How translation termination factor eRF1 Euplotes does not recognise UGA stop codon

In universal-code eukaryotes, a single class-1 translation termination factor eRF1 decodes all three stop codons, UAA, UAG, and UGA. In some ciliates with variant genetic codes one or two stop codons are used to encode amino acid(s) and are not recognized by eRF1. In Stylonychia, UAG and UAA codons are reassigned as glutamine codons, and in Euplotes, UGA is reassigned as cysteine codon. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of eRF1. Because variant-code ciliates most likely evolved from universal code ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. To find out amino acid residues which confer UAR-only specificity to Euplotes aediculatus eRF1, eRFI chimeras were constructed by swapping eRF1 E. aediculatus N-terminal domain sequences with the matching ones from the human protein. In these chimeras the MC-domain was from human eRF1. Functional analysis of these chimeric eRFI highlighted the crucial role of the two regions (positions 38-50 and 123-145) in the N-terminal domain of E. aediculatus eRF1 that restrict E. aediculatus eRF1 specificity toward UAR codons. Possibly, restriction of eRF1 specificity to UAR codons might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UGA to sense codons.     

Vacuolar ethylene formation does not depend on membrane potential

Enzymatic synthesis of ethylene in the vacuole is assumed to require membrane integrity. The possibility that this reflects dependence on the vacuolar membrane potential was investigated. Vacuoles were released from protoplasts isolated from leaves of Vicia faba L. cv. Cyprus. The dependence of the ethylene-forming activity on tonoplast integrity was re-examined by immobilization of the vacuoles in a cross-linked polymeric matrix and subsequent permeabilization of the tonoplast with toluene, a pore-forming reagent. The relationship between the vacuolar ethylene formation and the membrane potential of free vacuoles was investigated by following the uptake of thiocyanate using permeabilized, depolarized and hyperpolarized vacuoles. Toluene and the proton conductor carbonyl cyanide m -chlorophenylhydrazone (CCCP) caused loss of ethylene-forming activity and depolarized the vacuolar membrane potential. However, depolarization of the membrane potential with choline chloride and hyperpolarization by ATP did not affect ethylene biosynthesis. These conflicting results lead to the conclusion that vacuolar ethylene biosynthesis is not dependent on the vacuolar membrane potential. The possibility that the inhibition of ethylene biosynthesis by toluene and CCCP may result from direct hydrophobic interactions between these compounds and hydrophobic components of the ethylene-forming enzyme is discussed.     

Irreversible platelet aggregation does not depend on lipoxygenase metabolites

Previous investigations in our laboratory demonstrated the existence of an intrinsic mechanism, termed membrane modulation, capable of restoring sensitivity to aspirin treated platelets, resulting in irreversible aggregation in response to arachidonic acid (AA). The mechanism underlying correction of aspirin induced inhibition of platelet function, however, was not clear. In the present study we have evaluated the role of lipoxygenase (LO) metabolites of AA in securing irreversible aggregation of drug induced cyclooxygenase (CO) deficient platelets. Platelets treated with aspirin or Ibuprofen did not convert radiolabeled AA to thromboxane, but generated significant quantities of hydroxy acids via the LO pathway. However, drug exposed platelets, when stirred with epinephrine first and then challenged with AA, aggregated irreversibly. Eicosatetraynoic acid (ETYA 1, U53119) inhibited AA conversion by the LO pathway, whereas 5,8,11,14-eicosatetraynoic acid (ETYA 2) inhibited AA conversion by both CO and LO enzymes. Yet, at the inhibitory concentration these fatty acids failed to prevent AA induced irreversible aggregation of CO deficient, alpha adrenergic receptor stimulated platelets. Results of four studies show that the generation of LO metabolites of AA are not essential for securing irreversible aggregation of platelets.     

Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode

The main protease (M^pro) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for trans-cleavage activity. However, the auto-processing mechanism of M^pro, i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” M^pro. Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature M^pro, are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and trans-cleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of M^pro appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of M^pro from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV M^pro.     

Phospholipid rearrangement of apoptotic membrane does not depend on nuclear activity

 The behaviour of plasma membrane was studied in UV-treated cells to investigate its involvement in apoptosis. It was studied in HL60 cells, in which DNA oligonucleosomic cleavage occurs, and in Molt-4 cells, which are characterised by a different fragmentation pattern. During the early stages of apoptosis, a membrane lipid rearrangement occurs, which involves phosphatidylserine translocation from the inner to the outer leaflet. This molecular alteration was investigated by annexin V-FITC binding, analysed by flow cytometry and confocal microscopy. It was correlated with transmission electron microscopy, subdiploid peak appearance and DNA fragmentation. Our data indicate that the plasma membrane represents an early apoptotic target, even if its alterations are not detectable by ultrastructural analysis, which indicates its good preservation until late apoptotic stages. In addition, the study of apoptotic cells with absent or inactivated endonuclease demonstrates the independence of this membrane mechanism from nuclear activity. Accepted: 16 April 1998     

Oleamide-mediated sleep induction does not depend on perturbation of membrane homeoviscosity

To verify whether the sleep-inducing properties of oleamide were related to its ability to perturb membrane homeoviscosity, affecting 5-HT(2A) receptors, we compared the effects of oleamide and oleic acid, the latter lacking both the sleep-inducing effect and the action on 5-HT(2A) receptors. In binding studies the two compounds did not directly interact with rat brain cortex 5-HT(2A) receptors, nor did they increase the affinity of a 5-HT(2A) agonist, either in vitro or ex vivo. They had similar fluidizing effects, in vitro at high concentrations (>/=10 microM), and ex vivo after a dose of 100 mg/kg, and they reduced locomotor activity with similar potency. There thus appears to be no causal relationship between the fluidizing effects of oleamide and its sleep-inducing properties.     

Chemoattractant-stimulated calcium influx in Dictyostelium discoideum does not depend on cGMP

Chemoattractant stimulation of Dictyostelium cells leads to the opening of calcium channels in the plasma membrane, causing extracellular calcium to flux into the cell. The genetically uncharacterised mutants stmF and KI8 show strongly altered chemoattractant-stimulated cGMP responses. The aberrant calcium influx in these strains has provided evidence that the chemoattractant-stimulated calcium influx is potentiated by cGMP. We have tested this hypothesis in genetically defined mutants by measuring the calcium influx in a strain that lacks intracellular cGMP due to the disruption of two guanylyl cyclases, and in a strain with increased cGMP levels caused by the disruption of two cGMP-degrading phosphodiesterases. The results reveal that the calcium influx stimulated by cAMP or folic acid is essentially identical in these strains. We conclude that cGMP is not involved in chemoattractant-stimulated calcium influx.     

Novel roles for classical factors at the interface between translation termination and initiation.

The pathway of bacterial ribosome recycling following translation termination has remained obscure. Here, we elucidate two essential steps and describe the roles played by the three translation factors EF-G, RRF, and IF3. Release factor RF3 is known to catalyze the dissociation of RF1 or RF2 from ribosomes after polypeptide release. We show that the next step is dissociation of 50S subunits from the 70S posttermination complex and that it is catalyzed by RRF and EF-G and requires GTP hydrolysis. Removal of deacylated tRNA from the resulting 30S:mRNA:tRNA posttermination complex is then necessary to permit rapid 30S subunit recycling. We show that this step requires initiation factor IF3, whose role was previously thought to be restricted to promoting specific 30S initiation complex formation from free 30S subunits.     

Condensation of DNA by basic protiens does not depend on protien composition

We have studied by electron microscopy the size and morphology of the complexes obtained with different DNAs (between 500 and 5243 base pairs long) and four different proteins: sea urchin histone H1; sea cucumber histone ?₀, chicken erythrocyte histone H5, and clupeine. Surprisingly, the type of protein used has only a marginal influence on the complexes formed. The molecular weight and topology of DNA do not show any influence. The size of the complexes depends strongly on the ratio of positive to negative charges and also on the ionic conditions. Our studies have been mainly carried out at a ratio of 0.4. Under these conditions the average thickness of rods and toroids observed varies between 165 Å at 1.5 mM salt to 290 Å at 100 mM salt, with minor variations around these values depending on the type of DNA and protein used. We conclude that the formation of DNA condensates is mainly determined by a balance of electrostatic and intermolecular forces, the influence of specific interactions is only marginal. This conclusion seems to apply not only to the complexes described here, but also to chromatin fibers and to DNA condensed by low molecular weight counterions and other compounds (polyamines, inorganic ions, ethanol, etc.). © 1994 John Wiley & Sons, Inc.     

The influenza virus-induced fusion of erythrocyte ghosts does not depend on osmotic forces

The role of osmotic forces and cell swelling in the influenza virus-induced fusion of unsealed or resealed ghosts of human erythrocytes was investigated under isotonic and hypotonic conditions using a recently developed fluorescence assay (Hoekstra, D., De Boer, T., Klappe, K., Wilschut, J. (1984) Biochemistry 23, 5675-5681). The method is based on the relief of fluorescence selfquenching of the fluorescent amphiphile octadecyl rhodamine B chloride (R18) incorporated into the ghost membrane as occurs when labeled membranes fuse with unlabeled membranes. No effect neither of the external osmotic pressure nor of cell swelling on virally mediated ghost fusion was established. Influenza virus fused unsealed ghosts as effectively as resealed ghosts. It is concluded that neither osmotic forces nor osmotic swelling of cells is necessary for virus-induced cell fusion. This is supported by microscopic observations of virus-induced fusion of intact erythrocytes in hypotonic and hypertonic media. A disruption of the spectrin-actin network did not cause an enhanced cell fusion at acidic pH of about 5 or any fusion at pH 7.4.     

Probability of transition into cell cycle does not depend on growth factor concentration

When quiescent cells in monolayer culture are stimulated to proliferate with growth factor, the entry into S-phase or mitosis appears to follow first-order kinetics, with a probability to enter the cell cycle that depends on growth factor concentration (Smith and Martin, 1973). Suboptimal growth factor concentrations also lead to a decreased fraction of the cell population that responds to the stimulation (Brooks et al., 1984). Using flow cytometry, we have re-investigated this dual effect of growth factor concentration on cultures of quiescent normal human skin fibroblasts, stimulated with submaximal concentrations of fetal calf serum, epidermal growth factor, and platelet-derived growth factor. The size of the responding population decreased with decreasing concentration of growth factor, but the time course of cell division within this responding population was identical for all growth factor concentrations. This is in conflict with previous concepts and indicates that the entry into the proliferative state is based on a decision mechanism that cannot be adequately described using transition probabilities determined by mitogen concentration.     

Accumulation of epidermal growth factor within cells does not depend on receptor recycling

Quiescent cells seemingly have a constant number of surface epidermal growth factor receptors. However, exposure of cells to agents which interfere with normal protein turnover suggests that these receptors are internalized and degraded with an apparent half-life of ～6 hours. We show that the time course of maximal accumulation of ligand-receptor complexes is not altered under conditions where degradation of the ligand is inhibited, indicating that no degradation occurs during its first hour of exposure to cells. We also conclusively demonstrate that epidermal growth factor receptors are not recycled during the initial uptake of the ligand, and that a component of pinocytosis of this growth factor is dependent on $\text{de}\text{novo}$ protein synthesis.     

Activation of restriction endonuclease EcoRII does not depend on the cleavage of stimulator DNA.

The restriction endonuclease EcoRII is unable to cleave DNA molecules when recognition sites are very far apart. The enzyme, however can be activated in the presence of DNA molecules with a high frequency of EcoRII sites or by oligonucleotides containing recognition sites: Addition of the activator molecules stimulates cleavage of the refractory substrate. We now show that endonucleolysis of the stimulator molecules is not a necessary prerequisite of enzyme activation. A total EcoRII digest of pBR322 DNA or oligonucleotide duplexes with simulated EcoRII ends (containing the 5' phosphate group), as well as oligonucleotide duplexes containing modified bases within the EcoRII site, making them resistant to cleavage, are all capable of enzyme activation. For activation EcoRII requires the interaction with at least two recognition sites. The two sites may be on the same DNA molecule, on different oligonucleotide duplexes, or on one DNA molecule and one oligonucleotide duplex. The efficiency of functional intramolecular cooperation decreases with increasing distance between the sites. Intermolecular site interaction is inversely related to the size of the stimulator oligonucleotide duplex. The data are in agreement with a model whereby EcoRII simultaneously interacts with two recognition sites in the active complex, but cleavage of the site serving as an allosteric activator is not necessary.     

Fatigue resistance of rat extraocular muscles does not depend on creatine kinase activity

Background  

Creatine kinase (CK) links phosphocreatine, an energy storage system, to cellular ATPases. CK activity serves as a temporal and spatial buffer for ATP content, particularly in fast-twitch skeletal muscles. The extraocular muscles are notoriously fast and active, suggesting the need for efficient ATP buffering. This study tested the hypotheses that (1) CK isoform expression and activity in rat extraocular muscles would be higher, and (2) the resistance of these muscles to fatigue would depend on CK activity.     

Effect of endotoxin on oleic acid lung injury does not depend on priming.

Recent studies have demonstrated significant synergistic physiological and biochemical effects between low-dose endotoxin (Etx) administration and oleic acid (OA)-induced canine lung injury. To evaluate whether this interaction depends on Etx priming of some key cell population, we compared the effects of giving low-dose Etx both after as well as before inducing lung injury with OA. In addition to hemodynamic and blood-gas measurements, positron emission tomographic imaging was used to measure edema accumulation and intrapulmonary blood flow distribution. Biochemical measurements of the stable metabolites of prostacyclin and thromboxane were obtained as well as measurements of isoprostanes and reactive sulfhydryls as evidence for possible concomitant oxidant production. We found that the physiological and biochemical effects of low-dose Etx developed 30-45 min after its administration, regardless of whether Etx was administered before or after OA. No increase in either isoprostane or reactive sulfhydryl production after Etx and/or OA was detected. These data suggest that the synergistic effect of low-dose Etx and OA-induced lung injury is not due to a priming effect of Etx.