Proteins encoded by Agrobacterium tumefaciens Ti plasmid DNA (T-DNA) in crown gall tumors

Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions

Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-borne yellows virus (CABYV). We determined that efficient CABYV RNA translation requires the presence of a 3′-CITE in its 3′-UTR. We showed that this 3′-CITE requires the presence of the 5′-UTR in cis for its eIF4E-independent activity. Efficient virus multiplication depended on 3′-CITE activity. In CABYV isolates belonging to the three phylogenetic groups identified so far, the 3′-CITEs differ, and recombination prediction analyses suggest that these 3′-CITEs have been acquired through recombination with an unknown donor. Since these isolates have evolved in different geographical regions, this may suggest that their respective 3′-CITEs are possibly better adapted to each region. We propose that translation of other polerovirus genomes may also be 3′-CITE-dependent.

Recombination between higher plant DNA and the Ti plasmid of Agrobacterium tumefaciens

The Ti plasmid sequences (T-DNA) from the octopine-producing crown gall tumor A6S/2 were isolated by molecular cloning, using the bacteriophage lambda vector Charon 4A. Analysis of the cloned DNA segments indicates that the Ti plasmid sequences are covalently joined to plant nuclear DNA. These data demonstrate that genetic recombination between a eukaryote and a prokaryote can occur as a natural phenomenon.

Short direct repeats flank the T-DNA on a nopaline Ti plasmid

Crown gall disease results from the insertion of a segment of the Agrobacterium Ti plasmid, called T-DNA, into host plant nuclear DNA. We have subjected to sequence analysis the border regions of pTi T37 (ends of T-DNA) and one left T-DNA/plant DNA border fragment isolated from BT37 tobacco teratoma by molecular cloning. These sequence studies, taken together with published sequence of a right T-DNA/plant DNA border fragment, allowed us to identify the positions of left and right borders at the DNA sequence level. Comparison of left and right border regions of the Ti plasmid revealed a "core" direct repeat of 13 of 14 bases (12 contiguous) precisely at the borders of T-DNA. An extended repeat of 21 of 25 bases overlaps this core repeat. T-DNA on the Ti plasmid exhibits no longer direct or inverted repeats in the border regions, based on Southern hybridization studies. The physical structure of T-DNA differs from that of known prokaryotic and eukaryotic transposable elements but bears a structural resemblance to the prophage of bacteriophage lambda.

Differential expression of crown gall tumor markers in transformants obtained after in vitro Agrobacterium tumefaciens-induced transformation of cell wall regenerating protoplasts derived from Nicotiana tabacum

To obtain transformation of plant cells, we incubated 3-day-old cell wall-regenerating protoplasts from tobacco with Agrobacterium tumefaciens harboring tumor-inducing plasmids. Putative transformed tobacco cells were selected by phytohormone autotrophic growth and were shown to be transformed by the detection of the tumor cell specific enzymes lysopine dehydrogenase or nopaline dehydrogenase. This was substantiated by the detection, in transformed tumor tissues, of DNA sequences homologous to sequences in the tumor-inducing plasmid. Segregation of tumor markers has been observed among the transformants and it is suggested that this happened during the initiation of the transformation. The stable character of the transformed state was shown by the retention of tumor markers in subcloning of primary transformants under nonselective conditions. Suppression of the neoplastic state of transformants could take place, resulting in the development of transformed shoots. Indications were obtained for the inheritance of tumor markers through meiosis from seedlings obtained from seeds of flowering transformed plants that still expressed nopaline synthesis.

Revertant seedlings from crown gall tumors retain a portion of the bacterial Ti plasmid DNA sequences

BT37 is a crown gall teratoma incited on tobacco by Agrobacterium tumefaciens containing pTi-T37, a nopaline-type Ti plasmid. Treatment of this cloned tumor tissue with kinetin at 1 mg/liter results in the formation of relatively normal-appearing shoots. These shoots can be induced to root and set viable seed. In contrast to BT37 tissue, the derived tissues are not phytohormone independent and do not produce nopaline. The reverted plants, like normal tobacco plants, are susceptible to infection by A. tumefaciens. This loss of tumorous traits is accompanied by the loss of most of the Ti plasmid sequences (T-DNA) found in BT37 DNA. Southern blot analysis indicates that the revertant tissues have lost the central portion of the T-DNA, which contains the "common DNA" sequences, a highly conserved region of the Ti plasmid that has been found to be incorporated into all tumors studied. Thus, these sequences appear necessary for oncogenicity and tumor maintenance and their loss is probably directly related to tumor reversal. The reverted plants as well as the plants obtained from seed, however, do retain sequences homologous to the ends of the T-DNA present in the parental teratoma. The persistence of foreign DNA sequences during the process of meiosis and seed formation has important implications for the possibility of the genetic engineering of plants.

Octopine synthase mRNA isolated from sunflower crown gall callus is homologous to the Ti plasmid of Agrobacterium tumefaciens

We have shown that the structural gene for octopine synthase (a crown gall-specific enzyme) is located in a central portion of the T-DNA that came from the Ti plasmid of agrobacterium tumefaciens and is expressed after it has been transferred to the plant cells. Polyadenylylated RNA was prepared from polysomes isolated from an octopine-producing crown gall callus and purified by selective hybridization to one of five recombinant plasmids. Each such plasmid contained a different fragment of T-DNA of pTi-15955 (octopine-type Ti plasmid). Purified mRNA was translated in vitro in rabbit reticulocyte lysates, and the translation products were immunoprecipitated with antibody against octopine synthase. Total and immunoprecipitated products were characterized by their molecular weights. A polypeptide of M(r) 40,000 (the same as authentic octopine synthase) was synthesized in vitro by crown gall mRNA selectively hybridized to three of the five fragments of T-DNA and precipitated with antibody against octopine synthase. This polypeptide was not immunoprecipitated with normal rabbit antibody nor was it synthesized when mRNA from the habituated callus was substituted. A mRNA 1500 bases long was detected when total mRNA was fractionated on an agarose gel, transferred to nitrocellulose, and used for hybridization to three of the five (32)P-labeled T-DNA fragments. This apparent mRNA for octopine synthase hybridized to the same three fragments of T-DNA as the mRNA for the M(r) 40,000 polypeptide and was not detected in the habituated callus.

Mapping of promoter-proximal regions by in vitro transcription of two Agrobacterium tumefaciens Ti-plasmids

Transcription initiation sites were mapped on both the octopine pTi Ach5 and the nopaline pTI C58 plasmids of Agrobacterium tumefaciens. Transcription ternary complexes were subjected to electrophoresis on agarose gels, prior and/or subsequent to restriction endonuclease digestion of the DNA template, evidenced by autoradiography and located on the restriction maps of the two tumor-inducing plasmids. A. tumefaciens RNA polymerase promptly recognizes and starts transcription on a few sequences which include the T-DNA.

DNA sequence analysis of crown gall tumor T-DNA encoding the 0.7 kb transcript

Crown gall tumor formation involves integration into the plant genome of DNA sequences (the T-region) of tumor-inducing (Ti) plasmids present in Agrobacterium tumefaciens. The T-DNA of the tumor expresses several gene products. Little is known about the function or regulation of expression of the 0.7kb transcript, which represents a relatively abundant T-DNA transcript in octopine-type tumors. In this report, a detailed structural analysis of the gene encoding the 0.7 kb transcript has been obtained by DNA sequence analysis of T-DNA isolated from A6S/2 tumor line. An indication of the structural characteristics of the protein product is obtained from the predicted amino acid sequence. The sequences flanking the open reading frame show characteristics with other eucaryotic genes. The corresponding DNA sequence of the inducing Ti plasmid (pTiA6) is identical with that of the DNA sequence from the tumor. Comparison of this gene sequence with the corresponding region of another Ti plasmid (pTiAch5) shows several differences in the 5' flanking sequence, but the nucleotide sequence of the coding region and 3' flanking region are identical.

Map locations of five transcripts homologous to TR-DNA in tobacco and sunflower crown gall tumors

Polyadenylated RNA from two octopine type tumor lines (E1, PSCG-15955) was analyzed by RNA blot hybridization and shown to contain five major transcripts homologous to TR DNA. In tobacco E1 tissue, the molecular weights of the TR homologous RNAs are 1.65 kb, 1.55 kb, 1.45 kb, 1.05 kb, and 0.78 kb. The 5' - and 3'-termini of each of the five E1 tumor transcripts were determined by S1 nuclease hybrid protection mapping. The polarity of transcription for the 0.78, 1.05 and 1.65 kb RNAs is from left to right, while the 1.55 and 1.45 kb RNAs are transcribed from right to left. Although we see the same size transcripts in sunflower PSCG-15955 tissue (with the exception of a 0.89 kb RNA in place of the 1.55 kb transcript of E1) there is an apparent difference in the relative abundance of the various RNAs between the two tumor lines.

Nucleotide sequence of the T-DNA region from theA grobacterium tumefaciens octopine Ti plasmid pTi15955

The complete nucleotide sequence of the transferred region (T-DNA) of an octopine tumor inducing (Ti) plasmid fromAgrobacterium tumefaciens (pTi15955) has been determined. A total of 24 595 nucleotides extending approximately 900 bases to either side of the outermost, T-DNA boundaries was sequenced. Computer analysis of the sequenced portion of the Ti plasmid revealed that recognition sites for 72 restriction endonucleases are present in the DNA sequence at least once; no site forEcoK exists in this DNA sequence. Two imperfect 24 base repeats border the T-DNA sequence; the left starts at position 909 and the right ends at position 23 782, giving the T-DNA region a total length, of 22 874 nucleotides. Another two similar 24 base repeats lie within T-DNA and divide it, into three distinct domains: T-left (TL-DNA) 13 175 bp of apparently eukaryotic origin; T-center (TC-DNA) 1816 bp of prokaryotic origin; and T-right (TR-DNA) 7 883 bp of eukaryotic origin. The T-DNA contains nine reported transcripts, however, 26 open reading frames longer than 300 bases that start with an ATG initiation codon were found. Fourteen open reading frames are bounded by putative eukaryotic promoters, ribosome binding sites, and poly(A) addition sites and occur only in TL-and TR-DNAs. No open reading frames showing eukaryotic promoter sequences are located within the TC-DNA.

Two higher molecular weight forms related to ferritin are synthesizedin vitro by RNA from developing cotyledons and leaves ofPhaseolus vulgaris

Using RNA from developing cotyledons and leaves of bean two products were synthesizedin vitro, with Mr 31000 and 31500 which are antigenically related to the subunit of phytoferritin (Mr 26500). The relative abundance of the two products is dependent on the type of tissue from which the RNA was derived. Evidence is presented for the assumption that both products are precursors of the phytoferritin subunit. The hypothesis is put forward that different transit sequences direct the phytoferritin subunits to different cell organelles.

Structure and transcription of the nopaline synthase gene region of T-DNA

We present the DNA sequence and plant-tumor transcription pattern of some 2400 base pairs from the right border region of pTi T37 DNA from the virulent Agrobacterium tumefaciens strain T37. This region includes the entire transcription unit encompassing the nopaline synthase gene, together with parts of other transcription units. The strategy used to determine the sequence also produced two opposing series of defined, asymmetric deletions across the target DNA region, some of which may serve future purposes in the exploitation of this sequence, which is known to be expressed in a wide variety of host plant tissues.

Complementation analysis of Agrobacterium tumefaciens Ti plasmid mutations affecting oncogenicity

A wide host range cosmid vector has been constructed by insertion of the lambda cos site into the plasmid pRK2501. This cosmid, which is maintained in Agrobacterium tumefaciens and is compatible with the Ti plasmid, has been used to make a clone bank of the A. tumefaciens pTiA6 plasmid. Several pTiA6 cosmids have been used to complement Tn5-induced Ti plasmid mutations. Five avirulent mutations which map outside of the region of the plasmid maintained in plant tumours (T-DNA) could be complemented in a trans orientation. Two mutations which are located on a single HpaI restriction fragment outside of the T-DNA, as well as three mutations which map within the T-DNA region, could not be complemented in a trans orientation in a REC- host.

Sizes and map positions of several plasmid-DNA-encoded transcripts in octopine-type crown gall tumors

The sizes and relative map positions of RNA molecules encoded by the plasmid DNA of several octopine-type tobacco crown gall tumors were determined by blot hybridization. At least six discrete polyadenylylated RNAs (sizes 0.73-1.75 kilobases) were detected in octopine-producing tumors (lines A6S/2, E9, and 15955/01). In one tumor (line 15955/1) in which octopine could not be detected, one of the RNA species was missing and another was diminished in abundance. Evidence is presented suggesting that the transcripts are encoded entirely by the plasmid DNA and do not originate from the surrounding plant DNA sequences.

A coupled transcription-translation system from Agrobacterium tumefaciens and its application to study Ti plasmid expression in vitro

A coupled transcription-translation system was isolated from A. tumefaciens. Expression of plasmids pBR322 and pKT212 from E.coli, cloned fragments of Ti plasmid (plasmids pSS155 and pSS156) and Ti plasmid derivatives pAL2802, pAL2811, pAL2821 and pAL2832 was analysed in an A. tumefaciens cell-free system and compared with their expression in an E.coli cell-free system. New proteins of 41K and 44K appeared in A tumefaciens extracts, as the result of Ti plasmid expression. These proteins were not found in E.coli extracts.

Phytohormones in the formation of crown gall tumors

Crown gall tumors were initiated in a variety of plant species by infection with Agrobacterium tumefaciens strain B6 and the concomitant changes in the tissue levels of phytohormones, mainly indole-3-acetic acid (IAA) and cytokinins, were analyzed. A comparison was made of these hormones with those produced by virulent and avirulent strains of the bacterium in liquid culture and with those of bacteria-free crown gall callus cultures. Specific radioimmunoassays were employed for hormone determinations. An assay for the quantitation of femto-mol amounts of isopentenyladenosine and related cytokinins was newly developed and is described in detail. The results can be summarized as follows: Virulence in strain B 6 is associated with the ability to release trans-zeatin and increased amounts of IAA into the surrounding environment. In many, but not all plants analyzed, the development of crown gall tumors is also associated with a sharp rise in the levels of trans-zeatin-type zytokinins and IAA (e.g., Euphorbia lathyris, Catharanthus roseus). Crown gall calli growing on hormone-free media varied greatly in their cytokinin levels. In a culture of Nicotiana tabacum, both trans-zeatin and isopentenyladenine or related cytokinins were not detected. Thus, tumor growth cannot be explained on the basis of elevated levels of IAA and/or cytokinins alone.

Expression of plant tumor-specific proteins in minicells of Escherichia coli: a fusion protein of lysopine dehydrogenase with chloramphenicol acetyltransferase

Fragment EcoRI 7 from Ti-plasmid pTi Ach5, a part of the T-DNA in octopine tumors, was cloned in both orientations into pACYC184 and expressed in E. coli minicells. The cells synthesized four proteins from four different coding regions on EcoRI 7. Two of the proteins (Mr 25.000 and 26.000) were expressed with promoters from the Ti-plasmid fragment, while transcription for the two other proteins (Mr 18.000 and 74.000) started with a promoter on pACYC184. The Mr 18.000 protein represented a fusion product between chloramphenicol acetyltransferase (CAT) on pACYC184 and a part of lysopine dehydrogenase (LpDH), the enzyme synthesizing octopine and lysopine in plant tumor cells. The results suggest that E. coli minicells are a valuable system to study the proteins coded for by the T-region of Ti-plasmids.

Agrobacterium tumefaciens RNA polymerase: a new purification procedure and a study of the stable binding sites on homologous deoxyribonucleic acid

RNA polymerase (RNA nucleotidyltransferase, EC 2.7.7.6) of Agrobacterium tumefaciens has been purified according to a fast and efficient procedure. The method involves only two chromatographic steps and yields a highly active enzyme. The RNA polymerase was studied with respect to the ability to bind its homologous genome. A. tumefaciens deoxyribonucleic acid (DNA) binds the enzyme even when fragmented at undergenic size (300 base pairs). The general binding is unspecific and very labile at low concentrations of heparin (0.66 micrograms/mL). The number and distribution of the stable binding sites, class A sites [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157-185], have been calculated from the heparin-induced dissociation kinetics of binary complexes formed between the enzyme and DNA fragments of various sizes. A total of 3.5 x 10(3) class A sites (forming binary complexes with a half-life of 16.6 min) are present on A. tumefaciens genome, a large number of which show a distribution of 800-1000 base pairs. The rest have a more widely spaced distribution. The interactions between Escherichia coli RNA polymerase and the A. tumefaciens template have also been examined, and it has been observed that E. coli holoenzyme forms stable complexes with a shorter half-life and recognizes a lower number of class A sites on A. tumefaciens genome.

Strain-dependent temperature-sensitive phase in crown gall tumorigenesis

The effect of high temperature treatments on the early stages of crown gall tumorigenesis in sunflowers was investigated. Treatments of 32 C initiated at various times during the first ten days after infection had a similar effect on tumors induced by Agrobacterium tumefaciens strains B(6) and C58. Tumor growth was sensitive to 32 C until 60 to 72 hours after infection and was stimulated by 32 C after that time. Therefore, the "inception phase" for both C58 and B(6)-induced tumors ends between 60 to 72 hours after infection. In contrast, B(6) and C58 tumors varied in their response to 37 C treatments during the first 168 hours after infection. Both C58 and B(6) tumors were sensitive to 37 C during the first 72 hours; however, B(6) tumors became resistant to 37 C after 96 hours, whereas C58-induced tumors remained sensitive until 144 to 168 hours after infection.The growth rate of C58 and B(6) tumors in plants moved to 32 C at 90 hours after infection was the same. B(6) tumors in plants moved to 37 C at 90 hours after infection also continued to grow rapidly, whereas C58 tumors in plants moved to 37 C at 90 hours exhibited a complete cessation of tumor growth. The 37 C temperature-sensitive period specific to C58 tumors ceases by 168 hours after infection. This indicates that the temperature-sensitive functions are no longer required after 168 hours. The possible significance of this work with regard to the presence of a temperature-sensitive plasmid, pTiC58, in strain C58 and the mechanism of tumor-inducing plasmid DNA maintenance in incipient tumor cells is discussed.

Agrobacterium tumefaciens mutants affected in crown gall tumorigenesis and octopine catabolism

Mutants of Agrobacterium tumefaciens which affect virulence or the ability to catabolize octopine were isolated after Tn5-induced mutagenesis. Of 8,900 colonies tested, 7 mutants with Tn5 insertions in a specific region of other Ti plasmid unable to catabolize octopine were isolated. Thirty-seven mutants affected in tumorigenesis resulted from insertions in the Ti plasmid and the Agrobacterium chromosome. Of these mutations, 12 were chromosomal and 25 mapped on the plasmid. Twenty-three mapped within a 20-megadalton region, which is distinct from the Ti plasmid sequences found stably integrated into the plant cell genome T-deoxyribonucleic acid). Included in these were mutants that were either a virulent or produced tumors with unusual morphologies. Three mutants contained insertions in the T-deoxyribonucleic acid. These three mutants incited tumors which synthesized octopine but had an altered morphology due to either extensive proliferation of shoots or roots from the tumor callus. Three additional mutants not caused by Tn5 contained mutations in the Ti plasmid.