Chemical modification of hammerhead ribozymes. Catalytic activity and nuclease resistance.

A systematic study of selectively modified, 36-mer hammerhead ribozymes has resulted in the identification of a generic, catalytically active and nuclease stable ribozyme motif containing 5 ribose residues, 29-30 2'-O-Me nucleotides, 1-2 other 2'-modified nucleotides at positions U4 and U7, and a 3'-3'-linked nucleotide "cap." Eight 2'-modified uridine residues were introduced at positions U4 and U7. From the resulting set of ribozymes, several have almost wild-type catalytic activity and significantly improved stability. Specifically, ribozymes containing 2'-NH2 substitutions at U4 and U7, or 2'-C-allyl substitutions at U4, retain most of their catalytic activity when compared to the all-RNA parent. Their serum half-lives were 5-8 h in a variety of biological fluids, including human serum, while the all-RNA parent ribozyme exhibits a stability half-life of only approximately 0.1 min. The addition of a 3'-3'-linked nucleotide "cap" (inverted T) did not affect catalysis but increased the serum half-lives of these two ribozymes to > 260 h at nanomolar concentrations. This represents an overall increase in stability/activity of 53,000-80,000-fold compared to the all-RNA parent ribozyme.

Replacement of RNA hairpins by in vitro selected tetranucleotides.

An in vitro selection method based on the autolytic cleavage of yeast tRNA(Phe) by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides. Based on the rates of the site-specific cleavage by Pb2+ and the presence of a specific UV-induced crosslink, certain tetranucleotide sequences allow proper folding of the rest of the tRNA molecule, whereas others do not. One such successful tetramer sequence was also used to replace the acceptor stem of yeast tRNA(Phe) and the anticodon hairpin of E.coli tRNA(Phe) without disrupting folding. These experiments suggest that certain tetramers may be able to replace structurally nonessential hairpins in any RNA.

Recognition of yeast tRNA(Phe) by its cognate yeast phenylalanyl-tRNA synthetase: an analysis of specificity.

A kinetic analysis of aminoacylation of mutant yeast tRNA(Phe) transcripts by its cognate yeast phenylalanyl-tRNA synthetase (FRS) reveals five nucleotides in tRNA(Phe) as major recognition sites for FRS. The aminoacylation kinetics for two double mutants suggest that each of the five recognition sites contributes independently to kcat/KM. Measured kinetic values for the mutants presented here and those reported previously were then used to calculate the predicted kcat/KM of misacylation for a number of noncognate tRNAs. The predicted kcat/KM values are consistent with values measured by other investigators and thus support the five-nucleotide recognition model. The kcat/KM of misacylation for all known yeast tRNAs has been calculated on the basis of this model, and the specificity of FRS for tRNA(Phe) in yeast is discussed.

Lead-catalyzed cleavage of yeast tRNAPhe mutants.

Yeast tRNA(Phe) lacking modified nucleotides undergoes lead-catalyzed cleavage between nucleotides U17 and G18 at a rate very similar to that of its fully modified counterpart. The rates of cleavage for 28 tRNA(Phe) mutants were determined to define the structural requirements of this reaction. The cleavage rate was found to be very dependent on the identity and correct positioning of the two lead-coordinating pyrimidines defined by X-ray crystallography. Nucleotide changes that disrupted the tertiary interactions of tRNAPhe reduced the rate of cleavage even when they were distant from the lead binding pocket. However, nucleotide changes designed to maintain tertiary interactions showed normal rates of cleavage, thereby making the reaction of a useful probe for tRNA(Phe) structure. Certain mutants resulted in the enhancement of cleavage at a "cryptic" site at C48. The sequences of Escherichia coli tRNA(Phe) and yeast tRNA(Arg) were altered such that they acquired the ability to cleave at U17, confirming our understanding of the structural requirements for cleavage. This mutagenic analysis of the lead cleavage domain provides a useful guide for similar analysis of autocatalytic self-cleavage reactions.

Role of the tertiary nucleotides in the interaction of yeast phenylalanine tRNA with its cognate synthetase.

In vitro transcription by T7 RNA polymerase was used to prepare 32 different mutations in the 21 nucleotides that participate in the 9 tertiary base pairs or triples of yeast tRNAPhe. The mutations were designed either to disrupt the tertiary interaction or to change the sequence without disrupting the structure by transplanting tertiary interactions present in other tRNAs. Steady-state aminoacylation kinetics with purified yeast phenylalanyl synthetase revealed little change in reaction rate as long as a tertiary interaction was maintained. This suggests that the tertiary nucleotides only contribute to the folding of tRNAPhe and do not participate directly in sequence-specific interaction with the synthetase.

Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase.

An analysis of the aminoacylation kinetics of unmodified yeast tRNAPhe mutants revealed that five single-stranded nucleotides are important for its recognition by yeast phenylalanyl-tRNA synthetase, provided they were positioned correctly in a properly folded tRNA structure. When four other tRNAs were changed to have these five nucleotides, they became near-normal substrates for the enzyme.

Effect of volatile anesthetics on protein synthesis and secretion by rat hepatocyte suspensions.

The effect of volatile anesthetics on protein synthesis and secretion by isolated rat hepatocytes in suspension was investigated. Halothane and enflurane inhibited protein synthesis in a dose-dependent manner. Diethyl ether had little effect on protein synthesis while isoflurane caused a mild inhibition. This effect was more pronounced in hepatocytes from phenobarbital treated male rats when compared to hepatocytes from control rats. Protein synthesis in hepatocytes from phenobarbital treated female rats was inhibited similar to that seen with control male rat hepatocytes. Isoflurane, enflurane, and halothane also caused a dose-dependent inhibition of protein secretion, while diethyl ether was only mildly inhibitory. From these studies it appears that inhibition of protein synthesis and secretion might be an early and sensitive indicator of cellular injury by volatile anesthetics.

Toxicity and biotransformation of volatile halogenated anesthetics in rat hepatocyte suspensions.

This study examines the toxicity (as measured by reduced intracellular K+) and metabolism (defluorination) of halothane and enflurane in rat hepatocytes in suspension (RHS) with regards to O2 tension, time, and concentration. In 95% O2 halothane is more toxic than enflurane when RHS are exposed to 5-20 microliters of these anesthetics. At these levels halothane is not metabolized while enflurane is metabolized. At 21% O2 a similar pattern was seen with regards to toxicity. However, metabolism of halothane rapidly reached an elevated level while that of enflurane is reduced when compared to 95% O2. Thus toxicity of halothane and enflurane at these dose levels appears to be unrelated to metabolism and due solely to a solvent effect.

Effect of O2 tension on the bioactivation and metabolism of aliphatic halides by primary rat-hepatocyte cultures.

The covalent binding of CCl4 and CF3CHBrCl to cultured rat hepatocytes was enhanced by anoxic conditions, indicative of enhanced reductive biotransformation. The covalent binding of CHCl3 and CHCl2CH2Cl decreased as the O2 concentration was decreased, indicating a preference for oxidative metabolism. Lower O2 tensions decreased the formation of polar water-soluble metabolites with CHCl3 and CHCl2CH2Cl, while CCl4 and CF3CHBrCl were unaffected. The results indicate that primary cultured hepatocytes can reductively biotransform and bioactivate aliphatic halides under anoxic conditions.

Effect of senescence on the bioactivation of aliphatic halides.

Since the toxicity of xenobiotics is often related to their metabolism, this study was concerned with the relationship between aging and the bioactivation and covalent binding of certain aliphatic halides to microsomal protein and lipid. Hepatic microsomes were isolated from control and phenobarbital induced young (4 mo), adult (11 mo) and senescent (27 mo) Fischer 344 rats. Bioactivation and subsequent covalent binding were studied with 14C-labeled 1,2-dibromoethane, carbon tetrachloride, trichloroethylene, and 1, 1, 2-trichloroethane. With control rats, levels of binding increased slightly between 4 and 11 mo; however the values decreased 50-75% in the 27 mo group compared to the 11 mo group. No significant differences were noted between phenobarbital induced groups with regards to bioactivation of the aliphatic halides and their covalent binding to proteins and lipids. As an explanation for the decreased bioactivation ability in the senescent rats, they were also found to have significantly less hepatic cytochrome P-450 (-35%), NADPH cytochrome C reductase (-31%), and ethyl-morphine N-demethylase activity (-43%) when compared to the 11 mo age group. These differences were reduced when comparisons were made between the various age groups of phenobarbital induced animals. This suppression may indicate a decreased potential for the expression of toxicities requiring bioactivation.

Microsomal bioactivation and covalent binding of aliphatic halides to DNA.

Studies were carried out on the in vitro covalent binding of a series of 14C-labeled aliphatic halides to calf thymus DNA following bioactivation by hepatic microsomes isolated from phenobarbital-treated rats. Six compounds were shown to exhibit binding to DNA of greater than 0.3 nmol/mg DNA (1,2-dibromoethane, bromotrichloromethane, trichloroethylene, carbon tetrachloride, chloroform, and 1,1,2-trichloroethane). Covalent binding of the aliphatic halides to the nucleic acids was confirmed by sedimentation of the DNA-organohalogen adduct in a cesium chloride gradient and Sephadex LH-20 chromatography of the nucleosides released by enzymatic hydrolysis.

Bacteriophage T4 virion dihydrofolate reductase: approaches to quantitation and assessment of function.

This paper is concerned with the physiological role(s) of T4 phage-coded dihydrofolate reductase, which functions both in DNA precursor metabolism and as a virion protein. (i) We have detected enzyme activity in noninfectious particles produced under restrictive conditions by gene 11 mutants. This supports the conclusion of Kozloff et al. (J. Virol. 16:1401-1408, 1975) that the protein lies in the baseplate, covered by the gene 11 protein. (ii) We have obtained further evidence for virion dihydrofolate reductase as the target for neutralizing activity of T4 dihydrofolate reductase antiserum and as a determinant of the heat lability of the virion. This derives from our observation that the reductases specified by T4B and T4D differ in several properties. (iii) We have investigated several anomalous properties of T4 mutants bearing deletions that reportedly extend into or through the frd gene, which codes for dihydrofolate reductase. Evidence is presented that the deletions in fact do not extend through frd. These strains direct the synthesis of material that cross-reacts with antiserum to homogeneous dihydrofolate reductase. Moreover, they are all quite sensitive to the phage-neutralizing effects of this antiserum. In addition, they are restricted by several of the hospital strains, wild-type strains of Escherichia coli supplied by the California Institute of Technology group. (iv) We have attempted to detect dihydrofolate reductase among early-synthesized proteins present in T4 tails. Two such proteins are seen, one of which is evidently the gene 25 product and one that is a bacterial protein. Quantitation of our electrophoretic technique has allowed determination of the number of molecules of some T4 tail components present per virion. (v) Finally, we have compared the T4 dihydrofolate reductase with the corresponding enzyme specified by two plasmids conferring resistance to trimethoprim (Skold and Widh, J. Biol. Chem. 249:4324-4325, 1974). Although the enzymes are similar in some properties, they differ in several important respects, including immunological activity.