A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction.

We have investigated the chemical basis for a previously observed 7.8 A conformational change in the hammerhead ribozyme that positions the substrate for in-line attack. We have found that the conformational change can only be observed at or above pH 8.5 (in the presence of Co(2+)) and requires the presence of an ionizable 2'-OH at the cleavage site, and note that this observed apparent pK(a) of 8.5 for the conformational change is within experimental error (+/-0.5) of the previously reported apparent kinetic pK(a) of 8.5 for the hammerhead ribozyme in the presence of Co(2+). We have solved two crystal structures of hammerhead ribozymes having 2'-OCH(3) or 2'-F substitutions at the cleavage site and have found that these will not undergo a conformational change equivalent to that observed for the hammerhead ribozyme having an unmodified attacking nucleophile under otherwise identical conditions. We have also characterized the kinetics of cleavage in the crystal. In addition to verifying that the particular sequence of RNA that we crystallized cleaves faster in the crystal than in solution, we also find that the extent of cleavage in the crystal is complete, unlike in solution where this and most other hammerhead ribozyme substrates are cleaved only to about 70 % completion. The initial cleavage rate in the crystal obeys the expected log-linear relation between cleavage-rate and pH with a slope of 0.7, as has been observed for other hammerhead ribozyme sequences in solution, indicating that in both the crystal and in solution the pH-dependent step is rate-limiting. However, the cleavage rate in the crystal is biphasic, with the most dramatic distinction between initial (slower) and final (faster) phases appearing at pH 6.0. The initial phase corresponds to the pH-dependent cleavage rate observed in solution, but the second, faster phase is roughly pH-independent and closely parallels the cleavage rate observed at pH 8 (0.4/minute). This result is particularly remarkable because it entails that the rapidly cleaving phase at pH 6 is comparable to the cleavage rate for the fastest cleaving hammerhead ribozymes at pH 6. Based upon these observations, we conclude that the pH-dependent conformational change is the rate-determining step under standard conditions for the hammerhead ribozyme self-cleavage reaction, and that an ionizable 2'-proton at cleavage site is required for this conformational change. We further hypothesize that deprotonation of the cleavage-site 2'-oxygen drives this conformational change.     

Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors.

The ability of recombinant adeno-associated virus (AAV) to transduce cells with a marker gene in vitro was found to be substantially increased by the presence of adenovirus. Transfection experiments with adenovirus genomic DNA suggest that this increase is not facilitated by adenovirus-mediated viral uptake but is instead dependent on adenovirus gene expression. Using various adenovirus mutants, we were able to map this function to early-region E4 open reading frame 6. Plasmid expression of open reading frame 6 protein in cells infected with recombinant AAV increased transduction between 100- and 1,000-fold. The increase in transduction was not dependent on the recombinant AAV gene cassette but instead appeared to involve an immediate early step of the AAV life cycle. Chemical and physical agents that have been shown to induce helper-free replication of wild-type AAV were also able to stimulate recombinant AAV transduction, suggesting that the phenomenon might affect AAV DNA replication. Further experiments showed that viral uncoating was not affected and that the rate-limiting step involved synthesis of a second strand on the single-stranded genomic AAV DNA. These data suggest that the adenovirus E4 region, as well as chemical and physical agents, can play an essential role in an immediate-early step of the AAV life cycle, specifically in second-strand synthesis, and have important implications for the use of AAV vectors in gene therapy protocols.     

Study on the biosynthesis of dolichol in yeast: recognition of the prenyl chain length in polyprenol reduction

We synthesized three water-soluble biotin-tagged compounds with different prenyl chain lengths, biotinylated farnesal (BF), biotinylated C(55)-polyprenal (BP55), and biotinylated C(80)-polyprenal (BP80), and examined their effects on in vitro dolichol synthesis from farnesyl diphosphate. BF and BP55 did not affect the dolichol synthesis, whereas BP80 inhibited the reduction pathway from polyprenol to dolichol, accompanied by a decrease in the entire polyprenol and dolichol synthesis. Comparison of BP80 with eighteen detergents, including Triton X-100, CHAPS, octylglucoside, deoxycholate, and Tween 80, revealed the specific effect of BP80 on the reduction pathway. On SDS-polyacrylamide gel electrophoresis, BP80 was detected in an associated form with a 50 kDa protein. These results suggest that the reduction of polyprenol to dolichol in the dolichol biosynthetic pathway proceeds with the recognition of the polyprenol chain length by a 50 kDa protein.     

Beta-hydroxydecanoyl thio ester dehydrase does not catalyze a rate-limiting step in Escherichia coli unsaturated fatty acid synthesis

The intracellular level of beta-hydroxydecanoyl thio ester dehydrase, the product of the fabA gene of Escherichia coli, was increased by isolation of a putative promotor mutant (termed fabAup) or by molecular cloning of the wild-type fabA gene into plasmid pBR322. The fabAup and plasmid-carrying strains overproduced dehydrase by about 15- and 10-fold, respectively. The phospholipids of all strains that overproduced the dehydrase contained significantly higher levels of saturated fatty acids than isogenic strains producing a normal level of dehydrase. No increased levels of unsaturated fatty acids were observed. This result indicates that, although the dehydrase is required for unsaturated fatty acid synthesis, the level of dehydrase activity in wild-type cells does not limit the rate of unsaturated fatty acid synthesis. The introduction of a plasmid carrying the structural gene for beta-ketoacyl acyl carrier protein synthase I into a fabAup strain overcame the effect of dehydrase overproduction on fatty acid composition.     

Enzymatic synthesis of polyprenol monophosphate mannose in insects

Summary The microsomal fraction of insects was found to contain an enzyme which transfers mannose from guanosine diphosphate mannose to an endogenous or exogenous insect lipid and to other acceptors such as dolichol monophosphate or ficaprenol monophosphate. This activity depended on the presence of Triton X-100 and magnesium ions, the optimal concentration of the latter being 10mM. The optimal temperature of the reaction was 25 °C and the maximal activity was obtained at pH 7.9. The mannolipid formed behaved as a monophosphodiester when chromatographed on DEAE-cellulose. Weak acid treatment of the product liberated mannose. Its behaviour both on thin layer and Sephadex G-150 chromatography would indicate the presence of a number of isoprenyl units similar to the dolichol and different from the ficaprenol derivative. Stability to phenol treatment indicated that the lipid fraction of the mannolipid is an±-saturated polyprenol phosphate similar to dolichol monophosphate.Abbreviations DoIMP dolichol monophosphate - FMP ficaprenol monophosphate - IGAL insect glycosyl acceptor lipid Dedicated to ProfessorLuis F. Leloir on the occasion of his 70th birthday.     

Methods for finding genes a major rate-limiting step in positional cloning

Identification of transcribed sequences from within genomic regions has been a major rate-limiting step in the pursuit of genes involved in many human genetic diseases. Early efforts focused primarily on screening of cDNA libraries, identification of evolutionary conserved sequences, and northern blot hybridization. In recent years, several innovative techniques for gene identification have been devised. These techniques expand the size of the genomic region capable of being scanned for genes, while also allowing detection of genes regardless of their expression patterns. This article reviews several new and older techniques and discusses the advantages and limitations of each.     

Regulation of glucose metabolism in the lung: Hexokinase-catalyzed phosphorylation,a rate-limiting step

A measurement of uptake and phosphorylation of 2-deoxyglucose in rat lung slices under appropriately designed conditions showed that glucose metabolism in lung at the physiological concentration of the sugar will be limited by the rate of its phosphorylation and not by its transport into the cells.     

Lateral diffusion as a rate-limiting step in ubiquinone-mediated mitochondrial electron transport

Data are presented which indicate that the diffusion-based collisions of ubiquinone with its redox partners in the mitochondrial inner membrane are a rate-limiting step for maximum (uncoupled) rates of succinate-linked electron transport. Data were obtained from experimental analysis of a comparison of the apparent activation energies of lateral diffusion rates, collision frequencies, and electron transport rates in native and protein-diluted (phospholipid-enriched) inner membranes. Diffusion coefficients for Complex III (ubiquinol:cytochrome c oxidoreductase) and ubiquinone redox components were determined as a function of temperature using fluorescence recovery after photobleaching, and collision frequencies of appropriate redox partners were subsequently calculated. The data reveal that 1) the apparent activation energies for both diffusion and electron transport were highest in the native inner membrane and decreased with decreasing protein density, 2) the apparent activation energy for the diffusion step of ubiquinone made up the most significant portion of the activation energy for the overall kinetic activity, i.e. electron transport steps plus the diffusion steps, 3) the apparent activation energies for both diffusion and electron transport decreased in a proportionate manner as the membrane protein density was decreased, and 4) Arrhenius plots of the ratio of experimental electron transport productive collisions (turnovers) to calculated theoretically predicted, diffusion-based collisions for ubiquinone with its redox partners had little or no temperature dependence, indicating that as temperature increases, increases in electron transport rate are accounted for by the increases in diffusion-based collisions. These data support the Random Collision Model of mitochondrial electron transport in which the rates of diffusion and appropriate concentrations of redox components limit the maximum rates of electron transport in the inner membrane.     

Neurofibromatosis type 2 appears to be a genetically homogeneous disease

Neurofibromatosis type 2 (NF2) is an autosomal dominant syndrome characterized by the development of vestibular schwannomas and other tumors of the nervous system, including cranial and spinal meningiomas, schwannomas, and ependymomas. The presence of bilateral vestibular schwannomas is sufficient for the diagnosis. Skin manifestations are less common than in neurofibromatosis type 1 (NF1; von Recklinghausen disease). The apparent clinical distinction between NF1 and NF2 has been confirmed at the level of the gene locus by linkage studies; the gene for NF1 maps to chromosome 17, whereas the gene for NF2 has been assigned (in a single family) to chromosome 22. To increase the precision of the genetic mapping of NF2 and to determine whether additional susceptibility loci exist, we have performed linkage analysis on 12 families with NF2 by using four polymorphic markers from chromosome 22 and a marker at the NF1 locus on chromosome 17. Our results confirm the assignment of the gene for NF2 to chromosome 22 and do not support the hypothesis of genetic heterogeneity. We believe that chromosome 22 markers can now be used for presymptomatic diagnosis in selected families. The NF2 gene is tightly linked to the D22S32 locus (maximum lod score 4.12; recombination fraction 0). A CA-repeat polymorphism at the CRYB2 locus was the most informative marker in our families (lod score 5.99), but because the observed recombination fraction between NF2 and CRYB2 was 10 cM, predictions using this marker will need to be interpreted with caution.     

On the rate-limiting step in W-hydroxylation of lauric acid

Incubation of lauric acid with rat liver microsomes and NADPH yielded a mixture of 11-D-, 11-L-, and 12-hydroxylauric acids. 11-L- and 11-D-hydroxylations of 11-²H₂-lauric acid were accompanied by marked isotope effects, indicating that in these reactions splitting of the CH bond is rate limiting. When 11- and 12-hydroxylations of lauric acid were carried out in D₂O, 12-hydroxylation but not 11-hydroxylation was inhibited, showing that different steps are rate limiting in the two reactions.     

Analysis of the rate-limiting step in a ligand-cell receptor interaction: the immunoglobulin E system

Theory predicts that the kinetics of simple interactions between a ligand and a receptor bound on the surface of a cell will be affected by the occupancy of receptors on the same cell. In a diffusion-limited reaction the effect will be on the rate of dissociation but not on the rate of association until the cell is virtually saturated with ligand. If the rate of reaction is not diffusion limited, then the opposite holds; i.e., the forward velocities will be proportional to the concentration of vacant receptors, but the reverse reactions will not be. We examined the kinetics of reaction between immunoglobulin E (IgE) and its receptor and clearly demonstrated that the reaction is not diffusion controlled. The substantial (congruent to 30-fold) increase in the forward rate constant observed for the reaction of IgE with solubilized receptors as opposed to cell-bound receptors is therefore not an artifact of calculation. Since the reverse rate constants show little difference, we postulate that the presence of other surface components (rather than conformational differences in the receptor) affects the reaction with the cells. As an aid to the analysis, the theory has been extended so that not only the rate constants but also the entire course of the reaction of ligand with cell receptors can be predicted for diffusion-limited vs. non-diffusion-limited interactions.     

Enzymatic synthesis of polyprenol monophosphate mannose in insects.

The microsomal fraction of insects was found to contain an enzyme which transfers mannose from guanosine diphosphate mannose to an endogenous or exogenous insect lipid and to other acceptors such as dolichol monophosphate or ficaprenol monophosphate. This activity depended on the presence of Triton X-100 and magnesium ions, the optimal concentration of the latter being 10mM. The optimal temperature of the reaction was 25 degrees C and the maximal activity was obtained at pH 7.9. The mannolipid formed behaved as a monophosphodiester when chromatographed on DEAE-cellulose. Weak acid treatment of the product liberated mannose. Its behaviour both on thin layer and Sephadex G-150 chromatography would indicate the presence of a number of isoprenyl units similar to the dolichol and different from the ficaprenol derivative. Stability to phenol treatment indicated that the lipid fraction of the mannolipid is an alpha-saturated polyprenol phosphate similar to dolichol monophosphate.     

Identification of a protein from escherichia coli whose synthesis appears to be triggered by the initiation of DNA replication

Using a DNA temperature sensitive initiation mutant to synchronize the replication and cell division cycle, we have compared proteins which are synthesized during a period of DNA arrest with those synthesized after return to permissive temperature. This work has led to the identification of a DNA-binding protein of 60–65,000 molecular weight (SDS-gel electrophoresis) whose synthesis appears to be triggered by the initiation event.     

The rate-limiting step in hydrosmotic response of frog urinary bladder

Summary The ADH-induced water fluxes and the associated appearance of intramembranous particle aggregates in the luminal membrane of frog urinary bladders have been correlated in a time course study. Plots of the onset and reversal of the oxytocin-induced hydrosmotic response were sigmoidal in shape, symmetrical and slowed by low temperature to the same degree. Parallel freezefracture studies showed that the mean size distribution of the aggregates was constant at different temperatures and at different times during hormonal stimulation and washout. No qualitatively different picture of aggregate formation was detected at low temperature: this suggests that the insertion and removal of individual aggregates into or from the apical plasma membrane is a rather rapid process, both at 20 and at 6.5° C. As in the case of water permeability, both aggregate appearance and disappearance were similarly slowed by lowering the temperature.A similar time-course study of the inhibition of the hydrosmotic response by acidification of the medium was also made. In this case, lowering the incubation temperature induced a clear dissociation between net water flow and the surface area occupied by the aggregates. For the first time, a low water permeability was found associated with a high aggregate surface area in the apical membrane, indicating that cellular acidification induces an impairment of aggregate function rather than a reduction of surface area.J.C. is a career investigator at the Institut National de la Santé et de la Recherche Médicale, INSERM V.48     

Vision: Visual space is not what it appears to be

The location of visual objects in the world around us is reconstructed in a complex way from the image falling on the retina. Recent studies have begun to reveal the different ways in which the brain dynamically re-maps retinal information across eye movements to compute object locations for perception and directing actions.