A plant oncogene as a phosphatase

The plant oncogene rolD encodes a functional ornithine cyclodeaminase

The plant oncogene rolD stimulates the reproductive phase transition in plants. We define here the function of its gene product. We show that the RolD protein bears sequence homology with ornithine cyclodeaminase, an uncommon enzyme of specialized-niche eubacteria and archaea that catalyzes the unusual NAD(+)-dependent conversion of ornithine to proline. To confirm the prediction of the bioinformatic analysis, the RolD protein was expressed in Escherichia coli and purified. An ornithine-dependent NAD(+) reduction that can be ascribed only to ornithine cyclodeaminase (OCD) activity was detected both in bacterial extracts containing RolD and in assays on the purified RolD protein. Furthermore, OCD activity was observed in soluble extracts from plants overexpressing rolD. The role of rolD in plant pathogenesis and its effect on plant reproductive development are discussed in light of the newly demonstrated enzymatic activity of its gene product.

Role of threonines in the Arabidopsis thaliana somatic embryogenesis receptor kinase 1 activation loop in phosphorylation

The Arabidopsis thaliana somatic embryogenesis receptor kinase 1 (AtSERK1) gene encodes a receptor-like protein kinase that is transiently expressed during embryogenesis. To determine the intrinsic biochemical properties of the AtSERK1 protein, we have expressed the intracellular catalytic domain as a glutathione S-transferase fusion protein in Escherichia coli. The AtSERK1-glutathione S-transferase fusion protein mainly autophosphorylates on threonine residues (K(m) for ATP, 4 x 10(-6) m), and the reaction is Mg(2+) dependent and inhibited by Mn(2+). A K330E substitution in the kinase domain of AtSERK1 abolishes all kinase activity. The active AtSERK1(kin) can phosphorylate inactive AtSERK1(K330E) protein, suggesting an intermolecular mechanism of autophosphorylation. The AtSERK1 kinase protein was modeled using the insulin receptor kinase as a template. On the basis of this model, threonine residues in the AtSERK1 activation loop of catalytic subdomain VIII are potential targets for phosphorylation. AtSERK1 phosphorylation on myelin basic protein and casein showed tyrosine, serine, and threonine as targets, demonstrating that AtSERK1 is a dual specificity kinase. Replacing Thr-468 with either alanine or glutamic acid not only obliterated the ability of the AtSERK1 protein to be phosphorylated but also inhibited phosphorylation on myelin basic protein and casein, suggesting that Thr-468 is essential for AtSERK-mediated signaling.

The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana

With the aim of understanding better the distribution and evolution of Agrobacterium rhizogenes genes transferred in the genus Nicotiana, 42 species were screened for presence of rolB, rolC, ORF13, and ORF14. The transferred sequences were then compared within the genus and with current bacterial sequences. The results obtained showed the presence of at least one bacterial gene in 15 species belonging to different subgenera. Sequence analyses supported the hypothesis of coevolution of bacterial and plant sequences, thus suggesting a possible role for the transferred genes in the early events of Nicotiana species differentiation. The high level of conservation of Agrobacterium sequences and the dependence of their expression from the plant physiological context along with previous data suggesting their involvement in the determination of the plant hormonal balance were all consistent with this hypothesis. The results are finally discussed also as to their relevance for the hypothesis of mono and multi ancient infection by Agrobacterium.

Transformation of the apple rootstock M.9/29 with the rolB gene and its influence on rooting and growth

To improve the rooting ability, the dwarfing apple rootstock M.9/29 was transformed with the rolB gene by Agrobacterium-mediated gene transfer. The use of sorbitol in the induction medium resulted in a successful transformation, while the use of sucrose failed to give any transformants. Totally 14 putative clones, named ARB1-14, were obtained from ten different leaves. Polymerase chain reaction (PCR) and Southern analyses confirmed that all the clones contained the nptII and rolB genes, while only four of them contained the intact gus gene. The in vitro rooting test showed that all the tested clones rooted to 83-100% on the hormone free rooting medium, while only 1% for the control plants. The root number of the transgenic clones ranged from 3.5 to 9, while the control plants produced only one root. Growth analysis showed that the clone ARB9 and ARB10 had a significant reduced node number and stem length compared with the control plants. However, the relative growth rate (RGR) of the tested clones was similar to that of the control plants, indicating that RGR is not directly related to dwarfism of a plant. The clone ARB10 also showed a significant reduced internode length compared with the control plants. The root length and root morphology did not differ between the transgenic clones and the untransformed control plants.

Apraxia of single tool Use

We report a 72-year-old right-handed man who showed an 'apraxia of tool use' after a cerebral infarct in the territory of the left middle cerebral artery. His apraxia of tool use was characterized by a clear dissociation between the inability to use a single tool and the ability to use plural tools. Most of the errors occurred in selecting an appropriate target where a tool is expected to be applied. Detailed examinations confirmed that his conceptual knowledge of tool use was well preserved. Furthermore, when a target of a tool was provided as a cue, he used a single tool correctly. These results suggest that his inability to use a single tool originated from his inability to evoke a target image from an actual tool.

A structural model for the rolA protein and its interaction with DNA

The study of the plant oncogene rolA has been hampered by a lack of structural information. Here we show that, despite a lack of significant sequence similarity to proteins of known structure, the rolA sequence adopts a known fold; that of the papillomavirus E2 DNA-binding domain. This fold is reliably identified by modern threading programs, which consider predicted secondary structure, but not by others. Although the rolA sequence is only around 16% identical to those of the available template structures, a structural model could be built that performed well against protein structure verification programs. The adopted strategy involved alignment corrections, justified by multiple model building and evaluation, with particular attention paid to the hydrophobic core residues. We find that rolA protein is predicted to resemble the template proteins in two key aspects; existence as a dimer and ability to bind DNA. rolA protein has recently been shown experimentally to possess DNA binding ability. This model predicts Lys 24 and Arg 27 to be involved in sequence-specific interactions and eight other residues to hydrogen-bond phosphate groups of the DNA.

Gene for a protein capable of enhancing lateral root formation

Analysis of genes preferentially expressed in hairy roots caused by infection with Agrobacterium rhizogenes has provided insights into the regulation of lateral root formation. A hairy root preferential cDNA, HR7, has been cloned from hairy roots of Hyoscyamus niger. HR7 encodes a novel protein partially homologous to a metallocarboxypeptidase inhibitor and is expressed exclusively in the primordium and base of lateral roots in hairy roots. Overexpression of HR7 in transgenic roots of H. niger dramatically enhances the frequency of lateral root formation. The results of this study indicate that expression of HR7 plays a critical role in initiating lateral root formation.

The auxin-binding protein Nt-ERabp1 alone activates an auxin-like transduction pathway

Hyperpolarization of tobacco protoplasts is amongst the earliest auxin responses described. It has been proposed that the auxin-binding protein, ABP1, or a related protein could be involved in the first step of auxin perception at the plasma membrane. Using for the first time homologous conditions for interaction between the protein Nt-ERabp1 or a synthetic peptide corresponding to the C-terminus and tobacco protoplasts, we have demonstrated that both can induce the hyperpolarization response. The results show that Nt-ERabp1 or the C-terminal peptide alone activates the auxin pathway from the outer face of the plasma membrane.

Evidence suggesting protein tyrosine phosphorylation in plants depends on the developmental conditions

Protein tyrosine phosphorylation plays a central role in a variety of signal transduction pathways regulating animal cell growth and differentiation, but its relevance and role in plants are controversial and still largely unknown. We report here that a large number of proteins from all plant subcellular fractions are recognized by recombinant, highly specific, anti-phosphotyrosine antibodies. Protein tyrosine phosphorylation patterns vary among different adult plant tissues or somatic embryo stages and somatic embryogenesis is blocked in vivo by a cell-permeable tyrosyl-phosphorylation inhibitor, demonstrating the involvement of protein tyrosine phosphorylation in control of specific steps in plant development.

Gain of function assays identify non-rol genes from Agrobacterium rhizogenes TL-DNA that alter plant morphogenesis or hormone sensitivity

This study tested the morphogenetic potential of 15 open reading frames of the TL-DNA of Agrobacterium rhizogenes strain HRI. These open reading frames were expressed individually under the control of the 35S RNA promoter in transgenic tobacco plants (Nicotiana tabacum L.). Expression of three T-DNA loci, ORF3n, ORF8 and ORF13, alters plant morphogenesis or the response of transgenic tissues to plant hormones. ORF3n transgenic plants are characterized by retarded flowering, altered internode elongation, altered leaf shape and, in particular, leaf tip necrosis. ORF3n and ORF8 expression reduces the sensitivity to auxin and cytokinin in combination or auxin alone. Tetracycline-dependent expression of ORF13 overcomes a selection of low levels of expression during plant regeneration and reveals a strong inhibitory effect of the ORF13 gene product on cell division and cell elongation. We conclude that the A. rhizogenes TL-DNA harbors genetic information that is important for pathogenicity apart from the well studied rol genes. We propose that these genes play mainly a negative regulatory role during pathogenesis. Moreover, these loci might be relevant to successful infections in specific host plants.

Protein-tyrosine phosphatases: biological function, structural characteristics, and mechanism of catalysis

The protein-tyrosine phosphatases (PTPases) superfamily consists of tyrosine-specific phosphatases, dual specificity phosphatases, and the low-molecular-weight phosphatases. They are modulators of signal transduction pathways that regulate numerous cell functions. Malfunction of PTPases have been linked to a number of oncogenic and metabolic disease states, and PTPases are also employed by microbes and viruses for pathogenicity. There is little sequence similarity among the three subfamilies of phosphatases. Yet, three-dimensional structural data show that they share similar conserved structural elements, namely, the phosphate-binding loop encompassing the PTPase signature motif (H/V)C(X)5R(S/T) and an essential general acid/base Asp residue on a surface loop. Biochemical experiments demonstrate that phosphatases in the PTPase superfamily utilize a common mechanism for catalysis going through a covalent thiophosphate intermediate that involves the nucleophilic Cys residue in the PTPase signature motif. The transition states for phosphoenzyme intermediate formation and hydrolysis are dissociative in nature and are similar to those of the solution phosphate monoester reactions. One strategy used by these phosphatases for transition state stabilization is to neutralize the developing negative charge in the leaving group. A conformational change that is restricted to the movement of a flexible loop occurs during the catalytic cycle of the PTPases. However, the relationship between loop dynamics and enzyme catalysis remains to be established. The nature and identity of the rate-limiting step in the PTPase catalyzed reaction requires further investigation and may be dependent on the specific experimental conditions such as temperature, pH, buffer, and substrate used. In-depth kinetic and structural analysis of a representative number of phosphatases from each group of the PTPase superfamily will most likely continue to yield insightful mechanistic information that may be applicable to the rest of the family members.

The impact of Ti-plasmid-derived gene vectors on the study of the mechanism of action of phytohormones

The molecular basis of tumor formation on dicotyledonous plants by Agrobacterium relies on the transfer to the plant cell of a unique segment of bacterial DNA, the T-DNA. The T-DNA contains genes that are active in the plant cell and encode hormone biosynthetic enzymes, or proteins that deregulate the cell's response to phytohormones. Study of this process has yielded not only knowledge of how alterations in phytohormone homeostasis can affect plant cell growth, but also has provided the essential tools to study phytohormone signaling in transgenic plants. Furthermore, T-DNA insertion into the plant genome forms the basis of gene tagging, a versatile method for isolating genes involved in phytohormone signal transduction and action.