Development of a Rep-inducible, BBTV-based expression system in banana

Banana bunchy top is regarded as the most important viral disease of banana, causing significant yield losses worldwide. The disease is caused by Banana bunchy top virus (BBTV), which is a circular ssDNA virus belonging to the genus Babuvirus in the family Nanoviridae. There are currently few effective control strategies for this and other ssDNA viruses. “In Plant Activation” (InPAct) is a novel technology being developed at QUT for ssDNA virus-activated suicide gene expression. The technology exploits the rolling circle replication mechanism of ssDNA viruses and is based on a unique “split” gene design such that suicide gene expression is only activated in the presence of the viral Rep. This PhD project aimed to develop a BBTV-based InPAct system as a suicide gene strategy to control BBTV. The BBTV-based InPAct vector design requires a BBTV intergenic region (IR) to be embedded within an intron in the gene expression cassette. To ensure that the BBTV IR would not interfere with intron splicing, a TEST vector was initially generated that contained the entire BBTV IR embedded within an intron in a β-glucuronidase (GUS) expression vector. Transient GUS assays in banana embryogenic cell suspensions indicated that cryptic intron splice sites were present within the IR. Transcript analysis revealed two cryptic intron splice sites in the Domain III sequence of the CR-M within the IR. Removal of the CR-M from the TEST vector resulted in an enhancement of GUS expression suggesting that the cryptic intron splice sites had been removed. An InPAct GUS vector was subsequently generated that contained the modified BBTV IR, with the CR-M (minus Domain III) repositioned within the InPAct cassette. Using transient histochemical and fluorometric GUS assays in banana embryogenic cells, the InPAct GUS vector was shown to be activated in the presence of the BBTV Rep. However, the presence of both BBTV Rep and Clink was shown to have a deleterious effect on GUS expression suggesting that these proteins were cytotoxic at the levels expressed. Analysis of replication of the InPAct vectors by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector through the nicking/ligation activity of BBTV Rep. However, Rep-mediated episomal replicons, indicative of rolling circle replication of the released circularised cassettes, were not observed. The inability of the InPAct cassette to be replicated was further investigated. To examine whether the absence of Domain III of the CR-M was responsible, a suite of modified BBTV-based InPAct GUS vectors was constructed that contained the CR-M with the inclusion of Domain III, the CR-M with the inclusion of Domain III and additional upstream IR sequence, or no CR-M. Analysis of replication by Southern hybridisation revealed that neither the presence of Domain III, nor the entire CR-M, had an effect on replication levels. Since the InPAct cassette was significantly larger than the native BBTV genomic components (approximately 1 kb), the effect of InPAct cassette size on replication was also investigated. A suite of size variant BBTV-based vectors was constructed that increased the size of a replication competent cassette to 1.1 kbp through to 2.1 kbp.. Analysis of replication by Southern hybridisation revealed that an increase in vector size above approximately 1.5 - 1.7 kbp resulted in a decrease in replication. Following the demonstration of Rep-mediated release, circularisation and expression from the InPAct GUS vector, an InPAct vector was generated in which the uidA reporter gene was replaced with the ribonuclease-encoding suicide gene, barnase. Initially, a TEST vector was generated to assess the cytotoxicity of Barnase on banana cells. Although transient assays revealed a Barnase-induced cytotoxic effect in banana cells, the expression levels were sub-optimal. An InPAct BARNASE vector was generated and tested for BBTV Rep-activated Barnase expression using transient assays in banana embryogenic cells. High levels of background expression from the InPAct BARNASE vector made it difficult to accurately assess Rep-activated Barnase expression. Analysis of replication by Southern hybridisation revealed low levels of InPAct cassette-based episomal DNA released from the vector but no Rep-mediated episomal replicons indicative of rolling circle replication of the released circularised cassettes were again observed. Despite the inability of the InPAct vectors to replicate to enable high level gene expression, the InPAct BARNASE vector was assessed in planta for BBTV Rep-mediated activation of Barnase expression. Eleven lines of transgenic InPAct BARNASE banana plants were generated by Agrobacterium-mediated transformation and were challenged with viruliferous Pentalonia nigronervosa. At least one clonal plant in each line developed bunchy top symptoms and infection was confirmed by PCR. No localised lesions were observed on any plants, nor was there any localised GUS expression in the one InPAct GUS line challenged with viruliferous aphids. The results presented in this thesis are the first study towards the development of a BBTV-based InPAct system as a Rep-activatable suicide gene expression system to control BBTV. Although further optimisation of the vectors is necessary, the preliminary results suggest that this approach has the potential to be an effective control strategy for BBTV. The use of iterons within the InPAct vectors that are recognised by Reps from different ssDNA plant viruses may provide a broad-spectrum resistance strategy against multiple ssDNA plant viruses. Further, this technology holds great promise as a platform technology for the molecular farming of high-value proteins in vitro or in vivo through expression of the ssDNA virus Rep protein.

The manipulation of apoptosis-related genes to generate resistance to Fusarium wilt and water stress in banana

Bananas are susceptible to a diverse range of biotic and abiotic stresses, many of which cause serious production constraints worldwide. One of the most destructive banana diseases is Fusarium wilt caused by the soil-borne fungus, Fusarium oxysporum f. sp. cubense (Foc). No effective control strategy currently exists for this disease which threatens global banana production. Although disease resistance exists in some wild bananas, attempts to introduce resistance into commercially acceptable bananas by conventional breeding have been hampered by low fertility, long generation times and association of poor agronomical traits with resistance genes. With the advent of reliable banana transformation protocols, molecular breeding is now regarded as a viable alternative strategy to generate disease-resistant banana plants. Recently, a novel strategy involving the expression of anti-apoptosis genes in plants was shown to result in resistance against several necrotrophic fungi. Further, the transgenic plants showed increased resistance to a range of abiotic stresses. In this thesis, the use of anti-apoptosis genes to generate transgenic banana plants with resistance to Fusarium wilt was investigated. Since water stress is an important abiotic constraint to banana production, the resistance of the transgenic plants to water stress was also examined. Embryogenic cell suspensions (ECS) of two commercially important banana cultivars, Grand Naine (GN) and Lady Finger (LF), were transformed using Agrobacterium with the anti-apoptosis genes, Bcl-xL, Bcl-xL G138A, Ced-9 and Bcl- 2 3’ UTR. An interesting, and potentially important, outcome was that the use of anti-apoptosis genes resulted in up to a 50-fold increase in Agrobacterium-mediated transformation efficiency of both LF and GN cells over vector controls. Regenerated plants were subjected to a complete molecular characterisation in order to detect the presence of the transgene (PCR), transcript (RT-PCR) and gene product (Western blot) and to determine the gene copy number (Southern blot). A total of 36 independently-transformed GN lines (8 x Bcl-xL, 5 x Bcl-xL G138A, 15 x Ced-9 and 8 x Bcl-2 3’ UTR) and 41 independently-transformed LF lines (8 x Bcl-xL, 7 x BclxL G138A, 13 x Ced-9 and 13 x Bcl-2 3’ UTR) were identified. The 41 transgenic LF lines were multiplied and clones from each line were acclimatised and grown under glasshouse conditions for 8 weeks to allow monitoring for phenotypic abnormalities. Plants derived from 3 x Bcl-xL, 2 x Ced-9 and 5 x Bcl-2 3’ UTR lines displayed a variety of aberrant phenotypes. However, all but one of these abnormalities were off-types commonly observed in tissue-cultured, non-transgenic banana plants and were therefore unlikely to be transgene-related. Prior to determining the resistance of the transgenic plants to Foc race 1, the apoptotic effects of the fungus on both wild-type and Bcl-2 3’ UTR-transgenic LF banana cells were investigated using rapid in vitro root assays. The results from these assays showed that apoptotic-like cell death was elicited in wild-type banana root cells as early as 6 hours post-exposure to fungal spores. In contrast, these effects were attenuated in the root cells of Bcl-2 3’ UTR-transgenic lines that were exposed to fungal spores. Thirty eight of the 41 transgenic LF lines were subsequently assessed for resistance to Foc race 1 in small-plant glasshouse bioassays. To overcome inconsistencies in rating the internal (vascular discolouration) disease symptoms, a MatLab-based computer program was developed to accurately and reliably assess the level of vascular discolouration in banana corms. Of the transgenic LF banana lines challenged with Foc race 1, 2 x Bcl-xL, 3 x Ced-9, 2 x Bcl-2 3’ UTR and 1 x Bcl-xL G138A-transgenic line were found to show significantly less external and internal symptoms than wild-type LF banana plants used as susceptible controls at 12 weeks post-inoculation. Of these lines, Bcl-2 3’ UTR-transgenic line #6 appeared most resistant, displaying very mild symptoms similar to the wild-type Cavendish banana plants that were included as resistant controls. This line remained resistant for up to 23 weeks post-inoculation. Since anti-apoptosis genes have been shown to confer resistance to various abiotic stresses in other crops, the ability of these genes to confer resistance against water stress in banana was also investigated. Clonal plants derived from each of the 38 transgenic LF banana plants were subjected to water stress for a total of 32 days. Several different lines of transgenic plants transformed with either Bcl-xL, Bcl-xL G138A, Ced-9 or Bcl-2 3’ UTR showed a delay in visual water stress symptoms compared with the wild-type control plants. These plants all began producing new growth from the pseudostem following daily rewatering for one month. In an attempt to determine whether the protective effect of anti-apoptosis genes in transgenic banana plants was linked with reactive oxygen species (ROS)-associated programmed cell death (PCD), the effect of the chloroplast-targeting, ROS-inducing herbicide, Paraquat, on wild-type and transgenic LF was investigated. When leaf discs from wild-type LF banana plants were exposed to 10 ìM Paraquat, complete decolourisation occurred after 48 hours which was confirmed to be associated with cell death and ROS production by trypan blue and 3,3-diaminobenzidine (DAB) staining, respectively. When leaf discs from the transgenic lines were exposed to Paraquat, those derived from some lines showed a delay in decolourisation, suggesting only a weak protective effect from the transgenes. Finally, the protective effect of anti-apoptosis genes against juglone, a ROS-inducing phytotoxin produced by the causal agent of black Sigatoka, Mycosphaerella fijiensis, was investigated. When leaf discs from wild-type LF banana plants were exposed to 25 ppm juglone, complete decolourisation occurred after 48 hours which was again confirmed to be associated with cell death and ROS production by trypan blue and DAB staining, respectively. Further, TdT-mediated dUTP nick-end labelling (TUNEL) assays on these discs suggested that the cell death was apoptotic. When leaf discs from the transgenic lines were exposed to juglone, discs from some lines showed a clear delay in decolourisation, suggesting a protective effect. Whether these plants are resistant to black Sigatoka is unknown and will require future glasshouse and field trials. The work presented in this thesis provides the first report of the use of anti-apoptosis genes as a strategy to confer resistance to Fusarium wilt and water stress in a nongraminaceous monocot, banana. Such a strategy may be exploited to generate resistance to necrotrophic pathogens and abiotic stresses in other economically important crop plants.

Investigation of highly regulated promoters for the production of recombinant proteins in plants

Plants have been identified as promising expression systems for the commercial production of recombinant proteins. Plant-based protein production or “biofarming” offers a number of advantages over traditional expression systems in terms of scale of production, the capacity for post-translation processing, providing a product free of contaminants and cost effectiveness. A number of pharmaceutically important and commercially valuable proteins, such as antibodies, biopharmaceuticals and industrial enzymes are currently being produced in plant expression systems. However, several challenges still remain to improve recombinant protein yield with no ill effect on the host plant. The ability for transgenic plants to produce foreign proteins at commercially viable levels can be directly related to the level and cell specificity of the selected promoter driving the transgene. The accumulation of recombinant proteins may be controlled by a tissue-specific, developmentally-regulated or chemically-inducible promoter such that expression of recombinant proteins can be spatially- or temporally- controlled. The strict control of gene expression is particularly useful for proteins that are considered toxic and whose expression is likely to have a detrimental effect on plant growth. To date, the most commonly used promoter in plant biotechnology is the cauliflower mosaic virus (CaMV) 35S promoter which is used to drive strong, constitutive transgene expression in most organs of transgenic plants. Of particular interest to researchers in the Centre for Tropical Crops and Biocommodities at QUT are tissue-specific promoters for the accumulation of foreign proteins in the roots, seeds and fruit of various plant species, including tobacco, banana and sugarcane. Therefore this Masters project aimed to isolate and characterise root- and seed-specific promoters for the control of genes encoding recombinant proteins in plant-based expression systems. Additionally, the effects of matching cognate terminators with their respective gene promoters were assessed. The Arabidopsis root promoters ARSK1 and EIR1 were selected from the literature based on their reported limited root expression profiles. Both promoters were analysed using the PlantCARE database to identify putative motifs or cis-acting elements that may be associated with this activity. A number of motifs were identified in the ARSK1 promoter region including, WUN (wound-inducible), MBS (MYB binding site), Skn-1, and a RY core element (seed-specific) and in the EIR1 promoter region including, Skn-1 (seed-specific), Box-W1 (fungal elicitor), Aux-RR core (auxin response) and ABRE (ABA response). However, no previously reported root-specific cis-acting elements were observed in either promoter region. To confirm root specificity, both promoters, and truncated versions, were fused to the GUS reporter gene and the expression cassette introduced into Arabidopsis via Agrobacterium-mediated transformation. Despite the reported tissue-specific nature of these promoters, both upstream regulatory regions directed constitutive GUS expression in all transgenic plants. Further, similar levels of GUS expression from the ARSK1 promoter were directed by the control CaMV 35S promoter. The truncated version of the EIR1 promoter (1.2 Kb) showed some differences in the level of GUS expression compared to the 2.2 Kb promoter. Therefore, this suggests an enhancer element is contained in the 2.2 Kb upstream region that increases transgene expression. The Arabidopsis seed-specific genes ATS1 and ATS3 were selected from the literature based on their seed-specific expression profiles and gene expression confirmed in this study as seed-specific by RT-PCR analysis. The selected promoter regions were analysed using the PlantCARE database in order to identify any putative cis elements. The seed-specific motifs GCN4 and Skn-1 were identified in both promoter regions that are associated with elevated expression levels in the endosperm. Additionaly, the seed-specific RY element and the ABRE were located in the ATS1 promoter. Both promoters were fused to the GUS reporter gene and used to transform Arabidopsis plants. GUS expression from the putative promoters was consitutive in all transgenic Arabidopsis tissue tested. Importantly, the positive control FAE1 seed-specific promoter also directed constitutive GUS expression throughout transgenic Arabidopsis plants. The constitutive nature seen in all of the promoters used in this study was not anticipated. While variations in promoter activity can be caused by a number of influencing factors, the variation in promoter activity observed here would imply a major contributing factor common to all plant expression cassettes tested. All promoter constructs generated in this study were based on the binary vector pCAMBIA2300. This vector contains the plant selection gene (NPTII) under the transcriptional control of the duplicated CaMV 35S promoter. This CaMV 35S promoter contains two enhancer domains that confer strong, constitutive expression of the selection gene and is located immediately upstream of the promoter-GUS fusion. During the course of this project, Yoo et al. (2005) reported that transgene expression is significantly affected when the expression cassette is located on the same T-DNA as the 35S enhancer. It was concluded, the trans-acting effects of the enhancer activate and control transgene expression causing irregular expression patterns. This phenomenon seems the most plausible reason for the constitutive expression profiles observed with the root- and seed-specific promoters assessed in this study. The expression from some promoters can be influenced by their cognate terminator sequences. Therefore, the Arabidopsis ARSK1, EIR1, ATS1 and ATS3 terminator sequences were isolated and incorporated into expression cassettes containing the GUS reporter gene under the control of their cognate promoters. Again, unrestricted GUS activity was displayed throughout transgenic plants transformed with these reporter gene fusions. As previously discussed constitutive GUS expression was most likely due to the trans-acting effect of the upstream CaMV 35S promoter in the selection cassette located on the same T-DNA. The results obtained in this study make it impossible to assess the influence matching terminators with their cognate promoters have on transgene expression profiles. The obvious future direction of research continuing from this study would be to transform pBIN-based promoter-GUS fusions (ie. constructs containing no CaMV 35S promoter driving the plant selection gene) into Arabidopsis in order to determine the true tissue specificity of these promoters and evaluate the effects of their cognate 3’ terminator sequences. Further, promoter truncations based around the cis-elements identified here may assist in determining whether these motifs are in fact involved in the overall activity of the promoter.

Towards the biofortification of banana fruit for enhanced micronutrient content

In Uganda, vitamin A deficiency (VAD) and iron deficiency anaemia (IDA) are major public health problems with between 15-32% of children under 5 years of age showing VAD and 73% being anaemic. This is largely due to the fact that the staple food crop of the country, banana, is low in pro-vitamin A and iron, therefore leading to dietary deficiencies. Although worldwide progress has been made to control VAD and IDA through supplementation, food fortification and diet diversification, their long term sustainability and impact in developing countries such as Uganda is limited. The approach taken by researchers at Queensland University of Technology (QUT), Australia, in collaboration with the National Agricultural Research Organization (NARO), Uganda, to address this problem, is to generate consumer acceptable banana varieties with significantly increased levels of pro-vitamin A and iron in the fruit using genetic engineering techniques. Such an approach requires the use of suitable, well characterised genes and promoters for targeted transgene expression. Recently, a new banana phytoene synthase gene (APsy2a) involved in the synthesis of pro-vitamin A (pVA) carotenoids was isolated from a high â-carotene banana (F’ei cv Asupina). In addition, sequences of banana ferritin, an iron storage protein, have been isolated from Cavendish banana. The aim of the research described in this thesis was to evaluate the function of these genes to assess their suitability for the biofortification of banana fruit. In addition, a range of banana-derived promoters were characterised to determine their suitability for controlling the expression of transgenes in banana fruit. Due to the time constraints involved with generating transgenic banana fruit, rice was used as the model crop to investigate the functionality of the banana-derived APsy2a and ferritin genes. Using Agrobacterium-mediated transformation, rice callus was transformed with APsy2a +/- the bacterial-derived carotene desaturase gene (CrtI) each under the control of the constitutive maize poly-ubiquitin promoter (ZmUbi) or seed-specific rice glutelin1 (Gt1) promoter. The maize phytoene synthase (ZmPsy1) gene was included as a control. On selective media, with the exception of ZmUbi-CrtI-transgenic callus, all antibiotic resistant callus displayed a yellow-orange colour from which the presence of â-carotene was demonstrated using Raman spectroscopy. Although the regeneration of plants from yellow-orange callus was difficult, 16 transgenic plants were obtained and characterised from callus transformed with ZmUbi-APys2a alone. At least 50% of the T1 seeds developed a yellow-orange coloured callus which was found to contain levels of â-carotene ranging from 4.6-fold to 72-fold higher than that in non-transgenic rice callus. Using the seed-specific Gt1 promoter, 38 transgenic rice plants were generated from APsy2a-CrtI-transformed callus while 32 plants were regenerated from ZmPsy1-CrtI-transformed callus. However, when analysed for presence of transgene by PCR, all transgenic plants contained the APsy2a, ZmPsy1 or CrtI transgene, with none of the plants found to be co-transformed. Using Raman spectroscopy, no â-carotene was detected in-situ in representative T1 seeds. To investigate the potential of the banana-derived ferritin gene (BanFer1) to enhance iron content, rice callus was transformed with constitutively expressed BanFer1 using the soybean ferritin gene (SoyFer) as a control. A total of 12 and 11 callus lines independently transformed with BanFer1 and SoyFer, respectively, were multiplied and transgene expression was verified by RT-PCR. Pearl’s Prussian blue staining for in-situ detection of ferric iron showed a stronger blue colour in rice callus transformed with BanFer1 compared to SoyFer. Using flame atomic absorption spectrometry, the highest mean amount of iron quantified in callus transformed with BanFer1 was 30-fold while that obtained using the SoyFer was 14-fold higher than the controls. In addition, ~78% of BanFer1-transgenic callus lines and ~27% of SoyFer-transgenic callus lines had significantly higher iron content than the non-transformed controls. Since the genes used for enhancing micronutrient content need to be expressed in banana fruit, the activity of a range of banana-derived, potentially fruit-active promoters in banana was investigated. Using uidA (GUS) as a reporter gene, the function of the Expansin1 (MaExp1), Expansin1 containing the rice actin intron (MaExp1a), Expansin4 (MaExp4), Extensin (MaExt), ACS (MaACS), ACO (MaACO), Metallothionein (MaMT2a) and phytoene synthase (APsy2a) promoters were transiently analysed in intact banana fruit using two transformation methods, particle bombardment and Agrobacterium-mediated infiltration (agro-infiltration). Although a considerable amount of variation in promoter activity was observed both within and between experiments, similar trends were obtained using both transformation methods. The MaExp1 and MaExp1a directed high levels of GUS expression in banana fruit which were comparable to those observed from the ZmUbi and Banana bunchy top virus-derived BT4 promoters that were included as positive controls. Lower levels of promoter activity were obtained in both methods using the MaACO and MaExt promoters while the MaExp4, MaACS, and APsy2a promoters directed the lowest GUS activity in banana fruit. An attempt was subsequently made to use agro-infiltration to assess the expression of pVA biosynthesis genes in banana fruit by infiltrating fruit with constructs in which the ZmUbi promoter controlled the expression of APsy2a +/- CrtI, and with the maize phytoene synthase gene (ZmPsy1) included as a control. Unfortunately, the large amount of variation and inconsistency observed within and between experiments precluded any meaningful conclusions to be drawn. The final component of this research was to assess the level of promoter activity and specificity in non-target tissue. These analyses were done on leaves obtained from glasshouse-grown banana plants stably transformed with MaExp1, MaACO, APsy2a, BT4 and ZmUbi promoters driving the expression of the GUS gene in addition to leaves from a selection of the same transgenic plants which were growing in a field trial in North Queensland. The results from both histochemical and fluorometric GUS assays showed that the MaExp1 and MaACO promoters directed very low GUS activities in leaves of stably transformed banana plants compared to the constitutive ZmUbi and BT4 promoters. In summary, the results from this research provide evidence that the banana phytoene synthase gene (APsy2a) and the banana ferritin gene (BanFer1) are functional, since the constitutive over-expression of each of these transgenes led to increased levels of pVA carotenoids (for APsy2a) and iron content (for BanFer1) in transgenic rice callus. Further work is now required to determine the functionality of these genes in stably-transformed banana fruit. This research also demonstrated that the MaExp1 and MaACO promoters are fruit-active but have low activity in non-target tissue (leaves), characteristics that make them potentially useful for the biofortification of banana fruit. Ultimately, however, analysis of fruit from field-grown transgenic plants will be required to fully evaluate the suitability of pVA biosynthesis genes and the fruit-active promoters for fruit biofortification.

Generating transgenic banana (cv. Sukali Ndizi) resistant to Fusarium Wilt

Banana is one of the world’s most popular fruit crops and Sukali Ndizi is the most popular dessert banana in the East African region. Like other banana cultivars, Sukali Ndizi is threatened by several constraints, of which the Fusarium wilt disease is the most destructive. Fusarium wilt is caused by a soil-borne fungus, Fusarium oxysporum f.sp. cubense (Foc). No effective control strategy currently exists for this disease and although disease resistance exists in some banana cultivars, introducing resistance into commercial cultivars by conventional breeding is difficult because of low fertility. Considering that conventional breeding generates hybrids with additional undesirable traits, transformation is the most suitable way of introducing resistance in the banana genome. The success of this strategy depends on the availability of genes for genetic transformation. Recently, a novel strategy involving the expression of anti-apoptosis genes in plants was shown to result in resistance against several necrotrophic fungi, including Foc race 1 in banana cultivar Lady Finger. This thesis explores the potential of a plant-codon optimised nematode anti-apoptosis gene (Mced9) to provide resistance against Foc race 1 in dessert banana cultivar Sukali Ndizi. Agrobacterium-mediated transformation was used to transform embryogenic cell suspension of Sukali Ndizi with plant expression vector pYC11, harbouring maize ubiquitin promoter driven Mced9 gene and nptII as a plant selection marker. A total of 42 independently transformed lines were regenerated and characterized. The transgenic lines were multiplied, infected and evaluated for resistance to Foc race 1 in a small pot bioassay. The pathogenicity of the Ugandan Foc race 1 isolate used for infection was pre-determined and the spore concentration was standardised for consistent infection and symptom development. This process involved challenging tissue culture plants of Sukali Ndizi, a Foc race 1 susceptible cultivar and Nakinyika, an East African Highland cultivar known to be resistant to Foc race 1, with Fusarium inoculum and observing external and internal disease symptom development. Rhizome discolouration symptoms were the best indicators of Fusarium wilt with yellowing being an early sign of disease. Three transgenic lines were found to show significantly less disease severities compared to the wild-type control plants after 13 weeks of infection, indicating that Mced9 has the potential to provide tolerance to Fusarium wilt in Sukali Ndizi.

Improved molecular tools for sugar cane biotechnology

Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

Physiological basis of salt stress tolerance in rice expressing the antiapoptotic gene SfIAP

Programmed cell death-associated genes, especially antiapoptosis-related genes have been reported to confer tolerance to a wide range of biotic and abiotic stresses in dicotyledonous plants such as tobacco (Nicotiana tabacum L.) and tomato (Solanum lycopersicum L.). This is the first time the antiapoptotic gene SfIAP was transformed into a monocotyledonous representative: rice (Oryza sativa L.). Transgenic rice strains expressing SfIAP were generated by the Agrobacterium-mediated transformation method and rice embryogenic calli, and assessed for their ability to confer tolerance to salt stress at both the seedling and reproductive stages using a combination of molecular, agronomical, physiological and biochemical techniques. The results show that plants expressing SfIAP have higher salt tolerance levels in comparison to the wild-type and vector controls. By preventing cell death at the onset of salt stress and maintaining the cell membrane’s integrity, SfIAP transgenic rice plants can retain plant water status, ion homeostasis, photosynthetic efficiency and growth to combat salinity successfully.

Development of a transient, high-level expression platform for protein production in plants

Plants are an attractive alternative to conventional expression systems for the production of recombinant proteins and useful biologics, however, the economic viability of plant made proteins is strongly yield dependent. This study aimed to improve transgene expression levels in the plant host Nicotiana benthamiana using the Agroinfiltration transient expression platform. Independent investigation of the physical, chemical and genetic features associated with Agroinfiltration identified factors that improved transformation frequencies, elevated transgene expression levels and ultimately improved protein yield. The major outcome of this research was a novel hyper-expression system for biofarming recombinant proteins in plants.

Interactions between transgenic trees and mycorrhizal and pathogenic fungi

The development of biotechnology techniques in plant breeding and the new commercial applications have raised public and scientific concerns about the safety of genetically modified (GM) crops and trees. To find out the feasibility of these new technologies in the breeding of commercially important Finnish hardwood species and to estimate the ecological risks of the produced transgenic plants, the experiments of this study have been conducted as a part of a larger project focusing on the risk assessment of GM-trees. Transgenic Betula pendula and Populus trees were produced via Agrobacterium mediated transformation. Stilbene synthase (STS) gene from pine (Pinus sylvestris) and chitinase gene from sugar beet (Beta vulgaris) were transferred to (hybrid) aspen and birch, respectively, to improve disease resistance against fungal pathogens. To modify lignin biosynthesis, a 4-coumarate:coenzyme A ligase (4CL) gene fragment in antisense orientation was introduced into two birch clones. In in vitro test, one transgenic aspen line expressing pine STS gene showed increased resistance to decay fungus Phellinus tremulae. In the field, chitinase transgenic birch lines were more susceptible to leaf spot (Pyrenopeziza betulicola) than the non-transgenic control clone while the resistance against birch rust (Melampsoridium betulinum) was improved. No changes in the content or composition of lignin were detected in the 4CL antisense birch lines. In order to evaluate the ecological effects of the produced GM trees on non-target organisms, an in vitro mycorrhiza experiment with Paxillus involutus and a decomposition experiment in the field were performed. The expression of a transgenic chitinase did not disturb the establishment of mycorrhizal symbiosis between birch and P. involutus in vitro. 4CL antisense transformed birch lines showed retarded root growth but were able to form normal ectomycorrhizal associations with the mycorrhizal fungus in vitro. 4CL lines also showed normal litter decomposition. Unexpected growth reductions resulting from the gene transformation were observed in chitinase transgenic and 4CL antisense birch lines. These results indicate that genetic engineering can provide a tool in increasing disease resistance in Finnish tree species. More extensive data with several ectomycorrhizal species is needed to evaluate the consequences of transgene expression on beneficial plant-fungus symbioses. The potential pleiotropic effects of the transgene should also be taken into account when considering the safety of transgenic trees.

BADH基因转化番茄提高耐盐性的研究

甜菜碱是植物在盐、干旱或其它胁迫下在细胞中迅速积累的一种相容性有机小分子化合物，它在细胞中的积累与植物抗盐性的提高密切相关。甜菜碱醛脱氢酶（BADH）催化甜菜碱醛转化为甜菜碱。我们将来源于耐盐植物山菠菜（Atriplx hortensis L.）的BADH基因通过农杆菌介导法导入‘百丽春’番茄(Lycopersicon esculentum L. ‘Bailichun’)中，并获得15株转化植株，PCR、Southern和Northern检测表明，其中的6株有外源BADH基因的整合，5株中BADH基因能够正常表达，但不同植株间BADH基因的表达水平和BADH酶活力有较大差异。对叶片电导率的测定表明，转基因植株比野生型的耐盐性有较大提高。T1代分析表明，检测的两个转基因株系后代遵循孟德尔分离规律，90mmol/L NaCl胁迫下种子发芽率提高了2~4倍，幼苗的苗高、根长和须根数三个指标均明显优于对照。部分T1代植株在水培条件下能够耐受180mmol/L NaCl胁迫。 植物耐盐的另一机理就是利用液泡膜上存在的转运蛋白将细胞内的有毒离子区域化。我们将已转入编码转运蛋白基因AtNHX1的番茄品种‘Moneymaker’（L. esculentum‘Moneymaker’）株系X1OEA1通过农杆菌介导法转入山菠菜BADH基因，以期获得转双基因耐盐番茄。目前已获得转基因植株，PCR结果证明部分抗性幼苗中已整合了BADH基因，其它各项分子检测正在进行中。

农杆菌介导的双价抗盐基因转化番茄的研究

近年来，植物耐盐生物技术研究取得了可喜的进展，特别是通过抗盐基因转化在一定程度上使植物的耐盐性得到了提高。然而，植物的耐盐性是一个多基因控制的复杂性状，依赖于多个基因之间的相互作用。因此，只是将单个基因导入植物获得的抗逆性还是远不能达到满意的效果。一般认为，将多个与耐盐相关的基因转入到同一个植物（即所谓的“复合基因转化”）将会大大提高转基因植物的耐盐能力。 渗透调节是植物抵御盐胁迫的主要方式。植物渗透调节的方式分为两类：一是在细胞中吸收和积累无机盐，如通过离子通道、Na+/H+逆向运输蛋白和ATP酶/H+泵;二是在细胞中合成有机溶质，如脯氨酸和甘氨酸甜菜碱。 我们通过农杆菌介导法向转AtNHX1（拟南芥Na+/H+逆向运输蛋白编码基因）的番茄（Lycopersicum esculentum L. ‘Moneymaker’）株系X1OEA1自交二代植株（T2）中转入山菠菜甜菜碱醛脱氢酶基因（BADH）。PCR、Southern、RT-PCR和甜菜碱含量分析结果证明，BADH已经整合到目标植物基因组，并在转基因植株中转录和翻译表达。叶绿素荧光（Fv/Fm）、相对电导率（Rc/Rc’）、叶绿素含量（Chla+b）、叶绿素a/b比（Chla/b）和光合速率（Pn）测定结果表明，在200 mM NaCl 胁迫下，二次转化的番茄植株各项生理指标均优于转单基因AtNHX1的番茄。初步证明“复合基因转化”有助于进一步提高植物的耐盐性。同时对番茄的转化系统进行了优化，结果表明使用抗生素‘特美汀’作为抑制农杆菌的抗生素的转化效率明显高于使用头孢霉素。

二穗短柄草的遗传转化及VER2等基因在水稻中的功能初探

作为模式植物，水稻和拟南芥对于禾本科植物的研究都有其不足，二穗短柄草（Brachypodiumdistachyon）有望成为它们良好的补充。它具有作为一种模式植物所应该具有的各项优点，并且它与温带禾本科植物的亲缘关系比水稻更近。建立其良好转化体系是其成功应用的一环。本论文第一章以建立其农杆菌转化体系为目的，成功的诱导了其胚性愈伤组织，获得了潮霉素抗性愈伤，发现乙酰丁香酮浓度与转化效率的关系，并证明Silwet L-77对提高其转化效率有明显的作用，为进一步完善其转化体系打下了基础。 VER2是由本实验室发现的小麦春化相关基因，并己证明它可能参与春化过程中O-CJlcNAc介导的信号传导。本论文第二章研究了将VER2在水稻中过表达所引起的表型，发现VER2与光有类似的抑制根生长的作用，并且能够互相影响对方的表型，说明二者在水稻内调控根生长的信号途径既有共同的作用，但是又相互制约。进一步的研究有可能会找到水稻根内IAA响应的重要因子。 在第三章中，根据芯片数据克隆了水稻的十个可能与赤霉素、茉莉酸和减数分裂相关的上下调基因，并对其中四个利用过表达和RNAi技术进行了水稻转化，以研究它们在水稻中的功能。其中一个基因过表达的表型与赤霉素缺陷造成矮化和叶色深绿两个特征一致，而RNAi导致植株高度增加、叶色黄绿。而该基因受赤霉素诱导上调的程度在三个芯片杂交结果中最大(log2=2.3275)这一点也为其功能提供了很好的提示，即可能参与了赤霉素信号途径。

盐角草（Salicornia europaea L.）SePSY和SeLCY基因克隆及功能分析

盐角草（Salicornia europaea L.）是一种叶片退化而茎肉质化，不具有盐腺和盐囊泡的真盐生植物，可以在1020 mM NaCl下生存。其特殊的形态适应特点使其成为研究植物抗盐性的良好实验材料。但目前与盐角草抗盐机理相关的生理和分子方面的研究还非常有限。本文以盐角草为材料，首先探讨了盐分和渗透胁迫对其光合作用和渗透平衡的影响，在此基础上进一步克隆了盐角草类胡萝卜素合成途径中的两个关键酶，八氢番茄红素合成酶（SePSY）和番茄红素β-环化酶（SeLCY）基因，并进行了功能分析。该研究对于了解类胡萝卜素在植物抗盐性中所起的作用具有重要意义。 盐分和渗透胁迫对其光合作用和渗透平衡影响的实验结果表明：200 mM NaCl是盐生植物盐角草生长的最适盐浓度，在该盐度下盐角草中叶绿素a/b的比值和光饱和点升高，植株的光合作用表现出增强的效应，植株生长最佳。而27％ PEG-6000所模拟的渗透胁迫显著降低了盐角草中叶绿色a/b的比值，抑制其光合作用和生长。200 mM NaCl下，Na+的含量显著增加，但脯氨酸含量保持不变，说明Na+对盐角草渗透平衡的作用要强于脯氨酸。同时盐角草中液泡H+-ATPase（V-H+-ATPase）活性增强，而盐角草Na+/H+逆向转运蛋白基因（SeNHX1）在盐分和渗透胁迫下却表现为组成型表达;我们因此推断在盐分胁迫下，Na+的吸收是由于液泡H+-ATPase活性的增强，而不是诱导SeNHX1基因的表达。同时Na+的吸收可能进一步诱导了与光合作用相关基因的表达。 盐分对植物的影响涉及植物体内包括光合作用和活性氧代谢在内的多个代谢过程。在植物中，类胡萝卜素是植物捕光天线复合体（LHC）和光系统反应中心叶绿素结合蛋白的重要组成部分。植物体内类胡萝卜素能够清除植物叶绿体，线粒体和过氧化物体在电子传递过程中产生的活性氧。同时类胡萝卜素是植物激素ABA的前体。200 mM NaCl虽然增加了盐角草细胞的渗透势，但并没有对其造成氧化胁迫和离子毒害，相反提高了其光合能力。类胡萝卜素作为植物活性氧的淬灭剂和光系统的组成成分，可能在盐角草抗盐机理中发挥着比较重要的作用。在过去的十年中，类胡萝卜素研究大多集中在其生物合成和提高作物中类胡萝卜素含量方面，可是，在植物对非生物逆境（如氧化和盐分胁迫）的适应机制中，类胡萝卜素合成途径究竟发挥什么作用目前还不是很清楚。为了了解盐角草中类胡萝卜素合成途径在植物逆境的适应机制中所发挥的作用，本文采用RACE的方法克隆了盐角草类胡萝卜素合成途径中的两个关键酶基因 SePSY和SeLCY，将它们构建到植物表达载体SN1301中，转化拟南芥，并对它们进行了初步的功能分析。 研究发现盐角草SePSY基因全长1655 bp，编码419个氨基酸，推测分子量为47.2 kDa，等电点为8.92。其蛋白在1-65个氨基酸处有一个信号肽。在1-19和242-264氨基酸处有2个跨膜区。盐角草SeLCY基因全长1937 bp，编码498个氨基酸，推测分子量为56.1 kDa，等电点为8.41。其蛋白在1-37个氨基酸处有一个信号肽。在79-96，367-385和454-474氨基酸处有3个跨膜区。SePSY和SeLCY基因过量表达均促进转基因拟南芥的生长，转SePSY基因拟南芥次生根数目比野生型拟南芥明显增多。SePSY和SeLCY基因的过量表达还使转基因拟南芥对百草枯的抗性得到提高;SePSY基 因的过量表达增强了植株体内抗氧化保护酶过氧化物酶（POD），超氧化物歧化酶（SOD）活性，但过氧化氢酶 （CAT）的变化不显著;转SeLCY基因株系POD，SOD，CAT的活性都有所增强，但转SePSY基因株系中POD活性明显高于 转SeLCY基因株系。转SePSY和SeLCY基因拟南芥叶片中丙二醛（MDA）和H2O2含量均降低，但转SePSY基因株系中MDA和H2O2含量明显低于转SeLCY基因株系。说明转基因拟南芥对氧化胁迫的抗性得到了提高，同时使得光系统II（PSII）和细胞膜的结构和功能不被破坏。而转SePSY基因株系对盐分和氧化胁迫的抗性明显高于转SeLCY基因株系。SePSY和SeLCY基因的过量表达还提高了转基因拟南芥的光合效率，气孔导度和Fv/Fm比值。 SePSY和SeLCY基因转化拟南芥及其功能分析的初步结果表明，SePSY和SeLCY基因的过量表达提高了转基因拟南芥对体内活性氧（ROS）的清除能力，增强了拟南芥的光合能力，进而提高了拟南芥的抗盐性。

SeNHX1和BADH基因提高植物耐盐性的研究

土壤的盐碱化问题已经严重影响到世界范围内许多重要作物的生产。培育耐盐作物是解决这一问题的最有效途经。利用耐盐相关基因的转化可以在不改变或很少改变植物其它性状的情况下提高植物的耐盐性，因此基因工程方法对于改良植物耐盐性及其机理的研究具有重要的意义。目前植物耐盐基因工程从调控渗透调节物质和盐离子区隔化两个方面开展了较多的研究。已经获得一些耐盐性提高的转基因植物。 本研究拟用耐盐性较强植物山菠菜中的甜菜碱合成关键基因BADH和盐生植物盐角草的液泡膜Na+/H+ anitiporter基因SeNHX1对模式植物烟草进行转化，以确定其各自在耐盐性方面所起的作用。同时，现有的研究表明植物的耐盐性是多基因控制的复杂性状，因此拟把SeNHX1和BADH 这两个涉及不同耐盐机理的基因构建到同一个植物表达载体上，以比较单基因转化和双基因转化在提高植物耐盐性方面的优劣。除此之外，并对已经转入BADH基因番茄的耐盐性和遗传稳定性分析进行了研究。 转BADH基因番茄已经稳定遗传到T4世代。通过对5个转BADH基因番茄株系在T0世代、T3世代和T4世代的分析，表明除了株系T4-3由T0世代的3个拷贝变为1个拷贝外，其余各株系拷贝数均没有发生变化。外源基因编码的酶活性和最终催化产物甜菜碱在盐分胁迫下都能较容易的检测到，说明外源基因在番茄基因组中的遗传是稳定的，没有发生丢失。在连续2个世代的耐盐性鉴定中，各转基因株系的耐盐性较为一致，均比野生型有了较大的提高。其中株系T4-5连续2年表现出了较低的减产率，株系T4-8也在连续的2年中表现出了最高的单株产量。盐分胁迫下转BADH基因各个株系比野生型有较高的K+和Ca2+含量，较低的Na+含量，转基因株系较野生型有较低的脐腐病果率。 通过SeNHX1、BADH单独转化以及构建双价载体共转化的方法获得了3种类型的转基因烟草。Southern和Northern 检测结果表明，外源基因已经整合到烟草基因组中，并得到了正确的表达。转BADH基因烟草在盐分胁迫下能检测到明显的BADH酶活性和甜菜碱含量。转基因烟草T0代对盐分胁迫、氧化胁迫的抗性均较野生型对照有较大的提高。转基因株系在200 mM NaCl胁迫下较野生型有较高的光合速度。百草枯处理过的野生型叶盘比转基因株系积累了更多的丙二醛，表明野生型受到了更大的氧化胁迫。 已经获得3种转不同基因烟草的T1代，且T1代具有较强的耐渗透胁迫能力。转基因烟草的T0种子均能在含100 mg/L 卡钠霉素培养基上发芽和正常生长，其中部分种子能够在含200 mM NaCl 培养基上发芽并能较好的生长，而野生型根本不能发芽。从200 mM甘露醇胁迫1周后，又转移到营养液中的生长1周的情况来看，转基因烟草能较快的恢复正常的生长，有新的叶子和根长出，而野生型却不能，同时转基因株系比野生型具有更大的单株鲜重。 转BADH基因番茄在遗传上是稳定的，并且其耐盐性有了较大的提高。双基因转化烟草的抗盐性要好于单基因转化，但SeNHX1基因转化要好于BADH基因转化。说明SeNHX1基因在提高植物耐盐性方面要比BADH基因有更强的功能，同时，也表明多基因转化在植物的耐盐改良方面可能是一个更为有效的方法。