hinder the execution of such projects, but we also lack suitable technologies for sample handling and data management. This perspectives article will highlight current bottlenecks in PMF and offer potential solutions that combine PMF with existing technologies to build an integrated facility of the future for product development, testing, manufacturing and clinical translation. Ten major bottlenecks have been identified and are discussed in turn: automated cloning and simplified transformation options, reproducibility of bacterial cultivation, bioreactor integration with automated cell handling, options for rapid mid-scale candidate and product manufacturing, interconnection with (group-specific or personalized) clinical trials, diversity of (post-)infiltration conditions, development of downstream processing platforms, continuous process operation, compliance of manufacturing conditions with biosafety regulations, scaling requirements for cascading biomass.

Exploring Agrobacterium-mediated genetic transformation methods and its applications in Lilium

As a typical bulb flower, lily is widely cultivated worldwide because of its high ornamental, medicinal and edible value. Although breeding efforts evolved over the last 10000 years, there are still many problems in the face of increasing consumer demand. The approach of biotechnological methods would help to solve this problem and incorporate traits impossible by conventional breeding. Target traits are dormancy, development, color, floral fragrance and resistances against various biotic and abiotic stresses, so as to improve the quality of bulbs and cut flowers in planting, cultivation, postharvest, plant protection and marketing. Genetic transformation technology is an important method for varietal improvement and has become the foundation and core of plant functional genomics research, greatly assisting various plant improvement programs. However, achieving stable and efficient genetic transformation of lily has been difficult worldwide. Many gene function verification studies depend on the use of model plants, which greatly limits the pace of directed breeding and germplasm improvement in lily. Although significant progress has been made in the development and optimization of genetic transformation systems, shortcomings remain. Agrobacterium-mediated genetic transformation has been widely used in lily. However, severe genotypic dependence is the main bottleneck limiting the genetic transformation of lily. This review will summarizes the research progress in the genetic transformation of lily over the past 30 years to generate the material including a section how genome engineering using stable genetic transformation system, and give an overview about recent and future applications of lily transformation. The information provided in this paper includes ideas for optimizing and improving the efficiency of existing genetic transformation methods and for innovation, provides technical support for mining and identifying regulatory genes for key traits, and lays a foundation for genetic improvement and innovative germplasm development in lily.

Production of enzymes for the removal of odorous substances in plant biomass

Residual plant biomass collected from agricultural, technical or biopharmaceutical processes contains odorous substances. The latter are often unacceptable for customers if the biomass is used in sustainable products such as building materials, paints, glues or flame-resistant foils. The objective of this study was to identify enzymes that can prevent the formation or facilitate the degradation of odorous substances such as butanol, eugenol or ethyl acetate and their derivatives in residual biomass. We used plant cell packs (PCPs) as a small-scale screening platform to assess the expression of enzymes that break down odorous substances in tobacco biomass. First, we compiled a list of volatile compounds in residual plant biomass that may give rise to undesirable odors, refining the list to 10 diverse compounds representing a range of odors. We then selected five monomeric enzymes (a eugenol oxidase, laccase, oxidase, alkane mono-oxidase and ethyl acetate hydrolase) with the potential to degrade these substances. We transiently expressed the proteins in PCPs, targeting different subcellular compartments to identify optimal production conditions. The maximum yield we achieved was ∼20 mg kg-1 for Trametes hirsute laccase targeted to the chloroplast. Our results confirm that enzymes for the removal of odorous substances can be produced in plant systems, facilitating the upcycling of residual biomass as an ingredient for sustainable products.

Improvement of a Genetic Transformation System and Preliminary Study on the Function of LpABCB21 and LpPILS7 Based on Somatic Embryogenesis in Lilium pumilum DC. Fisch

Auxin transport mediates the asymmetric distribution of auxin that determines the fate of cell development. Agrobacterium-mediated genetic transformation is an important technical means to study gene function. Our previous study showed that the expression levels of LpABCB21 and LpPILS7 are significantly up-regulated in the somatic embryogenesis (SE) of Lilium pumilum DC. Fisch. (L. pumilum), but the functions of both genes remain unclear. Here, the genetic transformation technology previously developed by our team based on the L. pumilum system was improved, and the genetic transformation efficiency increased by 5.7-13.0%. Use of overexpression and CRISPR/Cas9 technology produced three overexpression and seven mutant lines of LpABCB21, and seven overexpression and six mutant lines of LpPILS7. Analysis of the differences in somatic embryo induction of transgenic lines confirmed that LpABCB21 regulates the early formation of the somatic embryo; however, excessive expression level of LpABCB21 inhibits somatic embryo induction efficiency. LpPILS7 mainly regulates somatic embryo induction efficiency. This study provides a more efficient method of genetic transformation of L. pumilum. LpABCB21 and LpPILS7 are confirmed to have important regulatory roles in L. pumilum SE thus laying the foundation for subsequent studies of the molecular mechanism of Lilium SE.

Agrobacterium-mediated and electroporation-mediated transformation of Chlamydomonas reinhardtii: a comparative study

Background

Chlamydomonas reinhardtii is an unicellular green alga used for functional genomics studies and heterologous protein expression. A major hindrance in these studies is the low level and instability of expression of nuclear transgenes, due to their rearrangement and/or silencing over time.

Results

We constructed dedicated vectors for Agrobacterium-mediated transformation carrying, within the T-DNA borders, the Paromomycin (Paro) selectable marker and an expression cassette containing the Luciferase (Luc) reporter gene. These vectors and newly developed co-cultivation methods were used to compare the efficiency, stability and insertion sites of Agrobacterium- versus electroporation-mediated transformation. The influence of different transformation methods, of the cell wall, of the virulence of different Agrobacterium strains, and of transgene orientation with respect to T-DNA borders were assessed. False positive transformants were more frequent in Agrobacterium-mediated transformation compared to electroporation, compensating for the slightly lower proportion of silenced transformants observed in Agrobacterium-mediated transformation than in electroporation. The proportion of silenced transformants remained stable after 20 cycles of subculture in selective medium. Next generation sequencing confirmed the nuclear insertion points, which occurred in exons or untraslated regions (UTRs) for 10 out of 10 Agrobacterium-mediated and 9 out of 13 of electroporation-mediated insertions. Electroporation also resulted in higher numbers of insertions at multiple loci.

Conclusions

Due to its labor-intensive nature, Agrobacterium transformation of Chlamydomonas does not present significant advantages over electroporation, with the possible exception of its use in insertional mutagenesis, due to the higher proportion of within-gene, single-locus insertions. Our data indirectly support the hypothesis that rearrangement of transforming DNA occurs in the Chlamydomonas cell, rather than in the extracellular space as previously proposed.

Electronic supplementary material

The online version of this article (10.1186/s12896-018-0416-3) contains supplementary material, which is available to authorized users.

An efficient protocol for the Agrobacterium-mediated genetic transformation of microalga Chlamydomonas reinhardtii

Algal-based recombinant protein production has gained immense interest in recent years. The development of algal expression system was earlier hindered due to the lack of efficient and cost-effective transformation techniques capable of heterologous gene integration and expression. The recent development of Agrobacterium-mediated genetic transformation method is expected to be the ideal solution for these problems. We have developed an efficient protocol for the Agrobacterium-mediated genetic transformation of microalga Chlamydomonas reinhardtii. Pre-treatment of Agrobacterium in TAP induction medium (pH 5.2) containing 100 μM acetosyringone and 1 mM glycine betaine and infection of Chlamydomonas with the induced Agrobacterium greatly improved transformation frequency. This protocol was found to double the number of transgenic events on selection media compared to that of previous reports. PCR was used successfully to amplify fragments of the hpt and GUS genes from transformed cells, while Southern blot confirmed the integration of GUS gene into the genome of C. reinhardtii. RT-PCR, Northern blot and GUS histochemical analyses confirm GUS gene expression in the transgenic cell lines of Chlamydomonas. This protocol provides a quick, efficient, economical and high-frequency transformation method for microalgae.

Quantitative image analysis and modeling indicate the Agrobacterium tumefaciens type IV secretion system is organized in a periodic pattern of foci

The Gram negative plant pathogen Agrobacterium tumefaciens is uniquely capable of genetically transforming eukaryotic host cells during the infection process. DNA and protein substrates are transferred into plant cells via a type IV secretion system (T4SS), which forms large cell-envelope spanning complexes at multiple sites around the bacterial circumference. To gain a detailed understanding of T4SS positioning, the spatial distribution of fluorescently labeled T4SS components was quantitatively assessed to distinguish between random and structured localization processes. Through deconvolution microscopy followed by Fourier analysis and modeling, T4SS foci were found to localize in a non-random periodic pattern. These results indicate that T4SS complexes are dependent on an underlying scaffold or assembly process to obtain an organized distribution suitable for effective delivery of substrates into host cells.

Agrobacterium-mediated transformation of the dwarf pomegranate (Punica granatum L. var. nana)

The dwarf pomegranate (Punica granatum L. var. nana) is a dwarf ornamental plant that has the potential to be the model plant of perennial fruit trees because it bears fruits within 1 year of seedling. We established an Agrobacterium-mediated transformation system for the dwarf pomegranate. Adventitious shoots regenerated from leaf segments were inoculated with A. tumefaciens strain EHA105 harboring the binary vector pBin19-sgfp, which contains neomycin phosphotransferase (npt II) and green fluorescent protein (gfp) gene as a selectable and visual marker, respectively. After co-cultivation, the inoculated adventitious shoots were cut into small pieces to induce regeneration, and then selected on MS medium supplemented with 0.5 muM alpha-naphthaleneacetic acid (NAA), 5 muM N(6)-benzyladenine (BA), 0.3% gellan gum, 50 mg/l kanamycin, and 10 mg/l meropenem. Putative transformed shoots were regenerated after 6-8 months of selection. PCR and PCR-Southern blot analysis revealed the integration of the transgene into the plant genome. Transformants bloomed and bore fruits within 3 months of being potted, and the inheritance of the transgene was confirmed in T(1) generations. The advantage of the transformation of dwarf pomegranate was shown to be the high transformation rate. The establishment of this transformation system is invaluable for investigating fruit-tree-specific phenomena.

Use of Agrobacterium expressing green fluorescent protein to evaluate colonization of sonication-assisted Agrobacterium-mediated transformation-treated soybean cotyledons

Colonization and infection of soybean cotyledons by Agrobacterium tumefaciens and subsequent elimination of bacteria from cotyledons were monitored using bacteria expressing green fluorescent protein (GFP). GFP provided a quick, non-destructive method to evaluate, in real time, Agrobacterium colonization of cotyledon surfaces as well as infection of internal cells. GFP was first detected 7 h following inoculation of the cotyledon. By 36 h, GFP expression was very intense, and was limited to the adaxial surface of the cotyledon. Expression of GFP also served as a useful indicator of successful elimination of the bacterium from plant tissue following antibiotic treatment.

Construction of an efficient expression system for Agrobacterium tumefaciens based on the coliphage T5 promoter

A versatile expression vector utilizing a promoter of coliphage T5, P(N25) (Gentz and Bujard, 1985. J. Bacteriol. 164, 70-77) and a derivative of the IncW broad-host-range plasmid pJB20 (Beaupré et al., 1997. J. Bacteriol. 179, 78-89) has been developed. This vector successfully expresses virulence proteins of Agrobacterium tumefaciens encoded by virG and a mutant allele of virA, virA (delta1-284, G665D) in Escherichia coli as well as in A. tumefaciens. The signal transduction proteins VirA (delta1-284, G665D) and VirG are fully functional when expressed in Agrobacterium, and the P(N25) driven expression overrides the complex transcriptional regulation present with the native promoters. This expression system will enable a more detailed analysis of the activation events in signal transduction in A. tumefaciens, and we expect it to be useful in other prokaryotes.

The chromosomal response regulatory gene chvI of Agrobacterium tumefaciens complements an Escherichia coli phoB mutation and is required for virulence

In an effort to identify the Agrobacterium tumefaciens phosphate regulatory gene(s), we isolated a clone from an A. tumefaciens cosmid library that restored regulated alkaline phosphatase activity to an Escherichia coli phoB mutant. The gene that complemented phoB was localized by subcloning and deletion analysis, and the DNA sequence was determined. An open reading frame, denoted chvI, was identified that encoded a predicted protein with amino acid similarity to the family of bacterial response regulators and 35% identify to PhoB. Surprisingly, an A. tumefaciens chvI mutant showed normal induction of phosphatase activity and normal virG expression when grown in phosphate-limiting media. However, this mutant was unable to grow in media containing tryptone, peptone, or Casamino Acids and was also more sensitive than the wild type to acidic extracellular pH. This mutant was avirulent on Kalanchoeë diagremontiana and was severely attenuated in vir gene expression. The pH-inducible expression of virG was also abolished. Growth of the chvI mutant was inhibited by K. diagremontiana wound sap, suggesting that avirulence may be due, in part, to the inability of this mutant to survive the plant wound environment.

Acetosyringone and osmoprotectants like betaine or proline synergistically enhance Agrobacterium-mediated transformation of apple

The effects of the plant signal molecule acetosyringone (AS) and the osmoprotectant betaine phosphate (BP) have been examined for their ability to increase the transformation efficiency of Agrobacterium tumefaciens (At), C58C1::pGV3850 harboring the binary vector pKIWI105. This binary plasmid encodes the β-glucuronidase (GUS) gene and was previously shown to be expressed exclusively in plant tissues. Bacteria were grown in one of two previously reported virulence induction media (MS20 and SIM) for 5h and GUS activity was measured fluorimetrically in individual 6 week old leaf discs as a quantitative measure of stable transformation events. Bacteria induced in MS20 supplemented with AS (0.1 mM) and BP (1 mM) showed a significant increase in GUS activity as compared to media containing AS or BP added singly or control media lacking the supplements. The effects of another osmoprotectant proline (1 mM) could replace the beneficial effects of betaine. No significant difference was observed among treatments with respect to the two induction media.

Factors influencing the efficiency of T-DNA transfer during co-cultivation of Antirrhinum majus with Agrobacterium tumefaciens

The effects of varying the pH of the cocultivation medium, additons of vir-inducing phenolic compounds and the strains of wild-type agrobacteria on transformation rates of a number of different varieties of Antirrhinum majus were studied. In general, optimal transformation was found with strains C58 or A281 and was favoured by low pH and the inclusion of acetosyringone in the co-cultivation medium. However, maximal transformation of the least susceptible variety was achieved at high pH and in the presence of syringaldehyde. This demonstrates the need for the optimization of a wide range of culture conditions when working with new genotypes and offers a rational approach towards the development of Agrobacterium-mediated transformation of new species or varieties.

Two-way chemical signaling in Agrobacterium-plant interactions

The discovery in 1977 that Agrobacterium species can transfer a discrete segment of oncogenic DNA (T-DNA) to the genome of host plant cells has stimulated an intense interest in the molecular biology underlying these plant-microbe associations. This attention in turn has resulted in a series of insights about the biology of these organisms that continue to accumulate at an ever-increasing rate. This excitement was due in part to the notion that this unprecedented interkingdom DNA transfer could be exploited to create transgenic plants containing foreign genes of scientific or commercial importance. In the course of these discoveries, Agrobacterium became one of the best available models for studying the molecular interactions between bacteria and higher organisms. One extensively studied aspect of this association concerns the exchange of chemical signals between Agrobacterium spp. and host plants. Agrobacterium spp. can recognize no fewer than five classes of low-molecular-weight compounds released from plants, and other classes probably await discovery. The most widely studied of these are phenolic compounds, which stimulate the transcription of the genes needed for infection. Other compounds include specific monosaccharides and acidic environments which potentiate vir gene induction, acidic polysaccharides which induce one or more chromosomal genes, and a family of compounds called opines which are released from tumorous plant cells to the bacteria as nutrient sources. Agrobacterium spp. in return release a variety of chemical compounds to plants. The best understood is the transferred DNA itself, which contains genes that in various ways upset the balance of phytohormones, ultimately causing neoplastic cell proliferation. In addition to transferring DNA, some Agrobacterium strains directly secrete phytohormones. Finally, at least some strains release a pectinase, which degrades a component of plant cell walls.

The Agrobacterium tumefaciens vir gene transcriptional activator virG is transcriptionally induced by acid pH and other stress stimuli

A set of Agrobacterium tumefaciens operons required for pathogenesis is coordinately induced during plant infection by the VirA and VirG proteins. The intracellular concentration of VirG increases in response to acidic media, and this response was proposed to be regulated at the level of transcription at a promoter (P2) that resembles the Escherichia coli heat shock promoters. To test this hypothesis, we first constructed a virG-lacZ transcriptional fusion. A strain containing this fusion had higher levels of beta-galactosidase activity in acidic media than in media at neutral pH. Second, primer extension analysis of virG indicated that acidic media stimulated the transcription of this promoter. To determine whether P2 is a member of a heat shock-like regulon in A. tumefaciens, five agents that induce E. coli heat shock genes were tested for their abilities to induce a P2-lacZ fusion in A. tumefaciens. P2 was most strongly induced by low pH, was moderately stimulated by CdCl2 or mitomycin C, and was slightly induced by P2 as measured by beta-galactosidase activity and primer extension analysis. Induction by these treatments did not require any Ti plasmid-encoded function or the chromosomally encoded RecA protein. We also pulse-labeled cellular proteins after a shift to low pH and detected several proteins whose synthesis was induced by these conditions. We conclude that P2 is primarily induced by acid pH and secondarily by certain other stimuli, each of which is stressful to cell growth. This stress induction is at least partly independent of the heat shock and SOS responses.

An Agrobacterium two-component regulatory system for the detection of chemicals released from plant wounds

Crown gall tumorigenesis by Agrobacterium tumefaciens requires the co-ordinate transcriptional induction of a set of pathogenesis genes. At least three classes of environmental stimuli act synergistically to induce these genes: (i) monocyclic aromatic hydrocarbons such as acetosyringone, coniferyl alcohol, and vanillin, (ii) neutral or acidic monosaccharides such as glucose and glucuronic acid, and (iii) acidic pH. Three proteins are required to sense and respond to these stimuli: (i) VirA, a transmembrane sensory protein and histidine protein kinase, (ii) VirG, a transcriptional activator which is phosphorylated by phosphoryl VirA, and (iii) ChvE, a periplasmic sugar-binding protein. VirA and VirG are members of the so-called two-component family of regulatory proteins. This regulatory system continues to offer new discoveries in the areas of signal transduction, host-microbe interactions, and host range.

The effects of acetosyringone and pH on Agrobacterium-mediated transformation vary according to plant species

Expiants of five plant species (Allium cepa, Antirrhinum majus, Brassica campestris. Glycine max, and Nicotiana tabacum) were co-cultivated with three Agrobacterium tumefaciens strains under different conditions to assess the effects of acetosyringone and medium pH on strain virulence. Tumours were incited on all dicotyledonous species by strains N2/73 and A281. The presence of acetosyringone during co-cultivation generally enhanced the virulence of these strains, most markedly N2/73 on A. majus and G. max, and A281 on G. max. Strain Ach5 was virulent only on N. tabacum in the absence of acetosyringone, which, when present, extended the host range to include A. majus. There was evidence to suggest that acetosyringone may suppress virulence in some strain/plant species interactions. Virulence was affected in some cases by medium pH, but there was no general effect across plant species.

Osmoregulation in Agrobacterium tumefaciens: accumulation of a novel disaccharide is controlled by osmotic strength and glycine betaine

We have investigated the mechanism of osmotic stress adaptation (osmoregulation) in Agrobacterium tumefaciens biotype I (salt-tolerant) and biotype II (salt-sensitive) strains. Using natural-abundance 13C nuclear magnetic resonance spectroscopy, we identified all organic solutes that accumulated to significant levels in osmotically stressed cultures. When stressed, biotype I strains (C58, NT1, and A348) accumulated glutamate and a novel disaccharide, beta-fructofuranosyl-alpha-mannopyranoside, commonly known as mannosucrose. In the salt-sensitive biotype II strain K84, glutamate was observed but mannosucrose was not. We speculate that mannosucrose confers the extra osmotic tolerance observed in the biotype I strains. In addition to identifying the osmoregulated solutes that this species synthesizes, we investigated the ability of A. tumefaciens to utilize the powerful osmotic stress protectant glycine betaine when it is supplied in the medium. Results from growth experiments, nuclear magnetic resonance spectroscopy, and a 14C labeling experiment demonstrated that in the absence of osmotic stress, glycine betaine was metabolized, while in stressed cultures, glycine betaine accumulated intracellularly and conferred enhanced osmotic stress tolerance. Furthermore, when glycine betaine was taken up in stressed cells, its accumulation caused the intracellular concentration of mannosucrose to drop significantly. The possible role of osmoregulation of A. tumefaciens in the transformation of plants is discussed.

Control of expression of Agrobacterium vir genes by synergistic actions of phenolic signal molecules and monosaccharides

Most virulence (vir) genes of Agrobacterium tumefaciens that are required for the formation of crown gall tumors are expressed in response to such plant signal molecules as acetosyringone and lignin precursors. The phenolic signals are transduced through a receptor VirA protein in the inner membrane of the bacterial cell. The expression of these genes triggers the transfer of a specific DNA segment, called transferred DNA (T-DNA), from the Ti plasmid to plant cells, and its integration into their nuclear DNA. We show here that a group of aldoses (L-arabinose, D-xylose, D-lyxose, D-glucose, D-mannose, D-idose, D-galactose, and D-talose) can markedly enhance acetosyringone-dependent expression of vir genes when the concentration of acetosyringone is limited (10 microM) but does not enhance the expression of noninducible genes. Likewise, a 2-deoxy-D-glucose, a nonmetabolized sugar, is also effective. When a deletion was introduced into the virA gene in the region encoding the periplasmic portion of the VirA protein, enhancement by glucose disappeared, but vir expression was induced by acetosyringone in this mutant. These results suggest that these sugars directly enhance a signaling process initiated by phenolic inducers that results in an increase in expression of the vir genes.