Molecular characterization of transforming plasmid rearrangements in transgenic rice reveals a recombination hotspot in the CaMV 35S promoter and confirms the predominance of microhomology mediated recombination

Gene silencing in transgenic soybean plants transformed via particle bombardment

Transgenes are susceptible to silencing in plants especially when multiple copies of the gene of interest are introduced. Transgenic plants derived by particle bombardment, which is the common method for transforming soybean, have a tendency to have multiple integration events. Three independent transgenic soybean plants obtained via particle bombardment were analyzed for transgene silencing. A GUS transgenic soybean line had at least 100 copies of the GUS gene while there were approximately 60 copies of the transgene in the two soybean lines transformed with a 15-kDa zein storage protein gene from maize. Soybean plants transformed with the GUS gene showed variable GUS expression. The coding region and promoter of the GUS gene in the plants with low expression of GUS were heavily methylated. Variability in GUS expression was observed in the progeny of the high expressors in the T(2) and T(3) generations as well. Expression level of the 15-kDa zein gene in transgenic soybean plants showed correlation with the level of transgene methylation. The helper component-proteinase from potyviruses is known to suppress post-transcriptional gene silencing. Transgenic plants were inoculated with the soybean mosaic potyvirus (SMV) to test possible effects on transgene silencing in soybean. Infection with SMV did not suppress transgene silencing in these plants and suggests that the silencing in these plants may not be due to post-transcriptional gene silencing.

T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites

A statistical analysis of 9000 flanking sequence tags characterizing transferred DNA (T-DNA) transformants in Arabidopsis sheds new light on T-DNA insertion by illegitimate recombination. T-DNA integration is favoured in plant DNA regions with an A-T-rich content. The formation of a short DNA duplex between the host DNA and the left end of the T-DNA sets the frame for the recombination. The sequence immediately downstream of the plant A-T-rich region is the master element for setting up the DNA duplex, and deletions into the left end of the integrated T-DNA depend on the location of a complementary sequence on the T-DNA. Recombination at the right end of the T-DNA with the host DNA involves another DNA duplex, 2-3 base pairs long, that preferentially includes a G close to the right end of the T-DNA.

Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement

To more fully characterize the internal structure of transgene loci and to gain further understanding of mechanisms of transgene locus formation, we sequenced more than 160 kb of complex transgene loci in two unrelated transgenic oat (Avena sativa L.) lines transformed using microprojectile bombardment. The transgene locus sequences from both lines exhibited extreme scrambling of non-contiguous transgene and genomic fragments recombined via illegitimate recombination. A perfect direct repeat of the delivered DNA, and inverted and imperfect direct repeats were detected in the same transgene locus indicating that homologous recombination and synthesis-dependent mechanism(s), respectively, were also involved in transgene locus rearrangement. The most unexpected result was the small size of the fragments of delivered and genomic DNA incorporated into the transgene loci via illegitimate recombination; 50 of the 82 delivered DNA fragments were shorter than 200 bp. Eleven transgene and genomic fragments were shorter than the DNA lengths required for Ku-mediated non-homologous end joining. Detection of these small fragments provided evidence that illegitimate recombination was most likely mediated by a synthesis-dependent strand-annealing mechanism that resulted in transgene scrambling. Taken together, these results indicate that transgene locus formation involves the concerted action of several DNA break-repair mechanisms.

Risk assessment of virus-resistant transgenic plants

Virus-resistant transgenic plants (VRTPs) hold the promise of enormous benefit for agriculture. However, over the past ten years, questions concerning the potential ecological impact of VRTPs have been raised. In some cases, detailed study of the mode of action of the resistance gene has made it possible to eliminate the source of potential risk, notably the possible effects of heterologous encapsidation on the transmission of viruses by their vectors. In other cases, the means of eliminating likely sources of risk have not yet been developed. When such residual risk still exists, the potential risks associated with the VRTP must be compared with those associated with nontransgenic plants so that risk assessment can fully play its role as part of an overall analysis of the advantages and disadvantages of practicable solutions to the problem solved by the VRTP.

Transformation vector based on promoter and intron sequences of a replacement histone H3 gene. A tool for high, constitutive gene expression in plants

This study explored the possibility of using non-viral, plant-based gene sequences to create strong and constitutive expression vectors. Replacement histone H3 genes are highly and constitutively expressed in all plants. Sequences of the cloned alfalfa histone H3.2 gene MsH3gl were tested. Constructs of the beta-glucuronidase (GUS) reporter gene were produced with H3.2 gene promoter and intron sequences. Their efficiency was compared with that of the commonly used strong 35S cauliflower mosaic virus promoter in transgenic tobacco plants. Combination of the H3.2 promoter and intron produced significantly higher GUS expression than the strong viral 35S promoter. Histochemical GUS analysis revealed a constitutive pattern of expression. Thus, alfalfa replacement H3 gene sequences can be used instead of viral promoters to drive heterologous gene expression in plants, avoiding perceived risks of viral sequences.

Controlling transgene integration in plants

The creation of transgenic plants has brought significant advances to light in plant biotechnology. However, in spite of the fact that transgenic plants are beginning to be grown widely, controlled transgene integration into a pre-determined site remains to be achieved. Here we suggest two alternative approaches for gene targeting in plants: manipulating the host and donor sequence, and targeting during active homologous recombination stages.

Rearrangements of the DNA in carbon ion-induced mutants of Arabidopsis thaliana

To elucidate the nature of structural alterations in plants, three carbon ion-induced mutations in Arabidopsis thaliana, gl1-3, tt4(C1), and ttg1-21, were analyzed. The gl1-3 mutation was found to be generated by an inversion of a fragment that contained GL1 and Atpk7 loci on chromosome 3. The size of the inverted fragment was a few hundred kilobase pairs. The inversion was found to accompany an insertion of a 107-bp fragment derived from chromosome 2. The tt4(C1) mutation was also found to be due to an inversion. The size of the intervening region between the breakpoints was also estimated to be a few hundred kilobase pairs. In the case of ttg1-21, it was found that a break occurred at the TTG1 locus on chromosome 5, and reciprocal translocation took place between it and chromosome 3. From the sequences flanking the breakpoints, the DNA strand breaks induced by carbon ions were found to be rejoined using, if present, only short homologous sequences. Small deletions were also observed around the breakpoints. These results suggest that the nonhomologous end-joining (NHEJ) pathway operates after plant cells are exposed to ion particles.

[The critical scientists' voice]

The intricate debate over genetically modified organisms (GMOs) involves powerful economic interests, as well as ethical, legal, emotional and scientific aspects, some of which are dealt with in this paper.(It is possible to identify two main groups of scientists across the GMOs divide: the triumphalist and the critical group.) Scientists in the triumphalist group state that GMOs and their derivatives are safe for the environment and do not offer health hazards any more than similar, non-genetically modified, products. This view is disputed by the critical scientists, who are prompted by the scarcity of studies on the environmental impacts and toxicity of GMOs, and who point out flaws in tests performed by the same companies which hold the patents. They are also critical of the current state of the process of gene transference, lacking accuracy, a fact which, coupled with the scant knowledge available about 97% of the genome functions, may produce unforseeable effects with risks for the environment and public health yet to be assessed. Examples of such effects are: the transference of alien genes [??] to other species, the emergence of toxins, the creation of new viruses, the impacts on beneficial insects and on biodiversity in general.

Linear transgene constructs lacking vector backbone sequences generate low-copy-number transgenic plants with simple integration patterns

Whole plasmids are used in both Agrobacterium-mediated transformation and direct DNA transfer, generally leading to the integration of vector backbone sequences into the host genome along with the transgene(s). This is undesirable, as vector backbone sequences often have negative effects on transgene or endogenous gene expression, and can promote transgene rearrangements. We, therefore, bombarded rice tissue with two constructs: a plasmid containing the bar gene, and a linear DNA fragment isolated from the same plasmid, corresponding to the minimal bar gene expression cassette (promoter, open reading frame and terminator). We recovered phosphinothricin-resistant plants from both experiments, showing that the selectable marker was efficiently expressed. Transformation with such constructs resulted in predominantly 'simple' integration events (one or two bands on Southern blots), producing low-copy-number transgenic plants with a low frequency of transgene rearrangements. Conversely, transformation with supercoiled or linearized whole plasmids generated plants with 'complex' integration patterns, that is, higher copy numbers and frequent transgene rearrangements. We monitored transgenic lines through to the R4 generation and observed no silencing in plants carrying minimal constructs. We also carried out experiments in which rice tissue was simultaneously bombarded with minimal linear hpt and gusA cassettes. We observed robust GUS activity in hygromycin-resistant plants, confirming co-expression of the selectable and nonselectable markers. Furthermore, the efficiency of cotransformation using minimal constructs was the same as that using supercoiled plasmid cointegrate vectors.