The Ypt1 GTPase is essential for the first two steps of the yeast secretory pathway

Small GTPases of the rab family are involved in the regulation of vesicular transport. The restricted distribution of each of these proteins in mammalian cells has led to the suggestion that different rab proteins act at different steps of transport (Pryer, N. K., L. J. Wuestehube, and R. Sheckman. 1992. Annu Rev. Biochem. 61:471-516; Zerial, M., and H. Stenmark. 1993. Curr. Opin. Cell Biol. 5:613-620). However, in this report we show that the Ypt1-GTPase, a member of the rab family, is essential for more than one step of the yeast secretory pathway. We determined the secretory defect conferred by a novel ypt1 mutation by comparing the processing of several transported glycoproteins in wild-type and mutant cells. The ypt1-A136D mutant has a change in an amino acid that is conserved among rab GTPases. This mutation leads to a rapid and tight secretory block upon a shift to the restrictive temperature, and allows for the identification of the specific steps in the secretory pathway that directly require Ypt1 protein (Ypt1p). The ypt1-A136D mutant exhibits tight blocks in two secretory steps, ER to cis-Golgi and cis- to medial-Golgi, but later steps are unaffected. Thus, it is unlikely that Ypt1p functions as the sole determinant of fusion specificity. Our results are more consistent with a role for Ypt1/rab proteins in determining the directionality or fidelity of protein sorting.     

Rate constants for the hexamer-dodecamer reaction of lobster hemocyanin

90° stopped-flow light scattering experiments have been used to determine the forward and reverse rate constants of the reversible hexamer-dodecamer reaction of lobster hemocyanin in glycine buffer at pH 9.6. Results were obtained at 20.5° and 25° at two different levels of calcium ion, and equilibrium constants derived from the data are in good agreement with those measured earlier with the ultracentrifuge.     

An RNA conformational change between the two chemical steps of group II self-splicing.

As for nuclear pre-mRNA introns, the splicing pathway of group II self-splicing introns proceeds by two successive transesterifications involving substrates with different chemical configurations. These two reactions have been proposed to be catalysed by two active sites, or alternatively by a single active site rearranging its components to accommodate the successive substrates. Here we show that the structural elements specific for the second splicing step are clustered in peripheral structures of domains II and VI. We show that these structures are not required for catalysis of the second chemical step but, instead, take part in a conformational change that occurs between the two catalytic steps. This rearrangement involves the formation of a tertiary contact between part of domain II and a GNRA tetraloop at the tip of domain VI. The fact that domain VI, which carries the branched structure, is involved in this structural rearrangement and the fact that modifications affecting the structures involved have almost no effect when splicing proceeds without branch formation, suggest that the conformational change results in the displacement of the first-step product out of the active site. These observations give further support to the existence of a single active site in group II introns.     

Resolving the first steps to multicellularity

Multicellular life has evolved many times, yet each origin requires free cells to integrate unselfishly into a higher-level individual. How can such transitions evolve? In a new paper, Herron and Michod investigate the recent origins of multicellularity in colonial algae. Their phylogenetic reconstructions provide a striking dissection of early steps, and altruistic traits are at the crux of it. Key evolutionary reversals are also revealed, where cellular selfishness might have thwarted multicellular integration.     

Enzyme kinetics in mammalian cells. II. Simultaneous determination of rate constants for the first three steps of galactose metabolism in red cells

The method for simultaneous measurement of the first two sequential enzymes of galactose metabolism of red cells has been extended to include the third step of the chain, epimerization of uridine diphosphogalactose to uridine diphosphoglucose. The method is rapid and precise and is applicable to a variety of genetic-biochemical problems.     

Rate constants for nitrification and denitrification in soils

Summary Rate constants for reactions in flowing solutions in soil can be calculated from extents of reactions as functions of depth, rates of flow, effective biomass of microbes and independent measurements of hydrodynamic dispersion. Constants have been calculated from data in the literature and are shown to be arbitrary unless all of these quantities have been evaluated. Good agreement of constants obtained in laboratory columns and in the field have been obtained for nitrification and denitrification in a few cases.Supported in part by a grant from The National Science Foundation-RANN.     

Rate constants and equilibrium constants for binding of actin to the 1:1 gelsolin-actin complex.

The rate constant and equilibrium constant of association of an actin monomer with 1:1 gelsolin-actin complex isolated from chicken were measured by using fluorescently labeled actin. According to fluorescence stopped-flow experiments, the rate constant of formation of the 1:2 gelsolin-actin complex from 1:1 gelsolin-actin complex and actin was found to be about 2 x 10(7) M-1 s-1 under conditions where gelsolin binds Ca2+. The rate of dissociation of one actin molecule from the 1:2 gelsolin-actin complex was determined by exchange of actin for fluorescently labeled actin. The rate constant of dissociation was about 0.02 s-1. Thus, the equilibrium constant for association of actin with 1:1 gelsolin-actin complex can be calculated to be in the range of 10(9) M-1. The rate of dissociation of actin from 1:2 gelsolin-actin complex was independent of the Ca2+ concentration. Ca2+ affects only the rate of association of actin with 1:1 gelsolin-actin complex.     

NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase.

The pentose-phosphate pathway provides reductive power and nucleotide precursors to the cell through oxidative and nonoxidative branches, respectively. 6-Phosphogluconolactonase is the second enzyme of the oxidative branch and catalyzes the hydrolysis of 6-phosphogluconolactones, the products of glucose 6-phosphate oxidation by glucose-6-phosphate dehydrogenase. The role of 6-phosphogluconolactonase was still questionable, because 6-phosphogluconolactones were believed to undergo rapid spontaneous hydrolysis. In this work, nuclear magnetic resonance spectroscopy was used to characterize the chemical scheme and kinetic features of the oxidative branch. We show that 6-phosphogluconolactones have in fact a nonnegligible lifetime and are highly electrophilic compounds. The delta form (1-5) of the lactone is the only product of glucose 6-phosphate oxidation. Subsequently, it leads to the gamma form (1-4) by intramolecular rearrangement. However, only the delta form undergoes spontaneous hydrolysis, the gamma form being a "dead end" of this branch. The delta form is the only substrate for 6-phosphogluconolactonase. Therefore, 6-phosphogluconolactonase activity accelerates hydrolysis of the delta form, thus preventing its conversion into the gamma form. Furthermore, 6-phosphogluconolactonase guards against the accumulation of delta-6-phosphogluconolactone, which may be toxic through its reaction with endogenous cellular nucleophiles. Finally, the difference between activity of human, Trypanosoma brucei, and Plasmodium falciparum 6-phosphogluconolactonases is reported and discussed.     

Determining rate constants for irreversible polymerization where the initial step and propagation steps have different rate constants: Consideration of polyadenylate polymerase

A new relationship is derived between the amount of monomer incorporated and the amount of initiated primer in an irreversible polymerization where the first step, initiation, has a rate constant differing from the elongation rate constants. It is valid for template directed and template independent polymerization. This relationship can be used in kinetic simulation. It suggests a simpler curve fitting technique to attain rate constants from a relatively small data set. Our analysis reveals some limitations of the model of irreversible polymerization; these limitations have not been obvious previously. For example, the initiation rate constant is not attainable from simple monomer incorporation data. Reliable rate constants can be obtained with minimal time course studies.     

Rate constants studies of the dye-sensitized photoinactivation of lysozyme

Summary The rate constants for the photodynamic inactivation of hen egg-white lysozyme at different temperatures were studied. Arrhenius plots of the methylene blue sensitized photo-inactivation of lysozyme gave an experimental activation energy of 7.5 kcal/mol. The rate constants for the photodynamic inactivation of lysozyme in the presence of riboflavin decreased almost linearly in the temperature range 4–38° C. The photosensitized oxidation of lysozyme at –20° C in freezing and non-freezing solvents was possible only in the presence of riboflavin. The effect of dye concentration on the quantum yield and rate constant for the photodynamic inactivation of lysozyme was examined. The quantum yields were lower when the concentrations of methylene blue used were low, and increased on increasing dye concentration, getting to a maximum and then declined at higher dye concentrations. It was found that in the case of riboflavin sensitized photo-inactivation of lysozyme both the rate constant and the quantum yield increased as the dye concentration increased. No maximum was observed over the range of dye concentrations studied. A new mechanism is postulated for the photodynamic action of lysozyme in the presence of riboflavin.     

Evidence for two growth steps in microtubule polymerization

For microtubule assembly, the data reported here support an initial nucleation phase followed by a growth or elongation phase. The nucleation phase was not detected kinetically. Evidence for this step was given by the existence of the critical concentration and the dependence of the number of microtubules on oligomer concentration.Kinetic evidence indicated the existence of two consecutive steps in the growth phase of microtubules. The fast process increased and the slow one decreased with the concentration of microtubule protein. Similar kinetics were found upon recombination of tubulin oligomer and dimer which had been resolved by agarose chromatography. The fast process increased with oligomer and decreased with dimer concentration while the slow one depended positively on dimer concentration. Microtubules were formed when the oligomeric fraction only was employed. In contrast, under identical conditions, no microtubule formation was detected turbidimetrically or by electron microscopy from dimer alone. When dimer caused elongation of seed tubules, there was only one growth step with a rate constant of the same order of magnitude as the slow process for the other experiments.     

Uncoupling the chemical steps of telomere resolution by ResT

ResT is the telomere resolvase of the spirochete Borrelia burgdorferi, the causative agent of Lyme disease. ResT is an essential cellular function that processes replication intermediates to produce linear replicons terminated by covalently closed hairpin telomeres. ResT generates these hairpin telomeres in a reaction with mechanistic similarities to those catalyzed by type IB topoisomerases and tyrosine recombinases. We report here, that like most of the tyrosine recombinases, ResT requires interprotomer communication, likely in an in-line synapse, to activate reaction chemistry. Unlike the tyrosine recombinases, however, we infer that the cleavage and strand transfer reactions on the two sides of the replicated telomere occur nearly simultaneously. Nonetheless, the chemical steps of the forward and reverse reactions performed by ResT can occur in a non-concerted fashion (i.e. events on the two sides of the replicated telomere can occur independently). We propose that uncoupling of reaction completion on the two sides of the substrate is facilitated by an early commitment to hairpin formation that is imposed by the precleavage action of the hairpin binding module of the ResT active site.     

Genetic knockout--the first steps and outlook for a neurophysiology of behavior

A review of modern data on genetic knockout strategy application to study the brain neurotransmitters and their role in the regulation of behavior. Advantages and shortcomings of genetic knockout of receptors and the enzymes of neurotransmitters metabolism models in comparison to other methods are discussed. Data on the effect of genetic knockout of various types of opioid, dopamine, serotonin and adrenoreceptors as well as enzymes in biosynthesis of catecholamines and serotonin on physiology and behavior is adduced. The data provide evidence that genetic knockout reproduces a principal effects of the lack of receptors and enzymes and allows to find new yet unknown properties. Mouse strains with genetic knockout represent unique models of hereditary neuropathology. At the same time the data presented clearly demonstrated that the lack of a single type of receptor or enzyme does not lead usually to disorganization of regulated by them physiological functions and behavior. The data witness to the complexity and multifactoriality of their regulations and evidenced the great compensatory potentials of organism.