Agrobacterium and plant genetic engineering

T-DNA insertion in Arabidopsis caused coexisting chromosomal inversion and duplication at megabase level

Agrobacteria-mediated transformation is widely used in plant genetic engineering to introduce exogenous genes and create mutant lines through random T-DNA insertion and gene disruption. When T-DNA fragments are inserted into the plant genome, it could cause chromosomal abnormalities. In this study, we investigated the genetic basis of pleiotropic phenotypes observed in the T-DNA insertion mutant lnc161. We discovered that there are four T-DNA insertions present in the lnc161 genome, which disrupted the genes LNC161 (AT3G05035), AT3G57400, AT5G05630, and AT5G16450, respectively. However, none of these insertions were the causative mutation that leads to the lnc161 phenotypes. Strikingly, through genetic analyses and high throughput sequencing, we found an inversion of about 19.8 Mb sequences between LNC161 and AT3G57400. Moreover, the sequences between AT5G05630 and AT5G16450 (about 3.7 Mb) were translocated from chromosome 5 to chromosome 3, adjacent to the inversion sequences, and were duplicated. This duplication led to an up-regulation of genes expression in this region, potentially resulting in pleiotropic morphological traits in lnc161. Overall, this study provides a case showing complex chromosomal re-arrangement induced by T-DNA insertion.

The translocated virulence protein VirD5 causes DNA damage and mutation during Agrobacterium-mediated transformation of yeast

The soil bacterium Agrobacterium tumefaciens is a preferred gene vector not only for plants but also for fungi. Agrobacterium delivers a small set of virulence proteins into host cells concomitantly with transferred DNA (T-DNA) to support the transformation process. Here, we find that expression of one of these proteins, called VirD5, in yeast host cells causes replication stress and DNA damage. This can result in both genomic rearrangements and local mutations, especially small deletions. Delivery of VirD5 during cocultivation with Agrobacterium led to mutations in the yeast genome that were unlinked to the integration of T-DNA. This load of mutations can be prevented by using a virD5 mutant for genome engineering, but this leads to a lower transformation frequency.

Tissue culture protocols for gene transfer and editing in maize (Zea mays L.)

Efficient methods for gene transfer to maize were developed in the 1990s, first mediated by particle bombardment and then by Agrobacterium tumefaciens. Both methods can efficiently create high-quality events. Genetically modified varieties were commercialized in 1996 and are now planted in more than 90% of the US corn field. Tissue culture protocols for both methods have been well developed and widely employed. Thus, various factors, including handling before gene delivery, techniques to protect cells during gene delivery, and culture media, have been well optimized for various genotypes. Typical protocols for both methods are herein presented to show major outputs from the studies conducted since the early 1990s. As the bombardment protocols tended to be optimized specifically for limited genotypes, the one for B104, a new public inbred with favorable agronomic characteristics, is shown. The Agrobacterium protocol is suitable for various inbred lines, including B104. These protocols are also useful starting points in the optimization of tissue culture for gene editing. The rate-limiting step in both transformation and gene editing is in tissue culture and plant regeneration from modified cells in elite germplasm. Despite the prolonged efforts, large varietal differences in tissue culture responses remain a serious issue in maize. Recently, protocols using morphogenic regulator genes, such as Bbm and Wus2, have been developed that show a strong potential of efficiently transforming recalcitrant varieties.

Plant Symbionts Are Engineers of the Plant-Associated Microbiome

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.

Overexpression of VIRE2-INTERACTING PROTEIN2 in Arabidopsis regulates genes involved in Agrobacterium-mediated plant transformation and abiotic stresses

Arabidopsis VIRE2-INTERACTING PROTEIN2 (VIP2) was previously described as a protein with a NOT domain, and Arabidopsis vip2 mutants are recalcitrant to Agrobacterium-mediated root transformation. Here we show that VIP2 is a transcription regulator and the C-terminal NOT2 domain of VIP2 interacts with VirE2. Interestingly, AtVIP2 overexpressor lines in Arabidopsis did not show an improvement in Agrobacterium-mediated stable root transformation, but the transcriptome analysis identified 1,634 differentially expressed genes compared to wild-type. These differentially expressed genes belonged to various functional categories such as membrane proteins, circadian rhythm, signaling, response to stimulus, regulation of plant hypersensitive response, sequence-specific DNA binding transcription factor activity and transcription regulatory region binding. In addition to regulating genes involved in Agrobacterium-mediated plant transformation, AtVIP2 overexpressor line showed differential expression of genes involved in abiotic stresses. The majority of the genes involved in abscisic acid (ABA) response pathway, containing the Abscisic Acid Responsive Element (ABRE) element within their promoters, were down-regulated in AtVIP2 overexpressor lines. Consistent with this observation, AtVIP2 overexpressor lines were more susceptible to ABA and other abiotic stresses. Based on the above findings, we hypothesize that VIP2 not only plays a role in Agrobacterium-mediated plant transformation but also acts as a general transcriptional regulator in plants.

In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation

One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.

An Improved Binary Vector and Escherichia coli Strain for Agrobacterium tumefaciens-Mediated Plant Transformation

The plasmid vector pGreenII is widely used to produce plant transformants via a process that involves propagation in Escherichia coli However, we show here that pGreenII-based constructs can be unstable in E. coli as a consequence of them hampering cell division and promoting cell death. In addition, we describe a new version of pGreenII that does not cause these effects, thereby removing the selective pressure for mutation, and a new strain of E. coli that better tolerates existing pGreenII-based constructs without reducing plasmid yield. The adoption of the new derivative of pGreenII and the E. coli strain, which we have named pViridis and MW906, respectively, should help to ensure the integrity of genes destined for study in plants while they are propagated and manipulated in E. coli The mechanism by which pGreenII perturbs E. coli growth appears to be dysregulation within the ColE1 origin of replication.

Heterologous DNA Uptake in Cultured Symbiodinium spp. Aided by Agrobacterium tumefaciens

Plant-targeted pCB302 plasmids containing sequences encoding gfp fusions with a microtubule-binding domain; gfp with the fimbrin actin-binding domain 2; and gfp with AtRACK1C from Arabidopsis thaliana, all harbored in Agrobacterium tumefaciens, were used to assay heterologous expression on three different clades of the photosynthetic dinoflagellate, Symbiodinium. Accessibility to the resistant cell wall and through the plasma membrane of these dinoflagellates was gained after brief but vigorous shaking in the presence of glass beads and polyethylene glycol. A resistance gene to the herbicide Basta allowed appropriate selection of the cells expressing the hybrid proteins, which showed a characteristic green fluorescence, although they appeared to lose their photosynthetic pigments and did not further divide. Cell GFP expression frequency measured as green fluorescence emission yielded 839 per every 10⁶ cells for Symbiodinium kawagutii, followed by 640 and 460 per every 10⁶ cells for Symbiodinium microadriaticum and Symbiodinium sp. Mf11, respectively. Genomic PCR with specific primers amplified the AtRACK1C and gfp sequences after selection in all clades, thus revealing their presence in the cells. RT-PCR from RNA of S. kawagutii co-incubated with A. tumefaciens harboring each of the three vectors with their respective constructs, amplified products corresponding to the heterologous gfp sequence while no products were obtained from three distinct negative controls. The reported procedure shows that mild abrasion followed by co-incubation with A. tumefaciens harboring heterologous plasmids with CaMV35S and nos promoters can lead to expression of the encoded proteins into the Symbiodinium cells in culture. Despite the obvious drawbacks of the procedure, this is an important first step towards a stable transformation of Symbiodinium.

Progress of cereal transformation technology mediated by Agrobacterium tumefaciens

Monocotyledonous plants were believed to be not transformable by the soil bacterium Agrobacterium tumefaciens until two decades ago, although convenient protocols for infection of leaf disks and subsequent regeneration of transgenic plants had been well established in a number of dicotyledonous species by then. This belief was reinforced by the fact that monocotyledons are mostly outside the host range of crown gall disease caused by the bacterium and by the failures in trials in monocotyledons to mimic the transformation protocols for dicotyledons. However, a key reason for the failure could have been the lack of active cell divisions at the wound sites in monocotyledons. The complexity and narrow optimal windows of critical factors, such as genotypes of plants, conditions of the plants from which explants are prepared, tissue culture methods and culture media, pre-treatments of explants, strains of A. tumefaciens, inducers of virulence genes, transformation vectors, selection marker genes and selective agents, kept technical hurdles high. Eventually it was demonstrated that rice and maize could be transformed by co-cultivating cells of callus cultures or immature embryos, which are actively dividing or about to divide, with A. tumefaciens. Subsequently, these initial difficulties were resolved one by one by many research groups, and the major cereals are now transformed quite efficiently. As many as 15 independent transgenic events may be regenerated from a single piece of immature embryo of rice. Maize transformation protocols are well established, and almost all transgenic events deregulated for commercialization after 2003 were generated by Agrobacterium-mediated transformation. Wheat, barley, and sorghum are also among those plants that can be efficiently transformed by A. tumefaciens.

Less is more: strategies to remove marker genes from transgenic plants

Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.

Architecture of the Helicobacter pylori Cag-type IV secretion system

Type IV secretion systems (T4SS) are macromolecular assemblies used by bacteria to transport material across their membranes. T4SS are generally composed of a set of twelve proteins (VirB1-11 and VirD4). This represents a dynamic machine powered by three ATPases. T4SS are widespread in pathogenic bacteria where they are often used to deliver effectors into host cells. For example, the human pathogen Helicobacter pylori encodes a T4SS, the Cag-T4SS, which mediates the injection of the toxin CagA. We review the progress made in the past decade in our understanding of T4SS architecture. We translate this new knowledge to derive an understanding of the structure of the H. pylori Cag system, and use recent protein-protein interaction data to refine this model.

Pili and flagella biology, structure, and biotechnological applications

Bacteria and Archaea expose on their outer surfaces a variety of thread-like proteinaceous organelles with which they interact with their environments. These structures are repetitive assemblies of covalently or non-covalently linked protein subunits, organized into filamentous polymers known as pili ("hair"), flagella ("whips") or injectisomes ("needles"). They serve different roles in cell motility, adhesion and host invasion, protein and DNA secretion and uptake, conductance, or cellular encapsulation. Here we describe the functional, morphological and genetic diversity of these bacterial filamentous protein structures. The organized, multi-copy build-up and/or the natural function of pili and flagella have lead to their biotechnological application as display and secretion tools, as therapeutic targets or as molecular motors. We review the documented and potential technological exploitation of bacterial surface filaments in light of their structural and functional traits.

New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation

Agrobacterium tumefaciens causes tumour formation in plants. Plant signals induce in the bacteria the expression of a range of virulence (Vir) proteins and the formation of a type IV secretion system (T4SS). On attachment to plant cells, a transfer DNA (T-DNA) and Vir proteins are imported into the host cells through the bacterial T4SS. Through interaction with a number of host proteins, the Vir proteins suppress the host innate immune system and support the transfer, nuclear targeting, and integration of T-DNA into host cell chromosomes. Owing to extensive genetic analyses, the bacterial side of the plant-Agrobacterium interaction is well understood. However, progress on the plant side has only been achieved recently, revealing a highly complex molecular choreography under the direction of the Vir proteins that impinge on multiple processes including transport, transcription, and chromosome status of their host cells.

Production of recombinant proteins in suspension-cultured plant cells

Plants have emerged in the past decade as a suitable alternative to the current production systems for recombinant pharmaceutical proteins and, today their potential for low-cost production of high quality, much safer and biologically active mammalian proteins is largely documented. Among various plant expression systems being explored, genetically modified suspension-cultured plant cells offer a promising system for production of biopharmaceuticals. Indeed, when compared to other plant-based production platforms that have been explored, suspension-cultured plant cells have the advantage of being totally devoid of problems associated with the vagaries of weather, pest, soil and gene flow in the environment. Because of short growth cycles, the timescale needed for the production of recombinant proteins in plant cell culture can be counted in days or weeks after transformation compared to months needed for the production in transgenic plants. Moreover, recovery and purification of recombinant proteins from plant biomass is an expensive and technically challenging business that may amount to 80-94% of the final product cost. One additional advantage of plant cell culture is that the recombinant protein fused with a signal sequence can be expressed and secreted into the culture medium, and therefore recovered and purified in the absence of large quantities of contaminating proteins. Consequently, the downstream processing of proteins extracted from plant cell culture medium is less expensive, which may/does balance the higher costs of fermentation. When needed for clinical use, recombinant proteins are easily produced in suspension-cultured plant cells under certified, controllable and sterile conditions that offer improved safety and provide advantages for good manufacturing practices and regulatory compliance. In this chapter, we present basic protocols for rapid generation of transgenic suspension-cultured cells of Nicotiana tabacum, Oriza sativa and Arabidopis thaliana. These systems are powerful tools for plant-made pharmaceuticals production in highly controlled conditions.

Transgenic wheat, barley and oats: production and characterization

Ever since the first developments in plant transformation technology using model plant species in the early 1980s, there has been a body of plant science research devoted to adapting these techniques to the transformation of crop plants. For some crop species progress was relatively rapid, but in other crop groups such as the small grain cereals, which were not readily amenable to culture in vitro and were not natural hosts to Agrobacterium, it has taken nearly two decades to develop reliable and robust transformation methods.In the following chapters of this book, transformation procedures for small grain cereals are presented, together with methods for gene and protein expression and the characterization of transgenic plants. In this introductory chapter we try to put these later chapters into context, giving an overview of the development of transformation technology for small grain cereals, discussing some of the pros and cons of the techniques and what limitations still exist.

Role of vitronectin-like protein in Agrobacterium attachment and transformation of Arabidopsis cells

The role of plant vitronectin-like protein (Vn) in Agrobacterium-host plant interactions and receptor-specific bacterial attachment is unclear and still open to debate. Using a well-established Agrobacterium-mediated Arabidopsis transformation system, the marker gene beta-glucuronidase (GUS) of Escherichia coli, and biochemical and cytological methods, such as ELISA tests, immunoblots, immunolocalization, and functional in vitro binding assays, we have reassessed the role of Vn in receptor-specific bacterial attachment and transformation. We provide evidence that Vn is present in the host plant cells and anti-human vitronectin antibody cross-reacts with a 65-kDa protein from Arabidopsis cells. The specificity of the immunological cross-reactivity of anti-vitronectin antibodies was further demonstrated by ELISA competition experiments. Immunogold labeling showed that Vn is localized in the plant cell wall, and its level increased considerably after phytohormone treatment of the petiole explants. However, Agrobacterium attachment was unaffected, and no inhibition of petiole cell transformation was detected in the presence of human vitronectin and anti-vitronectin antibodies in the media. Additionally, no correlation between the occurrence of Vn, attachment of bacteria to the cells, and susceptibility to Agrobacterium-mediated transformation was observed. Taken together, our data do not support a functional role of plant Vn as the receptor for site-specific Agrobacterium attachment leading to the transformation of Arabidopsis cells.

Molecular genetic improvement of cereals: transgenic wheat (Triticum aestivum L.)

Only modest progress has been made in the molecular genetic improvement of wheat following the production of the first transgenic plants in 1992, made possible by the development of efficient, long-term regenerable embryogenic cultures derived from immature embryos and use of the biolistics method for the direct delivery of DNA into regenerable cells. Transgenic lines expressing genes that confer resistance to environmentally friendly non-selective herbicides, and pests and pathogens have been produced, in addition to lines with improved bread-making and nutritional qualities; some of these are ready for commercial production. Reduction of losses caused by weeds, pests and pathogens in such plants not only indirectly increases available arable land and fresh water supplies, but also conserves energy and natural resources. Nevertheless, the work carried out thus far can be considered only the beginning, as many difficult tasks lie ahead and much remains to be done. The challenge now is to produce higher-yielding varieties that are more nutritious, and are resistant or tolerant to a wide variety of biotic as well as abiotic stresses (especially drought, salinity, heavy metal toxicity) that currently cause substantial losses in productivity. How well we will meet this challenge for wheat, and indeed for other cereal and non-cereal crops, will depend largely on establishing collaborative partnerships between breeders, molecular biologists, biotechnologists and industry, and on how effectively they make use of the knowledge and insights gained from basic studies in plant biology and genetics, the sequencing of plant/cereal genomes, the discovery of synteny in cereals, and the availability of DNA-based markers and increasingly detailed chromosomal maps.

Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer

Host recognition and macromolecular transfer of virulence-mediating effectors represent critical steps in the successful transformation of plant cells by Agrobacterium tumefaciens. This review focuses on bacterial and plant-encoded components that interact to mediate these two processes. First, we examine the means by which Agrobacterium recognizes the host, via both diffusible plant-derived chemicals and cell-cell contact, with emphasis on the mechanisms by which multiple host signals are recognized and activate the virulence process. Second, we characterize the recognition and transfer of protein and protein-DNA complexes through the bacterial and plant cell membrane and wall barriers, emphasizing the central role of a type IV secretion system-the VirB complex-in this process.

The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants

In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.

Genetic engineering for cut-flower improvement

The application of modern biotechnological approaches to cut flowers has clearly become instrumental and rewarding for the floriculture industry. In recent years, several gene-transfer procedures have been developed for some of the major commercial cut flowers. Using Agrobactrium or microprojectile bombardment, several basic protocols are now available. However, despite the great progress and interest in gene transfer to these crops, their transformation is routine in only a limited number of laboratories, and its application is still considered to be an "art form". This review summarizes the reported gene-transfer procedures for the main cut-flower crops, with an emphasis on the unique factors of each method and the recent progress in introducing new traits of horticultural interest into these species.

Factors affecting the genetic engineering of plants by microprojectile bombardment

Since its development in the mid-1980s, microprojectile bombardment has been widely employed as a method for direct gene transfer into a wide range of plants, including the previously difficult-to-transform monocotyledonous species. Although the numerous instruments available for microprojectile-mediated gene delivery and their applications have been widely discussed, less attention has been paid to the critical factors which affect the efficiency of this method of gene delivery. In this review we do not wish to describe the array of devices used for microprojectile delivery or their uses which have already been definitively described, but instead wish to report on research developments investigating the factors which affect microprojectile-mediated transformation of plants.

Plant transformation by coinoculation with a disarmed Agrobacterium tumefaciens strain and an Escherichia coli strain carrying mobilizable transgenes

Transformation of Nicotiana tabacum leaf explants was attempted with Escherichia coli as a DNA donor either alone or in combination with Agrobacterium tumefaciens. We constructed E. coli donor strains harboring either the promiscuous IncP-type or IncN-type conjugal transfer system and second plasmids containing the respective origins of transfer and plant-selectable markers. Neither of these conjugation systems was able to stably transform plant cells at detectable levels, even when VirE2 was expressed in the donor cells. However, when an E. coli strain expressing the IncN-type conjugation system was coinoculated with a disarmed A. tumefaciens strain, plant tumors arose at high frequencies. This was caused by a two-step process in which the IncN transfer system mobilized the entire shuttle plasmid from E. coli to the disarmed A. tumefaciens strain, which in turn processed the T-DNA and transferred it to recipient plant cells. The mobilizable plasmid does not require a broad-host-range replication origin for this process to occur, thus reducing its size and genetic complexity. Tumorigenesis efficiency was further enhanced by incubation of the bacterial strains on medium optimized for bacterial conjugation prior to inoculation of leaf explants. These techniques circumvent the need to construct A. tumefaciens strains containing binary vectors and could simplify the creation of transgenic plants.

Characterization of a wound-inducible cytochrome P450 gene ( CYP72A29) that is down-regulated during crown gall tumorigenesis in potato tuber

A cDNA for a putative cytochrome P450 (CYP72A29), which is down-regulated during Agrobacterium tumefaciens -mediated tumorigenesis, was isolated from potato ( Solanum tuberosumL. May Queen) tuber by differential display. Northern analysis indicated that the CYP72A29 gene was transiently up-regulated in tuber discs after a 24-h aging period, and expression gradually increased upon further incubation (up to 7 days). Inoculation of tuber discs with the non-pathogenic A. tumefaciens strain LBA4301 had a very similar effect, but inoculation with the wild-type strain A. tumefaciens A208 suppressed the accumulation of mRNA during further incubation. Furthermore, the accumulation of CYP72A29 mRNA was strongly suppressed by inoculation with mutant strains of A. tumefaciens that produce large amounts of indole-3-acetic acid. This down-regulation also occurred when the discs were treated with 2,4-dichlorophenoxyacetic acid or 1-naphthalenacetic acid. These results suggest that the expression of CYP72A29 is regulated by auxin. RT-PCR analysis revealed that the transcripts were most abundant in sprouts and eyes, less so in roots, and hardly detectable in leaves, flower buds and stems.

ARC5, a cytosolic dynamin-like protein from plants, is part of the chloroplast division machinery

Chloroplast division in plant cells is orchestrated by a complex macromolecular machine with components positioned on both the inner and outer envelope surfaces. The only plastid division proteins identified to date are of endosymbiotic origin and are localized inside the organelle. Employing positional cloning methods in Arabidopsis in conjunction with a novel strategy for pinpointing the mutant locus, we have identified a gene encoding a new chloroplast division protein, ARC5. Mutants of ARC5 exhibit defects in chloroplast constriction, have enlarged, dumbbell-shaped chloroplasts, and are rescued by a wild-type copy of ARC5. The ARC5 gene product shares similarity with the dynamin family of GTPases, which mediate endocytosis, mitochondrial division, and other organellar fission and fusion events in eukaryotes. Phylogenetic analysis showed that ARC5 is related to a group of dynamin-like proteins unique to plants. A GFP-ARC5 fusion protein localizes to a ring at the chloroplast division site. Chloroplast import and protease protection assays indicate that the ARC5 ring is positioned on the outer surface of the chloroplast. Thus, ARC5 is the first cytosolic component of the chloroplast division complex to be identified. ARC5 has no obvious counterparts in prokaryotes, suggesting that it evolved from a dynamin-related protein present in the eukaryotic ancestor of plants. These results indicate that the chloroplast division apparatus is of mixed evolutionary origin and that it shares structural and mechanistic similarities with both the cell division machinery of bacteria and the dynamin-mediated organellar fission machineries of eukaryotes.

Plant biotechnology in agriculture

Knowledge on plant genomes has progressed during the past few years. Two plant genomes, those of Arabidopsis thaliana and rice, have been sequenced. Our present knowledge of synteny also indicates that, despite plasticity contributing to the diversity of the plant genomes, the organization of genes is conserved within large sections of chromosomes. In parallel, novel plant transformation systems have been proposed, notably with regard to plastid transformation and the removal of selectable marker genes in transgenic plants. Furthermore, a number of recent works considerably widen the potential of plant biotechnology.

DNA transport in bacteria

DNA transport is important in various biological contexts--particularly chromosome segregation and intercellular gene transfer. Recently, progress has been made in understanding the function of a family of bacterial proteins involved in DNA transfer, and we focus here on one of the best-understood members, SpoIIIE. Studies of SpoIIIE-like proteins show that they might couple DNA transport to processes such as cell division, conjugation (mating) and the resolution of chromosome dimers.

Efficient vir gene induction in Agrobacterium tumefaciens requires virA, virG, and vir box from the same Ti plasmid

The vir genes of octopine, nopaline, and L,L-succinamopine Ti plasmids exhibit structural and functional similarities. However, we observed differences in the interactions between octopine and nopaline vir components. The induction of an octopine virE(A6)::lacZ fusion (pSM358cd) was 2.3-fold higher in an octopine strain (A348) than in a nopaline strain (C58). Supplementation of the octopine virG(A6) in a nopaline strain with pSM358 did not completely restore virE(A6) induction. However, addition of the octopine virA(A6) to the above strain increased virE(A6) induction to a level almost comparable to that in octopine strains. In a reciprocal analysis, the induction of a nopaline virE(C58)::cat fusion (pUCD1553) was two- to threefold higher in nopaline (C58 and T37) strains than in octopine (A348 and Ach5) and L,L-succinamopine (A281) strains. Supplementation of nopaline virA(C58) and virG(C58) in an octopine strain (A348) harboring pUCD1553 increased induction levels of virE(C58)::cat fusion to a level comparable to that in a nopaline strain (C58). Our results suggest that octopine and L,L-succinamopine VirG proteins induce the octopine virE(A6) more efficiently than they do the nopaline virE(C58). Conversely, the nopaline VirG protein induces the nopaline virE(C58) more efficiently than it does the octopine virE(A6). The ability of Bo542 virG to bring about supervirulence in tobacco is observed for an octopine vir helper (LBA4404) but not for a nopaline vir helper (PMP90). Our analyses reveal that quantitative differences exist in the interactions between VirG and vir boxes of different Ti plasmids. Efficient vir gene induction in octopine and nopaline strains requires virA, virG, and vir boxes from the respective Ti plasmids.

A second T-region of the soybean-supervirulent chrysopine-type Ti plasmid pTiChry5, and construction of a fully disarmed vir helper plasmid

Agrobacterium tumefaciens Chry5, which is particularly virulent on soybeans, induces tumors that produce a family of Amadori-type opines that includes deoxyfructosyl glutamine (Dfg) and its lactone, chrysopine (Chy). Cosmid clones mapping to the right of the known oncogenic T-region of pTiChry5 conferred Amadori opine production on tumors induced by the nopaline strain C58. Sequence analysis of DNA held in common among these cosmids identified two 25-bp, direct repeats flanking an 8.5-kb segment of pTiChry5. These probable border sequences are closely related to those of other known T-regions and define a second T-region of pTiChry5, called T-right (TR), that confers production of the Amadoriopines. The oncogenic T-left region (TL) was located precisely by identifying and sequencing the likely border repeats defining this segment. The two T-regions are separated by approximately 15 kb of plasmid DNA. Based on these results, we predicted that pKYRT1, a vir helper plasmid derived from pTiChry5, still contains all of TR and the leftmost 9 kb of TL. Consistent with this hypothesis, transgenic Arabidopsis thaliana plants selected for with a marker encoded by a binary plasmid following transformation with KYRT1 co-inherited production of the Amadori opines at high frequency. All opine-positive transgenic plants also contained TR-DNA, while those plants that lacked TR-DNA failed to produce the opines. Moreover, A. thaliana infected with KYRT1 in which an nptII gene driven by the 35S promoter of Cauliflower mosaic virus was inserted directly into the vir helper plasmid yielded kanamycin-resistant transformants at a low but detectable frequency. These results demonstrate that pKYRT1 is not disarmed, and can transfer Ti plasmid DNA to plants. A new vir helper plasmid was constructed from pTiChry5 by two rounds of sacB-mediated selection for deletion events. This plasmid, called pKPSF2, lacks both of the known T-regions and their borders. pKPSF2 failed to transfer Ti plasmid DNA to plants, but mobilized the T-region of a binary plasmid at an efficiency indistinguishable from those of pKYRT1 and the nopaline-type vir helper plasmid pMP90.

The N- and C-terminal portions of the Agrobacterium VirB1 protein independently enhance tumorigenesis

Genetic transformation of plants by Agrobacterium tumefaciens is mediated by a virulence (vir)-specific type IV secretion apparatus assembled from 11 VirB proteins and VirD4. VirB1, targeted to the periplasm by an N-terminal signal peptide, is processed to yield VirB1*, comprising the C-terminal 73 amino acids. The N-terminal segment, which shares homology with chicken egg white lysozyme as well as lytic transglycosylases, may provide local lysis of the peptidoglycan cell wall to create channels for transporter assembly. Synthesis of VirB1* followed by its secretion to the exterior of the cell suggests that VirB1* may also have a role in virulence. In the present study, we provide evidence for the dual roles of VirB1 in tumorigenesis as well as the requirements for processing and secretion of VirB1*. Complementation of a virB1 deletion strain with constructs expressing either the N-terminal lysozyme-homologous region or VirB1* results in tumors intermediate in size between those induced by a wild-type strain and a virB1 deletion strain, suggesting that each domain has a unique role in tumorigenesis. The secretion of VirB1* translationally fused to the signal peptide indicates that processing and secretion are not coupled. When expressed independently of all other vir genes, VirB1 was processed and VirB1* was secreted. When restricted to the cytoplasm by deletion of the signal peptide, VirB1 was neither processed nor secreted and did not restore virulence to the virB1 deletion strain. Thus, factors that mediate processing of VirB1 and secretion of VirB1* are localized in the periplasm or outer membrane and are not subject to vir regulation.

Phytoremediation of methylmercury pollution: merB expression in Arabidopsis thaliana confers resistance to organomercurials

Methylmercury is an environmental toxicant that biomagnifies and causes severe neurological degeneration in animals. It is produced by bacteria in soils and sediments that have been contaminated with mercury. To explore the potential of plants to extract and detoxify this chemical, we engineered a model plant, Arabidopsis thaliana, to express a modified bacterial gene, merBpe, encoding organomercurial lyase (MerB) under control of a plant promoter. MerB catalyzes the protonolysis of the carbon---mercury bond, removing the organic ligand and releasing Hg(II), a less mobile mercury species. Transgenic plants expressing merBpe grew vigorously on a wide range of concentrations of monomethylmercuric chloride and phenylmercuric acetate. Plants lacking the merBpe gene were severely inhibited or died at the same organomercurial concentrations. Six independently isolated transgenic lines produced merBpe mRNA and MerB protein at levels that varied over a 10- to 15-fold range, and even the lowest levels of merBpe expression conferred resistance to organomercurials. Our work suggests that native macrophytes (e.g., trees, shrubs, grasses) engineered to express merBpe may be used to degrade methylmercury at polluted sites and sequester Hg(II) for later removal.

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana

The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method was developed. The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77. Sucrose and surfactant were critical to the success of the floral dip method. Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate. Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities. Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold. Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold. Multiple ecotypes were transformable by this method. The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.

Characterization of transcription of genes involved in hairy root induction on pRi1724 core-T-DNA in two Ajuga reptans hairy root lines

The detailed status of the transcription of genes on pRil724 T-DNA in two independent hairy root lines of the plant Ajuga reptans, Ar-4 and Ar-24, which have several different characteristics, was obtained by Northern blotting and a reverse transcription-polymerase chain reaction (RT-PCR) analysis. In the Northern blotting analysis DNA fragments corresponding to the putative open reading frames (ORFs) as probes, transcripts from putative ORFs 10 (1724rolA), 11 (1724rolB), 12 (1724rolC), 13a and 14, which are homologs to each ORF on pRiA4, were detected in both hairy root lines, whereas no transcripts derived from ORF 13 were detected. The transcription of ORF 13 was, however, detected in the RT-PCR analysis, suggesting a minor expression of ORF 13. All of the putative ORFs were transcribed with their expected directions, since DNA fragments were amplified when the antisense primers were employed in the reverse transcription. We also found that different transcripts with a reverse direction were present at the locations of 1724rolA, 1724rolC and ORF 13a, because the DNA fragments were amplified from the templates when their sense primers were used in the reverse transcription.

PLANT TRANSFORMATION: Problems and Strategies for Practical Application

Plant transformation is now a core research tool in plant biology and a practical tool for cultivar improvement. There are verified methods for stable introduction of novel genes into the nuclear genomes of over 120 diverse plant species. This review examines the criteria to verify plant transformation; the biological and practical requirements for transformation systems; the integration of tissue culture, gene transfer, selection, and transgene expression strategies to achieve transformation in recalcitrant species; and other constraints to plant transformation including regulatory environment, public perceptions, intellectual property, and economics. Because the costs of screening populations showing diverse genetic changes can far exceed the costs of transformation, it is important to distinguish absolute and useful transformation efficiencies. The major technical challenge facing plant transformation biology is the development of methods and constructs to produce a high proportion of plants showing predictable transgene expression without collateral genetic damage. This will require answers to a series of biological and technical questions, some of which are defined.

Forest tree biotechnology

The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium.