The Experts below are selected from a list of 135 Experts worldwide ranked by ideXlab platform
Paul J J Hooykaas - One of the best experts on this subject based on the ideXlab platform.
-
complete sequence of succinamopine ti plasmid ptieu6 reveals its evolutionary relatedness with Nopaline type ti plasmids
Genome Biology and Evolution, 2019Co-Authors: Shuai Shao, Paul G H Van Heusden, Paul J J HooykaasAbstract:: Agrobacterium tumefaciens is the etiological agent of plant crown gall disease, which is induced by the delivery of a set of oncogenic genes into plant cells from its tumor-inducing (Ti) plasmid. Here we present the first complete sequence of a succinamopine-type Ti-plasmid. Plasmid pTiEU6 is comprised of 176,375 bp with an overall GC content of 56.1% and 195 putative protein-coding sequences could be identified. This Ti-plasmid is most closely related to Nopaline-type Ti-plasmids. It contains a single T-region which is somewhat smaller than that of the Nopaline-type Ti-plasmids and in which the gene for Nopaline synthesis is replaced by a gene (sus) for succinamopine synthesis. Also in pTiEU6 the Nopaline catabolic genes are replaced by genes for succinamopine catabolism. In order to trace the evolutionary origin of pTiEU6, we sequenced six Nopaline Ti-plasmids to enlarge the scope for comparison to this class of plasmids. Average nucleotide identity analysis revealed that pTiEU6 was most closely related to Nopaline Ti-plasmids pTiT37 and pTiSAKURA. In line with this traces of several transposable elements were present in all the Nopaline Ti plasmids and in pTiEU6, but one specific transposable element insertion, that of a copy of IS1182, was present at the same site only in pTiEU6, pTiT37, and pTiSAKURA, but not in the other Ti plasmids. This suggests that pTiEU6 evolved after diversification of Nopaline Ti-plasmids by DNA recombination between a pTiT37-like Nopaline Ti-plasmid and another plasmid, thus introducing amongst others new catabolic genes matching a new opine synthase gene for succinamopine synthesis.
-
transgenic n glauca plants expressing bacterial virulence gene virf are converted into hosts for Nopaline strains of a tumefaciens
Nature, 1993Co-Authors: A J G Regensburgtuink, Paul J J HooykaasAbstract:TUMOURS are induced by Agrobacterium tumefaciens on a variety of plants1–3. The virulence determinants of A. tumefaciens reside on a large tumour-inducing (Ti) plasmid. This plasmid carries two regions essential for tumour induction, namely the T region and the Vir region. During infection the T region is transferred to the plant cell, where it becomes stably integrated in one of the host chromosomes as T-DNA. Expression of T-DNA leads to the production of the plant hormones auxin and cytokinin, as well as to the synthesis of specific amino-acid derivatives termed opines. Agrobacterium strains are classified according to the types of opines produced by the tumours they induce. The Vir region contains genes that are expressed in the bacterium and are required for T-DNA transfer to plant cells, and several other genes that affect the efficiency of transfer and the host range. Vir regions from different Ti plasmids may vary slightly in the genes they contain: for instance, the virF gene, which is present in the Vir-region of octopine Ti plasmids, is absent from Nopaline Ti plasmids4,5. Mutation of the virF gene leads to a weakened virulence of octopine strains on tomato6 and Nicotiana glauca (shrub tobacco)4. Nopaline strains are strongly attenuated in N. glauca compared with octopine strains because of the absence of the virF virulence gene from the Ti plasmid in Nopaline strains4. The virF gene product may be transferred to and be active in plant cells. Here we isolate transgenic N. glauca plants in which the virF coding sequence is expressed using the cauliflower mosaic virus 35S promoter. The presence of the VirF protein converts the non-host N. glauca into a host for tumour formation by A. tumefaciens Nopaline strains and octopine virF mutants. Our results indicate that certain virulence gene products such as the VirF protein may be transferred to plant cells during tumour induction, where they function as mediators of T-DNA transfer.
-
octopine and Nopaline strains of agrobacterium tumefaciens differ in virulence molecular characterization of the virf locus
Plant Molecular Biology, 1990Co-Authors: Leo Sjoerd Melchers, R A Schilperoort, Michael J Maroney, Amke Den Dulkras, David V Thompson, Hanneke A J Van Vuuren, Paul J J HooykaasAbstract:Octopine and Nopaline strains of Agrobacterium tumefaciens were found to differ in virulence on Nicotiana glauca. This difference is due to the absence of a functional virF locus, which is necessary for efficient tumorigenesis on N. glauca, from the Nopaline Ti plasmids. Genetic studies and DNA sequence analysis of the virF locus revealed that virF embraces one open reading frame coding for a hydrophilic protein with a molecular mass of 22437 Da. Transcription of virF is directed from left to right, towards the T region, and is strongly induced by the phenolic compound acetosyringone. We established that virA and virG, two genes known to be essential for induction of the vir regulon, are necessary for acetosyringoneinduced virF expression, implying that virF is a member of this vir regulon. Agrobacterium virF mutants can be complemented for tumor induction by co-infection with avirulent Agrobacterium ‘helper’ strains. We found that such ‘helper’ strains must express not only the virF gene but also the vir operons virA, virB, virD and virG.
Joachim Schroder - One of the best experts on this subject based on the ideXlab platform.
-
octopine and Nopaline oxidases from ti plasmids of agrobacterium tumefaciens molecular analysis relationship and functional characterization
Journal of Bacteriology, 1994Co-Authors: H Zanker, G Lurz, U Langridge, Peter Langridge, D Kreusch, Joachim SchroderAbstract:The occ and noc regions of pTiAch5 (octopine) and pTiC58 (Nopaline) Ti plasmids are responsible for the catabolic utilization of octopine and Nopaline in Agrobacterium spp. The first enzymatic step is the oxidative cleavage into L-arginine and pyruvate or 2-ketoglutarate, respectively, by membrane-bound opine oxidases requiring two polypeptides (subunits B and A) for function. The DNA sequences showed that the subunits of pTiAch5 and pTiC58 are related, but none of the proteins revealed significant similarities to the biosynthetic enzymes expressed in transformed plant cells. The four proteins had no extensive overall similarity to other proteins, but the 35 N-terminal amino acids contained motifs found in many enzymes utilizing flavin adenine dinucleotide, flavin mononucleotide, or NAD(P)+ as cofactors. However, the activities were completely independent of added cofactors, and the nature of the electron acceptor remained unclear. Membrane solubilization led to complete loss of enzyme activity. The Nopaline oxidase accepted Nopaline and octopine (Vmax ratio, 5:1) with similar Km values (1.1 mM). The octopine oxidase had high activity with octopine (Km = 1 mM) and barely detectable activity with Nopaline. The subunits from the occ and the noc regions were exchangeable. The combinations ooxB-noxA and noxB-ooxA both produced active enzymes which oxidized octopine and Nopaline at similar rates, suggesting that both subunits contributed to the substrate specificity. These experiments also showed that the formation of functional enzyme required close proximity of the subunit genes on the same plasmid and that even a reversal of the gene order (A-B instead of B-A) led to reduced activity. Images
-
opine regulated promoters and lysr type regulators in the Nopaline noc and octopine occ catabolic regions of ti plasmids of agrobacterium tumefaciens
Journal of Bacteriology, 1994Co-Authors: J Von Lintig, D Kreusch, Joachim SchroderAbstract:Essential steps in the uptake and catabolism of the plant tumor metabolites Nopaline and octopine in Agrobacterium spp. are performed by proteins encoded in the Nopaline catabolic (noc) and octopine catabolic (occ) regions of Ti plasmids. We investigated the opine activation of the genes by using (i) promoter studies of Agrobacterium spp. and (ii) analysis of the promoter interaction with the regulatory proteins NocR (noc) and OccR (occ). The noc region contained two Nopaline-induced promoters (Pi1[noc] and Pi2[noc]) and one autogenously regulated promoter (Pr [control of NocR expression]). Pi2 and Pr overlapped and were divergently oriented (Pi2 [noc]). DNA binding studies and DNase I footprints indicated that NocR bound specifically to single binding sites in Pi1[noc] and Pi2/Pr[noc] and that Pi2 and Pr were regulated from the same binding site. The binding was independent of the inducer Nopaline, and Nopaline caused small changes in the footprint. The promoters in the noc and occ regions shared sequence motif and contained the sequence T-N11-A, which is characteristic for LysR-type-regulated promoters. The occ region contained one octopine-induced and one autogenously regulated promoter (Pi/Pr[occ]) in the same arrangement as Pi2/Pr[noc] in the noc region. Promoter deletions indicated that sequences flanking the OccR binding site determined the extent of induction, although they did not bind OccR. The promoter bound OccR in the absence and presence of octopine. The opine caused a change in the mobility of the DNA-protein complex with the complete promoter. The resected fragments did not reveal this opine-induced shift, and it was also not detectable with the DNA-NocR complexes with the two promoters of the noc region. Images
-
characterization of a Nopaline induced gene for a 40 kda protein in the Nopaline catabolic noc region of ti plasmid ptic58
Biochimica et Biophysica Acta, 1993Co-Authors: Andreas Schrell, Joachim SchroderAbstract:Abstract The Nopaline catabolic region (noc) in Ti plasmid pTiC58 codes for functions in the utilization of Nopaline. The enzymes are identified, except for a 40 kDa protein (40k gene). The sequence reveals a polypeptide with no homology to other known proteins, except for similarities in two out of three motifs characteristic for d -isomer specific 2-hydroxyacid dehydrogenases.
-
opine transport genes in the octopine occ and Nopaline noc catabolic regions in ti plasmids of agrobacterium tumefaciens
Journal of Bacteriology, 1992Co-Authors: H Zanker, J Von Lintig, Joachim SchroderAbstract:The occ and noc regions of octopine and Nopaline Ti plasmids in Agrobacterium tumefaciens are responsible for the catabolic utilization of octopine and Nopaline, respectively. Opine-inducible promoters, genes for regulatory proteins and for catabolic enzymes, had been identified in previous work. However, both regions contained additional DNA stretches which were under the control of opine-inducible promoters, but the functions were unknown. We investigated these stretches by DNA sequence and functional analyses. The sequences showed that both of the catabolic regions contain a set of four genes which are transcribed in the same direction. The occ and noc region genes are related, but the arrangement of the genes is different. The deduced polypeptides are related to those of binding protein-dependent transport systems of basic amino acids in other bacteria. The comparison suggested that three of the polypeptides are located in the membrane and that one is a periplasmic protein. We constructed cassettes which contained either the putative transport genes only or the complete occ or noc region; all constructs, however, included the elements necessary for opine-induced expression of the genes (the regulatory gene and the inducible promoters). Uptake studies with 3H-labelled octopine showed that the putative transport genes in the occ region code for octopine uptake proteins. The corresponding studies with 3H-labelled Nopaline and the noc region cassettes indicated that the uptake of Nopaline requires the putative transport genes and additional functions from the left part of the noc region.
-
functional organization of the regions responsible for Nopaline and octopine catabolism in ti plasmids of agrobacterium tumefaciens
1991Co-Authors: Joachim Schroder, J Von Lintig, H ZankerAbstract:The catabolism of opines synthesized in transformed plant cells by Agrobacterium is an important aspect in the bacteria/plant interaction. We investigate Ti plasmid genes in the noc-region of pTiC58 and in the occ-region of pTiAch5 which are necessary for catabolism of Nopaline and octopine, respectively. Results with a binary vector system indicate that both regions code for constitutively expressed proteins which are necessary and sufficient for activation in trans of the catabolic functions in presence of the opines. These proteins from the noc- and the occ-region reveal significant similarities to each other and to regulatory proteins characterized in other bacteria. The positions of the inducible promoters have been mapped to regions of less than 0.5 kbp. Apart from proteins directly involved in opine catabolism, both regions code for at least two proteins which are related to transport proteins in other bacteria. These and previous results indicate that several genes in the noc- and the occ-region are related, but adapted for function in Nopaline and octopine utilization.
Vitaly Citovsky - One of the best experts on this subject based on the ideXlab platform.
-
Nopaline type ti plasmid of agrobacterium encodes a virf like functional f box protein
Scientific Reports, 2015Co-Authors: Benoit Lacroix, Vitaly CitovskyAbstract:During Agrobacterium-mediated genetic transformation of plants, several bacterial virulence (Vir) proteins are translocated into the host cell to facilitate infection. One of the most important of such translocated factors is VirF, an F-box protein produced by octopine strains of Agrobacterium, which presumably facilitates proteasomal uncoating of the invading T-DNA from its associated proteins. The presence of VirF also is thought to be involved in differences in host specificity between octopine and Nopaline strains of Agrobacterium, with the current dogma being that no functional VirF is encoded by Nopaline strains. Here, we show that a protein with homology to octopine VirF is encoded by the Ti plasmid of the Nopaline C58 strain of Agrobacterium. This protein, C58VirF, possesses the hallmarks of functional F-box proteins: it contains an active F-box domain and specifically interacts, via its F-box domain, with SKP1-like (ASK) protein components of the plant ubiquitin/proteasome system. Thus, our data suggest that Nopaline strains of Agrobacterium have evolved to encode a functional F-box protein VirF.
-
comparison between nuclear localization of Nopaline and octopine specific agrobacterium vire2 proteins in plant yeast and mammalian cells
Molecular Plant Pathology, 2001Co-Authors: Tzvi Tzfira, Vitaly CitovskyAbstract:SUMMARY In a unique case of trans-kingdom DNA transfer, Agrobacterium genetically transforms plants by transferring its DNA segment into the host cell nucleus and integrating it into the plant genome. One of the central players in this process is the bacterial virulence protein, VirE2, which binds the transported DNA molecule and facilitates its nuclear import. Nuclear import of VirE2 proteins encoded by two major Agrobacterium strains, Nopaline and octopine, has been hypothesized to occur by different mechanisms, i.e. the Nopaline VirE2 was imported only into the nuclei of plant cells while the octopine VirE2 also accumulated in the nuclei of animal cells. Here, this notion was tested by a systematic comparison of nuclear import of Nopaline- and octopine-specific VirE2 in dicotyledonous and monocotyledonous plants and in living mammalian and yeast cells. These experiments showed that nuclear import of both Nopaline and octopine VirE2 proteins is plant-specific, occurring in plant but not in non-plant systems.
-
Comparison between nuclear localization of Nopaline‐ and octopine‐specific Agrobacterium VirE2 proteins in plant, yeast and mammalian cells
Molecular Plant Pathology, 2001Co-Authors: Tzvi Tzfira, Vitaly CitovskyAbstract:SUMMARY In a unique case of trans-kingdom DNA transfer, Agrobacterium genetically transforms plants by transferring its DNA segment into the host cell nucleus and integrating it into the plant genome. One of the central players in this process is the bacterial virulence protein, VirE2, which binds the transported DNA molecule and facilitates its nuclear import. Nuclear import of VirE2 proteins encoded by two major Agrobacterium strains, Nopaline and octopine, has been hypothesized to occur by different mechanisms, i.e. the Nopaline VirE2 was imported only into the nuclei of plant cells while the octopine VirE2 also accumulated in the nuclei of animal cells. Here, this notion was tested by a systematic comparison of nuclear import of Nopaline- and octopine-specific VirE2 in dicotyledonous and monocotyledonous plants and in living mammalian and yeast cells. These experiments showed that nuclear import of both Nopaline and octopine VirE2 proteins is plant-specific, occurring in plant but not in non-plant systems.
Steven J Rothstein - One of the best experts on this subject based on the ideXlab platform.
-
transformation of a partial Nopaline synthase gene into tobacco suppresses the expression of a resident wild type gene
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: Daphne R Goring, Lisa Thomson, Steven J RothsteinAbstract:Abstract A portion of the Nopaline synthase gene under the control of the cauliflower mosaic virus 35S promoter was used to transform a tobacco plant that had previously been transformed with a wild-type Nopaline synthase (nos) gene. Unexpectedly, in all nine primary transformants tested the wild-type nos expression was virtually completely suppressed. In contrast, plants transformed with the control vector DNA, which differed only in the absence of the partial nos gene, did not show any inhibition of nos expression. Progeny plants were analyzed for the stability of the gene-silencing phenotype. All of the progeny that carried both the wild-type and partial nos genes had no detectable Nopaline synthase activity. In addition, wild-type nos mRNA could not be detected in these plants. In most plants in which the wild-type gene was segregated away from the partial nos gene, wild-type levels of activity were detected. Although DNA methylation has been shown to be correlated with a decrease in promoter activity in plants, none of the progeny appeared to carry a methylated nos promoter. The underlying mechanism causing this gene suppression phenomenon is unclear at this time.
Leon Otten - One of the best experts on this subject based on the ideXlab platform.
-
sequence and functional analysis of the left hand part of the t region from the Nopaline type ti plasmid ptic58
Plant Molecular Biology, 1999Co-Authors: Leon Otten, Jeanyves Salomone, Anne Helfer, Julien Schmidt, Philippe Hammann, Patrice De RuffrayAbstract:The Agrobacterium tumefaciens Nopaline strain C58 transfers a large, 29 kb T-DNA into plant cells during infection. Part of this DNA (the `common DNA') is also found on the T-DNA of octopine strains, the remaining DNA is Nopaline strain-specific. Up to now, only parts of the C58 T-DNA and related T37 T-DNA have been sequenced. We have sequenced the remainder of the Nopaline-specific T-DNA (containing genes a to d) and acs to iaaM. Gene c codes for a new unknown T-DNA protein. Gene a is homologous to the agrocinopine synthase gene. Genes b, c′, d and e are part of a larger family: they are related to the T-DNA genes 5, rolB, lso and 3′. Genes 5, rolB and lso induce or modify plant growth and have been called T-DNA oncogenes. Our studies show that gene 3′ (located on the TR-DNA of octopine strains) is also oncogenic. Although the b–e T-DNA fragment from C58 and its individual genes lack growth-inducing activity, an a-acs deletion mutant was distinctly less virulent on Kalanchoe daigremontiana and showed reduced shoot formation on Kalanchoe tubiflora. Shoot formation could be restored by genes c and c′ in co-infection experiments. Contrary to an earlier report, a C58 e gene deletion mutant was fully virulent on all plants tested.
-
agrobacterium vitis Nopaline ti plasmid ptiab4 relationship to other ti plasmids and t dna structure
Molecular Genetics and Genomics, 1994Co-Authors: Leon Otten, P De RuffrayAbstract:The Ti plasmid of the Agrobacterium vitis Nopaline-type strain AB4 was subcloned and mapped. Several regions of the 157 kb Ti plasmid are similar or identical to parts of the A. vitis octopine/cucumopine (o/c)-type Ti plasmids, and other regions are homologous to the Nopaline-type Ti plasmid pTiC58. The T-DNA of pTiAB4 is a chimaeric structure of recent origin: the left part is 99.2% homologous to the left part of the TA-DNA of the o/c-type Ti plasmids, while the right part is 97.1 % homologous to the right part of an unusual Nopaline T-DNA recently identified in strain 82.139, a biotype Il strain from wild cherry. The 3′ non-coding regions of the ipt genes from pTiAB4 and pTi82.139 are different from those of other ipt genes and contain a 62 by fragment derived from the coding sequence of an ipt gene of unknown origin. A comparison of different ipt gene sequences indicates that the corresponding 62 by sequence within the coding region of the AB4 ipt gene has been modified during the course of its evolution, apparently by sequence transfer from the 62 by sequence in the 3′ non-coding region. In pTi82.139 the original coding region of the ipt gene has remained largely unmodified. The pTiAB4 6b gene differs from its pTi82.139 counterpart by the lack of a 12 by repeat in the 3′ part of the coding sequence. This leads to the loss of four glutamic acid residues from a series of ten. In spite of these differences, the ipt and 6b genes of pTiAB4 are functional. Our results provide new insight into the evolution of Agrobacterium Ti plasmids and confirm the remarkable plasticity of these genetic elements. Possible implications for the study of bacterial phylogeny are discussed.
