Jan-Peter Nap

pBINPLUS: an improved plant transformation vector based on pBIN19

We describe the construction of a new plant transformation vector, pBINPLUS, based on the popular pBIN19 vector. Improvements over pBIN19 include location of the selectable marker gene at the left T-DNA border, a higher copy number inE. coli, and two rare restriction sites around the multiple cloning site for easier cloning and analysis of T-DNA insertions in plant genomes.

Developmental Biology of a Plant-Prokaryote Symbiosis: The Legume Root Nodule

The development of nitrogen fixing root nodules on the roots of leguminous plants is induced by soil bacteria (for example, from the genus Rhizobium). The formation of this plant organ involves specific activation of genes in both plant and bacterium. Analysis of these genes gives insight into the way in which plant and bacterium succeed in coordinating plant development.

Reduced Position Effect in Mature Transgenic Plants Conferred by the Chicken Lysozyme Matrix-Associated Region

Matrix-associated regions may be useful for studying the role of chromatin architecture in transgene activity of transformed plants. The chicken lysozyme A element was shown to have specific affinity for tobacco nuclear matrices, and its influence on the variability of transgene expression in tobacco plants was studied. T-DNA constructs in which this element flanked either the [beta]-glucuronidase (GUS) reporter gene or both reporter and selection gene were introduced in tobacco. The variation in GUS gene activity was reduced significantly among mature first-generation transgenic plants carrying the A element. Average GUS activity became somewhat higher, but the maximum attainable level of gene expression was similar for all three constructs. Transient gene expression assays showed that the A element did not contain general enhancer functions; therefore, its presence seemed to prevent the lower levels of transgene expression. The strongest reduction in variability was found in plants transformed with the construct carrying the A elements at the borders of the T-DNA. In this population, expression levels became copy number dependent. The presence of two A elements in the T-DNA did not interfere with meiosis.

The MAR-Mediated Reduction in Position Effect Can Be Uncoupled from Copy Number-Dependent Expression in Transgenic Plants

To study the role of matrix-associated regions (MARs) in establishing independent chromatin domains in plants, two transgenes were cloned between chicken lysozyme A elements. These transgenes were the neomycin phosphotransferase (NPTII) gene under control of the nopaline synthase (nos) promoter and the [beta]-glucuronidase (GUS) gene controlled by the double cauliflower mosaic virus (dCaMV) 35S promoter. The A elements are supposed to establish an artificial chromatin domain upon integration into the plant DNA, resulting in an independent unit of transcriptional regulation. Such a domain is thought to be characterized by a correlated and position-independent, hence copy number-dependent, expression of the genes within the domain. The presence of MARs resulted in a higher relative transformation efficiency, demonstrating MAR influence on NPTII gene expression. However, variation in NPTII gene expression was not significantly reduced. The selection bias for NPTII gene expression during transformation could not fully account for the lack of reduction in variation of NPTII gene expression. Topological interactions between the promoter and A element may interfere with the A element as a domain boundary. In contrast, the GUS gene on the same putative chromatin domain showed a highly significant reduction in variation of gene expression, as expected from previous results. Surprisingly, no copy number-dependent GUS gene expression was observed: all plants showed approximately the same GUS activity. We concluded, therefore, that dCaMV 35S-GUS gene expression in mature tobacco plants is regulated by some form of dosage compensation.

Isolation of High Quality DNA and RNA from Leaves of the Carnivorous Plant Drosera rotundifolia

Drosera rotundifolia belongs to the family of the sundews, a large group of carnivorous plants that carry stalked glands on the upper leaf surface to attract, trap and digest insects for food. Therefore, such plants can live in relatively poor ecosystems. They are frequently used as medicinal herbs and have various other interesting characteristics associated with them. In attempts to evaluate the gene pool of these plants, we experienced that many published protocols for nucleic acid isolation failed to yield DNA and RNA of sufficient quality for analysis. Therefore, we have developed CTAB (hexadecyltrimethylammoniumbromide)-based extraction protocols for the routine isolation of high-quality DNA and RNA from small amounts of in vitro-grown Drosera rotundifolia leaves. The methods developed are simple, fast and effective. The obtained DNA could be analyzed by PCR, restriction endonucleases and DNA gel blotting, and the obtained RNA was of sufficient quality for RT-PCR and RNA gel blotting.

Biosafety of kanamycin-resistant transgenic plants.

Kanamycin resistance is one of the most frequently used selection markers for obtaining transgenic plants. The introduction of these transgenic plants into agricultural practice will cause the kanamycin resistance gene and the gene product to be present on a large scale. The desirability of this situation is analysed. The nature, properties and applications of the antibiotic kanamycin are briefly reviewed, as are the mechanisms of kanamycin resistance. It is argued that the gene used for resistance is an excellent choice because of the high substrate specificity of the enzyme encoded. Human or veterinary antibiotic therapies will not be compromised. Also, the physico-chemical characteristics of the antibiotic exclude the existence of selective conditions in the environment. Therefore, a transgenic plant or any other organism that might have acquired the gene will not get any selective advantage because of this gene. Evidence further suggests there is no toxicity or predictable harm of both gene or gene product for human or animal consumption. Full legislative clearance of this transgenic trait is therefore acceptable.

Allermatch™, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

BackgroundNovel proteins entering the food chain, for example by genetic modification of plants, have to be tested for allergenicity. Allermatch™ http://allermatch.org is a webtool for the efficient and standardized prediction of potential allergenicity of proteins and peptides according to the current recommendations of the FAO/WHO Expert Consultation, as outlined in the Codex alimentarius.DescriptionA query amino acid sequence is compared with all known allergenic proteins retrieved from the protein databases using a sliding window approach. This identifies stretches of 80 amino acids with more than 35% similarity or small identical stretches of at least six amino acids. The outcome of the analysis is presented in a concise format. The predictive performance of the FAO/WHO criteria is evaluated by screening sets of allergens and non-allergens against the Allermatch databases. Besides correct predictions, both methods are shown to generate false positive and false negative hits and the outcomes should therefore be combined with other methods of allergenicity assessment, as advised by the FAO/WHO.ConclusionsAllermatch™ provides an accessible, efficient, and useful webtool for analysis of potential allergenicity of proteins introduced in genetically modified food prior to market release that complies with current FAO/WHO guidelines.

The impact on biosafety of the phosphinothricin-tolerance transgene in inter-specific B. rapa×B. napus hybrids and their successive backcrosses

Abstract There is strong evidence indicating that gene flow from transgenic B. napus into weedy wild relatives is inevitable following commercial release. Research should now focus on the transmission, stability, and impact of transgene expression after the initial hybridization event. The present study investigated the transfer of a phosphinothricin-tolerance transgene by inter-specific hybridization between B. rapa and two transgenic B. napus lines. The expression of the transgene was monitored in the F1 hybrids and in subsequent backcross generations. The transgene was transmitted relatively easily into the F1 hybrids and retained activity. Large differences in the transmission frequency of the transgene were noted between offspring of the two transgenic lines during backcrossing. The most plausible explanation of these results is that the line showing least transmission during backcrossing contains a transgene integrated into a C-genome chromosome. Approximately 10% of offspring retained the tolerant trait in the BC3 and BC4 generations. The implications of these findings for the stable introgression of transgenes carried on one of the chromosomes of the C-genome from B. napus and into B. rapa are briefly discussed.

Approaching the Lower Limits of Transgene Variability.

The inclusion of chicken lysozyme matrix-associated regions (MARs) in T-DNA has been demonstrated to reduce the variation in [beta]-glucuronidase (GUS) gene expression among first-generation transformed plants. The residual variation observed between transgenic plant lines with MARs at the T-DNA borders was investigated. By definition, any phenotypic variance between or within genetically identical plants is caused by random or environmental variation. This variation therefore sets a lower limit to the variation in GUS activities. The variance of GUS activity in offspring plant populations of genetically identical individuals was used as an estimate of environmental variation. For transgenic plants with MARs at the T-DNA borders, the variation between independent transformants could not be distinguished from the environmental variation. The variation could be attributed mainly to the variation in the GUS activity measurement. Therefore, the MAR element approached the maximal possible reduction of transgene variability given current technology and sample sizes. The role of MARs in offspring plants was evaluated by comparing such populations of transgenic plants for the magnitude of and variation in GUS activity. Pairwise comparisons showed that the presence of MARs reduced variation in offspring generations in the same manner as demonstrated for primary transformants. The populations carrying a doubled cauliflower mosaic virus 35S promoter-GUS gene tended to be more variable than the Lhca3.St.1 promoter-GUS gene-carrying populations. This tendency indicated an intrinsic susceptibility of the doubled cauliflower mosaic virus 35S promoter to variation. Homozygous plants were approximately twice as active as the corresponding hemizygous plants and tended to be more variable than the hemizygous plants. We hypothesized that the magnitude of environmental variations is related to a higher susceptibility to transgene silencing.

Local Coexpression Domains of Two to Four Genes in the Genome of Arabidopsis

Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearsons correlation coefficient larger than 0.7. This number is approximately 1- to 5-fold higher than the numbers expected by chance. A small (5%–10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.