Determination of the angle between the acceptor and anticodon stems of a truncated mitochondrial tRNA

Significant departures from the canonical (cloverleaf) secondary structure of transfer (t)RNAs can be found among the mitochondrial (m)tRNAs of higher metazoans; these mtRNAs thus pose a challenge to the concept of an invariant, L-shaped tertiary conformation for all tRNAs. For bovine mtRNASer(AGY), which lacks the entire "dihydrouridine" (dhU) arm, two distinct tertiary models have been proposed: the first model preserves the L-shaped conformation at the expense of overall size; the second model preserves the absolute distance between the 3' terminus and the anticodon loop, while allowing the acceptor-anticodon interstem angle to vary. We have tested the central predictions of these two models by performing a series of transient electric birefringence measurements on bovine mtRNASer(AGY) constructs in which the aminoacyl-acceptor and anticodon stems were each extended by approximately 70 bp. This mtRNA species is particularly amenable to analysis, since the native bovine (heart) mtRNA is completely unmodified outside of the anticodon loop. For magnesium ion concentrations above 1 mM, the interstem angle for the extended mtRNA, 120(+/-5) degrees, is approximately 50% larger than the corresponding angle for yeast tRNAPhe (70-80 degrees) under the same ionic conditions. Furthermore, the interstem angles of the two tRNAs exhibit strikingly different responses to the addition of magnesium ions: the interstem angle for yeast tRNAPhe is reduced by nearly 50 % upon addition of 2 mM magnesium ions, whereas the angle for mtRNASer(AGY) increases by about 10%. Our data thus support a central prediction of the second model; namely, that truncated mtRNAs will possess more open interstem angles. In addition, we demonstrate that birefringence amplitude data can be used to provide model-independent estimates for the interstem angles.     

Unfolding of the tRNA(Phe) structure by complementary oligonucleotides

The effect of ribonuclease and cytochrome c on electrophoretic mobility of liposomes composed of phosphatidylcholine and diphosphatidylglycerol has been studied. zeta-Potential of lipid vesicles was found to decrease in the presence of proteins. Parameters of proteins binding to phospholipids were evaluated from the changes of surface charge density of model membranes. The constants of protein association with phospholipids were calculated to be about 4 x 10(4) M-1 for ribonuclease and about 5.4 x 10(4) M-1 for cytochrome c.     

The anticodon and discriminator base are important for aminoacylation of Escherichia coli tRNA(Asn)

A gel shift assay that distinguishes the aminoacylated form from the deacylated form of tRNAs was used to study the requirements for aminoacylation of Escherichia coli tRNA(Asn) in vivo. tRNA(Asn) derivatives containing single base changes in their anticodons or discriminator bases were constructed, and the extent of in vivo aminoacylation was determined directly. Substitution of U35 with C35 or U36 with C36 abolished aminoacylation of the tRNA. Substitution of G34 with C34 converted tRNA(Asn) into a lysine acceptor. Thus, each of the anticodon nucleotides are important for aminoacylation of tRNA(Asn). Substitution of discriminator base G73 with A73 affected the extent of aminoacylation in vivo indicating that the discriminator base also contributes to aminoacylation of tRNA(Asn).     

The chemical synthesis of E. coli tRNA(Lys) anticodon loop fragment and its analogues

E. coli tRNA(Lys) anticodon loop fragment (Umnm5s2UUUt6A) 1 and its analogues 2-6 were synthesized by the classical phosphotriester approach in solution. The preparation of suitably protected derivatives of N6-threonylcarbamoyladenosine 18 is also described.     

A tRNA identity switch mediated by the binding interaction between a tRNA anticodon and the accessory domain of a class II aminoacyl-tRNA synthetase

Identity elements in tRNAs and the intracellular balance of tRNAs allow accurate selection of tRNAs by aminoacyl-tRNA synthetases. The histidyl-tRNA from Escherichia coli is distinguished by a unique G-1.C73 base pair that upon exchange with other nucleotides leads to a marked decrease in the rate of aminoacylation in vitro. G-1.C73 is also a major identity element for histidine acceptance, such that the substitution of C73 brings about mischarging by glycyl-, glutaminyl-, and leucyl-tRNA synthetases. These identity conversions mediated by the G-1.C73 base pair were exploited to isolate secondary site revertants in the histidyl-tRNA synthetase from E. coli which restore histidine identity to a histidyl-tRNA suppressor carrying U73. The revertant substitutions confer a 3-4 fold reduction in the Michaelis constant for tRNAs carrying the amber-suppressing anticodon and map to the C-terminal domain of HisRS and its interface with the catalytic core. These findings demonstrate that the histidine tRNA anticodon plays a significant role in tRNA selection in vivo and that the C-terminal domain of HisRS is in large part responsible for recognizing this trinucleotide. The kinetic parameters determined also show a small degree of anticooperativity (delta delta G = -1.24 kcal/mol) between recognition of the discriminator base and the anticodon, suggesting that the two helical domains of the tRNA are not recognized independently. We propose that these effects substantially account for the ability of small changes in tRNA binding far removed from the site of a major determinant to bring about a complete conversion of tRNA identity.     

5-formylcytidine (f5C) found at the wobble position of the anticodon of squid mitochondrial tRNA(Met)CAU

In squid (Loligo breekeri) mitochondria, AUA codons are translated as methionine instead of the universal isoleucine. Here, we present the nucleotide sequence of squid mitochondrial tRNA(Met)CAU. This tRNA(Met)CAU has 5-formylcytidine (f5C) at the wobble position of the anticodon, though it is partially modified. This result indicates the common feature with bovine and nematoda mitochondrial systems in that f5C at the wobble position of the anticodon is very likely involved in translation of AUA codons as methionine in squid mitochondria.     

The aminoacceptor stem of the yeast tRNA(Lys) contains determinants of mitochondrial import selectivity

The effect of quinine, a cinchona alkaloid, was studied on gastrointestinal transit in mice. Intraperitoneal (i.p.) administration of quinine inhibited the intestinal propulsion of a charcoal suspension at a dose of 100 mg/kg, comparing favorably with 5 mg/kg morphine. In an attempt to probe into the mechanism underlying this inhibition, a possible modulation by minoxidil (1 mg/kg, p.o.) and glibenclamide (1 mg/kg, p.o.), the drugs that, respectively, open and close ATP-sensitive K+ channels was tested on gastrointestinal transit in animals treated or not with quinine or morphine. While minoxidil produced no significant change of normal transit, glibenclamide significantly increased it. However, both drugs blocked the quinine-induced reduction in gastrointestinal transit. In contrast, the inhibitory effect of morphine on gastrointestinal transit was not modified by either drug. The effects of quinine as well as of morphine on gastrointestinal transit were significantly antagonized by naloxone (2 mg/kg, s.c.), a mu-opioid receptor antagonist but not by yohimbine (1 mg/kg, i.p.), an alpha2-adrenoceptor antagonist. Furthermore, quinine at a lower dose (25 mg/kg) that showed no per se effect on gastrointestinal transit, significantly potentiated the response to 2.5 mg/kg morphine. Although the role of ATP-sensitive K+ channels in the action of quinine and morphine was not clarified by the present results, a possible involvement of endogenous opioid(s) in the quinine-induced inhibition of gastrointestinal transit can be suggested.     

The relationship between smoking and triglyceride-rich lipoproteins is modulated by genetic variation in the glycoprotein IIIa gene

In the last year, several studies have reported conflicting results concerning an association between the PI(A2) allele of the PI(A1/A2) polymorphism of platelet glycoprotein IIIa and the risk of myocardial infarction. In the present study, we analyzed the hypothesis of whether glycoprotein IIIa genotypes have any association with lipids and lipoproteins as classical cardiovascular risk factors. Smoking, associated with changes in triglyceride-rich lipoprotein (TRL) concentrations and with both hypercoagulability and reduced fibrinolysis, was also analyzed as an environmental factor. Blood samples were obtained from 170 subjects (83 men and 87 women; mean age, 57 years; SD 15) recruited by random sampling from the census of Girona, Spain. Subjects were classified as current smokers (n=41) and nonsmokers or exsmokers (n=129). Whereas no differences were found in lipid and lipoprotein concentrations between smokers and nonsmokers in subjects with the PI(A1/A1) genotype, smokers with the PI(A1/A2) or PI(A2/A2) genotypes showed significantly higher triglyceride and very-low-density lipoprotein (VLDL) triglyceride concentrations than nonsmokers or exsmokers with the same genotypes. Similarly, the VLDL triglyceride/HDL cholesterol ratio was significantly different in subjects with the PI(A1/A2) or PI(A2/A2) genotypes stratified according to smoking status. Further analysis revealed a significant interaction between smoking and genotype when those homozygous for the allele PI(A1) were compared with one or two PI(A2) alleles for the three lipidic parameters. The observed effects appear to show links between smoking, triglyceride metabolism, and a glycoprotein involved in platelet aggregation. It is likely that the pI(A) polymorphism is in linkage disequilibrium with other functional mutations that might influence triglyceride metabolism under some environmental factors such as smoking. This finding may provide a new perspective in the complex relationship between glycoprotein IIIa gene, environment, and their interactions.     

NMR evidence for helix geometry modifications by a G-U wobble base pair in the acceptor arm of E. coli tRNA(Ala)

The length, width and position of the nucleus of Babesia bovis and Babesia bigemina kinetes from the haemolymph of Boophilus microplus engorged female ticks were recorded. Additionally, the shape of Babesia bovis kinetes were registered as curved, semi-curved or straight. To this aim Boophilus microplus tick larvae from a colony free of Babesia were fed on splenectomised calves artificially infected with either Babesia bovis or Babesia bigemina pathogenic strains. Six engorged female ticks showing an infection of at least ten mature kinetes of Babesia bovis in a sample of haemolymph 5 days after detachment were also monitored 7, 9 and 10 days after collection. The same procedure was followed with six engorged female ticks infected with Babesia bigemina. One hundred and twenty kinetes of each species of Babesia were evaluated. The mean length +/- standard deviation and ranges for Babesia bovis kinetes were 14.30 +/- 0.922 microns and 11.9-16.3 microns, while the corresponding measures for the kinetes of Babesia bigemina were 11.27 +/- 0.900 microns and 9.0-13.1 microns (P < 0.001, t-test). The width was 3.33 +/- 0.315 microns, 2.6-4.0 microns for Babesia bovis and 2.24 +/- 0.287 microns, 1.5-2.8 microns for Babesia bigemina kinetes (P < 0.001). The most common position of the nucleus was central for both species of Babesia. A total of 58% of Babesia bovis kinetes showed the typical curved tail. No effect of time post-collection and individual host ticks in the kinete of Babesia bigemina was found while an unexpected influence of individual host tick in the width of Babesia bovis kinetes was detected (P < 0.01, analysis of variance). The overlap in the sizes of kinetes from both species of Babesia makes it difficult to apply the results to ticks of unknown babesial infection status. This finding is further complicated by the intra-specific size variations of Babesia kinetes from different geographical origins.     

Effects of osmomolarity, calcium and magnesium ions on the structuredness of cytoplasmic matrix (SCM)

A study of forty patients with active lichen planus and a negative family history for diabetes showed that 42% had unequivocally abnormal oral glucose tolerance. The pattern of insulin response to glucose is similar to that seen in typical mild maturity-onset diabetes. There was no association between the presence of glucose intolerance and the duration or type of lesions. None of the patients with glucose intolerance had demonstrable islet-cell antibodies.     

Binding of a fragment of yeast phenylalanyl tRNA containing an anticodon loop with 30S and 70S ribosomes from Escherichia coli. The role of guanosine-42 in this interaction

Poly(U)-dependent binding of isolated yeast tRNA(Phe) anticodon hairpin (15-nucleotide-long, corresponding to nucleotides 28-42 within the tRNA) and several its derivatives to the P site of Escherichia coli 30S and 70S ribosomes was studied quantitatively. The affinity for the hairpin binding to 70S ribosomes was shown to be only 30-fold weaker than that for the binding of total tRNA(Phe). Within the anticodon hairpin, removal of the 3'-terminal nucleotide corresponding to guanosine-42 in tRNA(Phe) decreases the association constant for the anticodon arm-ribosome interaction 15-fold. Replacement of this guanosine with other nucleosides does not affect the affinity, regardless of involvement in the hairpin secondary structure. These data indicate that G-42 affects the anticodon arm affinity most likely by forming a direct contact with the ribosome. One can assume that this nucleotide within intact tRNA also forms a contact with the P site. Since the 3'-terminal ribose modifications (oxidation, oxidation and reduction) as well as the presence or absence of the 3'-terminal phosphate does not affect the affinity of the anticodon arm fragment, the latter is obviously involved in the interaction through 3'-terminal nucleotide base groups which does not take part in base pairing.     

Stimulation of Stat5 by granulocyte colony-stimulating factor (G-CSF) is modulated by two distinct cytoplasmic regions of the G-CSF receptor

In a manner similar to many other cytokines, treatment of cells with granulocyte CSF (G-CSF) has been shown to induce the tyrosine phosphorylation of the STAT proteins. Activation of Stat1 and Stat5 by G-CSF requires the membrane-proximal cytoplasmic domain of the receptor, including box1 and box2, while G-CSF-stimulated tyrosine phosphorylation of Stat3 also requires a region distal to box 2. In this study, we show that although the membrane-proximal 55 amino acids of the G-CSF receptor are sufficient for activation of Stat5, the maximal rate of Stat5 activation requires an additional 30 amino acids of the cytoplasmic domain. In contrast, the distal carboxyl-terminal region of the receptor appears to down-regulate Stat5 activation in that deletion of this carboxyl terminus results in increased amplitude and prolonged duration of Stat5 activation by G-CSF. Significantly, expression of a truncated dominant-negative Stat5 protein in hemopoietic cells not only inhibits G-CSF-dependent cell proliferation, but also suppresses cell survival upon G-CSF withdrawal. We further show that a potential protein tyrosine phosphatase may play a critical role in the down-regulation of G-CSF-stimulated Stat5 activation. These results demonstrate that two distinct cytoplasmic regions of the G-CSF receptor are involved in the regulation of the intensity and duration of Stat5 activation, and that Stat5 may be an important player in G-CSF-mediated cell proliferation and survival.     

Modified nucleosides in the first positions of the anticodons of tRNA(Leu)4 and tRNA(Leu)5 from Escherichia coli

Minor leucine tRNA species, tRNA(Leu)4 and tRNA(Leu)5, from Escherichia coli B have been reported to recognize leucine codons UUA and UUG [Goldman, E., Holmes, W. M., and Hatfield, G. W. (1979) J. Mol. Biol. 129, 567-585]. In the present study, these two tRNA(Leu) species were purified from E. coli A19, and the nucleotide sequences were determined by a post-labeling method. tRNA(Leu)5 was found to correspond to the tRNA gene reported as su degrees6 tRNA [Yoshimura, M., Inokuchi, H., and Ozeki, H. (1984) J. Mol. Biol. 177, 627-644]. The first letter of the anticodon was identified to be 2'-O-methylcytidine (Cm). tRNA(Leu)4 was identified as the minor leucine tRNA that has been sequenced previously (tRNA(Leu)UUR) [Yamaizumi, Z., Kuchino, Y., Harada, F., Nishimura, S., and McCloskey, J. A. (1980) J. Biol. Chem. 255, 2220-2225]. There was an unidentified modified nucleoside (N*) in the first position of the anticodon of tRNA(Leu)4. Nucleoside N* was isolated to homogeneity (1 A260 unit). By 1H NMR spectroscopy, nucleoside N was found to be a 2'-O-methyluridine derivative with a substituent having a -CH2NH2+CH2COO- moiety in position 5 of the uracil ring. On the basis of these NMR analyses together with mass spectrometry, the chemical structure of nucleoside N* was determined as 5-carboxymethylaminomethyl-2'-O-methyluridine (cmnm5Um). Nucleoside N* was thus found to be a novel type of naturally occurring modified uridine. Because of the conformational rigidity of Cm and cmnm5Um in the first position of the anticodon, these tRNA(Leu) species recognize the leucine codons UUA++ and UUG correctly, but never recognize the phenylalanine codons UUU and UUC.     

NMR studies of the effects of the 5'-phosphate group on conformational properties of 5-methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4

5-Methylaminomethyluridine (mnm5U) exists in the first position of the anticodon (position 34) of Escherichia coli tRNA4Arg for codons AGA/AGG. In the present study, the temperature dependence of the ribose-puckering equilibrium of pmnm5U was analyzed by proton NMR spectroscopy. Thus, the enthalpy difference (delta H) between the C2'-endo and C3'-endo forms was obtained at 0.65 kcal.mol-1. By comparison of the delta H values of pU and pmnm5U, the 5-substitution was found to increase the relative stability of the C3'-endo form over the C2'-endo form significantly (by 0.56 kcal.mol-1). Furthermore, this conformational "rigidity" was concluded to depend on the 5'-phosphate group, because nucleoside U exhibits only a negligible change in the ribose-puckering equilibrium upon the 5-methylaminomethyl substitution. Further NMR analyses and molecular dynamics calculations revealed that interactions between the 5-methylaminomethyl and 5'-phosphate groups of pmnm5U restrict the conformation about the glycosidic bond to a low anti form, enhancing steric repulsion between the 2-carbonyl and 2'-hydroxyl groups in the C2'-endo form. This intrinsic conformational rigidity of the mnm5U residue in position 34 may contribute to the correct codon recognition.     

Pleiotropic phenotype of acetyl-CoA-carboxylase-defective yeast cells--viability of a BPL1-amber mutation depending on its readthrough by normal tRNA(Gln)(CAG)

The Saccharomyces cerevisiae gene BPL1 encodes the enzyme biotin:protein ligase (BPL), which is required for acetyl-CoA carboxylase (ACC) holoenzyme formation. Disruption of one of the two BPL1 alleles present in diploid cells results, upon sporulation, in a 2+:2(0) segregation of cell viability, with none of the two viable spores being BPL1 negative. In contrast to BPL1 deletants, BPL1 base-substitution mutants are potentially viable and may be isolated as long-chain-fatty-acid-requiring auxotrophs. In addition to ACC pyruvate carboxylase and an additional biotin-containing protein of unknown function fail to be biotinylated in BPL1-defective yeast mutants. In this study, one of these mutants, bpl1-C25/17, is shown to contain an amber stop codon at position 151 of the 689-amino-acid BPL sequence. In bpl1-C25/17 cells, de novo fatty acid synthesis is almost absent (< 2% of the wild type), while very-long-chain fatty acid (VLCFA) synthesis and, to some extent, medium-long-chain fatty acid elongation are still active. Hence, endogenous malonyl-CoA synthesis is reduced but not abolished by the translational stop mutation. A low rate of intact-BPL synthesis is accomplished in the mutant by occasional readthrough of the bpl1-C25/17 UAG nonsense triplet by normal yeast tRNA(Gln)(CAG). Correspondingly, ACC biotinylation is severely reduced though not completely absent in the two bpl1 mutants studied in this work. Residual BPL1 expression in bpl1-C25/17 cells is increased to a level allowing wild-type-like growth by transformation with high copy numbers of either the wild-type tRNA(Gln)(CAG) or the mutant bpl1-C25/17 genes. It is concluded that the lethality of BPL1 deletants is due to the lack of malonyl-CoA-dependent VLCFA synthesis and that the viability of distinct ACC-defective point mutants is due to their maintenance of a critical level of malonyl-CoA and, hence, VLCFA production. The residual capacity of malonyl-CoA synthesis, though, is inadequate to allow cytoplasmic bulk de novo fatty acid synthesis, nor does it support mutant growth on 13:0 as the only dietary fatty acid. ACC-defective mutants are respiratory deficient, which is attributed to the failure of mitochondrial fatty acid synthesis. Since lipoic acid levels of ACC1 and BPL1 mutants are essentially normal, an unknown product of mitochondrial fatty acid synthesis appears to be critically reduced in malonyl-CoA-deficient yeast cells.