Evaluation of four Agrobacterium tumefaciens strains for the genetic transformation of tomato (Solanum lycopersicum L.) cultivar Micro-Tom.

KEY MESSAGE : Agrobacterium tumefaciens strains differ not only in their ability to transform tomato Micro-Tom, but also in the number of transgene copies that the strains integrate in the genome. The transformation efficiency of tomato (Solanum lycopersicum L.) cv. Micro-Tom with Agrobacterium tumefaciens strains AGL1, EHA105, GV3101, and MP90, harboring the plasmid pBI121 was compared. The presence of the nptII and/or uidA transgenes in regenerated T(0) plants was determined by PCR, Southern blotting, and/or GUS histochemical analyses. In addition, a rapid and reliable duplex, qPCR TaqMan assay was standardized to estimate transgene copy number. The highest transformation rate (65 %) was obtained with the Agrobacterium strain GV3101, followed by EHA105 (40 %), AGL1 (35 %), and MP90 (15 %). The mortality rate of cotyledons due to Agrobacterium overgrowth was the lowest with the strain GV3101. The Agrobacterium strain EHA105 was more efficient than GV3101 in the transfer of single T-DNA insertions of nptII and uidA transgenes into the tomato genome. Even though Agrobacterium strain MP90 had the lowest transformation rate of 15 %, the qPCR analysis showed that the strain MP90 was the most efficient in the transfer of single transgene insertions, and none of the transgenic plants produced with this strain had more than two insertion events in their genome. The combination of higher transformation efficiency and fewer transgene insertions in plants transformed using EHA105 makes this Agrobacterium strain optimal for functional genomics and biotechnological applications in tomato.

Hexokinase and 'glucokinase' in liver metabolism.

Rat liver contains four hexokinase isoenzymes, one of which, despite often being called 'glucokinase', is no more specific for glucose than the others. However, it does differ from them in displaying a sigmoid kinetic response to glucose, requiring much higher glucose concentrations for activity, and being insensitive to physiological concentrations of glucose 6-phosphate.

A Sulfhydryl Reagent Modulates Systemic Signaling for Wound-Induced and Systemin-Induced Proteinase Inhibitor Synthesis.

The sulfhydryl group reagent p-chloromecuribenzene sulfonic acid (PCMBS), an established inhibitor of active apoplastic phloem loading of sucrose in several plant species, is shown to be a powerful inhibitor of wound-induced and systemin-induced activation of proteinase inhibitor synthesis and accumulation in leaves of tomato plants (Lycopersicon esculentum cv Castlemart). PCMBS, supplied to young tomato plants through their cut stems, blocks accumulation of proteinase inhibitors in leaves in response to wounding. The application of systemin directly to fresh wounds enhances systemic accumulation of proteinase inhibitors to levels higher than wounding alone. Placed on fresh wounds, PCMBS severely inhibits systemic induction of proteinase inhibitors, in both the presence and absence of exogenous systemin. PCMBS inhibition can be reversed by cysteine, dithiothreitol, and glutathione. Radiolabeled systemin placed on fresh wounds is readily transported from the wounded leaves to upper leaves. However, in the presence of PCMBS, radiolabeled systemin is not transported away from wound sites. Induction of proteinase inhibitor I synthesis by oligouronides (degree of polymerization [almost equal to] 20), linolenic acid, or methyl jasmonate was not inhibited by PCMBS. The cumulative data support a possible role for sulfhydryl groups in mediating the translocation of systemin from wound sites to distal receptor sites in tomato plants and further support a role for systemin as a systemic wound signal.

Systems biology may work when we learn to understand the parts in terms of the whole.

The first point to note about whether systems biology will work is that the essential idea of systems biology is not new: there has been interest in it, as well as efforts to apply it, since the middle of the 20th century. The difference now is that it has become fashionable, with an explosion in the number of publications using the two words, albeit not always with the same meaning. The reductionist approach remains dominant, however, and systems biology is often seen as no more than integration of diverse data into models of systems. This way of thinking needs to be changed if systems biology is to lead to an understanding of life and to provide the benefits that are expected from it. The emphasis ought to be on the needs of the system as a whole for understanding the components, not the converse. General properties of metabolic systems, such as feed-back inhibition, can be properly understood by taking account of supply and demand, i.e. the requirements of the system as a whole, but this is often overlooked. Metabolism tends to be viewed as static, although enzymes (and proteins in general) are continuously synthesized and degraded. The fact that they are themselves therefore metabolites introduces great complexity to metabolism, including an implication of infinite regress; understanding how living organisms escape from this will be an essential step towards understanding life.

The competition plot: A kinetic method to assess whether an enzyme that catalyzes multiple reactions does so at a unique site.

Enzymes often act on more than one substrate, and the question then arises as to whether this can be attributed to the existence of two different enzymes that have not been separated or, more interesting, to the presence of two different active sites in the same enzyme. The competition plot is a kinetic method that allows us to test with little experimentation whether the two reactions occur at the same site or at different sites. It consists of making mixtures of the two substrates and plotting the total rate against a parameter p that defines the concentrations of the two substrates in terms of reference concentrations chosen to give the same rates at p = 0 and p = 1, i.e., when only one of the substrates is present. With a slight modification of the equations it can also be applied to enzymes that deviate from Michaelis-Menten kinetics. If the two substrates react at the same site, the competition plot gives a horizontal straight line; i.e., the total rate is independent of p. In contrast, if the two reactions occur at two separate and independent sites a curve with a maximum is obtained; separate reactions with cross-inhibition generate curves with either maxima or minima according to whether the Michaelis constants of the two substrates are smaller or larger than their inhibition constants in the other reactions. Strategies to avoid ambiguous results and to improve the sensitivity of the plot are described. A practical example is given to facilitate the experimental protocol for this plot.

Characteristics necessary for an interconvertible enzyme cascade to generate a highly sensitive response to an effector.

A monocyclic interconvertible enzyme cascade, in which active and inactive states of an enzyme are interconverted by two opposing enzyme-catalysed reactions, does not necessarily produce a greater degree of sensitivity to an effector than one could expect from direct interaction between effector and target reaction. On the contrary, a cascade in which an effector acts on one of the enzymes catalysing the interconversion reactions by altering the apparent value of its specificity constant will always generate a less sensitive response than direct interaction would give. Nonetheless, even if both interconversion reactions obey Michaelis-Menten kinetics with the ordinary types of inhibition and activation, one can easily generate an enormous sensitivity in which a 0.5% change in concentration can increase the proportion of target enzyme in the active state from 10% to 90%: this corresponds approximately to a Hill coefficient of 800. To maximize the sensitivity, the following conditions must be satisfied: (1) both modifier enzymes must act under conditions of near saturation; (2) the effector must act on both of them in opposite directions; (3) it must alter the apparent values of their catalytic constants; (4) the enzyme subject to inhibition by the effector must respond at much lower effector concentrations than the enzyme subject to activation. As the last of these conditions appears to be counter-intuitive, it suggests that feeble activation of modifier enzymes in real systems may have passed unnoticed, or been dismissed as physiologically insignificant, although in reality crucial to the effective response of the system.

Cooperative behaviour in monomeric enzymes. Change of negative to positive cooperativity by effect of a ligand.

Three steady-state models were analysed to see if they could reproduce the following kinetic characteristics in a monomeric enzyme with two substrates: a) kinetic cooperativity with respect to the first substrate but not to the second; b) modulation of the kinetic cooperativity for the first substrate by the concentration of the second; c) change in the sign of the kinetic cooperativity at very low concentrations of the second substrate. A slow transition model previously proposed for vertebrate "glucokinase" (hexokinase D), model I, (Olavarría et al., 1982) was able to reproduce characteristics a and b, but never c. The "mnemonical" model (Ricard et al., 1974), model II, also reproduced characteristics a and b, and failed to reproduce c. Thus when observations were performed at concentrations of the first substrate around K0.5 it was possible to observe a decrease in the Hill coefficient (h) relative to the decrease in the concentration of the second substrate, but values lower than 1.0 were never obtained. At extremely high substrate concentrations, the second substrated did not affect the cooperativity of the enzyme for the first substrate. Model III was similar to Model I, but it was considered that only the enzyme conformer with the higher affinity for the first substrate was catalytically active. With this model it was possible to change positive cooperativity into negative if the second substrated altered the frequency of the conformational transition.

[Concurrence of multiple and integrated mechanisms in the modulation of enzyme activities: significance for the regulation of metabolic fluxes]. / Concurrencia de mecanismos múltiples e integrados en la modulación de la actividad enzimática: significado para la regulación de flujos metabólicos.

The activity of some enzymes in a given metabolic pathway is modulated through multiple mechanisms, which operate in a simultaneous and coherent way to produce either stimulation or inhibition. The operation of these mechanisms is illustrated with several enzymes involved in glucose metabolism, by choosing examples from the presentations at the Symposium. Thus the reciprocal interactions of the regulatory mechanisms acting upon hexokinase D ('glucokinase'), phosphofructokinase, fructose 1,6-bisphosphatase and pyruvate kinase were discussed, as well as their relationships with the induction of enzyme conformational changes. In addition, the effects of covalent interconversions on glutamine synthetase activity were briefly analyzed. An outstanding feature exhibited by all these enzymes is the display of a great number of elasticity coefficients, which are differential quotients measuring the dependence of enzymatic activity on each variable that modulates it. A general assumption is that these enzymes make an important contribution to the control of the metabolic flux in which they participate. The flux control, however, appears to be shared in different degrees by all the components of the system, and may be quantified through the differential quotient denominated control coefficient. Some of the problems that emerge in any attempt to estimate these coefficients in the living cells are discussed. The problems derive partly from the complex subcellular structure, the formation of functional compartments resulting from reversible association of the enzymes, one to another and to different cellular components, and the actual state of cell water. These problems make that the results obtained with purified and highly diluted enzymes in most enzymological studies should not be extrapolated directly to what happens in vivo, without a careful evaluation of each particular case. The regulatory role of enzyme activity of fructose 2,6-bisphosphate and its eventual participation as an intermediary in the hormonal control of glycolytic and gluconeogenic fluxes are emphasized. The regulation of yeast fructose 1,6-bisphosphate activity is discussed in relation to the eventual role of allosteric modulators and covalents interconversions as signals for the initiation of intracellular degradation of the enzyme during catabolic inactivation.

Co-operativity in monomeric enzymes.

It has been known for at least 20 years that monomeric enzymes can in principle show kinetic behaviour similar in appearance to the binding of ligands to oligomeric proteins in which there are co-operative interactions between multiple binding sites. However, the initial lack of experimental examples of kinetic co-operativity suggested that in nature co-operativity always arose from interactions between binding sites. Now, however, several examples are known, most of which cannot be explained in terms of multiple binding sites on one polypeptide chain. All current theoretical models for monomeric co-operativity postulate that it arises from the presence in the mechanism of parallel pathways for substrate binding that are slow compared with the possible rate of the catalytic reaction. Rapid removal of the intermediates produced in the slow steps prevents them from approaching equilibrium and allows the appearance of kinetic properties that would not be possible in systems at equilibrium.

All hexokinase isoenzymes coexist in rat hepatocytes.

The cellular distribution of hexokinase isoenzymes, N-acetylglucosamine Kinase and pyruvate kinases in rat liver was studied. Hepatocytes and non-parenchymal cells with high viability and almost no cross-contamination were obtained by perfusion in situ of the liver with collagenase, with the use of an enriched cell-culture medium in all steps of cell isolation. Separation of hexokinase isoenzymes was done by DEAE-cellulose chromatography, and enzyme activities were measured by a specific radioassay. Cytosol from isolated hepatocytes contained high-affinity hexokinases A, B and C, in addition to hexokinase D. The last-mentioned represented about 95% of total glucose-phosphorylating activity. Only hexokinase A was found associated t the particulate fraction. Isolated non-parenchymal cells contained only hexokinases A, B and C. N-Acetylglucosamine kinase was measured with a specific radioassay and was found as a single enzyme form in both hepatocytes and non-parenchymal cells, with higher activities in the former. Pyruvate kinase isoenzyme L was present only in the hepatocytes and isoenzyme K only in the non-parenchymal liver cells, confirming that they are good cellular markers.

Information transfer in metabolic pathways. Effects of irreversible steps in computer models.

Various metabolic models have been studied by computer simulation in an effort to understand why allowing for the reversibility of the reaction catalysed by pyruvate kinase, normally considered as irreversible for all practical purposes, significantly altered the behaviour of the model of glycolysis in Trypanosoma brucei [Eisenthal, R. & Cornish-Bowden, A. (1998) J. Biol. Chem. 273, 5500-5505]. Studies of several much simpler models indicate that the enzymes catalysing early steps in a pathway must receive information about the concentrations of the metabolites at the end of the pathway if a model is to be able to reach a steady state; treating all internal steps as reversible is just one way of ensuring this. Feedback inhibition provides a much better way, and as long as feedback loops are present in a model it makes almost no difference to the behaviour whether the intermediate steps with large equilibrium constants are treated as irreversible. In the absence of feedback loops, ordinary product inhibition of all the enzymes in the chain can also transfer information; this is efficient for regulating fluxes but very inefficient for regulating intermediate concentrations. More complicated patterns of regulation, such as activation of a competing branch or forcing flux through a parallel route, can also serve to some degree as ways of passing information around an irreversible step. However, they normally do so less efficiently than inhibition, because the extent to which an enzyme or a pathway can be activated always has an upper limit (which may be below what is required), whereas most enzymes are inhibited completely at saturating concentrations of inhibitor.

The glucose-induced switch between glycogen phosphorylase and glycogen synthase in the liver: outlines of a theoretical approach.

The glucose-induced switch between glycogen phosphorylase and glycogen synthase in the liver is investigated by means of a theoretical approach based on a minimal, bicyclic cascade model involving the reversible phosphorylation of the two enzymes. The aim of the analysis is to evaluate the contribution of different factors to the sequential changes in the activity of glycogen phosphorylase and glycogen synthase observed following the addition of suprathreshold amounts of glucose.

Rounding error, an unexpected fault in the output from a recording spectrophotometer: implications for model discrimination.

Although commonly ignored in discussions of experimental error, rounding may sometimes be the major source of error, especially with modern precision instruments: some recording spectrophotometers are optically and photometrically capable of making absorbance measurements with errors less than 0.0003, but provide no numerical information more precise than +/- 0.001. The problem may be diagnosed by a characteristic arrangement of points in a residual plot, which resembles the result of cutting a stroboscopic picture of a bouncing ball into several strips and modifying it by sliding the strips relative to one another to bring the points closer to the axis. Harmful effects of rounding error can be critical in experiments designed for model discrimination.

Channelling can affect concentrations of metabolic intermediates at constant net flux: artefact or reality?

We show that if a metabolic intermediate is directly transferred ('channelled') from an enzyme that catalyses its production to another that uses it as substrate, there is no change in its free concentration compared with a system with the same net flux in which there is no direct transfer. Thus the widespread idea that channelling provides a mechanism for decreasing metabolite concentrations at constant flux is false. Results from computer simulation that suggest otherwise [Mendes, P., Kell, D. B. & Westerhoff, H. V. (1992) Eur. J. Biochem. 204, 257-266] are artefacts either of variations in flux or of alterations in opposite directions of the activities of the relevant enzymes.

Suppression of kinetic cooperativity of hexokinase D (glucokinase) by competitive inhibitors. A slow transition model.

Hexokinase D ('glucokinase') displays positive cooperativity with mannose with the same h values (1.5-1.6) as with glucose but with higher K0.5 values (8 mM at pH 8.0 and 12 mM at pH 7.5). In contrast, fructose and 2-deoxyglucose exhibit Michaelian kinetics [Cárdenas, M. L., Rabajille, E., and Niemeyer, H. (1979) Arch. Biol. Med. Exp. 12, 571-580; Cárdenas, M. L., Rabajille, E., and Niemeyer, H. (1984) Biochem. J. 222, 363-370]. Mannose, fructose, 2-deoxyglucose and N-acetylglucosamine acted as competitive inhibitors of glucose phosphorylation and decreased the cooperativity with glucose. Their relative efficiency for reducing the value of h to 1.0 was: fructose greater than mannose greater than 2-deoxyglucose greater than N-acetylglucosamine. Galactose, which is not a substrate nor an inhibitor, was unable to change the cooperativity. The competitive inhibition of glucose phosphorylation by N-acetylglucosamine or mannose was cooperative at very low glucose concentrations (less than 0.5 K0.5), suggesting the interaction of the inhibitors with more than one enzyme form. These and previously reported results are discussed on the basis of a slow transition model, which assumes that hexokinase D exists mainly in one conformation state (E1) in the absence of ligands and that the binding of glucose (or mannose) induces a conformational transition to EII. This new conformation would have a higher affinity for the sugar substrates and a higher catalytic activity than EI. Cooperativity would emerge from shifts of the steady-state distribution between the two enzyme forms as the sugar concentration increase. The inhibitors would suppress cooperativity with glucose by inducing or trapping the EII conformation. In addition, the model postulates that the different kinetic behaviour of hexokinase D with the different sugar substrates, cooperative with glucose and mannose and Michaelian with 2-deoxyglucose and fructose, is the consequence of differences in the velocities of the conformational transitions induced by the sugar substrates.

Fructose is a good substrate for rat liver 'glucokinase' (hexokinase D).

Rat liver 'glucokinase' (hexokinase D) catalyses the phosphorylation of fructose with a maximal velocity about 2.5-fold higher than that for the phosphorylation of glucose. The saturation function is hyperbolic and the half-saturation concentration is about 300 mM. Fructose is a competitive inhibitor of the phosphorylation of glucose with a Ki of 107 mM. Fructose protects hexokinase D against inactivation by 5,5'-dithiobis-(2-nitrobenzoic acid), and the apparent dissociation constants are about 300 mM in the presence of different concentrations of the inhibitor. The co-operativity of the enzyme in the phosphorylation of glucose can be abolished by addition of fructose to the reaction medium. Fructose appears to be no better as a substrate for the other mammalian hexokinases than it is for hexokinase D. It is proposed that the name 'glucokinase' ought to be reserved for enzymes that are truly specific for glucose, such as those of micro-organisms and invertebrates, and that liver glucokinase must be called hexokinase D (or hexokinase IV) within the classification EC 2.7.1.1.