Isolation of single-copy-sequence clones from a yeast artificial chromosome library of randomly-sheared Arabidopsis thaliana DNA.

We describe the construction of a yeast artificial chromosome (YAC) library from the Arabidopsis thaliana genome. Randomly sheared high molecular weight source DNA was extracted from frozen, ground leaf tissue and blunt-end-ligated to the vector pYAC3. By size-fractionating the ligation products, we achieved an average clone size of 150 kb. Approximately 6% of the YACs contained inserts from the chloroplast genome. We screened clones equivalent to greater than four A. thaliana haploid nuclear genomes and isolated YACs homologous to five single-copy-sequence probes. The library should be useful for chromosome walking and genome mapping experiments. In addition, the approach used for its construction should be applicable to other higher plant species.

Nucleotide sequence of an insertion sequence (IS) element identified in the T-DNA region of a spontaneous variant of the Ti-plasmid pTiT37.

We have identified and determined the nucleotide sequence of an IS element (IS136) of Agrobacterium tumefaciens. This is the first IS element isolated and sequenced from a nopaline type Ti-plasmid. Our IS element has 32/30 bp inverted repeats with 6 mismatches, is 1,313 bp long and generates 9 bp direct repeats upon integration. IS136 has 3 main open reading frames (ORF's). Only ORF1 (159 codons) is preceded by sequences that are proposed to serve functional roles in transcriptional and translational initiation. No DNA sequence homology was found between IS136 and IS66, an IS element isolated from an octopine type Ti-plasmid.

The right border region of pTiT37 T-DNA is intrinsically more active than the left border region in promoting T-DNA transformation.

Deletions of border regions of T-DNA on Agrobacterium Ti plasmid or mini-T plasmid have shown the right border region of pTiT37 T-DNA to be more active than the left border region in promoting T-DNA transformation. In this study we examine the possibility that the apparent difference in activity of left and right border regions may be due to position or orientation differences between the left and right borders with respect to the transferred onc genes. We have constructed eight similar single-border mini-T plasmids that contain a left border segment or a right border segment of pTiT37 T-DNA at various positions with either orientation with respect to the onc genes. We assayed the plant tumor-inducing activity of these mini-T plasmids in Agrobacterium tumefaciens LBA4404 containing the virulence helper plasmid pAL4404. Regardless of the position and orientation of the border-containing segment in the mini-T plasmid, mini-T plasmids with the right border segment were highly virulent, whereas those with the left border segment were only weakly so. These results indicate that the difference in transformational activity between the left and right border regions is intrinsic and not an effect of position or orientation with respect to the onc genes. The pattern of the mini-T plasmid sequences integrated into the plant genome suggests that T-DNA transformation involves the directional transfer of a linear intermediate bounded by the border repeats.

Activity of T-DNA borders in plant cell transformation by mini-T plasmids.

By using a binary vector system, we examined the requirements for border sequences in T-DNA transformation of plant genomes. Mini-T plasmids consisting of small replicons with different extents of pTiT37 T-DNA were tested for plant tumor-inducing ability in Agrobacterium tumefaciens strain LBA4404 containing helper plasmid pAL4404 (which encodes virulence genes needed for T-DNA transfer). Assays of these bacteria on carrot disks, Kalanchoë leaves, and SR1 Nicotiana tabacum plantlets showed that mini-T plasmid containing full length T-DNA including left and right borders was highly virulent, as were mini-T plasmids containing all onc (oncogenicity) genes and only the right border. In contrast, mini-T plasmids containing all onc genes and only the left border induced tumors only rarely, and a mini-T plasmid containing all onc genes but no T-DNA borders was completely avirulent. Southern hybridization analyses of tumor DNA showed that T-DNA border sequences delimited the extent of the two-border mini-T plasmid transferred and integrated into the plant genome. When only one T-DNA border was present, it formed one end of the transferred DNA, and the other end mapped in the vector sequences. The implications of these results for the mechanism of T-DNA transfer and integration are discussed.