The role of guanyl nucleotide binding proteins in the formation of inositol phosphates in adrenal glomerulosa cells

A non-hydrolysable GTP analogue enhanced the formation of [3H]inositol polyphosphates in permeabilized adrenal glomerulosa cells. Pertussis toxin, which ADP-ribosylated Ni, failed to influence angiotensin-induced formation of 3H-labelled inositol phosphates and the incorporation of [32F]phosphate into phosphatidylinositol and phosphatidic acid. These results show that Ni is present and a G-protein activates phospholipase C also in glomerulosa cells, however, it is not Ni which couples angiotensin receptors to the enzyme.     

Hairpin formation in the self-complementary dodecamer d-GGTACGCGTACC and derivatives containing GA and IA mispairs

The dodecamer d-GGTACGCGTACC and four derivatives with GA and IA mispairs in the 6,7 and 5,8 positions have been examined in dilute solution and 0.01-0.1 M sodium chloride. Concentration dependence of Tm, gel electrophoresis, and equilibrium centrifugation indicate that these self-complementary oligomers can form hairpins under the present conditions. Thermal transitions measured in the ultraviolet primarily represent melting of hairpin to coil [cf. Scheffler et al. (1968, 1970)]. The Tm values show little or no depression for 6,7 substitution but rather large depression for 5,8 replacement. We interpret the results to indicate that the 6,7 sequences have two-base loops and five base pair stems and that the 5,8 sequences have four-base loops and four base pair stems. A concurrent theoretical modeling study [Raghunathan et al. (1991) Biochemistry (following paper in this issue)] provides support for this interpretation.     

The role of phosphoric acid residues in the formation of antigenic determinants of the structural components of DNA

The inhibitory activity of thymidine, thymidine triphosphate and thymidyl oligonucleotides was studied in thymidine-antithymidine antibodies reaction. Thymidine was shown to have the greatest inhibitory effect, with thymidine triphosphate and thymidyl oligonucleotide inhibitory activity less expressed and reducing with the increase in oligonucleotide length. The effect of thymidine, thymidine triphosphate and thymidyl oligonucleotides on the interaction of antisera and SLE patients' sera with denatured DNA was studied. It was shown that thymidine triphosphate and particularly thymidyl oligonucleotides are characterized by greater inhibitory capacity, as compared to thymidine. It was found that only thymine dimers bound by phosphate groups can inhibit the interaction of UV-irradiated DNA with antiserum specific for UV-modified DNA. The data obtained suggest that the charge determined by phosphoric acid residues plays an essential role in the interaction of antibodies induced to charged structural DNA components.     

Cell-cell junction formation: The role of Rap1 and Rap1 guanine nucleotide exchange factors

Rap proteins are Ras-like small GTP-binding proteins that amongst others are involved in the control of cell-cell and cell-matrix adhesion. Several Rap guanine nucleotide exchange factors (RapGEFs) function to activate Rap. These multi-domain proteins, which include C3G, Epacs, PDZ-GEFs, RapGRPs and DOCK4, are regulated by various different stimuli and may function at different levels in junction formation. Downstream of Rap, a number of effector proteins have been implicated in junctional control, most notably the adaptor proteins AF6 and KRIT/CCM1. In this review, we will highlight the latest findings on the Rap signaling network in the control of epithelial and endothelial cell-cell junctions.     

The role of zooplankton grazing in the formation of `clear water phase' in a shallow charophyte-dominated lake

In Chara-dominated shallow eutrophic Lake Prossa (Estonia), the collapse of spring phytoplankton community occurred in late May after which both primary production (PP) and phytoplankton biomass (B&pinf;) stayed at a very low level. By mid-June the Secchi depth had increased up to 2.6 m indicating the achievement of the `clear water phase', which persisted thoughout the rest of the vegetation period. The biomass of `edible' phytoplankton formed on average 53% of the total phytoplankton biomass, and the share of herbivorous zooplankton was on average 61% of the total zooplankton biomass. In spring zooplankton removed daily 27% of the total B&pinf; and 29% of PP by grazing while in summer these values rarely exceeded 5%. Zooplankton grazing was responsible for the decrease of `edible' (<31 μm) phytoplankton after its spring peak as well as for maintaining its biomass at a very low level during the whole vegetation period. Depletion of mineral forms of nitrogen and phosphorus that occurred most probably because of the development of charophytes by the end of May supported the collapse of the whole phytoplankton community and kept the water clear throughout the summer and autumn.

     

The role of the bound nucleotide in the polymerization of actin.

Three mucleotides, ATP, ADP, and an unsplit-table analog of ATP (adenylyl imidodiphosphate (AMPPNP)), were bound to monomeric actin, and their effects on the rate and extent of the actin polymerization were studied. The kinetics of polymerization, assayed by the change in OD232, followed a simple exponential curve. The rates of polymerization were equal for bound ATP and AMPPNP; both of which were three to five times faster than the rate for ADP. The concentration of actin monomers in apparent equilibrium with the polymer, G(180 degrees longitude), was determined. Values of G(180 degrees longitude) in 100 mM KCl were found for different nucleotides to be: G-ATP(180 degrees longitude) = 0.7 mu-M, G-AMPPNP(180 degrees longitude) = 0.8 MU-M, and G-ADP(180 degrees longitude) = 3.4 mu-M. The equilibrium constant of the polymerization is given by K = [G(180 degrees longitude)]-minus 1 when no nucleotide is split. The polymerization of actin-ATP is more complex due to the splitting of the nucleotide and our data require that this polymerization involves more than one step. The kinetic parameters for the polymerization of actin-ATP can be explained by a simple scheme in which the nucleotide dephosphorylation occurs in a step following the polymerization step. The conclusions are: (1) the binding of ATP to actin monomer promotes polymerization slightly more than the binding of ADP, (2) actin bound ATP provides less than 4 kJ/mol of free energy to promote polymerization, and (3) the dephosphorylation of the nucleotide is not coupled to polymerization.     

The emerging role of deubiquitination in nucleotide excision repair

Nucleotide excision repair (NER) protects genome stability by eliminating DNA helix distorting lesions, such as those induced by UV radiation. The addition and removal of ubiquitin, namely, ubiquitination and deubiquitination, have recently been demonstrated as general mechanisms to regulate protein functions. Accumulating evidence shows that several NER factors are subjected to extensive regulation by ubiquitination and deubiquitination. Thus, the balance between E3 ligases and deubiquitinating enzyme activities can dynamically alter the ubiquitin landscape at DNA damage sites, thereby regulating NER efficiency. Current knowledge about XPC ubiquitination by different ubiquitin E3 ligases highlights the importance of ubiquitin linkage types in regulating XPC binding and release from damaged DNA. Here, we discuss the emerging roles of deubiquitinating enzymes and their ubiquitin linkage specificities in NER.     

The role of nucleotide pyrophosphatase in Mullerian duct regression

Mullerian inhibiting substance (MIS), a glycoprotein from the fetal testis causing regression of the embryonic Mullerian duct, can be inhibited in vitro in the presence of Mn²⁺ by a wide range of nucleotides including GTP, NAD, ATP, AMP, and several nonhydrolyzable synthetic ATP analogs. Extracellular nucleotide pyrophosphatase (NPPase), an enzyme able to hydrolyze the wide variety of the nucleotides and analogs found to inhibit Mullerian duct regression, was studied by histochemical staining (H. Sierakowska and D. Shugar (1963) to determine if NPPase localized in or around the Mullerian duct during regression. Frozen sections of urogenital ridges from to rat fetuses (n = 77) were incubated with a-naphthyl thymidine-5′-phosphate (naphthyl TMP) and Fast Red TR. Nucleotide pyrophosphatase hydrolyzes naphthyl TMP, releasing naphthol, which then reacts with Fast Red to produce color at the enzyme site. Nucleotide hydrolysis was detected around regressing male (n = 16) Mullerian duct cells at days of gestation, but no hydrolysis was detected around female (n = 17) Mullerian duct cells at any stage. Controls (n = 24) incubated without substrate did not stain. Addition of exogenous ATP (n = 20) to the histochemical incubation medium inhibited nucleotide hydrolysis on male Mullerian ducts, suggesting that this staining is specific for pyrophosphatase activity. Results in vivo were confirmed in vitro by incubating day female rat urogenital ridges with MIS for 72 hr prior to histochemical staining. The addition of testosterone to MIS was obligatory to detect staining in vitro (n = 10). The localized NPPase activity around the regressing Mullerian duct suggests that NPPase may appear as a consequence of duct regression and may act to control the degree of membrane phosphorylation by degrading excess trinucleotides.     

The role of structural genomic variants in population differentiation and ecotype formation in Timema cristinae walking sticks

Theory predicts that structural genomic variants such as inversions can promote adaptive diversification and speciation. Despite increasing empirical evidence that adaptive divergence can be triggered by one or a few large inversions, the degree to which widespread genomic regions under divergent selection are associated with structural variants remains unclear. Here we test for an association between structural variants and genomic regions that underlie parallel host‐plant‐associated ecotype formation in Timema cristinae stick insects. Using mate‐pair resequencing of 20 new whole genomes we find that moderately sized structural variants such as inversions, deletions and duplications are widespread across the genome, being retained as standing variation within and among populations. Using 160 previously published, standard‐orientation whole genome sequences we find little to no evidence that the DNA sequences within inversions exhibit accentuated differentiation between ecotypes. In contrast, a formerly described large region of reduced recombination that harbours genes controlling colour‐pattern exhibits evidence for accentuated differentiation between ecotypes, which is consistent with differences in the frequency of colour‐pattern morphs between host‐associated ecotypes. Our results suggest that some types of structural variants (e.g., large inversions) are more likely to underlie adaptive divergence than others, and that structural variants are not required for subtle yet genome‐wide genetic differentiation with gene flow.     

The role of cyclic nucleotide phosphodiesterases in the regulation of adipocyte lipolysis

This study assessed the effects of selective inhibitors of 3',5'-cyclic nucleotide phosphodiesterases (PDEs) on adipocyte lipolysis. IC224, a selective inhibitor of type 1 phosphodiesterase (PDE1), suppressed lipolysis in murine 3T3-L1 adipocytes (69.6 +/- 5.4% of vehicle control) but had no effect in human adipocytes. IC933, a selective inhibitor of PDE2, had no effect on lipolysis in either cultured murine 3T3-L1 adipocytes or human adipocytes. Inhibition of PDE3 with cilostamide moderately stimulated lipolysis in murine 3T3-L1 and rat adipocytes (397 +/- 25% and 235 +/- 26% of control, respectively) and markedly stimulated lipolysis in human adipocytes (932 +/- 7.6% of control). Inhibition of PDE4 with rolipram moderately stimulated lipolysis in murine 3T3-L1 adipocytes (291 +/- 13% of control) and weakly stimulated lipolysis in rat adipocytes (149 +/- 7.0% of control) but had no effect on lipolysis in human adipocytes. Cultured adipocytes also responded differently to a combination of PDE3 and PDE4 inhibitors. Simultaneous exposure to cilostamide and rolipram had a synergistic effect on lipolysis in murine 3T3-L1 and rat adipocytes but not in human adipocytes. Hence, the relative importance of PDE3 and PDE4 in regulating lipolysis differed in cultured murine, rat, and human adipocytes.     

The role of protein phosphorylation in the regulation of cyclic nucleotide phosphodiesterases

The cyclic nucleotide phosphodiesterases constitute a complex superfamily of enzymes responsible for catalyzing the hydrolysis of cyclic nucleotides. Regulation of cyclic nucleotide phosphodiesterases is one of the two major mechanisms by which intracellular cyclic nucleotide levels are controlled. In many cases the fluctuations in cyclic nucleotide cAMP-specific, calmodulin-stimulated and cGMP-binding phosphodiesterases have been demonstrated to be substrates for protein kinases. Here we review the evidence that hormonally responsive phosphorylation acts to regulate cyclic nucleotide phosphodiesterases. In particular, the cGMP-inhibited phosphodiesterases, which can be phosphorylated by at least two different protein kinases, are activated as a result of phosphorylation. In contrast, phosphorylation of the calmodulin-stimulated phosphodiesterases, which coincides with, a decreased sensitivity to activation by calmodulin, results in decreased phosphodiesterase activity.     

Substrate specificity of T4 RNA-ligase. The role of phosphate nucleotide residues in the formation of a covalent AMP-RNA-ligase complex]

The inhibiting effect of adenosine, AMP, ADP, ATP, gamma-thio ATP (I), beta,gamma-imine ATP (II), beta,gamma-methylene ATP (III), P1,P3-di(adenosine-5') triphosphate (IV), P1,P4-di(adenosine-5') tetraphosphate (V) and adenosine 5'-tetraphosphate (VI) on the first step of the T4 RNA ligase reaction was studied. All the compounds tested, with the exception of adenosine, appeared to be competitive inhibitors of the first step of the enzymatic reaction. The inhibition constants (Ki) for the ATP analogs were determined. The data obtained suggest that the efficiency of inhibition depends on the number of phosphate groups and on the structure of ATP analogs. All the compounds under study (I-VI), except for AMP and ADP, form covalent AMP-RNA ligase complexes.     

The role of the conserved switch II glutamate in guanine nucleotide exchange factor-mediated nucleotide exchange of GTP-binding proteins

Guanine nucleotide exchange factors (GEFs) regulate the activity of small G proteins by catalysing the intrinsically slow exchange of GDP for GTP. The mechanism involves the formation of trimeric G protein-nucleotide-GEF complexes, followed by the release of nucleotide to form stable binary G protein-GEF complexes. A number of structural studies of G protein-GEF complexes have shown large structural changes induced in the nucleotide binding site. Together with a recent structure of a trimeric complex, these studies have suggested not only some common principles but also large differences in detail in the GEF-mediated exchange reaction. Several structures suggested that a glutamic acid residue in switch II, which is part of the DxxGQE motif and highly conserved in Ras-like G proteins, might have a decisive mechanistic role in GEF-mediated nucleotide exchange reactions. Here we show that mutation of the switch II glutamate to Ala severely impairs GEF-catalysed nucleotide exchange in most, but not all, Ras family G proteins, explaining its high sequence conservation. The residue determines the initial approach of GEF to the nucleotide-loaded G protein and does not appreciably affect the formation of a binary nucleotide-free complex. Its major effect thus appears to be the removal of the P-loop lysine from its interaction with the nucleotide.     

The role of nucleotide sugar transporters in development of eukaryotes

The Golgi apparatus membrane of all eukaryotes has nucleotide sugar transporters which play essential roles in the glycosylation of glycoproteins, proteoglycans and glycolipids. Mutations of these transporters have broad developmental phenotypes across many species including diseases in humans and cattle.     

Interaction of nucleic acid bases with water molecules and formation of mismatched nucleotide pairs

The possibility of the inclusion of water molecules in the formation of mismatched nucleotide pairs was considered in relation to the mechanisms of point errors in template directed biosynthesis. Calculations of the intermolecular interaction energy for systems containing two bases and one water molecule were carried out by the method of atom-atom potential functions. There exist energy minima for each base pair, corresponding to a single N--H...O or N--H...N H-bond between the bases and H-bonding of the water molecule with both bases. The relative positions of glycosyl bonds in some of these minima are closer to those for Watson--Crick pairs, than the positions of minima for these pairs without water. For other minima, the H-bond formation between the water molecule and the two bases additionally stabilizes the relative base position in wobble-pairs with two H-bonds between the bases. The base and water positions in energy minima are compared with the positions in some pairs proposed on the basis of NMR and X-ray data for double helical oligonucleotides.