Genetic analysis of T-DNA transcripts in nopaline crown galls

Plant crown gall tumor cells result from the insertion and expression of a defined DNA sequence, called T-DNA, which is derived from the Ti plasmid, harbored by Agrobacterium tumefaciens strains. To study the function of the genes of the T-DNA of the nopaline Ti plasmid, pTiC58, a collection of mutants was isolated so that T-DNA genes are inactivated either separately or in various combinations. It was found that no single T-DNA gene or T-region border is absolutely essential for stable tumor formation. We have identified the gene responsible for synthesis in transformed cells of the phosphorylated sugar, agrocinopine, and at least three additional genes controlling the morphology of plant tumors. Two of these latter genes work together to inhibit shoot formation and ensure efficient tumorous growth. Inactivation of these genes can be suppressed by the addition of auxins. The third gene inhibits root formation and appears to play a role in the cytokinin-independent growth of transformed cells. Mutants missing all three genes do not induce tumors, nor shoot or root formation, although the mutant T-DNA sequence is transferred to plant cells.     

Retention of tumor markers in F1 progeny plants from in vitro induced octopine and nopaline tumor tissues

Tumorous tobacco shoots have been derived from callus tissues produced by Agrobacterium tumefaciens-induced transformation of tobacco protoplasts and by fusion of normal protoplasts with those from crown gall tumors. The continued presence of T-DNA sequences in shoots is directly demonstrated by Southern blotting and is also revealed by the presence of the tumor markers octopine and nopaline. When grafted onto normal tobacco plants, both octopine- and nopaline-type shoots (including those from somatic hybrids) produced flowers and set seed. Germination of these seeds gave F1 progeny that showed retention of morphological markers of their parental shoots, and one seedling retained the ability to synthesize nopaline. The data demonstrate that T-DNA markers can be retained during meiosis and are expressed in F1 plants.     

Internal organization,boundaries and integration of Ti-plasmid DNA in nopaline crown gall tumours

Eight lines of nopaline crown gall tumours were analysed by Southern (1975) blot hybridization to determine the size, internal organization, boundaries, possible plant DNA integration and accuracy of transfer of the Ti-plasmid DNA segment (T-DNA) transferred from Agrobacterium tumefaciens to crown gall plant cells. The conservation of this T-DNA in tumour tissues and tissues derived from plants regenerated from crown gall teratomas was also studied.A defined plasmid segment (the T-region) of about 15 × 10⁶M_r is accurately transferred and integrated into nuclear plant DNA without any major internal rearrangements. Furthermore, common composite fragments covalently linking the left and the right boundary of the T-region were observed, thus indicating either tandem duplications of integrated T-DNA segments or polymeric circles of T-DNA segments. The length of the transferred segment is not determined by size, since insertions in the T-region were found to be co-transferred with the T-DNA. The results indicate that sequences at the boundaries of the region may play a role in the transfer mechanism, although the right boundary could be replaced by a Tn1 insertion. Cells from plants regenerated from crown gall teratomas were shown to contain T-DNA without internal rearrangements but with minor modifications of the boundary fragments. In plants obtained from meiotic products of teratomaderived regenerated plants no T-DNA was observed.     

Purification and characterization of the crown gall specific enzyme nopaline synthase.

Nopaline synthase of sunflower (Helianthus annuus L.) crown gall tissue induced by Agrobacterium tumefaciens strain C58 or T37 (nopaline utilizers) was purified to homogeneity as judged by analytical disc gel electrophoresis. The native enzyme elutes from a column of Ultrogen AcA 34 as a single peak with an estimated molecular weight of 158,000. The dissociated enzyme migrates on NaDodSO4-polyacrylamide gels as a single band with a molecular weight of 40,000. Thus, the native enzyme appears to be composed of four equal-weight subunits. Nopaline synthesizing activity is found exclusively in crown gall tissues induced by strains of A. tumefaciens that utilize nopaline (e.g., C58 and T37). We found the same tissue specificity for the purified protein that we believe represents nopaline synthase. The results of kinetic studies of the purified enzyme are consistent with a ter-bi rapid-equilibrium random-order mechanism. Nopaline synthase is probably responsible for the in vivo synthesis of both N2-(1,3-dicarboxypropyl)arginine (nopaline) and N2-(1,3-dicarboxypropyl)ornithine (ornaline) in crown gall tissues since substrate specificities and Km values do not change during purification.     

Characterization of the enzyme responsible for nopaline and ornaline synthesis in sunflower crown gall tissues

Extracts prepared from sunflower (Helianthus annuus L.) crown gall tissues induced by Agrobacterium tumefaciens strains C58 and T37 (nopaline utilizers) catalyze the synthesis of nopaline and ornaline. These compounds are not synthesized in extracts of crown gall tissues induced by strains B6, 15955 (octopine utilizers), and AT1 (utilizes neither octopine nor nopaline) or in extracts of habituated sunflower callus. Both synthetic activities require NADPH, α-ketoglutarate, and either arginine or ornithine; histidine and lysine will not substitute. Incorporation of arginine or ornithine into product is inhibited by the other substrate but not by histidine or lysine. On the basis of inhibition and K_m data, both activities appear to be catalyzed by one enzyme and the same enzyme is apparently present in crown gall tissues induced by strains C58 and T37.     

Sequence comparisons betweenAgrobacterium tumefaciens T-DNA-encoded octopine and nopaline dehydrogenases and other nucleotide-requiring enzymes: Structural and evolutionary implications

Summary The nucleotide sequences of the two T-DNA-encoded crown gall imino acid dehydrogenases octopine dehydrogenase and nopaline dehydrogenase were compared with each other and with the sequences of other dehydrogenases. A multistep strategy comprising computer sequence analysis and secondary- and antigenic-structure predictions was used. An alignment of octopine and nopaline dehydrogenase was obtained in which a 20-amino-acid N-terminal arm and six fairly long gaps in the C-terminal moiety were introduced. The aligned sequences have identities of 26% at the amino acid level and 38% at the nucleotide level. They appear to contain two domains. The N-terminal coenzyme-binding domains are similar to those of the well-characterized NAD(P) dehydrogenases. Conserved fragments were found in the C-terminal catalytic domains that likely contain essential residues for catalysis. Comparison of the sequences with those of two other 2-keto acid dehydrogenases, lactate and malate dehydrogenase, suggests that as in those enzymes, histidine, aspartic acid, and arginine residues are located at the octopine and nopaline dehydrogenase active sites. The crown gall enzymes could not be classified with any known family of dehydrogenases. Their evolutionary origin remains unknown. However, predictions concerning their internal organization may provide new insight into protein evolution.     

Studies on the structure of cointegrates between octopine and nopaline Ti-plasmids and their tumour-inducing properties

Stable cointegrates between incRh-1 octopine (Ach5) and nopaline (C58) Ti-plasmids, present in ten independently isolated Agrobacterium tumefaciens strains, showed identical restriction endonuclease patterns. Each cointegration event had taken place in the common sequence between the T-regions of both Ti-plasmids. This illustrates a high preference for this region when used in the formation of cointegrates. Four crown gall tissues, obtained after transformation of Nicotiana tabacum cells by one of the mutants, were analysed by using Southern blot analysis for their T-DNA structure. The borders of T-DNA frequently appeared to differ from T-DNA borders previously detected in tumour tissues that had been induced by Agrobacterium strain C58 or Ach5. Therefore, it was concluded that possibly a less stringent mechanism exists for the integration into plant DNA of T-DNA, derived from a composite (octopine/nopaline) T-region than for integration of T-DNA from a normal (octopine or nopaline) T-region.Abbreviations Agr sensitivity to agrocin 84 - Ape phage Apl exclusion - Cb resistance to carbenicillin - Occ octopine catabolism - Ocs octopine synthesis - Noc nopaline catabolism - Nos nopaline synthesis - Rec recombination - Tra transfer - Vir virulence     

Isolation and characterization of diverse nopaline type Ti plasmids of Agrobacterium tumefaciens from Japan

Ninety Agrobacterium strains were isolated from naturally appearing crown galls in Japan. They were classified into several groups based on opine type, biovars, tumorigenicity, and indigeneous plasmid profiles. Twenty-nine strains utilized nopaline, but none utilized octopine. Eighteen isolates were tumorigenic, nopaline type strains and thus classified as Agrobacterium tumefaciens. Some strains possessed anomalous traits such as lysine utilization, resistance to agrocin 84, and a lack of motility. Pathogenic strains contained Ti plasmids of either 200 kb or 260 kb, as identified by hybridization to T-DNA of the known Ti plasmid. However, the restriction enzyme cleavage patterns, arising from hybridization to the probe, were different from each other and indicated that nopaline type Ti plasmids possess more diverse T-DNA structures than previously reported. Five of 6 representative strains induced tumors on 6 plant species (tomato, petunia, poplar, kalanköe, apple, and grape). Among these, apple was notable, since only a few strains have been reported to be pathogenic to this plant. On petunia, 4 strains developed large tumors while 2 produced only small tumors. Teratomas were formed on poplar in a strain-dependent manner, but not on tomato. These results suggest that our isolates are wide host range strains, and that host-specificity of these strains is related to diverse T-DNA structures.     

The opine synthase genes carried by Ti plasmids contain all signals necessary for expression in plants

Signals necessary for in vivo expression of Ti plasmid T-DNA-encoded octopine and nopaline synthase genes were studied in crown gall tumors by constructing mutated genes carrying various lengths of sequences upstream of the 5' initiation site of their mRNAs. Deletions upstream of position -294 did not interfere with expression of the octopine synthase gene while those extending upstream of position -170 greatly reduced the gene expression. The estimated size of the octopine synthase promoter is therefore 295 bp. The maximal length of 5' upstream sequences involved in the in vivo expression of the nopaline synthase gene is 261 bp. Our results also demonstrated that Ti plasmid-derived sequences contain all signals essential for expression of opine synthase genes in plants. Expression of these genes, therefore, is independent of the direct vicinity of the plant DNA sequences and is not activated by formation of plant DNA and T-DNA border junction.     

Regeneration of intact tobacco plants containing full length copies of genetically engineered T-DNA,and transmission of T-DNA to R1 progeny

Cloned DNA sequences encoding yeast alcohol dehydrogenase and a bacterial neomycin phosphotransferase have been inserted into the T-DNA of Agrobacterium tumefaciens plasmid pTiT37 at the “rooty” locus. Transformation of tobacco stem segments with the engineered bacterial strains produced attenuated crown gall tumors that were capable of regeneration into intact, normal tobacco plants. The yeast gene and entire transferred DNA (T-DNA) were present in the regenerated plants in multiple copies, and nopaline was found in all tissues. The plants were fertile, and seedlings resulting from self-pollination also contained intact and multiple copies of the engineered T-DNA. Expression of nopaline in the germinated seedlings derived from one regenerated plant was variable and did not correlate with the levels of T-DNA present in the seedlings. Preliminary evidence indicates that nopaline in progeny of other similarly engineered plants is more uniform. The disarming of pTiT37 by insertions at the “rooty” locus thus appears to produce a useful gene vector for higher plants.     

Methylation of the T-DNA in Agrobacterium tumefaciens and in several crown gall tumors.

Methylation of the T-DNA in Agrobacterium tumefaciens and in four octopine-type (A6S/2, E9, 15955/1, 15955/01) and one nopaline-type (HT37#15) crown gall tumors was investigated using the isoschizomeric restriction endonucleases Msp I and Hpa II. T-DNA in the octopine-type Ti-plasmid pTiB6(806) was not methylated at the sequence 5'CCGG3' in Agrobacterium. With two possible exceptions, neither was the T-DNA of the nopaline-type Ti-plasmid pTiT37 methylated in the bacterium. In all tumor lines investigated, at least one copy of the T-DNA was not methylated. DNA methylation was not detected in the lines A6S/2, 15955/1, HT37#15, and the TL region of E9. DNA methylation of some copies of TR in the E9 tumor line, and possibly in the 15955/01 line, was detected. The methylation of some copies of TR in the E9 line may indicate that not all copies of TR are transcribed in this tumor.     

T-DNA organization in homogeneous and heterogeneous octopine-type crown gall tissues of nicotiana tabacum

Octopine-type tumor tissue was obtained both by infection of plants or isolated protoplasts with Agrobacterium tumefaciens and by somatic hybridization of normal and crown gall tobacco cells. Analysis of T-DNA by Southern blotting of clones and uncloned tissue reveals that, whereas tumors induced on plants are heterogeneous mixtures of cells differing in T-DNA organization, each tissue derived from transformed protoplasts or from somatic hybridization is homogeneous. Detailed analysis of T-DNA organization showed that T_L- or “core” T-DNA was always present at one or two copies per diploid genome. However, sometimes it was present in a modified form, either deleted, extended, tandemly duplicated or probably methylated. T_R-DNA was not detected. The observed variation in the organization of T-DNA in octopine crown gall tissue did not appear to be a characteristic of the way the tissue was derived.     

Expression of nopaline synthesis in tumorous and regenerant tobacco crown galls

Summary Tissues formed in liquid cultures of tobacco (Nicotiana tabacum cv. Wisconsin 38) crown galls incited byAgrobacterium tumefaciens C58 were of three types: unorganized callus, organized teratoma, and organized normal appearing. These tissues contained 400±12, 410±17, and 614±53 μg nopaline/g fresh weight, respectively. Using [¹⁴C]arginine, methods were developed for measuring in vivo nopaline biosynthetic rates. Tissues were incubated in a low concentration (i.e., 3 μM) of [¹⁴C]arginine to minimize disruption of the internal pool (approximately 140 μM free arginine). Radioactivity in the tissue was assayed and the specific radioactivity of free arginine, the precursor of nopaline, was determined. The linear rate of incorporation of radioactivity into nopaline was used to calculate the following biosynthetic rates (expressed as microgram nopaline per gram fresh weight per 24 h): callus, 14; teratoma, 21; normal appearing, 24. These results show conclusively that normal appearing tissues obtained from crown gall tumors can synthesize nopaline. Abnormal growth and opine biosynthesis, therfore, can be expressed independently.     

Regeneration of tobacco plants from crown gall tumors

Summary Tissue culture methods have been developed for regeneration of normal appearing tobacco plants from bacteria-free crown gall strains incited byAgrobacterium tumefaciens C58, IIBV7, B6, CGIC, A6NC, 27, and AT4. Regenerants fall into two categories depending on the properties of tissues from these plants. The first type of regenerant was obtained from tumors incited byA. tumefaciens C58 and it retained the potential for expression of tumor characteristics such as a nonrequirement for phytohormones (auxin and cytokinin) by explants in vitro and the presence of detectable concentrations of nopaline. Normal appearing plants obtained from C58 tumors had much lower concentrations of nopaline than the corresponding tumor tissue (130 versus 1700 μg per g dry wt) indicating a parallel repression of abnormal growth and nopaline concentrations in regenerants. The second type of regenerant was obtained from tumors incited by the otherA. tumefaciens strains and was characterized by requirements for phytohormones by explants in vitro and the apparent lack of octopine or nopaline in regenerant tissues.     

Differences in susceptibility of Arabidopsis ecotypes to crown gall disease may result from a deficiency in T-DNA integration.

We show that among ecotypes of Arabidopsis, there is considerable variation in their susceptibility to crown gall disease. Differences in susceptibility are heritable and, in one ecotype, segregate as a single major contributing locus. In several ecotypes, recalcitrance to tumorigenesis results from decreased binding of Agrobacterium to inoculated root explants. The recalcitrance of another ecotype occurs at a late step in T-DNA transfer. Transient expression of a T-DNA-encoded beta-glucuronidase gusA gene is efficient, but the ecotype is deficient in crown gall tumorigenesis, transformation to kanamycin resistance, and stable GUS expression. This ecotype is also more sensitive to gamma radiation than is a susceptible ecotype. DNA gel blot analysis showed that after infection by Agrobacterium, less T-DNA was integrated into the genome of the recalcitrant ecotype than was integrated into the genome of a highly susceptible ecotype.