Studies on Agrobacterium tumefaciens: characterization of strains 1D135 and B6, and analysis of the bacterial chromosome, transfer RNA and ribosomes for tumor-inducing ability

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops.

Iodate and nitrate transformation by Agrobacterium/Rhizobium related strain DVZ35 isolated from contaminated Hanford groundwater

Nitrate and radioiodine (¹²⁹I) contamination is widespread in groundwater underneath the Central Plateau of the Hanford Site. ¹²⁹I, a byproduct of nuclear fission, is of concern due to a 15.7 million year half-life, and toxicity. The Hanford 200 West Area contains plumes covering 4.3 km² with average ¹²⁹I concentrations of 3.5 pCi/L. Iodate accounts for 70.6% of the iodine present and organo-iodine and iodide make up 25.8% and 3.6%, respectively. Nitrate plumes encompassing the ¹²⁹I plumes have a surface area of 16 km² averaging 130 mg/L. A nitrate and iodate reducing bacterium closely related to Agrobacterium, strain DVZ35, was isolated from sediment incubated in a ¹²⁹I plume. Iodate removal efficiency was 36.3% in transition cultures, and 47.8% in anaerobic cultures. Nitrate (10 mM) was also reduced in the microcosm. When nitrate was spiked into the microcosms, iodate removal efficiency was 84.0% and 69.2% in transition and anaerobic cultures, respectively. Iodate reduction was lacking when nitrate was absent from the growth medium. These data indicate there is simultaneous reduction of nitrate and iodate by DVZ35, and iodate is reduced to iodide. Results provide the scientific basis for combined nitrogen and iodine cycling throughout the Hanford Site.

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 transcriptional regulator Ros is a prokaryotic zinc finger protein that regulates the plant oncogene ipt

Virulence genes of Agrobacterium tumefaciens are under the control of positive and negative transcriptional regulators. We found that the transcriptional regulator Ros controls expression of the plant oncogene ipt, which encodes isopentenyl transferase, in A. tumefaciens. This enzyme is involved in biosynthesis of the plant growth hormone cytokinin in the host plant. An ipt promoter::cat reporter gene fusion showed a 10-fold increase in ipt promoter activity in A. tumefaciens ros mutant strains when compared with wild type. Also, increased levels (10- to 20-fold) of isopentenyl adenosine, the product of the reaction catalyzed by isopentenyl transferase, were detected in ros mutant strains. In vitro studies using purified Ros showed it binds directly to the ipt promoter. Analysis of the deduced Ros amino acid sequence identified a novel type of C2H2 zinc finger. In Ros the peptide loop spacing of the zinc finger is 9 amino acids as opposed to the invariant 12 amino acids in the classical C2H2 motif. Site-directed mutagenesis of Cys-82 and His-92 in this motif showed that these residues are essential for Zn2+ and DNA binding activities of Ros. The existence of such a regulator in Agrobacterium may be due to horizontal interkingdom retrotransfer of the ros gene from plant to bacteria.

Identification by PCR of genes encoding multiple response regulators

Environmental sensing in bacteria often involves the concerted action of sensor kinases and response regulators. Degenerate oligonucleotide primers were designed on the basis of amino acid similarity in the response regulators of these two-component systems. The primers were used in PCR to specifically amplify an internal DNA segment corresponding to the receiver module domain from genes encoding response regulators. Amplification products of the expected size were obtained from 12 different Gram-positive and Gram-negative bacteria. Sequence analysis revealed that 22 DNA fragments, which clearly originated from response regulator genes, were amplified from Escherichia coli, Agrobacterium tumefaciens, Bacillus subtilis and Lactobacillus bulgaricus. In each of these four species the receiver module of putative response regulator genes, which do not seem to be related to any of the already characterized genes, was identified. This simple and powerful method is therefore particularly useful for discovering new signal transduction systems which cannot be revealed by usual genetic studies.

Relationship between Symptom Development and Actual Sites of Infection in Leaves of Anthurium Inoculated with a Bioluminescent Strain of Xanthomonas campestris pv. dieffenbachiae

The infection process of bacterial blight of anthurium was monitored with a bioluminescent strain of Xanthomonas campestris pv. dieffenbachiae. The relationship between symptom expression on infected leaves (assessed visually) and the extent of bacterial movement within tissues (evaluated by bioluminescence emission) varied among anthurium cultivars. In several cultivars previously considered susceptible on the basis of symptom development alone, bacterial invasion of leaves extended far beyond the visually affected areas. In other cultivars previously considered resistant, bacterial invasion was restricted to areas with visible symptoms. In three cultivars previously considered resistant, leaves were extensively invaded by the bacterium, and yet few or no symptoms were seen on infected leaves. The pathogen was consistently recovered from leaf sections emitting bioluminescence but not from sections emitting no light. At an early stage of infection, no significant differences in the percentages of infected areas as determined by visual assessment were observed in any of the cultivars. However, differences among cultivars were detected by bioluminescence as the disease progressed, because bacterial invasion was not always accompanied by symptom expression. In susceptible cultivars, the advancing border of infection was 5 to 10 cm inward from the margins of the visible symptoms and often reached to the leaf petiole even when symptoms were visible in <10% of the total leaf area. Comparisons of anthurium cultivars in which a nondestructive method was used to quantify the severity of leaf infection by a bioluminescent pathogen have enabled us to evaluate susceptibility and resistance to bacterial blight accurately. Such evaluations will be of importance in breeding resistant cultivars for disease control.

Role of Pore Size Location in Determining Bacterial Activity during Predation by Protozoa in Soil

The predation of a luminescence-marked strain of Pseudomonas fluorescens by the soil ciliate Colpoda steinii was studied in soil microcosms. Bacterial cells were introduced in either small (neck diameter, <6 (mu)m) or intermediate-sized (neck diameter, 6 to 30 (mu)m) pores in the soil by inoculation at appropriate matric potentials, and ciliates were introduced into large pores (neck diameter, 30 to 60 (mu)m). Viable cell concentrations of bacteria introduced into intermediate-sized pores decreased at a greater rate than those in small pores, with reductions in bacterial populations being accompanied by an increase in viable cell numbers of the ciliate. The data indicate that the location of bacteria in small pores provides significant protection from predation. In the absence of C. steinii, the level of metabolic activity of the bacterial population, measured by luminometry, decreased at a greater rate than cell number, and the level of luminescence cell(sup-1) consequently decreased. The decrease in levels of luminescence indicates a loss of activity due to starvation. During predation by C. steinii, the level of the activity of cells introduced into small pores fell in a similar manner. The level of cell activity was, however, significantly greater for cells introduced into intermediate-sized pores, despite their greater susceptibility to predation. The data suggest that increased activity arises from a release of nutrients by the predator and the greater accessibility of bacteria to nutrients in larger pores. Nutrient amendment of microcosms resulted in increases in bacterial populations to sustained, higher levels, while levels of luminescence increased transiently. The predation of cells introduced into intermediate-sized pores was greater, and there was also evidence that the level of activity of surviving bacteria was greater for bacteria in intermediate-sized but not small pores.

Inhibition of Agrobacterium tumefaciens oncogenicity by the osa gene of pSa

The IncW plasmid pSa originally derived from Shigella flexneri completely inhibits the tumor-inducing ability of Agrobacterium tumefaciens when it is resident in this organism. Oncogenic inhibition is mediated through the expression of the osa gene on pSa. This gene is part of a 3.1-kb DNA segment of pSa that contains four open reading frames revealed by sequencing. Specific deletions and TnCAT insertions within this segment localized the oncogenic inhibitory activity to the last open reading frame, orf-4, designated osa (for oncogenic suppression activity). No promoter exists immediately upstream of the coding sequence of osa since TnCAT insertions or deletions into orf-3 caused the loss of oncogenic inhibition. Deletion analysis showed that the promoter of orf-1 is required for osa transcription. The first three orfs have no role in oncogenic inhibition, since osa alone placed under the control of a constitutive Pkm promoter completely inhibited A. tumefaciens oncogenicity. This inhibition of oncogenicity by osa is not limited to a specific host plant but appears to show broad host specificity. Because the osa-encoded product has close homologies to the fiwA-encoded product of the IncP plasmid RP1, osa may be involved in fertility inhibition that would prevent or reduce the formation of stable mating pairs and T-DNA transfer between A. tumefaciens and plants.

The virD4 gene is required for virulence while virD3 and orf5 are not required for virulence of Agrobacterium tumefaciens

The virD operon of the resident Ti plasmid of Agrobacterium tumefaciens contains loci involved in T-DNA processing and undefined virulence functions. Nucleotide sequence of the entire virD operon of pTiC58 revealed similarities to the virD operon of the root-inducing plasmid pRiA4b and to that of the octopine-type plasmid pTiA6NC. However, comparative sequence data show that virD of pTiC58 is more akin to that of the pRiA4b than to that of the pTiA6NC. T7f10::virD gene fusions were used to generate polypeptides that confirm the presence of four open reading frames virD1, virD2, virD3, and virD4 within virD which have a coding capacity for proteins of 16.1, 49.5, 72.6, and 73.5 kDa, respectively. virD3 therefore encodes a polypeptide 3.4 times larger (72.6 versus 21.3 kDa) than that encoded by virD3 of octopine Ti plasmids. Non-polar virD4 mutants could not be complemented by a distant homologue, TraG protein of plasmid RP4. An independently regulated fifth ORF (orf5) is located immediately downstream of 3' end of virD4 and encodes a polypeptide of 97.4 kDa. The expression of orf5 is dependent on its own promoter and is independent of acetosyringone induction in A. tumefaciens. Recently, it has been shown that virD3 of octopine Ri or Ti plasmids is not required for virulence. In this report, we confirm and extend these findings on a nopaline Ti plasmid by using several virD non-polar mutants that were tested for virulence. virD3 and orf5 non-polar mutants showed no effect on tumorigenicity on 14 different plant species, while virD4 mutants lost their tumorigenicity completely on all these test plants. These data suggest that virD3 and orf5 are not essential for virulence whereas virD4 is absolutely required on a wide range of host plants.

The region essential for efficient autonomous replication of pSa in Escherichia coli

Comparative analyses were made between plasmid pSa17, a deletion derivative of pSa that is capable of replicating efficiently in Escherichia coli and plasmid pSa3, a derivative that is defective for replication. By comparing the restriction maps of these two derivatives, the regions essential for replication and for stable maintenance of the plasmid were determined. A 2.5 kb DNA segment bearing the origin of DNA replication of pSa17 was sequenced. A 36 kDa RepA protein was encoded in the region essential for replication. Downstream of the RepA coding region was a characteristic sequence including six 17 bp direct repeats, the possible binding sites of RepA protein, followed by AT-rich and GC-rich sequences. Furthermore, an 8 bp incomplete copy of the 17 bp repeat was found in the promoter region of the repA gene. Based on the hypothesis that RepA protein binds to this partial sequence as well as to intact 17 bp sequences, an autoregulatory system for the synthesis of RepA protein may be operative. Another open reading frame (ORF) was found in the region required for the stability of the plasmid. The putative protein encoded in this ORF showed significant homology to several site-specific recombination proteins. A possible role of this putative protein in stable maintenance of the plasmid is discussed.

Rapid generation of directed and unmarked deletions in Xanthomonas

We have devised a rapid four-step procedure for the generation of directed and unmarked chromosomal deletions in bacteria, based on the use of a novel cloning vector containing the Bacillus subtilis sacB gene that encodes levansucrase and confers sucrose sensitivity, which can be used for counter-selection. Using this technique, we describe the construction of a 6.5 kb directed and unmarked deletion in a phytopathogenicity region of the chromosome in Xanthomonas campestris. This procedure allows rapid and easy transfer of a wide variety of mutant allelic DNA to the bacterial chromosome, and should be adaptable to various bacteria besides Xanthomonas spp.

A correlation with type of sulfonamide resistance gene in Escherichia coli and synergy between trimethoprim and sulfamethoxazole

Plasmids carrying type I or II sulfonamide-resistance (Sur) genes were evaluated for their effect on synergy between trimethoprim (Tmp) and sulfamethoxyzole (Smx) in E. coli. Strain J53 containing each of three plasmids (R1, pSa, and R388) with the type I Sur gene displayed a synergistic response to Tmp/Smx; strain LE392 containing a plasmid (RSF1010) with the type II Sur gene displayed no synergy. The difference in synergy between type I and type II Sur genes might be explained by the difference in amount of resistant enzyme produced.

The osa gene of pSa encodes a 21.1-kilodalton protein that suppresses Agrobacterium tumefaciens oncogenicity

The incompatibility group W plasmid pSa suppresses Agrobacterium tumefaciens oncogenicity (J. Loper and C. Kado, J. Bacteriol. 139:591-596, 1979). The oncogenic suppressive activity was localized to a 3.1-kb region of pSa by Tn5 mutagenesis and deletion analysis. Within this fragment, a 1.1-kb subclone bearing oncogenic suppressive activity was subjected to further characterization. Nucleotide sequencing of the 1.1-kb fragment revealed a 570-bp open reading frame (ORF1) that has a coding capacity for a protein of 21.1 kDa. Sequencing of flanking regions revealed a second ORF (ORF2) located 3 bp upstream of ORF1, with a coding capacity for a protein of 22.8 kDa. Gene fusions of these ORFs to a T7 phi 10 expression system in Escherichia coli resulted in the synthesis of polypeptides of the predicted sizes. An E. coli promoter consensus sequence was not found in the expected positions in the region preceding ORF1. However, several sequences with similarity to the consensus -10 sequence of the A. tumefaciens vir gene promoters were found upstream of ORF1. Potential translational start signals are upstream of ORF1 and ORF2. These sequences showed no significant similarity at the nucleotide or amino acid levels with those in available data bases. However, the C-terminal portion of the ORF1 protein is rich in hydrophobic residues. Perhaps oncogenicity suppression is effected by an association of this protein with the Agrobacterium membrane such that T-DNA transfer is blocked.

The virC and virD operons of the Agrobacterium Ti plasmid are regulated by the ros chromosomal gene: analysis of the cloned ros gene

The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid. The ros gene was cloned from a genomic bank by electroporation and complementation in Agrobacterium cells. Reporter fusion to the ros gene indicates that the level of transcription is controlled in part by autoregulation. A consensus inverted repeat sequence present in the ros promoter and in the virC and virD promoters of pTiC58, pTiA6, and pRiA4b suggests that a specific Ros binding site exists in these promoters. In the virC and virD promoter region, this binding site is within a cluster of vir box consensus sequences in which the VirG protein binds. This suggests possible binding competition between Ros and VirG at the virC and virD promoters. That the Ros protein binds DNA is suggested by the presence of a 'zinc finger' consensus sequence in the protein.

A plant-inducible gene of Xanthomonas campestris pv. campestris encodes an exocellular component required for growth in the host and hypersensitivity on nonhosts

Using Tn4431, a transposon that allows transcriptional fusions to a promoterless luciferase (lux) operon, we have isolated a nonpathogenic mutant of Xanthomonas campestris pv. campestris, i.e., JS111, that does not incite any of the black rot symptoms on all tested cruciferous host plants (J. J. Shaw, L. G. Settles, and C. I. Kado, Mol. Plant Microbe Interact. 1:39-45, 1988). In the study reported here, we determined that in contrast to the wild-type strain, JS111 is unable to induce a hypersensitive necrotic response on nonhost plants such as datura, tomato, and cucumber, suggesting that JS111 is a nonpathogenic, nonhypersensitive Hrp mutant. JS111 displayed culture growth rates, exopolysaccharide production, and protease, pectate lysase, cellulase, amylase, and phosphatase activities comparable to those of the wild-type strain. However, the growth of JS111 in host leaves was markedly attenuated. Coinoculation of JS111 with the wild-type strain in cauliflower or radish leaves rescued the growth deficiency of the mutant to normal levels. The locus mutated in JS111 was cloned and named hrpXc, and transcriptional and genetic complementation analyses of the hrpXc locus were conducted. The regulation of hrpXc expression was also investigated in vitro and in planta, using fusions to a lux or chloramphenicol acetyltransferase reporter gene. The hrpXc gene was found to be strongly induced in radish leaves. This is the first report and analysis of a hrp locus from a Xanthomonas species.

Use of Ti Plasmid DNA Probes for Determining Tumorigenicity of Agrobacterium Strains

Probes consisting of T-DNA genes from the Ti plasmid of Agrobacterium tumefaciens were used for determining tumorigenicity of strains. Two 32 P-labeled probes hybridized with 28 of 28 tumorigenic strains of the pathogen but not with 20 of 22 nontumorigenic strains. One probe, pTHE17, consists of all but the far left portion of the T-DNA of strain C58. Probe Sma I7 consists of Sma I fragment 7 of pTiC58, including onc genes 1, 4, and 6a and most of 2. Another probe, pAL4044, consisting of the vir region of strain Ach-5, hybridized with several nontumorigenic as well as tumorigenic strains. Colony hybridizations were done with 28 tumorigenic and 22 nontumorigenic Agrobacterium strains. About 10 6 CFU of the different tumorigenic strains were detectable with this method. Southern analyses confirmed the presence or absence of Ti plasmids in strains for which tumorigenicity was questioned. Colony hybridization with the T-DNA probes provides a rapid and sensitive means for determining the tumorigenic nature of Agrobacterium strains.

Molecular characterization of the vir regulon of Agrobacterium tumefaciens: complete nucleotide sequence and gene organization of the 28.63-kbp regulon cloned as a single unit

The entire vir regulon of Agrobacterium tumefaciens was subcloned and the complete 28.6-kbp nucleotide sequence was determined. The regulon was cloned as a single unit into two replicons, one of which replicates at a high copy number in this bacterium, and a second which has broad-host-range features to replicate in other Gram-negative bacteria. These vir region plasmids are able to confer in trans the processing and transfer activities on a second plasmid containing the T-DNA. In the high copy number vir region plasmid pUCD2614, a moderate increase in basal vir gene expression was observed as judged by virE::cat fusion expression assays relative to the wild-type control plasmid. Furthermore, higher efficiencies of tobacco leaf disk transformation were observed than with the widely used vir helper plasmid pAL4404. The nucleotide sequence studies showed that the vir region consists of 28,631 bp comprising 24 open reading frames which encode proteins involved in tumorigenicity. Two open reading frames not previously characterized, virH and ORF5, were uncovered within the virD/virE intervening spacer region. Together these studies more completely characterize the structure and function of the vir regulon.

virG of Agrobacterium tumefaciens plasmid pTiC58 encodes a DNA-binding protein

Virulence genes of the Agrobacterium tumefaciens Ti plasmid are positively regulated by the products of virA and virG. To study the DNA-binding properties of the VirG protein, a translational fusion between virG and the trpE gene of Escherichia coli was constructed, and antiserum was raised against the encoded fusion protein. Using this antiserum, a protein of Mr congruent to 29,000, a size similar to that calculated from the virG nucleotide sequence, was detected in an E. coli strain harbouring a virG expression vector. Both the virG protein and the fusion protein were found, by filter-binding and gel retardation analyses, to bind DNA nonspecifically. These data support an existing model for the two-component regulatory systems of bacteria.

Two chromosomal loci involved in production of exopolysaccharide in Agrobacterium tumefaciens

The chromosomal locus pscA (exoC) of Agrobacterium tumefaciens LBA4301 has been cloned by complementation of the avirulent and exopolysaccharide (EPS)-deficient mutant LBA4301 pscA. We have also identified a new locus, termed psdA (polysaccharide depression) and located 16 kilobases from pscA in the A. tumefaciens chromosome, that negatively affects EPS production when it is present in more than one copy in A. tumefaciens LBA4301. Subcloning, transposon mutagenesis, and transcriptional analysis have been conducted for both loci and indicate that pscA and psdA are transcribed in the same orientation. Acidic-EPS assays showed that psdA depresses succinoglycan production and that its negative effect increases with the copy number of the gene. Virulence tests of psdA transconjugants on Datura stramonium showed no visible alteration in virulence, while LBA4301 pscA was totally avirulent.

Minimal region necessary for autonomous replication of pTAR

The native 44-kilobase-pair plasmid pTAR, discovered in a grapevine strain of Agrobacterium tumefaciens, contains a single origin of DNA replication confined to a 1.0-kilobase-pair region of the macromolecule. This region (ori) confers functions sufficient for replication in Agrobacterium and Rhizobium species but not in Pseudomonas solanacearum, Pseudomonas glumae, Pseudomonas syringae pv. savastanoi, Xanthomonas campestris pv. campestris, and Escherichia coli. ori contains a repA gene that encodes a 28,000-dalton protein required for replication. Nucleotide sequencing of repA and its promoter region revealed four 8-base-pair palindromic repeats upstream of the repA coding region. Deletion of these repeats alters repA expression and plasmid copy number. Downstream of repA are three additional repeats in a region essential for replication. A locus responsible for plasmid partitioning (parA) and a putative second locus regulating plasmid copy number are part of the origin region and are required for stable plasmid maintenance.

Regulation of the virC and virD promoters of pTiC58 by the ros chromosomal mutation of Agrobacterium tumefaciens

The virC and virD operons of the virulence region of the Ti plasmid are highly regulated, requiring a transcriptional regulator that is encoded by virG and is activated by the product of virA and plant phenolics such as acetosyringone. Full expression of virC and virD of octopine and nopaline Ti plasmids is also obtained by a mutation in the ros gene of the Agrobacterium tumefaciens chromosome. S1-nuclease analysis, in vitro transcription, and DNase I protection experiments with A. tumefaciens RNA polymerase revealed virD promoters tandemly arranged, both of which are functional in the Ros mutant, while only one is functional in the presence of acetosyringone. A third (overlapping) promoter appears to be responsible for transcription of virC. Expression of virC and virD appears to be modulated by factors within the bacterium by means of a mechanism that is independent of factors produced during infection of the host plant.

Regulation of the vir genes of Agrobacterium tumefaciens plasmid pTiC58

The virulence (vir) region of pTiC58 was screened for promoter activities by using gene fusions to a promoterless lux operon in the broad-host-range vector pUCD615. Active vir fragments contained the strongly acetosyringone-inducible promoters of virB, virC, virD, and virE and the weakly inducible promoters of virA and virG. Identical induction patterns were obtained with freshly sliced carrot disks, suggesting that an inducer is released after plant tissue is wounded. Optimal conditions for vir gene induction were pH 5.7 for 50 microM acetosyringone or sinapic acid. The induction of virB and virE by acetosyringone was strictly dependent on intact virA and virG loci. An increase in the copy number of virG resulted in a proportional, acetosyringone-independent increase in vir gene expression, and a further increase occurred only if an inducing compound and virA were present.

Molecular characterization of the virC genes of the Ti plasmid

The virC (formerly bak) complementation group of the nopaline-type Ti plasmid pTiC58 encodes two proteins, VirC1 and VirC2. According to the primary structure of the polypeptides predicted by the nucleotide sequence, VirC1 is composed of 231 amino acids with a total molecular mass of 25.5 kilodaltons, and VirC2 is composed of 202 amino acids with a molecular mass of 22.1 kilodaltons. The pTiC58 VirC1 and VirC2 polypeptides are equal in length to VirC1 and VirC2 of the octopine-type plasmid pTiA6NC. VirC1 proteins of pTiC58 and pTiA6NC are identical at 202 (87.4%) of the amino acid residues, and this homology is distributed fairly evenly throughout the protein. VirC2 identities occur at 142 residues (70.3%), but fall predominantly into two blocks of higher homology (84.6 and 78.5%) separated by a 41-residue segment of much lower homology (29.3%). Mutations in virC resulted in attenuated virulence on all hosts tested, the severity of attenuation varying markedly depending on the type of plant inoculated. For example, the attenuation was more pronounced on Kalanchoe than on sunflower or jimson weed. Virulence was restored to normal on all hosts by in-trans complementation with corresponding nonmutant DNA fragments of pTiC58 or of the octopine-type plasmid pTi15955. Two oligopeptides from within the predicted pTiC58 VirC1 polypeptide were synthesized and used to raise antibodies. These antibodies were used to detect the VirC1 product of both pTiC58 and pTi15955. In both cases, virC was expressed constitutively in the Agrobacterium tumefaciens ros mutant. The homology between virC genes of octopine- and nopaline-type Ti plasmids thus includes a conservation of genetic regulatory control mechanisms as well as considerable conservation of the primary structure of the protein products.

Characterization of the virE locus of Agrobacterium tumefaciens plasmid pTiC58

The virE locus that is responsible for the efficiency of infection by Agrobacterium tumefaciens (T. Hirooka and C. Kado, J. Bacteriol. 168:237-243, 1986) is located next to the right boundary of the virulence (Vir) region of the nopaline plasmid pTiC58. This locus is very similar to the virE locus of octopine type Ti plasmids on the basis of nucleotide and amino acid sequence comparisons as well as genetic complementation analyses. The nucleotide sequence of virE revealed three open reading frames, arranged as an operon, with a potential coding capacity for proteins of 9, 7.1, and 63.5 kilodaltons. The promoter region of virE was analyzed by using gene fusions to promoterless cat and lux genes. Two different promoters were detected, one which operates in A. tumefaciens and one which operates in Escherichia coli. virE is transcribed from left to right toward the T region. In A. tumefaciens, the expression of virE was induced by acetosyringone and required the presence of pTiC58.

Agrobacterium tumefaciens pTAR parA promoter region involved in autoregulation, incompatibility and plasmid partitioning

The locus responsible for directing proper plasmid partitioning of Agrobacterium tumefaciens pTAR is contained within a 1259 base-pair region. Insertions or deletions within this locus can result in the loss of the plasmid's ability to partition properly. One protein product (parA), approximately 25,000 Mr, is expressed from the par locus in Escherichia coli and A. tumefaciens protein analysis systems in vitro. DNA sequence analysis of the locus revealed a single 23,500 Mr open reading frame, confirming the protein data. A 248 base-pair region immediately upstream from the 23,500 Mr open reading frame, containing an array of 12 seven-base-pair palindromic repeats each of which are separated by exactly ten base-pairs of A + T-rich (75%) sequence, not only serves to provide the promoter but is also involved in parA autoregulation. In addition, this region containing a set of 12 seven-base-pair palindromic repeats, is responsible for plasmid-associated incompatibility within Inc Ag-1 and also functions as the cis-acting recognition site at which parA interacts to bring about partitioning. Transcriptional analysis indicated that only the DNA strand responsible for parA is actively transcribed, and that active transcription of the opposite strand of par can inhibit the production of parA, resulting in plasmid destabilization. The presence of the par locus in a plasmid results in stable inheritance within a wide range of members of Rhizobiaceae. Segregation rates of par-defective derivatives can be influenced by the host.

Location of the right boundary of the virulence region on Agrobacterium tumefaciens plasmid pTiC58 and a host-specifying gene next to the boundary

The right boundary of the virulence (Vir) region of the nopaline plasmid pTiC58 of Agrobacterium tumefaciens was determined by transposon insertion, cartridge emplacement, and deletion mutagenesis. Genetic complementation with mutant and wild-type alleles led to the identification of the virE locus at the right boundary, which was located about 6 kilobases from the left border of the segment of DNA that is transferred into the plant genome. virE is 2.0 kilobases long and encodes at least one protein of 69 kilodaltons. Various mutations in virE resulted in different truncated lengths of the 69-kilodalton protein. As this protein was increasingly truncated from the carboxy terminus, the host range of A. tumefaciens and the frequency of tumor formation diminished concomitantly. Thus, as one of its functions, the 69-kilodalton protein of virE is probably involved in some aspect of the host range specificity of A. tumefaciens and in infection efficiency.

Regulation of Ti plasmid virulence genes by a chromosomal locus of Agrobacterium tumefaciens

We isolated a mutant strain of Agrobacterium tumefaciens, designated Ros, that has a pleiotropic phenotype which includes elevated levels of expression of certain genes in the virulence (Vir) region of tumor-inducing plasmid pTiC58. This mutant and others were isolated by fusing the promoter of the Vir bak gene to a promoterless gene (cat) that encodes chloramphenicol acetyltransferase and then selecting for increased expression of cat in A. tumefaciens. The ros mutation is chromosomal in nature and is characterized by a more-than-300-fold increase in the level of expression of bak and a 12-fold increase in the level of expression of an adjacent divergent operon containing the hdv genes, which are involved in some aspect of host specificity. The Ros mutant is fully virulent and is typified by its unusual colony morphology; the colonies have rough surfaces, uneven edges, and a pit in the center at 24 degrees C and vary markedly in appearance from one growth temperature to another. The Ros mutant is not able to form colonies at 12 degrees C, a temperature at which the wild-type strain forms colonies in 14 days. The ros mutation occurs spontaneously with a frequency of 5 X 10(-8). Genetic and biochemical evidence indicates that the product of the ros locus is a negative regulator of Ti plasmid genes and is related to undefined chromosomally encoded functions that are involved in the mutant phenotype.

Analysis of Agrobacterium tumefaciens plasmid pTiC58 replication region with a novel high-copy-number derivative

The origin of replication, ori, of the nopaline tumor-inducing plasmid, pTiC58, mapped in a region that shares sequence homology with octopine plasmids pTiAch5 and pTiB6. Within this region, the minimum amount of DNA necessary for maintaining autonomous replication was a 2.6-kilobase region, which also comprised the incompatibility function inc. pTiC58 derivatives containing inc were incompatible with Agrobacterium tumefaciens plasmids pTiC58, pTiD1439, pTiAch5, pTi15955, and pTiA5 and were compatible with A. rhizogenes plasmid pRi12. Situated adjacent to the origin region was a 1.5-kilobase par segment involved in stable inheritance of pTiC58 under nonselective growth conditions. When par was present, plasmid maintenance approached that of the wild-type pTiC58. Rapid loss from the cell population was observed for plasmids not containing this locus. Another 1.5-kilobase region, cop, positively regulated pTiC58 copy number, enabling certain pTiC58 derivatives to exist at a copy number up to 80 times higher than that of wild-type pTiC58. Deletions within the cop locus resulted in reduced copy number. The ori/inc regions were flanked on either side by the par and cop loci.

Design and development of amplifiable broad-host-range cloning vectors: analysis of the vir region of Agrobacterium tumefaciens plasmid pTiC58

The construction of a set of new plasmids that are suitable as general cloning vectors in Escherichia coli and Agrobacterium tumefaciens is described. Plasmid pUCD2 is amplifiable in E. coli, replicates in a wide range of gram-negative hosts and contains a number of useful restriction endonuclear cleavage sites and antibiotic resistance genes. This includes unique sites for KpnI, SacI, SacII, PstI, ClaI, SalI, EcoRV, and PvuII and the genes for resistance to kanamycin, tetracycline, ampicillin, and spectinomycin/streptomycin. Derivatives of pUCD2 include pUCD4, which has a unique XbaI site and the cosmid pUCD5, which also contains a unique EcoRI site. Two smaller plasmids pUCD9P and pUCD9X, contain many of the same unique sites as pUCD2 and pUCD4, but carry only the pBR322 replication origin and therefore do not display the extensive host-range of pSa. These plasmids were used to isolate and manipulate fragments of the A. tumefaciens pTiC58 plasmid in both E. coli and A. tumefaciens. Fragments from the virulence (vir) region of pTiC58 inserted immediately upstream of the spectinomycin resistance gene of pUCD2 resulted in spectinomycin resistance levels that varied greatly depending on the particular fragment and its orientation of insertion. Using this property we find that a major portion of the vir region of pTiC58 is transcribed in A. tumefaciens and E. coli from left to right toward the T region.

Characterization of the replication and stability regions of Agrobacterium tumefaciens plasmid pTAR

A 5.4-kilobase region containing the origin of replication and stability maintenance of the 44-kilobase Agrobacterium tumefaciens plasmid pTAR has been mapped and characterized. Within this region is a 1.3-kilobase segment that is capable of directing autonomous replication. The remaining segment contains the stability locus for maintenance of pTAR during nonselective growth. Approximately 35% of pTAR shares sequence homology with pAg119, a 44-kilobase cryptic plasmid in grapevine strain 1D1119. However, no homology was detected between pTAR DNA and several Ti plasmids or several other small cryptic plasmids in many A. tumefaciens strains. A recombinant plasmid containing the origin of replication and stability maintenance region of pTAR was compatible with pTiC58, pTi15955, and pTi119 and incompatible with pAg119. A new compatibility group, Inc Ag-1, is discussed.

Genetic complementation of Agrobacterium tumefaciens Ti plasmid mutants in the virulence region

Mutants with Tn5 insertions in the vir region of the Agrobacterium tumefaciens TiC58 plasmid are unable to form crown-gall tumors. Complementation tests of these vir region mutants were carried out by constructing merodiploids in a recombination-deficient strain. Each merodiploid possessed a mutant TiC58 plasmid and a recombinant plasmid containing either the homologous wild-type DNA region or the homologous region containing a second Tn5 insertion. The analysis identified six complementation groups. Mutations in one of these complementation groups were not complemented in trans and represent a cis-dominant locus. The mutation in one complementation group showed variation in host range.

Detailed restriction enzyme map of crown gall-suppressive IncW plasmid pSa, showing ends of deletion causing chloramphenicol sensitivity

Detailed restriction enzyme maps of the antibiotic resistance plasmid pSa and of a chloramphenicol-sensitive spontaneous deletion mutant of pSa were constructed. The smaller plasmid contained one set of three restriction enzyme sites that appeared at both ends of the deleted region in the intact plasmid. The frequency of loss of chloramphenicol resistance was 1% after eight logs of growth and was dependent on the recA gene function of Escherichia coli. A previously published map lacks an 11-kilobase-pair SstII fragment present on this map.

Ti plasmid and chromosomal ornithine catabolism genes of Agrobacterium tumefaciens C58

The pTiC58 plasmid noc genes of Agrobacterium tumefaciens C58 code for nopaline oxidase (nocC), nopaline permease (nocP), the inducible periplasmic protein n1 (nocB), and a function(s) required for ornithine catabolism (nocA). In addition, strains C58 and Ach-5 of A. tumefaciens have chromosomal ornithine catabolism genes. The chromosomal orc gene codes for ornithine dehydrogenase. Strain C58 is normally orc, but orc+ mutants can be selected. We have characterized both chromosomal orc and pTiC58 nocA plasmid genes. Complementation of most chromosomal orc mutants by pTiC58 restored growth on both nopaline and L-ornithine but did not restore ornithine dehydrogenase activity. We conclude that ornithine is an intermediate of nopaline degradation and that the Ti plasmid and chromosome both code for ornithine-degradative enzymes. A model for nopaline catabolism is presented.

A functional map of the nopaline catabolism genes on the Ti plasmid of Agrobacterium tumefaciens C58

The nopaline catabolism (noc) genes are located in a 14.4 kb region on the pTiC58 plasmid of A. tumefaciens C58. These genes permit the bacterium to grow on nopaline N2-(1,3-dicarboxylpropyl) arginine, a substrate produced in plant tumors initiated by strain C58. The functions of the noc genes include the use of nopaline and L-ornithine as sole carbon and nitrogen sources. Using Tn5 insertional mutants, we have identified and mapped the positions of the genes that are responsible for nopaline catabolism (NopC), ornithine catabolism (OrnC) and nopaline uptake (NopU). A polar relationship was found between these phenotypes, which extended leftward over the noc region to the T-region. The NopC mutants were also deficient in nopaline oxidase, an enzyme that liberates free arginine from nopaline. The noc region also encodes the synthesis of a periplasmic protein, n1 that was induced by nopaline. Tn5 insertional mutations and molecular cloning were used to map the n1 production locus. The recombinant plasmids, pSa4480 and pSa4481, containing the 8.9 kb right-hand end of the noc region, conferred n1 production when introduced into a pTi-free strain of A. tumefaciens. Production of n1 by the strains carrying these plasmids required nopaline induction. We have identified in toto three noc loci: nocB, nocC, and nocA, which confer n1 production, nopaline oxidase production and ornithine catabolism respectively. A model is proposed whereby the noc genes of pTiC58 are contained on a leftward reading operon in the order nocB, nocC, and nocA.

Indoleacetic acid complementation and its relation to host range specifying genes on the Ti plasmid of Agrobacterium tumefaciens

Host range variations were noted when 23 wild-type strains of Agrobacterium tumefaciens were tested on 27 different plant species. Because we have shown previously that host range specificity is conferred by the pTi plasmid, these variations in host specificity implicated genetic differences among pTi plasmids within the A. tumefaciens population that was tested. Host specificity was independent of the type of opine utilized and biotype of the strain used. These data suggested that separate genetic determinants operate for host specificity. This hypothesis was confirmed by Tn5 mutagenesis of the pTi plasmid, which generated mutants affected in host specificity. The regions of host specifying genes were located by displacement analysis of mutant pTi-plasmid-DNA restriction fragments. There are at least two sites on the pTiC58 plasmid: one within the T-region and the other about 75-77 kb to the right of this region. Mutations within the T-region were chemically complemented by indoleacetic acid, which restored the host range of the mutants. Such complementations were not observed with mutants outside the T-region.

Characteristics of Ti plasmids from broad-host-range and ecologically specific biotype 2 and 3 strains of Agrobacterium tumefaciens

Agrobacterium tumefaciens strains isolated from crown gall tumors on grapevines in California were consistently of the biotype 3 group. All 11 of these strains were limited in their host range and harbored Ti plasmids with molecular masses between 119 and 142 megadaltons (Mdal) as well as a larger cryptic plasmid of greater than 200 Mdal; occasionally a smaller cryptic plasmid of 65 Mdal was also present. Ti plasmids o these strains have DNA sequences in common with Ti plasmids of octopine and nopaline strains belonging to the biotype 1 group and exhibited sequence homologies with the conserved region of the T-DNA. Ten of the 11 strains utilized octopine as a sole source of carbon and nitrogen and 3 strains catabolized both octopine and nopaline, whereas 1 strain catabolized only nopaline. All of these strains were resistant to the bacteriocin agrocin-84, except one grapevine strain that belonged to the biotype 1 group and was agrocin sensitive; it is also differed in its plasmid and virulence characteristics. Isolations from Rubus ursinus ollalieberry galls yielded exclusively biotype 2 strains. These strans were insensitive to agrocin-84, utilized nopaline as a sole carbon and nitrogen source, and were highly virulent on all host plants tested. They contained Ti plasmids ranging between 100 and 130 Mdal and occasionally a cryptic plasmid of 69 Mdal. Their Ti plasmids have DNA sequences in common with Ti plasmids of biotype 1 strains and with the conserved region of the T-DNA.

Host range conferred by the virulence-specifying plasmid of Agrobacterium tumefaciens

The host range of Agrobacterium tumefaciens 1D1109, known to induce crown gall only on grapevine (Vitis spp.), was extended to include many plant species by transferring a tumor-inducing plasmid (pTi) from strain 1D1, a broad-host-range pathogen. The pTi plasmid was mobilized by the conjugative plasmid pRK2, which was inserted into 1D1 by mating with Escherichia coli J53(pRK2). The resulting transconjugants were screened for their ability to induce crown gall tumors on hosts other than grapevine by inoculation into sunflower. Transconjugants that were virulent on sunflower were then tested on 36 different host plants and compared with host-limited strain 1D1109 and the donor strain. Two transconjugants induced tumors on the same 28 plant species as those of the original plasmid donor 1D1(pRK2) (pTi). These results show that pRK2 promoted transfer of the pTi plasmid and suggest that the pTi plasmid rather than the A. tumefaciens chromosome determined the host range of the pathogen. Insertion of pRK2 alone did not extend the host range of strain 1D1109. Insertion of pS-a into A. tumefaciens 1D1 by mating with E. coli J53-1 (pS-a) resulted in the concomitant loss of pTi and virulence. There appears to be incompatibility between pTi and pS-a.