New vectors and marker excision systems mark progress in engineering the plastid genome of higher plants

Dynamic morphology of plastids and stromules in angiosperm plants

Labelling of plastids with fluorescent proteins has revealed the diversity of their sizes and shapes in different tissues of vascular plants. Stromules, stroma-filled tubules comprising thin extensions of the stroma surrounded by the double envelope membrane, have been observed to emanate from all major types of plastid, though less common on chloroplasts. In some tissue types, stromules are highly dynamic, forming, shrinking, attaching, releasing and fragmenting. Stromule formation is negatively affected by treatment of tissue with cytoskeletal inhibitors. Plastids can be connected by stromules, through which green fluorescent protein (GFP) and fluorescently tagged chloroplast protein complexes have been observed to flow. Within the highly viscous stroma, proteins traffic by diffusion as well as by an active process of directional travel, whose mechanism is unknown. In addition to exchanging materials between plastids, stromules may also serve to increase the surface area of the envelope for import and export, reduce diffusion distance between plastids and other organelles for exchange of materials, and anchor the plastid onto attachment points for proper positioning with the plant cell. Future studies should reveal how these functions may affect plants in adapting to the challenges of a changing environment.

Improving containment strategies in biopharming

This review examines the challenges of segregating biopharmed crops expressing pharmaceutical or veterinary agents from mainstream crops, particularly those destined for food or feed use. The strategy of using major food crops as production vehicles for the expression of pharmaceutical or veterinary agents is critically analysed in the light of several recent episodes of contamination of the human food chain by non-approved crop varieties. Commercially viable strategies to limit or avoid biopharming intrusion into the human food chain require the more rigorous segregation of food and non-food varieties of the same crop species via a range of either physical or biological methods. Even more secure segregation is possible by the use of non-food crops, non-crop plants or in vitro plant cultures as production platforms for biopharming. Such platforms already under development range from outdoor-grown Nicotiana spp. to glasshouse-grown Arabidopsis, lotus and moss. Amongst the more effective methods for biocontainment are the plastid expression of transgenes, inducible and transient expression systems, and physical containment of plants or cell cultures. In the current atmosphere of heightened concerns over food safety and biosecurity, the future of biopharming may be largely determined by the extent to which the sector is able to maintain public confidence via a more considered approach to containment and security of its plant production systems.

Dicamba resistance: enlarging and preserving biotechnology-based weed management strategies

The advent of biotechnology-derived, herbicide-resistant crops has revolutionized farming practices in many countries. Facile, highly effective, environmentally sound, and profitable weed control methods have been rapidly adopted by crop producers who value the benefits associated with biotechnology-derived weed management traits. But a rapid rise in the populations of several troublesome weeds that are tolerant or resistant to herbicides currently used in conjunction with herbicide-resistant crops may signify that the useful lifetime of these economically important weed management traits will be cut short. We describe the development of soybean and other broadleaf plant species resistant to dicamba, a widely used, inexpensive, and environmentally safe herbicide. The dicamba resistance technology will augment current herbicide resistance technologies and extend their effective lifetime. Attributes of both nuclear- and chloroplast-encoded dicamba resistance genes that affect the potency and expected durability of the herbicide resistance trait are examined.

The genetic transformation of plastids

Biolistic delivery of DNA initiated plastid transformation research and still is the most widelyused approach to generate transplastomic lines in both algae and higher plants. The principal designof transformation vectors is similar in both phylogenetic groups. Although important additions tothe list of species transformed in their plastomes have been made in algae and in higher plants, thekey organisms in the area are still the two species, in which stable plastid transformation was initiallysuccessful, i.e., Chlamydomonas reinhardtii and tobacco. Basicresearch into organelle biology has substantially benefited from the homologous recombination-basedcapability to precisely insert at predetermined loci, delete, disrupt, or exchange plastid genomesequences. Successful expression of recombinant proteins, including pharmaceutical proteins, hasbeen demonstrated in Chlamydomonas as well as in higher plants,where some interesting agronomic traits were also engineered through plastid transformation.

Construction of marker-free transplastomic plants

Because of its prokaryotic-type gene expression machinery, maternal inheritance and the opportunity to express proteins at a high level, the plastid genome (plastome or ptDNA) is an increasingly popular target for engineering. The ptDNA is present as up to 10,000 copies per cell, making selection for marker genes essential to obtain plants with uniformly transformed ptDNA. However, the marker gene is no longer desirable when homoplastomic plants are obtained. Marker-free transplastomic plants can now be obtained with four recently developed protocols: homology-based excision via directly repeated sequences, excision by phage site-specific recombinanses, transient cointegration of the marker gene, and the cotransformation-segregation approach. Marker excision technology will benefit applications in agriculture and in molecular farming.

Transformation of the plastid genome to study RNA editing

In this chapter we provide an overview of cytosine-to-uridine (C-to-U) RNA editing in the plastids of higher plants. Particular emphasis will be placed on the role plastid transformation played in understanding the editing process. We discuss how plastid transformation enabled identification of mRNA cis elements for editing and gave the first insight into the role of editing trans factors. The introduction will be followed by a protocol for plastid transformation, including vector design employed to identify editing cis elements. We also discuss how to test RNA editing in vivo by cDNA sequencing. At the end, we summarize the status of the field and outline future directions.

Gene activation in plastids by the CRE site-specific recombinase

We developed a novel system for gene activation in plastids that uses the CRE/loxP site-specific recombination system to create a translatable reading frame by excision of a blocking sequence. To test the system, we introduced an inactive gfp* gene into the tobacco plastid genome downstream of the selectable spectinomcyin resistance (aadA) marker gene. The aadA gene is the blocking sequence, and is flanked by directly oriented loxP sites for excision by the CRE. In the non-activated state, gfp* is transcribed from the aadA promoter, but the mRNA is not translated due to the lack of an AUG translation initiation codon. Green Fluorescent Protein (GFP) expression is activated by excision of the aadA coding segment to link up the gfp* coding region with the translation initiation codon of aadA. Tobacco plants that carry the inactive gfp* gene do not contain detectable levels of GFP. However, activation of gfp* resulted in GFP accumulation, proving the utility of CRE-induced protein expression in tobacco chloroplasts. The gene activation system described here will be useful to probe plastid gene function and for the production of recombinant proteins in chloroplasts.

Isolation of precise plastid deletion mutants by homology-based excision: a resource for site-directed mutagenesis, multi-gene changes and high-throughput plastid transformation

We describe a simple and efficient homology-based excision method to delete plastid genes. The procedure allows one or more adjacent plastid genes to be deleted without the retention of a marker gene. We used aadA-based transformation to duplicate a 649 bp region of plastid DNA corresponding to the atpB promoter region. Efficient recombination between atpB repeats deletes the intervening foreign genes and 1,984 bp of plastid DNA (co-ordinates 57,424-59,317) containing the rbcL gene. Only five foreign bases are present in DeltarbcL plants illustrating the precision of homology-based excision. Sequence analysis of non-functional rbcL-related sequences in DeltarbcL plants indicated an extra-plastidic origin. Mutant DeltarbcL plants were heterotrophic, pale-green and contained round plastids with reduced amounts of thylakoids. Restoration of autotrophy and leaf pigmentation following aadA-based transformation with the wild-type rbcL gene ruled out mutations in other genes. Excision and re-use of aadA shows that, despite the multiplicity of plastid genomes, homology-based excision ensures complete removal of functional aadA genes. Rescue of the DeltarbcL mutation and autotrophic growth stabilizes transgenic plastids in heteroplasmic transformants following antibiotic withdrawal, enhancing the overall efficiency of plastid transformation. Unlike the available set of homoplasmic knockout mutants in 25 plastid genes, the rbcL deletion mutant isolated here is readily transformed with the efficient aadA marker gene. This improvement in deletion design facilitates advanced studies that require the isolation of double mutants in distant plastid genes and the replacement of the deleted locus with site-directed mutant alleles and is not easily achieved using other methods.

Construction of marker-free transplastomic tobacco using the Cre-loxP site-specific recombination system

Incorporation of a selectable marker gene in the plastid genome is essential to uniformly alter the thousands of genome copies in a tobacco cell. When transformation is accomplished, however, the marker gene becomes undesirable. Here we describe plastid transformation vectors, the method of plastid transformation using tobacco leaves and alternative protocols for marker gene excision with the P1 bacteriophage Cre-loxP site-specific recombination system. Plastid vectors carry a marker gene flanked with directly oriented loxP sites and a gene of interest, which are introduced into plastids by the biolistic process. The transforming DNA integrates into the plastid genome by homologous recombination via plastid targeting sequences. Marker gene excision is accomplished by a plastid-targeted Cre protein expressed from a nuclear gene. Expression may be from an integrated gene introduced by Agrobacterium transformation (Transformation Protocol), by pollination (Pollination Protocol) or from a transient, non-integrated T-DNA (Transient Protocol). Transplastomic plants are obtained in about 3 months, yielding seed after 2 months. The time required to remove the plastid marker and nuclear genes and to obtain seed takes 10-16 months, depending on which protocol is used.