Ti plasmid and chromosomal ornithine catabolism genes of Agrobacterium tumefaciens C58

Isolation and Characterization of Avirulent and Virulent Strains of Agrobacterium tumefaciens from Rose Crown Gall in Selected Regions of South Korea

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease in various hosts across kingdoms. In the present study, five regions (Wonju, Jincheon, Taean, Suncheon, and Kimhae) of South Korea were chosen to isolate A. tumefaciens strains on roses and assess their opine metabolism (agrocinopine, nopaline, and octopine) genes based on PCR amplification. These isolated strains were confirmed as Agrobacterium using morphological, biochemical, and 16S rDNA analyses; and pathogenicity tests, including the growth characteristics of the white colony appearance on ammonium sulfate glucose minimal media, enzyme activities, 16S rDNA sequence alignment, and pathogenicity on tomato (Solanum lycopersicum). Carbon utilization, biofilm formation, tumorigenicity, and motility assays were performed to demarcate opine metabolism genes. Of 87 isolates, 18 pathogenic isolates were affirmative for having opine plasmid genes. Most of these isolates showed the presence of an agrocinopine type of carbon utilization. Two isolates showed nopaline types. However, none of these isolates showed octopine metabolic genes. The objectives of the present study were to isolate and confirm virulent strains from rose crown galls grown in the different regions of Korea and characterize their physiology and opine types. This is the first report to describe the absence of the octopine type inciting the crown gall disease of rose in South Korea.

Bases moléculaires de l’infection de plantes parAgrobacterium tumefaciensvia un système de sécrétion de type IV

Agrobacterium tumefaciens is a well studied phytopathogen given its various applications for deciphering host-pathogen interactions, bacterial communication, and capacity to transfer DNA fragments into host cells via a membrane protein system, the type IV secretion system (T4SS). T4SS mechanism is similar to the one responsible for antibiotic resistance gene transmission, and new knowledge gained could be applied to other organisms using such a mechanism. As well, A. tumefaciens is of economic importance in biotechnology due to its capacity to generate genetically modified plants. Agrobacterium tumefaciens harbours a plasmid known as Ti plasmid encoding T4SS function genes used for transferring genetic information and plant colonization. In this review, the authors describe the molecular basis of infection, from detection of host signals, to the description of different regions of Ti plasmid key to infection, ending with substrate transfer through bacterial wall. [Journal translation].

Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host

By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K_D of 0.6 µM) greater than that for nopaline (K_D of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche construction paradigm in bacterial pathogens.

An ecological niche is defined, in a given environment, by the availability of nutritive resources, which can be specifically assimilated by certain living organisms to promote their proliferation. The bacterial pathogen Agrobacterium tumefaciens is able to engineer an ecological niche in the infected host via the transformation of the plant genome and diversion of the plant metabolism towards production of the opine nutrients. In this work, we quantified the selective advantage conferred to a member of the phytopathogenic species A. tumefaciens which is able to assimilate the opine nopaline. This opine is a condensate of arginine and α-ketoglurate that is produced both under linear and cyclic forms in the plant tumour environment. We further determined at the molecular and atomistic levels how A. tumefaciens is able to sense the nopaline molecules, and which metabolic pathways are activated in response. Overall, this work deciphered some key molecular events in the niche construction of the pathogen A. tumefaciens that is unique among living organisms and used to develop bioengineering tools.

Fungal catabolism of crown gall opines

This study was conducted to determine the capacities of 37 fungi to utilize various crown gall opines as their sole carbon and nitrogen source. One strain of Fusarium solani, two of Cylindrocarpon destructans, and six of Cylindrocarpon heteronema catabolized octopine, mannopine, octopinic acid, succinamopine, or a combination of these opines. One C. heteronema and one Fusarium dimerum strain grew only on succinamopine. None of the fungal isolates had the ability to grow on nopaline. The catabolism of opines by fungi was confirmed by the disappearance of the opine from the growth medium and by an increase in final mycelial dry weight with rising initial concentration of test substrate. This study thus shows that the catabolism of opines is not restricted to bacteria.

The ntrC gene of Agrobacterium tumefaciens C58 controls glutamine synthetase (GSII) activity, growth on nitrate and chromosomal but not Ti-encoded arginine catabolism pathways

The ntrC locus of Agrobacterium tumefaciens C58 has been cloned using the Azorhizobium sesbaniae ORS571 ntrC gene as a DNA hybridization probe. Transposon Tn5 mutagenesis of the cloned ntrC locus was carried out and one Tn5 insertion within the region of highest DNA homology with A. sesbaniae ORS571 ntrC was used for gene replacement of the wild-type C58 ntrC gene. The A. tumefaciens ntrC::Tn5 mutant was found to be unable to grow on nitrate as sole nitrogen (N) source, to lack glutamine synthetase (GSII) activity and to be unable to use arginine (or ornithine) as sole N source, unless the Ti-encoded arginine catabolism pathway was induced with small amounts of nopaline. Thus the A. tumefaciens ntrC regulatory gene is essential for (transcriptional) activation of the GSII and nitrate reductase genes, as well as for the chromosomal but not the Ti-borne arginine catabolism pathways.

Identification of Agrobacterium tumefaciens genes that direct the complete catabolism of octopine

Agrobacterium tumefaciens R10 was mutagenized by using the promoter probe transposon Tn5-gusA7, and a library of approximately 5,000 transcriptional fusions was screened for octopine-inducible patterns of gene expression. Twenty-one mutants carrying strongly inducible gusA fusions, 20 of which showed defects in the catabolism of octopine or its metabolites, were obtained. One group of mutants could not use octopine as a carbon source, while a second group of mutants could not utilize arginine or ornithine and a third group could not utilize octopine, arginine, ornithine, or proline as a carbon source. Utilization of these compounds as nitrogen sources showed similar but not identical patterns. Fifteen fusions were subcloned together with adjacent DNA. Sequence analysis and further genetic analysis indicated that insertions of the first group are localized in the occ region of the Ti plasmid. Insertions of the second group were localized to a gene encoding ornithine cyclodeaminase. This gene is very similar to, but distinct from, a homolog located on the Ti plasmid. This gene is located immediately downstream from a gene encoding an arginase. Genetic experiments indicated that this arginase gene is essential for octopine and arginine catabolism. Insertions of the third group was localized to a gene whose product is required for degradation of proline. We therefore have identified all steps required for the catabolism of octopine to glutamate.

Nopaline causes a conformational change in the NocR regulatory protein-nocR promoter complex of Agrobacterium tumefaciens Ti plasmid pTiT37

The nocR gene of Agrobacterium tumefaciens Ti plasmid pTiT37 is the regulatory gene of the nopaline catabolism (noc) operon of pTiT37. We have cloned and sequenced nocR, which encodes a DNA-binding protein. The deduced amino acid sequence is similar to those of members of the LysR family of prokaryotic activator proteins. Gel retardation experiments demonstrated that the NocR protein binds to the nocR promoter in both the presence and absence of nopaline. The increased mobility of the complex and alterations in the DNase I footprints revealed a nopaline-induced conformational change in the NocR-DNA complex. Sequence analysis of the NocR binding site indicated the presence immediately downstream of the -10 sequence of the nocR promoter of a 12 bp putative operator overlapping a consensus gyrase recognition sequence and an 18 bp long alternating purine-pyrimidine sequence. These results suggest that nopaline-induced alterations in the NocR protein-nocR promoter complex might control gene expression in the noc operon.

Arginase of Agrobacterium Ti plasmid C58. DNA sequence, properties, and comparison with eucaryotic enzymes

Agrobacterium nopaline Ti plasmids code for three enzymes of nopaline [N2-(1,3-dicarboxypropyl)-L-arginine] degradation: nopaline oxidase, arginase, and ornithine cyclodeaminase. We describe the DNA sequence of the arginase gene, a comparison of the deduced protein sequence with eucaryotic arginases, and properties of the procaryotic enzyme. The results show that the agrobacterial arginase is related with arginases from yeast, rat liver, and human liver (28-33% identity). The Ti plasmid enzyme revealed several properties which appear common to all arginases, but it does not utilize L-canavanine as substrate, and its Mn2+ requirement is not satisfied by Fe2+, Co2+, or Ni2+. The properties of arginase and ornithine cyclodeaminase are discussed as part of the mechanisms which avoid depletion of L-arginine and L-ornithine pools for biosynthetic reactions during catabolic utilization of nopaline.

Ornithine cyclodeaminase from octopine Ti plasmid Ach5: identification, DNA sequence, enzyme properties, and comparison with gene and enzyme from nopaline Ti plasmid C58

Octopine and nopaline are two arginine-derived opines synthesized in plant cells transformed with octopine or nopaline plasmids. Utilization in Agrobacterium tumefaciens is mediated by Ti plasmid regions called occ or noc (octopine or nopaline catabolism), and recent experiments showed that noc in pTiC58 codes for a pathway from nopaline to L-proline. The last enzyme is ornithine cyclodeaminase (OCD), an unusual protein converting L-ornithine directly into L-proline. We investigated whether octopine plasmid pTiAch5 also harbors a gene for OCD. The results revealed an ocd gene which is induced by octopine and maps in the occ region. DNA sequence analysis and comparison with the gene from pTiC58 showed that the two genes are related (69% homology in DNA and deduced amino acid sequence), and antiserum against OCD(C58) also reacted with OCD(Ach5). The enzyme activity was characterized, and a comparison with OCD(C58) showed that the properties are similar, but not identical. Differences were detected in the regulation of enzyme activity by L-arginine and L-proline and in the response to varying ratios of NAD+/NADH. It is proposed that this reflects different mechanisms for integration of opine catabolism into general metabolism.

Ornithine cyclodeaminase from Ti plasmid C58: DNA sequence, enzyme properties and regulation of activity by arginine

Nopaline, an abundant opine in plant cells transformed with nopaline-type Ti plasmids, is catabolized in Agrobacterium by three Ti-plasmid-coded steps via arginine and ornithine to proline. The last enzyme, ornithine cyclodeaminase (OCD), converts ornithine directly into proline with release of ammonia. We describe the DNA sequence of the ocd gene from Ti plasmid C58, antiserum against an OCD fusion protein overexpressed in Escherichia coli, induction and identification of the gene product in Agrobacterium and enzymatic properties of the protein. The DNA sequence suggests a soluble protein with a stretch of some homology with ornithine carbamoyltransferases from other bacteria. OCD activity is subject to substrate inhibition, is stimulated by NAD+ (presumably acting as a catalytic cofactor) and is regulated by L-arginine which has pronounced effects on the optima for pH and temperature and on the Km for ornithine. The regulation of OCD activity by L-arginine is discussed as part of the mechanisms which integrate the pathway of Ti-plasmid-coded opine utilization with general metabolism in Agrobacterium.

The Noc region of Ti plasmid C58 codes for arginase and ornithine cyclodeaminase

Plant tumors induced by Agrobacterium tumefaciens synthesize a group of substances (opines) which can serve as sole source of carbon and nitrogen for the bacteria. We investigate Ti-plasmid-coded genes and enzymes involved in catabolism of the opine N2-(1,3-dicarboxypropyl)-L-arginine (nopaline) with a novel approach: expression and mapping of protein-coding regions in Escherichia coli minicells, followed by identification of enzyme functions in the heterologous E. coli background. The results show that a specific part of the nopaline catabolism (Noc) region of Ti plasmid C58 is packed with closely spaced protein-coding regions which can be expressed into polypeptides of distinct sizes in E. coli. We identify and map three enzyme activities: nopaline oxidase, arginase and ornithine cyclodeaminase, an unusual protein converting ornithine directly into proline. Nopaline oxidase requires two different Noc-gene-encoded proteins for function and the latter two enzymes are new discoveries in the Noc region. These three enzyme activities together constitute a catabolic pathway leading from nopaline through arginine and ornithine to proline.

Proline biosynthesis encoded by the noc and occ loci of Agrobacterium Ti plasmids

Octopine or nopaline Ti plasmids, or clones encoding their occ or noc loci, allowed proline auxotrophs of Agrobacterium tumefaciens to utilize the appropriate arginyl opine as a proline substitute. Arginine and ornithine substituted for proline only if the occ or noc loci were induced or made constitutive by mutation. These results support a report demonstrating a Ti plasmid-encoded activity in A. tumefaciens which cyclizes ornithine to proline.

Arginine catabolism in Agrobacterium strains: role of the Ti plasmid

We present a study of the enzymatic activities involved in the pathway for arginine catabolism by Agrobacterium tumefaciens. Nitrogen from arginine is recovered through the arginase-urease pathway; the genes for these two activities are probably chromosomally born. Arginase was found to be inducible during growth in the presence of arginine or ornithine. Urease was constitutively expressed. Ornithine, resulting from the action of arginase on arginine, could be used as a nitrogen source via transamination to delta 1-pyrroline-5-carboxylate and reduction of the latter compound to proline by a reductase (both enzymatic activities are probably chromosomally encoded). Ornithine could also be used as a carbon source. Thus, we identified an ornithine cyclase activity that was responsible for direct conversion of ornithine to proline. This activity was found to be Ti plasmid encoded and inducible by growth in medium containing octopine or nopaline. The same activity was also chromosomally encoded in some Agrobacterium strains. In such strains, this activity was inducible during growth in arginine-containing medium.