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

Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens

The plant tumor disease known as crown gall was not called by that name until more recent times. Galls on plants were described by Malpighi (1679) who believed that these extraordinary growth are spontaneously produced. Agrobacterium was first isolated from tumors in 1897 by Fridiano Cavara in Napoli, Italy. After this bacterium was recognized to be the cause of crown gall disease, questions were raised on the mechanism by which it caused tumors on a variety of plants. Numerous very detailed studies led to the identification of Agrobacterium tumefaciens as the causal bacterium that cleverly transferred a genetic principle to plant host cells and integrated it into their chromosomes. Such studies have led to a variety of sophisticated mechanisms used by this organism to aid in its survival against competing microorganisms. Knowledge gained from these fundamental discoveries has opened many avenues for researchers to examine their primary organisms of study for similar mechanisms of pathogenesis in both plants and animals. These discoveries also advanced the genetic engineering of domesticated plants for improved food and fiber.

Agrobacterium: nature's genetic engineer

Agrobacterium was identified as the agent causing the plant tumor, crown gall over 100 years ago. Since then, studies have resulted in many surprising observations. Armin Braun demonstrated that Agrobacterium infected cells had unusual nutritional properties, and that the bacterium was necessary to start the infection but not for continued tumor development. He developed the concept of a tumor inducing principle (TIP), the factor that actually caused the disease. Thirty years later the TIP was shown to be a piece of a tumor inducing (Ti) plasmid excised by an endonuclease. In the next 20 years, most of the key features of the disease were described. The single-strand DNA (T-DNA) with the endonuclease attached is transferred through a type IV secretion system into the host cell where it is likely coated and protected from nucleases by a bacterial secreted protein to form the T-complex. A nuclear localization signal in the endonuclease guides the transferred strand (T-strand), into the nucleus where it is integrated randomly into the host chromosome. Other secreted proteins likely aid in uncoating the T-complex. The T-DNA encodes enzymes of auxin, cytokinin, and opine synthesis, the latter a food source for Agrobacterium. The genes associated with T-strand formation and transfer (vir) map to the Ti plasmid and are only expressed when the bacteria are in close association with a plant. Plant signals are recognized by a two-component regulatory system which activates vir genes. Chromosomal genes with pleiotropic functions also play important roles in plant transformation. The data now explain Braun's old observations and also explain why Agrobacterium is nature's genetic engineer. Any DNA inserted between the border sequences which define the T-DNA will be transferred and integrated into host cells. Thus, Agrobacterium has become the major vector in plant genetic engineering.

Membrane and core periplasmic Agrobacterium tumefaciens virulence Type IV secretion system components localize to multiple sites around the bacterial perimeter during lateral attachment to plant cells

Type IV secretion systems (T4SS) transfer DNA and/or proteins into recipient cells. Here we performed immunofluorescence deconvolution microscopy to localize the assembled T4SS by detection of its native components VirB1, VirB2, VirB4, VirB5, VirB7, VirB8, VirB9, VirB10, and VirB11 in the C58 nopaline strain of Agrobacterium tumefaciens, following induction of virulence (vir) gene expression. These different proteins represent T4SS components spanning the inner membrane, periplasm, or outer membrane. Native VirB2, VirB5, VirB7, and VirB8 were also localized in the A. tumefaciens octopine strain A348. Quantitative analyses of the localization of all the above Vir proteins in nopaline and octopine strains revealed multiple foci in single optical sections in over 80% and 70% of the bacterial cells, respectively. Green fluorescent protein (GFP)-VirB8 expression following vir induction was used to monitor bacterial binding to live host plant cells; bacteria bind predominantly along their lengths, with few bacteria binding via their poles or subpoles. vir-induced attachment-defective bacteria or bacteria without the Ti plasmid do not bind to plant cells. These data support a model where multiple vir-T4SS around the perimeter of the bacterium maximize effective contact with the host to facilitate efficient transfer of DNA and protein substrates.

IMPORTANCE

Transfer of DNA and/or proteins to host cells through multiprotein type IV secretion system (T4SS) complexes that span the bacterial cell envelope is critical to bacterial pathogenesis. Early reports suggested that T4SS components localized at the cell poles. Now, higher-resolution deconvolution fluorescence microscopy reveals that all structural components of the Agrobacterium tumefaciens vir-T4SS, as well as its transported protein substrates, localize to multiple foci around the cell perimeter. These results lead to a new model of A. tumefaciens attachment to a plant cell, where A. tumefaciens takes advantage of the multiple vir-T4SS along its length to make intimate lateral contact with plant cells and thereby effectively transfer DNA and/or proteins through the vir-T4SS. The T4SS of A. tumefaciens is among the best-studied T4SS, and the majority of its components are highly conserved in different pathogenic bacterial species. Thus, the results presented can be applied to a broad range of pathogens that utilize T4SS.

Cytokinin/auxin balance in crown gall tumors is regulated by specific loci in the T-DNA

Insertion of the transposon Tn5 into the T-region of the octopine Ti plasmid of Agrobacterium tumefaciens gives rise to crown gall tumors having altered morphology. Three loci within the T-DNA that control tumor morphology have been detected [Garfinkel, D. J., Simpson, R. B., Ream, L. W., White, F. F., Gordon, M. P. & Nester, E. W. (1981) Cell 27, 143-153]. They influence tumor size (tml), production of roots (tmr), or production of shoots (tms). Cytokinin and auxin levels in such mutant tumors were examined by HPLC/radioimmunoassay and HPLC/fluorescence assay, respectively. Free indoleacetic acid levels (in pmol/g) were: uninfected tobacco stem tissues, 128; wild-type A348 tumors, 295; tml mutant tumors, 307; tmr mutant tumors, 129; and tms mutant tumors, 70. Average trans-ribosylzeatin levels were correspondingly: 0.97, 48, 40, 0.54, and 1,400 pmol/g. trans-Ribosylzeatin/indoleacetic acid ratios were as high as 24 in shoot-producing tumors and as low as 0.003 in root-producing tumors. The evidence strongly suggests that tumor phytohormone levels are determined by genes in the T-DNA.

Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression

Agrobacterium tumefaciens transfers DNA (T-DNA) to plant cells, where it integrates into the plant genome. Little is known about how T-DNA chooses sites within the plant chromosome for integration. Previous studies indicated that T-DNA preferentially integrates into transcriptionally active regions of the genome, especially in 5'-promoter regions. This would make sense, considering that chromatin structure surrounding active promoters may be more "open" and accessible to foreign DNA. However, recent results suggest that this seemingly non-random pattern of integration may be an artifact of selection bias, and that T-DNA may integrate more randomly than previously thought. In this chapter, I discuss the history of these observations and the role chromatin proteins may play in T-DNA integration and transgene expression. Understanding how chromatin conformation may influence T-DNA integration will be important in developing strategies for reproducible and stable transgene expression, and for gene targeting.

Will you let me use your nucleus? How Agrobacterium gets its T-DNA expressed in the host plant cell

Agrobacterium is the only known bacterium capable of natural DNA transfer into a eukaryotic host. The genes transferred to host plants are contained on a T-DNA (transferred DNA) molecule, the transfer of which begins with its translocation, along with several effector proteins, from the bacterial cell to the host-cell cytoplasm. In the host cytoplasm, the T-complex is formed from a single-stranded copy of the T-DNA (T-strand) associated with several bacterial and host proteins and it is imported into the host nucleus via interactions with the host nuclear import machinery. Once inside the nucleus, the T-complex is most likely directed to the host genome by associating with histones. Finally, the chromatin-associated T-complex is uncoated from its escorting proteins prior to the conversion of the T-strand to a double-stranded form and its integration into the host genome.

A 20 nucleotide upstream element is essential for the nopaline synthase (nos) promoter activity

The nopaline synthase (nos) promoter is expressed in a wide range of plant cell types and regulated by various developmental and environmental factors. The nos upstream control region essential for this regulation was studied by means of synthetic oligomers using transient and stable transformation systems. Insertion of a 20 nucleotide sequence containing two hexamer motifs and a spacer region into deletion mutants lacking the upstream control region was essential for promoter activity. Mutation of one or more nucleotides of either hexamer sequence significantly altered the strength of expression of the nos promoter. Point mutations within the spacer region also strongly influenced promoter strength. Insertion of multiple copies of the 20 nucleotide sequence into the nonfunctional deletion mutants proportionally increased the promoter activity. These results suggest that this twenty nucleotide sequence is essential for the nos promoter to function. Substitution of the nos element with the ocs or 35S as-1 which contain similar hexamer motifs restored not only promoter activity but also responses to wounding, auxin, methyl jasmonate, and salicylic acid.

Levels and location of expression of the Agrobacterium tumefaciens pTiA6 ipt gene promoter in transgenic tobacco

The location of gene expression of the Agrobacterium tumefaciens ipt gene promoter in transgenic tobacco plants was examined using the beta-glucuronidase (GUS) reporter gene. Expression of GUS was detected in every organ and most cell types examined. The highest levels of GUS activity were found in roots. To further examine the transcriptional basis of this broad expression pattern, deletions in the 5' non-coding region of the gene were translationally fused to two promoterless reporter genes, encoding the enzymes chloramphenicol acetyl transferase (CAT) and beta-glucuronidase (GUS). Reporter enzyme assays revealed the existence of an upstream segment required for maximal promoter function, the 5' end of which is between -442 and -408 of the Pipt ATG codon. This upstream segment is required for maximal levels of GUS expression in roots, but not in other organs, and a tobacco suspension-cultured cell line. The implications of broad ipt expression on the process of crown gall tumorigenesis are discussed.

A chromosomal Agrobacterium tumefaciens gene required for effective plant signal transduction

The vir gene products of Agrobacterium tumefaciens carry out the transfer of T-DNA to the plant genome. Effective transcriptional induction of the vir genes by plant signal molecules is controlled by two vir gene products, VirA and VirG. In this study we have identified and cloned a chromosomal region which is also required for vir gene induction. Transposon insertions within this region reduce induction significantly and strongly attenuate virulence, resulting in a restricted host range for infection. The reduction in vir gene transcription can be partially overcome by high concentrations of the inducer molecule acetosyringone. Expression of virG at low pH and low phosphate concentrations, which is independent of plant signals, is not affected by these mutations. Sequence analysis of the region revealed two divergent open reading frames, which we have designated chvE and ORF1. Several transposon insertions mapped in chvE; this resulted in attenuated virulence. chvE codes for a putative protein which is homologous to two periplasmic receptor proteins involved in chemotaxis and uptake of sugars. Whether ORF1 is required for virulence is uncertain. One transposon insertion resulting in avirulence maps in or near the 5' end of ORF1, and several which do not affect virulence map in its 3' end. ORF1 codes for a putative protein which is homologous to a family of transcriptional activator proteins.

Nopaline synthase promoter is wound inducible and auxin inducible

The activity of the nopaline synthase (nos) promoter is differentially regulated in several plant organs. In this article we demonstrate that the nos promoter is wound inducible in both vegetative and reproductive organs. The induction of the nos promoter was observed in leaves, stems, cotyledons, and various reproductive organs, suggesting that the response is not organ specific. The wound response was further enhanced by addition of auxins. Other growth substances had no effect on the wound-inducible nos promoter activity. Deletion analysis of the nos promoter indicated that the 10-base pair (GCACATACGT) Z element located between -123 and -114 or an element overlapping with this sequence is essential for the wound and auxin responses.

Altered imino diacid synthesis and transcription in crown gall tumors with transposon Tn5 insertions in the 3' end of the octopine synthase gene

Octopine synthase encoded by the T-DNA (transferred DNA) locus ocs synthesizes N2-(D-1-carboxyethyl)-L-amino acids in octopine-type crown gall tumors. So far, derivatives of only basic amino acids have been isolated. We have detected a glutamine derivative and called it heliopine. Tumors induced by several Ti plasmids with transposon Tn5 insertions in the 3' end of ocs still synthesized small quantities of N2-(1-carboxyethyl)-arginine and N2-(1-carboxyethyl)-glutamine. In addition, N2-(1,3-dicarboxypropyl)-asparagine, which is absent in wild-type octopine tumors, was detected in these tumors. These three imino diacids (octopine, heliopine, and asparaginopine, respectively, or their isomers) were undetectable in tumors induced by Ti plasmids harboring deletions of the ocs gene. Poly(A)+ RNAs which hybridize to the ocs sequence can also be detected in the ocs::Tn5 tumors; these RNAs, however, were heterogeneous in size and shorter in length than the normal ocs mRNA. These results indicate that mutant ocs products synthesize imino diacids in these ocs::Tn5 tumors.

Organ-specific and developmental regulation of the nopaline synthase promoter in transgenic tobacco plants

Control regions of the nopaline synthase (nos) gene have been widely used to express foreign genes in plants since the promoter is active in a wide variety of plant tissues. We report here the characteristics of the nos promoter activity in transgenic tobacco (Nicotiana tabacum) plants at various developmental stages. The promoter was highly active in the lower parts of a plant and gradually decreased in the upper parts. This vertical gradient was maintained throughout plant growth until the flowering stage when the overall promoter strength decreased significantly in the vegetative organs. However, in various flower organs, the nos promoter activities increased dramatically. Higher activity was observed in calyx, corolla, and stamens although the maximum promoter activity in each organ was found at different stages of flower development. The promoter activity in pistils was low and gradually increased in the ovaries after anthesis. In developing fruits, the nos promoter activity was strongly induced during the mid-stage of embryogenesis. These results indicate that the expression of the nos promoter is developmentally regulated and organ specific in transgenic tobacco plants.

Deletion analysis of the mannopine synthase gene promoter in sunflower crown gall tumors and Agrobacterium tumefaciens

We have used deletion mutagenesis to analyze a TR-DNA promoter from the octopine-type Ti plasmid pTiB6806. The promoter for the gene encoding mannopine synthase (mas) was cloned upstream of the bacterial kanamycin-resistance gene neomycin phosphotransferase II (NPT II). Bal31 deletion mutagenesis was used to generate deletion derivatives of the mas/NPTII gene beginning 1353 bp upstream of the initiation of transcription and extending to 120 bp downstream from the mRNA start site. Deletions that left intact 318 bp upstream of transcription initiation had no detectable effect on the ability of tumors harboring the deletion to synthesize correctly initiated mRNA or to grow on the kanamycin analogue G418. Deletion to-138 destroyed the ability of sunflower crown gall tumors to grow on G418 although low levels of the mas/NPTII transcript were detected in one tumor line. Deletions that left only 57 bp upstream of transcription initiation allowed neither growth on G418 nor detectable mas/NPTII synthesis, even though the CCAAT and TATAA homologies were intact. The mas promoter is functional in Agrobacterium tumefaciens and we present data concerning the effects of the Bal31 deletions on the growth of A. tumefaciens on kanamycin.

Localization of kinetoplast DNA maxicircle transcripts in bloodstream and procyclic form Trypanosoma brucei

Over 80% of the maxicircle and numerous minicircles of Trypanosoma brucei kinetoplast DNA have been cloned. The uncloned maxicircle segment contains few restriction endonuclease cleavage sites, varies in size among strains, and may be unstable in conventional cloning systems. cDNA prepared to bloodstream or procyclic trypomastigote RNA hybridized to all but one maxicircle segment, but did not hybridize to minicircles. Fourteen maxicircle transcripts were detected in RNA from both bloodstream and procyclic trypomastigotes. The coding sequences for these transcripts were localized and account for most of the maxicircle. One region of the maxicircle, which borders the variable region, was not found to be transcribed. We conclude that the maxicircle is largely but not completely transcribed in both bloodstream and procyclic trypomastigotes, whereas minicircle transcription is minimal or absent in these stages. Qualitative transcriptional differences which could account for mitochondrial respiratory differences between the bloodstream and procyclic trypomastigotes were not observed.

Sustained ethylene production in Agrobacterium-transformed carrot disks caused by expression of the T-DNA tms gene products

Agrobacterium-infected carrot disks continually produced elevated levels of ethylene. Ethylene production was mediated by the elevated levels of auxin synthesized in transformed tissues.

Physical and functional map of supervirulent Agrobacterium tumefaciens tumor-inducing plasmid pTiBo542

Agrobacterium tumefaciens strains carrying pTiBo542 induce large, fast-appearing tumors and have an unusually wide host range. A clone bank was made from this 250-kilobase plasmid in a wide-host-range vector, and restriction maps were determined for BamHI and SalI. The virulence genes, transferred DNA genes, plasmid incompatibility region, and a region that inhibits growth of certain A. tumefaciens strains were localized. The six virulence genes and two tms genes were highly homologous to the genes of pTiA6, but the tmr gene was not. Mutations in each of the six vir loci of pTiA6 were complemented by clones from the vir region of pTiBo542.

Structure and expression of DNA transferred to tobacco via transformation of protoplasts with Ti-plasmid DNA: co-transfer of T-DNA and non T-DNA sequences

The T-DNA structure and organization in tissues obtained via transformation of tobacco protoplasts with Ti-plasmid DNA was found to be completely different from the T-DNA introduced via Agrobacterium tumefaciens. It is often fragmented. Overlapping copies of T-DNA, having various sizes, as well as separated fragments of T-DNA were detected. The border sequences of 23 basepairs (bp), flanking the T-region in the Ti-plasmid as direct repeats are not used as preferred sequences for integration. Similar results were obtained with a T-region clone lacking one of the TL-borders. This clone, which carried the cytokinin locus and only the right border sequence of TL and the left border sequence of TR, still had the capacity to transform protoplasts. Also the Vir-region of the Ti-plasmid is not required for integration of foreign DNA via DNA transformation. This is demonstrated by the results with the T-region clone mentioned and by the transforming capacity of a Ti-plasmid carrying a mutated Vir-region. Nevertheless, in a number of Ti-plasmid DNA transformants Vir-region fragments were found to be stably integrated. Furthermore, it has been established that co-transformation can occur with plant cells. Besides the detection of Ti-plasmid fragments from outside the T-region also DNA sequences originating from two DNA sources, which were both independently present in transformation experiments, have been found in some DNA transformants, e.g. calf thymus DNA, which was used as carrier DNA. No expression of the co-transferred DNA was observed. In total three phenotypical classes of DNA transformants were isolated. Although the T-DNA was often scrambled, polyA(+) mRNA studies indicated that the different phenotypes studied can be explained by the presence of active T-DNA genes with known functions.

Site-specific mutagenesis in the TR-DNA region of octopine-type Ti plasmids

Site-specific insertion and deletion mutations affecting all six of the eukaryotic-like genes in the TR-DNA region of the octopine-type Ti plasmids pTil5955 or pTiA6 have been generated. None of the mutations affected virulence or tumor morphology on sunflower. Mutations in the coding regions of two of the genes resulted in tumors without any detectable mannopine, mannopinic acid or agropine, and mutations in either the coding region or in the 3' untranslated region of a third gene eliminated biosynthesis of agropine, but not mannopine or mannopinic acid. Detection of two previously unobserved silver nitrate-positive substance in tumors incited by one of the mutant strains, together with data on the presence of opines in tumors incited by coinoculation with mixtures of different mutant strains, allowed us to propose the functional order of all three genes involved in the biosynthesis of mannopine, mannopinic acid and agropine. TR-DNA was absent in tumors incited by anAgrobacterium tumefaciens strain harboring a Ti plasmid in which the right border of the TR-DNA region was deleted.

The nucleosome structure of the rRNA genes of some tumorous and nontumorous Nicotiana cell lines

The nucleosome structure of the nuclear rRNA genes was investigated in a variety of tumorous and nontumorous Nicotiana tabacum cell lines, and in a genetic tumor produced by crossing Nicotiana langsdorffii with Nicotiana glauca. The rRNA genes from two unorganized octopine type crown gall tumors were found in an altered nucleosome conformation compared to those of the other cell lines and N. tabacum leaves. The altered nucleosome structure of the rRNA genes in the octopine type crown gall lines was not due to the tumorous state of the tissue, nor was it related directly to the morphology of the tumor. These two lines did have, however, a greatly reduced rRNA gene copy number. Several Eco R1 fragments homologous to the rRNA gene probe were preferentially lost from one of these tumor lines. The alteration of the nucleosome structure of the remaining rRNA genes in the octopine type crown gall tumors may result from rapid transcription necessitated by their reduced copy number.

Limited-host-range plasmid of Agrobacterium tumefaciens: molecular and genetic analyses of transferred DNA

A tumor-inducing (Ti) plasmid from a strain of Agrobacterium tumefaciens that induces tumors on only a limited range of plants was characterized and compared with the Ti plasmids from strains that induce tumors on a wide range of plants. Whereas all wide-host-range Ti plasmids characterized to date contain closely linked oncogenic loci within a single transferred DNA (T-DNA) region, homology to these loci is divided into two widely separated T-DNA regions on the limited-host-range plasmid. These two plasmid regions, TA-DNA and TB-DNA, are separated by approximately 25 kilobases of DNA which is not maintained in the tumor. The TA-DNA region resembles a deleted form of the wide-host-range TL-DNA and contains a region homologous to the cytokinin biosynthetic gene. However, a region homologous to the two auxin biosynthetic loci of the wide-host-range plasmid mapped within the TB-DNA region. These latter genes play an important role in tumor formation because mutations in these loci result in a loss of virulence on Nicotiana plants. Furthermore, the TB-DNA region alone conferred tumorigenicity onto strains with an intact set of vir genes. Our results suggest that factors within both the T-DNA and the vir regions contribute to the expression of host range in Agrobacterium species. There was a tremendous variation among plants in susceptibility to tumor formation by various A. tumefaciens strains. This variation occurred not only among different plant species, but also among different varieties of plants within the same genus.

Identification and genetic analysis of an Agrobacterium tumefaciens chromosomal virulence region

A genetic analysis of Agrobacterium tumefaciens chromosomal functions required for virulence was undertaken. Large Tn5-containing cosmid clones were isolated from DNA of avirulent A. tumefaciens mutants having chromosomal Tn5 insertions and exhibiting defective attachment to plant cells. The clones from several different mutants each contained overlapping segments of a 30-kilobase A. tumefaciens chromosomal region, which were physically mapped. All chromosomal Tn5 insertions leading to the avirulent, attachment-defective phenotype were localized within an 11-kilobase portion of this chromosomal virulence region. Transposon Tn3::HoHo1 (Tn3 containing lacZ) was used to simultaneously mutagenize and create lac fusions within the virulence region. This analysis demonstrated the presence of two distinct chromosomal virulence loci, which were 1.5 and 5 kilobases long; transposon insertions into these loci led to avirulence and defective attachment. The beta-galactosidase activity associated with various Tn3::HoHo1-created lac fusions indicated that the loci are transcribed in opposite directions, and complementation studies suggested that each locus consists of a single transcriptional unit. A cosmid clone of the chromosomal virulence region containing a lac fusion in the extreme 3' portion of the 5-kilobase locus was used to demonstrate that expression of this region is dependent on the presence of sequences in the 5' portion of the locus, confirming its operon-like nature.

Specific attachment of Agrobacterium tumefaciens to bamboo cells in suspension cultures

Agrobacterium tumefaciens was tested for its ability to attach to tissue culture cells of bamboo, a monocotyledonous plant. Phase-contrast microscopy and kinetic experiments with radiolabeled bacteria showed that attachment to bamboo cells was indistinguishable from attachment to cells of dicotyledonous plants. Bacterial mutants defective in attachment to dicotyledonous plants showed similar behavior with bamboo, and extensive washing of the bamboo cells had no effect on the number of bacteria which attached.

Changes in T-DNA methylation and expression are associated with phenotypic variation and plant regeneration in a crown gall tumor line

Phenotypic variation of an octopine-type crown gall tumor line resulting from changes in the pattern of T-DNA methylation and expression is described. Variants that grow as unorganized callus always express T-DNA transcripts 1 and 2. In shoot-forming variants (teratomas) only T-DNA transcript 4 is expressed. This line also regenerates normal-appearing, rooted plants in which all T-DNA expression is suppressed. Tissues from these plants require phytohormones for growth in vitro. These plants are self-fertile and transmit T-DNA through meiosis, and T-DNA suppression is maintained in the next generation. After treatment of regenerated plant tissue with 5-azacytidine, an inhibitor of DNA methylation, T-DNA transcription and phytohormone-independent tumorous growth resume. The T-DNA of cell lines in which T-DNA is not expressed is highly methylated, whereas the level of T-DNA methylation is reduced in 5-azacytidine treated cells that resume T-DNA expression and phytohormone-independent growth. The correlation between the degree of T-DNA methylation and the level of T-DNA expression indicates that hypermethylation is responsible for the suppression of T-DNA transcription.

Physical and functional map of an Agrobacterium tumefaciens tumor-inducing plasmid that confers a narrow host range

Agrobacterium tumefaciens Ag162 induces crown gall disease on an unusually narrow range of host plants. The 231-kilobase Ti plasmid which has been shown to determine host range, was subcloned into the vector pVCK102. By comparing overlaps of cloned insets, maps were constructed for the restriction endonucleases SalI, XhoI, EcoRI, and KpnI. Plasmid incompatibility, octopine catabolism, and at least six virulence genes were localized. Plasmid incompatibility between pTiAg162 and the wide host range plasmid pTiA6 consists of two components: mutual incompatibility and the apparent ability of pTiA6 to block RK2 replication if the pTiAg162 incompatibility locus is linked to the vector pVK102. The octopine catabolism locus maps within the 30 kilobases of DNA separating the two T-DNA regions of pTiAg162. Complementation of avirulent vir mutants of pTiA6 with clones of pTiAg162 DNA did not confer the host range of pTiAg162 but rather restored the wide host range of pTiA6. One potentially important difference between pTiA6 and pTiAg162 is that pTiAg162 T-DNA regions are widely separated.

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 tms genes of the pTiA6NC octopine Ti plasmid: two gene products involved in plant tumorigenesis

The nucleotide sequence of the tumor morphology locus, tms, from pTiA6NC has been determined. The sequence analysis indicates that each of two polyadenylylated transcripts encoded by this locus contains an open reading frame; the predicted transcript 1 gene product has a molecular size of 83,769 daltons, and the predicted transcript 2 gene product, of 49,588 daltons. The precise start and stop positions of the transcript 2 RNA have been mapped with S1 nuclease. Several insertion mutations have been constructed. One of these localizes the transcript 2 promoter within the 72 base pairs 5' to transcription initiation. Significant homology was observed between the protein encoded by transcript 1 and the adenine binding region of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens, suggesting that the transcript 1 protein binds adenine either as substrate or cofactor.

The sequence of the tms transcript 2 locus of the A. tumefaciens plasmid pTiA6 and characterization of the mutation in pTiA66 that is responsible for auxin attenuation

The incorporation of Ti plasmid sequences, the T-DNA, into the genomes of dicotyledenous plants causes the formation of tumors. Here we report the nucleotide sequence of one of the T-DNA "oncogenes", the transcript 2 gene of pTiA6 and we further characterize the 2.7 Kb element that has spontaneously inserted into this gene in plasmid pTiA66. The results indicate that the transcript 2 portion of the T-DNA has an open reading frame that could encode a polypeptide of 49.8 Kd. The open reading frame is surrounded by sequences that typically have roles in eucaryotic gene expression. Nucleotide sequence and Southern blot analysis also indicates that the 2.7 Kb insert in the transcript 2 gene of pTiA66 is located within the coding sequence of the gene and suggests that the element is an insertion sequence. We designate this element, IS66.

Clonal analysis of heterogeneous crown gall tumor tissues induced by wild-type and shooter mutant strains ofAgrobacterium tumefaciens-expression of T-DNA genes

Tumors were induced by anAgrobacterium tumefaciens strain with a wild-type octopine Ti plasmid and by shooter mutants with a transposon insertion in the auxin-locus of the T-region. Cloning of isolated axenic tumor tissues revealed that in all cases they consisted of tumor cells (10-26%) next to a majority of normal cells. The tumor clones that had been induced by the strain with the wild-type Ti plasmid all grew as amorphous calli. Tumor, clones induced by a shooter mutant were of two different types. One type of clone grew well on phytohormone-free medium. this type invariably regenerated tumorous shoots abundantly on this medium. The other type of clone only grew after the addition of auxin and cytokinin to the culture medium, but slow growth also took place in the presence of only auxin. This type never regenerated shoots spontaneously. After stimulation by a high level of kinetin, however, a few shoots were also obtained from these clones. One of these shoots, like other tumorous shoots, contained the tumor-specific enzyme octopinesynthase (Ocs), but in contrast to other tumorous shoots formed a root-system.The expression of T-DNA genes in shoots proliferating from the cloned tumor tissues induced by a mutant with an insertion in the region for transcript tr. 2 was studied by northern blot hybridization. Except for tr.2 the T-DNA transcripts were detected in the tumorous shoots analysed, including the transcript, tr.1 from the auxin-locus and tr.4 from the cytokinin-locus. This shows that the presence of these transcripts, which are assumed to be responsible for the tumorigenic character of tumor cells, does not interfere with the differentiation of shoot cells.One of the shooty tumor clones (TSO38) showed an unstable character with regard to octopine synthase activity (Ocs±). For, TSO38 and some of its subclones, it was found that only 4% of the regenerated shoots were Ocs(+). Northern blot hybridization revealed that the mRNA for octopine synthase was present in extremely low quantity in the population of TSO38 derived shoots.The finding that it was possible to force shoots from clone TSO38 and from subclone TSO38-23(-) that were Ocs(-) to become Ocs(+), proved that the gene for octopine synthase was present in the Ocs(-) shoots and that this gene showed unstable expression due to regulation at the level of transcription.

Nucleotide sequence of the Agrobacterium tumefaciens octopine Ti plasmid-encoded tmr gene

The nucleotide sequence of the tmr gene, encoded by the octopine Ti plasmid from Agrobacterium tumefaciens (pTiAch5), was determined. The T-DNA, which encompasses this gene, is involved in tumor formation and maintenance, and probably mediates the cytokinin-independent growth of transformed plant cells. The nucleotide sequence of the tmr gene displays a continuous open reading frame specifying a polypeptide chain of 240 amino acids. The 5'- terminus of the polyadenylated tmr mRNA isolated from octopine tobacco tumor cell lines was determined by nuclease S1 mapping. The nucleotide sequence 5'-TATAAAA-3', which sequence is identical to the canonical "TATA" box, was found 29 nucleotides upstream from the major initiation site for RNA synthesis. Two potential polyadenylation signals 5'-AATAAA-3' were found at 207 and 275 nucleotides downstream from the TAG stopcodon of the tmr gene. A comparison was made of nucleotide stretches, involved in transcription control of T-DNA genes.

Studies on the use of toxic precursor analogs of opines to select transformed plant cells

S-(2-aminoethyl-)L-cysteine and L-canavanine were less toxic for octopine-type crown gall tissues that contained lysopine dehydrogenase than for other crown gall or habituated tissues. These analogs are substrates for lysopine dehydrogenase in vitro and in vivo. Thus toxic analogs of amino acid precursors of opines may be useful in selecting for cells that contain an opine dehydrogenase.

Host and T-DNA determinants of cytokinin autonomy in tobacco cells transformed byAgrobacterium tumefaciens

The hormone autonomy of tobacco (Nicotiana tabacum L.) cells transformed byAgrobacterium tumefaciens containing mutations attmr (the "rooty" locus) of the pTiT37 plasmid has been examined. These cells require cytokinin, but not auxin for continuous growth in culture, indicating that the function of thetmr locus is to specify or induce cytokinin autonomy. Examination of tissues from plants regenerated from cells transformed by the mutant bacteria showed that the auxin independent phenotype is suppressed, but can be reinitiated in culture by exposure to an exogenous supply of auxin. In addition the developmental state of the cells from such regenerated plants can exert a profound influence on their cytokinin autonomy phenotype.

Multiple mutations in the T region of the Agrobacterium tumefaciens tumor-inducing plasmid

Three genetic loci affecting tumor morphology lie within pTiA6NC T-DNA: tms, tmr, and tml. Using deletions and multiple transposon insertions, we constructed tumor-inducing (Ti) plasmids representing every possible double and triple mutant combination. tms tmr and tms tmr tml mutants did not incite tumors on most plants and produced a very weak response on a few other hosts but tms tml and tmr tml mutants were virulent. Thus, either tms+ or tmr+ alone can promote significant tumor growth but tml+ by itself is not sufficient. On hosts where tms mutants induce tumors accompanied by shoot proliferation, addition of a tml mutation reduces or eliminates shoot proliferation, suggesting that tml+ promotes shoot development. The small calli incited by tms tmr and tms tmr tml mutants contain agropine, an indication that these plant cells incorporate T-DNA in the absence of substantial tumor growth.