Biomedical subjects
Publications and source records attributed to D Labuda.
RNase A4 is a new RNase activity found as a contaminant in commercial polynucleotide phosphorylase. This enzyme has the ability of hydrolyzing the phosphodiester bond between pyrimidine-A in both loop and paired regions of RNA.
The steps of UUC recognition by tRNAPhe were analysed by temperature-jump measurements. At ion concentrations close to physiological conditions we found three relaxation processes, which we assigned to (1) formation of codon-anticodon complexes, (2) a conformational change of the anticodon loop coupled with Mg2+ binding, and (3) codon-induced association of tRNA. The relaxation data were evaluated both by the usual procedure (fitting the exponentials evaluated from the individual experiments of a set to a reaction model) and by "global fitting", i.e. fitting a set of relaxation curves obtained at various concentrations directly to a reaction model, thus leaving out the intermediate exponential fitting step. The data can be represented quantitatively by a three-step model: the codon binds to the anticodon at a rate of 4 X 10(6) to 6 X 10(6) M-1S-1 as is usual for the formation of oligomer helices; the conformation change of the anticodon loop is associated with inner sphere complexation of Mg2+ at a rate of 10(3) S-1; the codon-tRNA complexes form dimers at a rate of 5 X 10(6) to 15 X 10(6) M-1S-1. A similar mechanism is found for the binding of the wobble codon UUU to tRNAPhe at increased concentrations of Mg2+. Measurements at different Mg2+ concentrations demonstrate the distinct role of this ion in the codon recognition and the codon-induced tRNA dimerization. We propose a simple mechanism, based upon the special properties of magnesium ions, for long-distance transfer of reaction signals along nucleic acid chains.
It is shown by equilibrium sedimentation that the binding of cognate codons to tRNAPhe (yeast), tRNAPhe (Escherichia coli), tRNALys, tRNAfMet and of the wobble codon UUU to tRNAPhe (yeast) induces dimerization of codon transfer RNA complexes. Analysis of the sedimentation profiles with a quantitative evaluation of the coupling between sedimentation and association equilibrium provides dimerization constants in the range from 1 X 10(4) to 6 X 10(4) M-1. These results on various tRNAs from different organisms suggest that the codon-induced tRNA association is a general phenomenon. Probably the codon-induced tRNA association facilitates the aminoacyl transfer reaction.
In order to learn about the effect of the G:U wobble interaction we characterized to codon:anticodon binding between triplets: UUC, UUU and yeast tRNAPhe (anticodon GmAA) as well as the anticodon:anticodon binding between Escherichia coli tRNAGlu2, E. coli tRNALys (anticodons: mam5s2UUC, and mam5S2UUU, respectively) and tRNAPhe from yeast and E. coli (anticodon GAA) using equilibrium fluorescence titrations and temperature jump measurements with fluorescence and absorption detection. The difference in stability constants between complexes involving a G:U pair rather than a usual G:C basepair is in the range of one order magnitude and is mainly due to the shorter lifetime of the complex involving G:U in the wobble position. This difference is more pronounced when the codon triplet is structured, i.e., is built in the anticodon loop of a tRNA. The reaction enthalpies of the anticodon:anticodon complexes involving G:U mismatching were found to be about 4 kcal/mol smaller, and the melting temperatures more than 20 degrees C lower, than those of the corresponding complexes with the G:C basepair. The results are discussed in terms of different strategies that might be used in the cell in order to minimize the effect of different lifetimes of codon-tRNA complexes. Differences in these lifetimes may be used for the modulation of the translation efficiency.
The binding of Ca2+ and Mg2+ to tRNAPhe is analyzed by equilibrium titrations and temperature-jump measurements using the Wye base fluorescence as a label. Titration experiments starting with the folded structure of the tRNA (high salt and low temperature) show that Ca2+ and Mg2+ binding detected by Wye base fluorescence changes is associated with equilibrium constants between 1 x 10(3) and 3 x 10(3) M-1. The binding of Ca2+ leads to an increase of the relaxation time associated with a conformation change of the anticodon loop and to a decrease of the corresponding amplitude. These data are represented quantitatively by a two-step reaction scheme with a preferential binding of Ca2+ to one of the anticodon conformations. When Mg2+ is added, an extra relaxation process is observed with time constants around 1 ms. This process demonstrates the formation of a Mg2+ inner sphere complex. Relaxation time constants and amplitudes are represented quantitatively by a three-step reaction scheme. Mg2+ binds preferentially to one of the anticodon conformations. In the absence of Mg2+, these conformations are populated almost equally with a transition rate constant around 5 x 10(3) s-1. The Mg2+ inner sphere complex is formed with a relatively low rate constant of (1--2) x 10(3) s-1, indicating a conformational barrier. These data strongly suggest that the Mg2+ site analyzed in the present investigation corresponds to the anticodon site with a distorted octahedral coordination characterized by X-ray analysis. The results are discussed in terms of the anticodon function and also with respect to their implications upon Mg2+ binding to nucleic acids in general.
It is shown by measurements of the sedimentation equilibrium that binding of the codon UUC to tRNAPhe from yeast induces an association of tRNA molecules. Sedimentation measurements at different concentrations demonstrate that the tRNA-codon complexes form dimers. The sedimentation profiles are analyzed quantitatively in terms of a simple monomer-dimer model as well as a model which considers the sedimentation of four species (tRNA, tRNA.UUC, (tRNA.UUC)2, and UUC) separately. The information resulting from the conservation of mass relation is used directly in the determination of equilibrium constants via integration o the sedimentation profiles. Using this procedure, we determine the equilibrium constants for dimerization of the tRNAPhe.UUC complex, KD = 8.6 x 10(4) M-1, and for the binding of UUC to tRNAPhe, KL = 1800 M-1 (5 degrees C). The large free energy for dimerization of the tRNA-codon complex suggests that interactions between adjacent tRNAs are important for the ribosomal translation process.
Explore the source record for details and available documents.
The sodium ion concentration dependent conformational changes of transfer RNA (unfractionated tRNA from baker's yeast) have been studied in unbuffered aqueous solutions by Rayleigh light scattering. Changes of the optical parameters of the molecule indicated the following conformational changes of tRNA with increasing NaCl concentration: in salt-free solution tRNA molecules have an irregular hairpin loop-like structure in which the orientation of base rings is not correlated. Upon addition of a small amount of NaCl (0.005 M) an increasing ordering of this structure is observed. In 0.1 M-NaCl the molecule has an extended structure with ordered regions (arms). Further increase of sodium ion concentration up to 2 M results in folding of the extended structure and formation of a compact and rigid conformation in which most of the bases are nearly perpendicular to the symmetry axis of the molecule.
The mechanism of codon recognition by tRNA is investigated in the system tRNAPhe + UUC by temperature-jump measurements using the Wye base fluorescence as a label. In 0.4 M Na+ and 5 mM Mg2+ a two-step reaction is observed and described quantitatively; UUC is shown to bind preferentially to one of two conformations on the anticodon loop. In 0.1 m Na+ and 10 mM Mg2+ an additional relaxation effect is observed, which indicates a codon-induced conformation change leading to an association of tRNA molecules. The codon-induced tRNA association is demonstrated independently by equilibrium sedimentation. The present results suggest a more active role of tRNA during translation than anticipated.
Explore the source record for details and available documents.
Explore the source record for details and available documents.
Dependence of barley phenylalanine tRNA (tRNAPhe) fluorescence intensity at 430 nm upon LiCl, NaCl, KCl, CsCl or NH4Cl concentration was measured in 0.01 M Tris-HCl, pH 7.5, 0.001 M Na2EDTA solutions. Increase of monovalent cation concentration in the solvent from 0 to 2 M induced about 3-fold fluorescence intensity enhancement. The fractional fluorescence change was used as a measure of bound ligand concentration. Fluorescence Scatchard plots revealed three classes of monovalent cation binding sites on the tRNA molecule: interacting (strong) and independent (weak and very weak) sites. Calculated from Scatchard plots binding constants (K), for strong and weak binding of monovalent cations (in the case of Na+ binding: Ks = 26 M-1 and Kw = 4.3 M-1 respectively) exhibit linear dependence upon ionic radius (r). Two limiting values obtained from the plot of K versus r: K(max) at r = 0 r(max) at K = 0, characterize additionally strong and weak monovalent cation binding sites (Ks(max) = 42 M-1 Kw(max) = 8.5 M-1, rs(max) = 0.23 nm and rw(max) = 0.22 nm). A model of the relationship between weak Mg2+ binding sites and monovalent cation binding sites as well as of monovalent cations binding to tRNA is proposed.
Explore the source record for details and available documents.
1. Large-scale isolation of tRNA from barley embryos is described, involving: phenol extraction, RNA deproteinization with the chloroform-isoamyl alcohol mixture, batch sorption on DEAE-cellulose, NaCl gradient elution of tRNA from DEAE-cellulose, and deaminoacylation of tRNA in the presence of bentonite. The procedure yielded tRNA free of protein and RNase activity. 2. The amino acid acceptor activity of the crude barley tRNA, its melting profiles and chromatographic patterns on Sephadex G-100 and BD-cellulose were similar to those of tRNA from other sources.
Explore the source record for details and available documents.
Two fractions of phenylalanine tRNA (tRNA(Phe) (1) and tRNA(Phe) (2)) were purified by BD-cellulose and RPC-5 chromatography of crude tRNA isolated from barley embryos. Successive RPC-5 rechromatography runs of tRNA(Phe) (2) showed its conversion into more stable tRNA(Phe) (1), suggesting that the two fractions have essentially the same primary structure. Both tRNA(Phe) (1) and tRNA(Phe) (2) had about the same acceptor activity, but tRNA(Phe) (2) was aminoacylated much faster than tRNA(Phe) (1). RPC-5 chromatography of crude aminoacylated tRNA showed higher contents of phe-tRNA(Phe) (2) than of phe-tRNA(Phe) (1) but the ratio of these two fractions estimated by relative fluorescence intensity was about 1. Fluorescence spectra of tRNA(Phe) from barley embryos suggest that it contains Y base similar to Y(w) from wheat tRNA(Phe).
The single-strand conformational polymorphism technique was used to search for neutral polymorphisms in 18 PCR-amplified dystrophin gene fragments. Out of the seven polymorphisms (six intronic and one exonic) detected in Caucasians, one was absent from the Oriental population. Significant differences in allele frequencies between the two populations were observed for three of the intronic polymorphisms. In Caucasians, one variant position occurred per 728 bp of the total DNA or one per 483 bp of the intronic sequence; the corresponding average heterozygosities were 0.04 and 0.06%, respectively.
The origin of acute lymphoblastic leukemia (ALL), the most common pediatric cancer, can be explained by a combination of genetic factors and environmental exposure. The environmental toxicants to which an individual is exposed are biotransformed and eliminated from the body after metabolic conversion mediated by Phase I and Phase II xenobiotic-metabolizing enzymes. Phase I enzymes catalyze hydroxylation, reduction and oxidation reactions of xenobiotics (carcinogens/drugs), often converting them into more active or toxic compounds. Phase II enzymes catalyze conjugation reactions (glucuronidation, acetylation, methylation), thereby converting the metabolites into non-reactive, water-soluble products that are eliminated from the organism. The genetic polymorphism underlying the variation in enzyme activity can modify susceptibility to diverse adult cancers, probably by influencing the activation and removal of toxicants or drugs. Here we present an overview of the role of genetic variants of certain Phase I and Phase II enzymes in the development of childhood ALL, a good model for such studies because of its short latency period. The genetic contribution to the development of ALL is examined by association studies that analyze the loci of Phase I enzymes (cytochrome P-450, myeloperoxidase) and Phase II enzymes (quinone-oxidoreductase, glutathione-S-transferase, N-acetyltransferase). The loci of the enzyme variants CYPlA1, CYP2E1, NQO1, GSTM1, GSTP1, NAT2 are associated with disease development, and evidence of gene-gene interactions has emerged as well. Despite the improvements in treatment, resistant cases of ALL remain a leading cause of cancer-related death in children. Although the underlying mechanism of drug resistance is not well understood, differences in the capacity of ALL patients to process drugs and environmental carcinogens could play a role by modifying the risk of recurrent malignancy, as well as the response to therapy. Therefore, polymorphic genes encoding carcinogen- and drug-metabolizing enzymes may not only increase the risk of ALL but also influence the risk of relapse in patients. We found that the prognosis of patients with CYPlA1 and NQO1 variants was worse than that of patients who lack these variants. We conclude that genotyping ALL patients for functional polymorphisms of candidate genes can become an important tool in predicting disease outcome.